Biology

13 pages, 1643 KB

Open AccessArticle

Characterization and Comparative Analyses of Nuclear Mitochondrial DNAs in Genomes of the Leaf-Roller Moths (Lepidoptera: Tortricidae)

by Weifeng Peng, Jiayi Yu, Zhengbing Wang, Zhen Li, Xin Miao, Jin Liu, Jiahui Zhang, Liuyong Xie, Weili Ding, Keshi Ma and Mingsheng Yang

Biology 2026, 15(6), 517; https://doi.org/10.3390/biology15060517 - 23 Mar 2026

Viewed by 490

Abstract

During eukaryotes evolution, mitochondrial DNA (mtDNA) fragments integrate into nuclear genomes, forming nuclear mitochondrial DNA sequences (Numts). Tortricidae (Lepidoptera), a species-rich and economically critical family, lacks systematic characterization of Numts, which hinders reliable molecular research. Here, we systematically characterized Numts in 27 Tortricidae [...] Read more.

During eukaryotes evolution, mitochondrial DNA (mtDNA) fragments integrate into nuclear genomes, forming nuclear mitochondrial DNA sequences (Numts). Tortricidae (Lepidoptera), a species-rich and economically critical family, lacks systematic characterization of Numts, which hinders reliable molecular research. Here, we systematically characterized Numts in 27 Tortricidae species spanning two subfamilies via genome download, mitochondrial genome annotation, and Numt identification and characterization. With each species’ mtDNA as query, Numt identification was performed with an E-value threshold of 10⁻⁴ and a sequence similarity cut-off of >60%, with a minimum length of 50 bp to exclude spurious hits. Results showed that all species contained Numts, with copy numbers varying drastically (9–208). Numt numbers positively correlated with nuclear genome length, but not mitochondrial genome length. Numts insertion flanking regions had significantly higher AT content than nuclear genome, indicating the insertion preference for AT-rich regions. Numts were predominantly derived from the mitochondrial cox1 gene, highlighting the risk of co-amplification when cox1 is used as a DNA barcode for species identification or phylogenetic studies. This study represents a systematic charaterizition of copy number, length distribution, insertion sequence preferences, and mitochondrial gene origins of Numts in Tortricidae, offering valuable references for refining molecular systematics, comparative genomics, and pest management in Tortricidae and related lepidopteran groups. Full article

(This article belongs to the Section Genetics and Genomics)

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27 pages, 420 KB

Open AccessReview

The Role of GDF-15 in Heart Failure and Biomarker Potential—From Basic Science to Clinical Praxis

by Mário Barbosa, Maria Ana Martins, Joana Fernandes-Silva, Ana Melício and Álvaro M. Martins

Biology 2026, 15(6), 516; https://doi.org/10.3390/biology15060516 - 23 Mar 2026

Viewed by 638

Abstract

Heart failure (HF) prognosis, particularly readmission and mortality, remains poor irrespective of advances in its management. Growth differentiation factor-15 (GDF-15) is a member of the transforming growth factor-beta (TGF-β) superfamily that arises as a promising biomarker to improve HF management, still despite two [...] Read more.

Heart failure (HF) prognosis, particularly readmission and mortality, remains poor irrespective of advances in its management. Growth differentiation factor-15 (GDF-15) is a member of the transforming growth factor-beta (TGF-β) superfamily that arises as a promising biomarker to improve HF management, still despite two decades of extensive investigation some issues remain controversial. We performed a search in PubMed using the following Medical Subject Headings (MeSH) to identify relevant studies published in the last five years (after the latest updates of the guidelines by major Scientific Societies): “Growth differentiation factor-15 (GDF-15)”, “heart failure”, “prognosis” and “diagnosis”. The search was supplemented by data previous to this period, considered of utmost importance. A total of 115 articles written in English were retrieved. Extensive evidence supports GDF-15 as an independent predictor of adverse outcomes across the heterogeneous HF spectrum and its addition to risk scores based on traditional biomarkers improves prognostic power. However, limited tissue specificity restricts its diagnostic value. Tailored treatment strategies and its role as a therapeutic target remain speculative, as the effect of HF therapies on GDF-15 levels is unclear and clinical trials have been unsuccessful. Large prospective studies are needed to validate its reliability for routine clinical use. Full article

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16 pages, 2895 KB

Open AccessArticle

Effects of High-Monounsaturated-Fatty-Acid (MUFA) Diet and Melatonin Supplementation on Lipid Metabolism in Female Rats

by Jun-Ling Luo and Yi-Wen Chien

Biology 2026, 15(6), 515; https://doi.org/10.3390/biology15060515 - 23 Mar 2026

Viewed by 427

Abstract

Background: This study investigated the effects of melatonin (50 mg/kg/day) and a high-monounsaturated-fatty-acid (MUFA) diet (60% MUFAs; PUFA/SFA ratio = 5), alone or combined, on lipid metabolism-related gene expression in female Sprague–Dawley rats. Methods: Thirty-two eight-week-old rats were randomized into four groups: control [...] Read more.

Background: This study investigated the effects of melatonin (50 mg/kg/day) and a high-monounsaturated-fatty-acid (MUFA) diet (60% MUFAs; PUFA/SFA ratio = 5), alone or combined, on lipid metabolism-related gene expression in female Sprague–Dawley rats. Methods: Thirty-two eight-week-old rats were randomized into four groups: control (C), melatonin (M), experimental oil diet (E), and combined melatonin plus experimental oil diet (ME). Treatments lasted eight weeks, with melatonin given orally at 17:00–19:00 daily. Results: In the ME group, hepatic expression of peroxisome proliferator-activated receptor α (PPARα) and acyl-CoA oxidase (ACO) mRNA was markedly upregulated, while the E group showed significantly higher expression of hormone-sensitive lipase (HSL) in white adipose tissue. Additionally, ME rats exhibited increased fibronectin type III domain-containing protein 5 (FNDC5) mRNA with reduced peroxisome proliferator-activated receptor gamma coactivator-1α (PGC-1α), but serum irisin remained unchanged. Conclusions: Melatonin and a high-MUFA diet induced modest and non-uniform changes in lipid metabolism-related gene expression. However, these transcriptional responses were not accompanied by measurable physiological or metabolic outcomes, indicating that the observed effects represent early molecular adaptations rather than functional metabolic modulation. Full article

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21 pages, 6863 KB

Open AccessArticle

Identification of the ZmDUF966 Gene Family in Maize, Analysis of Its Expression Under Cold Stress, and Preliminary Investigation of the ZmDUF966-10 Regulatory Network

by Minghao Sun, Wenyue Li, Yunlong Li, Sinan Li, Yan Sun, Shujun Li, Yue Yin, Enhao Zhou, Yue Wang, Tao Yu, Wei Zhao, Quan Cai, Xin Li and Jianguo Zhang

Biology 2026, 15(6), 514; https://doi.org/10.3390/biology15060514 - 23 Mar 2026

Viewed by 453

Abstract

Maize (Zea mays L.) originated in tropical and subtropical regions. During its growth and development, cold stress severely threatens seedling survival rates and final yield by inducing oxidative stress, compromising cell membrane integrity, and causing “physiological drought.” The Domain of Unknown Function [...] Read more.

Maize (Zea mays L.) originated in tropical and subtropical regions. During its growth and development, cold stress severely threatens seedling survival rates and final yield by inducing oxidative stress, compromising cell membrane integrity, and causing “physiological drought.” The Domain of Unknown Function 966 (DUF966) gene family comprises a class of regulatory factors containing conserved domains of undetermined function. Although they are considered to be extensively involved in plant growth, development, and stress response, their specific roles within the maize cold-tolerance regulatory network remain to be explored. In this study, 10 ZmDUF966 family members were identified via genome-wide analysis, and their phylogenetic relationships, gene structures, conserved motifs, chromosomal localizations, and cis-acting elements were systematically analyzed. The results indicate that the ZmDUF966 family is highly conserved among Poaceae species, and its promoters are enriched with stress-responsive elements such as LTR and ABRE. The core gene, ZmDUF966-10, was significantly up-regulated (approximately 35-fold at 48 h, p < 0.05) as validated by RT-qPCR under cold stress and is post-transcriptionally regulated by conserved miRNAs such as zma-miR159. Further yeast two-hybrid experiments revealed a preliminary physical interaction between the ZmDUF966-10 protein and an ABA/WDS-induced protein, suggesting its potential involvement in ABA-mediated stress signaling, though functional validation remains to be conducted. In conclusion, this study identifies ZmDUF966-10 as a promising candidate gene that responds to cold signals through multi-level regulatory networks, providing a valuable gene resource for further functional characterization and potential application in cold-tolerant maize improvement. Full article

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19 pages, 635 KB

Open AccessReview

Snapshot on Cell-to-Cell Communication Nanotubes: From Bacteria to Humans

by Loredana Moro

Biology 2026, 15(6), 513; https://doi.org/10.3390/biology15060513 - 23 Mar 2026

Viewed by 685

Abstract

From bacteria to higher vertebrates, cells have developed different systems to communicate with each other and transmit specific signals in a dynamic interplay with neighborhood cells. This review focuses on cell-to-cell communication mediated by nanotubes, membrane protrusions present during evolution from bacteria to [...] Read more.

From bacteria to higher vertebrates, cells have developed different systems to communicate with each other and transmit specific signals in a dynamic interplay with neighborhood cells. This review focuses on cell-to-cell communication mediated by nanotubes, membrane protrusions present during evolution from bacteria to higher plants and animals. We describe the basic structure of nanotubes in different organisms and cell types and their functions, which cover transfer of signaling molecules, ions, organelles and pathogens in a cell- and context-dependent manner, thereby promoting cell survival, tissue development, response to stress, pathogens’ spreading and drug resistance. We also provide an overview of recent studies that are broadening our understanding of the role of these conduits in the pathogenesis of high-incidence diseases in humans, such as cancer and neurodegeneration. Full article

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

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16 pages, 3006 KB

Open AccessArticle

Effects of Simulated Precipitation Treatment on Denitrifying Microbial Communities in the Wayan Mountains

by Shijia Zhou, Kelong Chen, Ni Zhang, Zhiyun Zhou and Siyu Wang

Biology 2026, 15(6), 512; https://doi.org/10.3390/biology15060512 - 23 Mar 2026

Viewed by 389

Abstract

The Qinghai–Tibet Plateau is undergoing rapid warming and humidification, with altered precipitation regimes increasingly affecting soil nitrogen cycling and N₂O emissions. Denitrification—a key nitrogen transformation pathway—is particularly sensitive to these hydrological changes. Here, we investigated the response of nirK-type denitrifying [...] Read more.

The Qinghai–Tibet Plateau is undergoing rapid warming and humidification, with altered precipitation regimes increasingly affecting soil nitrogen cycling and N₂O emissions. Denitrification—a key nitrogen transformation pathway—is particularly sensitive to these hydrological changes. Here, we investigated the response of nirK-type denitrifying microbial communities to altered precipitation in an alpine wetland on the northern shore of Qinghai Lake. Using a long-term precipitation manipulation platform with five gradients (ambient, ±25%, and ±50%), we integrated high-throughput sequencing with bioinformatics to systematically assess community shifts. Short-term precipitation treatments did not significantly alter alpha diversity, but markedly restructured community composition. Extreme wetting (+50%) increased within-group heterogeneity. At the phylum level, Proteobacteria remained dominant across all treatments, whereas extreme drought (−50%) suppressed Planctomycetes. At the genus level, Ochrobactrum was enriched under reduced precipitation, while Rhodopseudomonas increased under increased precipitation. Functional predictions indicated that reduced precipitation enhanced nitrogen fixation potential, whereas increased precipitation favored nitrate respiration. Soil pH and carbon fractions were the key environmental filters driving community variation. Ecological process analysis revealed that community assembly was entirely governed by deterministic processes, specifically variable selection. Together, these findings elucidate how precipitation shifts reconfigure the structure and functional potential of denitrifying microbial communities in alpine wetlands, primarily via changes in soil pH and moisture under variable selection. This work provides critical insights into microbial regulation of the nitrogen cycle on the Tibetan Plateau under ongoing climate change. Full article

(This article belongs to the Section Microbiology)

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20 pages, 3021 KB

Open AccessArticle

Agronomic Performance, Mineral Composition, and Biochemical Characteristics of Basil (Ocimum basilicum L.) Grown in Trout (Oncorhynchus mykiss) Aquaponic Systems

by Mohammed Elakrouch, Marouane Mohaddab, Sarah Elmoussaoui, Arthur Libault, Ahmed Rachid and M. Haissam Jijakli

Biology 2026, 15(6), 511; https://doi.org/10.3390/biology15060511 - 22 Mar 2026

Viewed by 481

Abstract

Aquaponic systems are among the sustainable approaches for combining fish farming and plant cultivation and have been proposed as potentially economically viable food production technologies. Their performance depends on the balanced environmental conditions shared by fish, nitrifying bacteria, and plants. This study assessed [...] Read more.

Aquaponic systems are among the sustainable approaches for combining fish farming and plant cultivation and have been proposed as potentially economically viable food production technologies. Their performance depends on the balanced environmental conditions shared by fish, nitrifying bacteria, and plants. This study assessed the performance of a trout-based (Oncorhynchus mykiss) decoupled aquaponic system for basil (Ocimum basilicum L.) growth and essential oil composition. Two cultivation strategies were compared over 60 days: a non-supplemented system relying exclusively on trout rearing water, and a system supplemented with mineral nutrients formulated according to the recommendations of the Hoagland nutrient solution. Basil grown without mineral supplementation maintained a healthy appearance and stable physiological status, with satisfactory growth, although it remained lower than in supplemented plants. The mineral profile of the plants showed similar nitrate and phosphorus concentrations between non-supplemented and supplemented plants, with nitrate levels of 5.40 ± 0.29 mg g⁻¹ and 5.52 ± 0.29 mg g⁻¹, respectively, and phosphorus levels of 5.46 ± 0.23 mg g⁻¹ and 6.14 ± 0.91 mg g⁻¹, respectively. In contrast, potassium concentration was lower in non-supplemented plants (36.89 ± 3.31 mg g⁻¹) compared to supplemented plants (55.56 ± 7.16 mg g⁻¹). Essential oil yield expressed per cultivated surface area remained comparable between systems, reaching 2.96 and 3.09 mL m⁻² in the supplemented and non-supplemented systems, respectively. GC–MS analysis revealed that linalool (≈24%) was the predominant compound in both systems. Notably, estragole content was higher in non-supplemented plants (21.35 ± 1.46%) compared to supplemented plants (5.24 ± 0.68%). Overall, trout-based aquaponic systems not only support satisfactory basil growth but also enhance the production of essential oils with desirable aromatic characteristics, representing a sustainable and efficient strategy for aromatic plant cultivation. Full article

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33 pages, 3117 KB

Open AccessReview

The Therapeutic Crossroad Between Mitochondria and Cannabidiol: A Mini-Review

by Mihaela Jorgovan, Tamara Maksimović, Oana Bătrîna, Codruța Șoica, Alexandra Mioc and Marius Mioc

Biology 2026, 15(6), 510; https://doi.org/10.3390/biology15060510 - 22 Mar 2026

Viewed by 904

Abstract

Cannabidiol is a non-psychoactive compound originating from Cannabis sativa L., with a promising therapeutic profile that influences numerous cellular processes. A major area of interest is its impact on mitochondria, organelles essential for cellular metabolism, ATP production, calcium homeostasis, and stress response. This [...] Read more.

Cannabidiol is a non-psychoactive compound originating from Cannabis sativa L., with a promising therapeutic profile that influences numerous cellular processes. A major area of interest is its impact on mitochondria, organelles essential for cellular metabolism, ATP production, calcium homeostasis, and stress response. This article explores the available data on contribution of CBD effect on mitochondria to its therapeutic potential in treatment of various pathologies: cancer, cardiovascular, lung, neurological, gastrointestinal and liver disease, and muscle pathologies. Regarding cancer, the cytotoxic effects of cannabidiol on glioma, leukaemia, non-Hodgkin lymphoma, prostate, gastric, and breast cancer are analysed. In the case of cardiomyopathies and heart failure, cannabidiol plays an important role in reducing oxidative stress and promoting mitochondrial biogenesis. In lung diseases, cannabidiol reduces the expression of mitochondrial fission genes and increases the expression of fusion genes. When it comes to neurological pathologies, cannabidiol protects neurons and exhibits a strong antioxidant effect, while in gastrointestinal and liver diseases, cannabidiol stabilises mitochondrial membrane potential, increases ATP production, and reduces oxidative stress. In muscle affections, cannabidiol improves mitochondrial function by inhibiting excessive mitophagy. Although modern formulations may improve the low bioavailability of CBD, its potential non-selective cytotoxicity toward non-malignant cells remains an important concern that warrants further investigation. Nevertheless, cannabidiol possesses a remarkable therapeutic potential, and its effects on mitochondria open new perspectives in the treatment of numerous diseases. Full article

(This article belongs to the Special Issue New Insights into Mitochondria in Health and Disease)

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20 pages, 11070 KB

Open AccessArticle

A Comparative Transcriptome and WGCNA of Tomato Reveals Hub Genes and a Hormone-Mediated Defense Network Against Ralstonia solanacearum

by Chuying Yu, Xiaofang Wang, Chunchun Qin, Yi Liu, Guiyun Gan, Liangyu Cai, Rui Xiang, Yaqin Jiang, Weiliu Li, Qihong Yang and Yikui Wang

Biology 2026, 15(6), 509; https://doi.org/10.3390/biology15060509 - 22 Mar 2026

Viewed by 608

Abstract

Bacterial wilt caused by Ralstonia solanacearum is a major constraint on tomato (Solanum lycopersicum L.) production, yet the molecular basis of quantitative resistance remains poorly understood. In this study, comparative transcriptome profiling was performed on resistant (‘ZM3’) and susceptible (‘ZM86’) tomato inbred [...] Read more.

Bacterial wilt caused by Ralstonia solanacearum is a major constraint on tomato (Solanum lycopersicum L.) production, yet the molecular basis of quantitative resistance remains poorly understood. In this study, comparative transcriptome profiling was performed on resistant (‘ZM3’) and susceptible (‘ZM86’) tomato inbred lines following pathogen inoculation in roots, stems, and leaves. Differential expression analysis and weighted gene co-expression network analysis (WGCNA) were conducted to identify resistance-associated regulatory modules and hub genes. The results revealed distinct gene expression patterns between the two genotypes after infection. Several co-expression modules were significantly associated with resistance or susceptibility traits. Functional enrichment analysis showed that differentially expressed genes were mainly involved in plant hormone signal transduction, plant–pathogen interaction, phenylpropanoid biosynthesis, and cell wall modification. Genes related to ethylene and salicylic acid signaling were strongly induced following infection, whereas brassinosteroid-associated genes showed genotype-dependent expression patterns. Network analysis further identified several hub genes within defense-related modules, including ACO (Solyc04g007980), ERF1 (Solyc09g091950), MAPK9, receptor-like kinase RLK (Solyc07g006770), and a dirigent family gene (Solyc10g008900). Taken together, our results suggest that tomato resistance to Ralstonia solanacearum involves a coordinated defense network integrating hormone-mediated transcriptional regulation and structural reinforcement, and provides candidate genes for breeding bacterial wilt-resistant cultivars. Full article

(This article belongs to the Special Issue The Potential of Genetics and Plant Breeding in Crop Improvement)

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20 pages, 22059 KB

Open AccessArticle

Physio-Transcriptomic Mechanism of Antimony Tin Oxide Nanoparticle-Induced Midgut Toxicity in Bombyx mori

by Yang Fang, Xuan Li, Fengchao Zhang, Yang Liu, Liang Ma, Liping Chen and Qijun Xie

Biology 2026, 15(6), 508; https://doi.org/10.3390/biology15060508 - 22 Mar 2026

Viewed by 414

Abstract

The silkworm (Bombyx mori) is an economically important insect that plays a crucial role in agricultural development. Antimony tin oxide, a high-tech multifunctional nanomaterial, is extensively utilized in contemporary industries due to its properties of transparency, conductivity, and stability. Nevertheless, the [...] Read more.

The silkworm (Bombyx mori) is an economically important insect that plays a crucial role in agricultural development. Antimony tin oxide, a high-tech multifunctional nanomaterial, is extensively utilized in contemporary industries due to its properties of transparency, conductivity, and stability. Nevertheless, the toxicity and potential adverse effects of antimony tin oxide on living organisms remain poorly understood. In this study, we evaluated the effects of antimony tin oxide at varying concentrations (0–3.2 μg/μL) on the growth, oxidative stress response, gene expression, and midgut integrity of fifth-instar silkworm larvae. Exposure to high concentrations of antimony tin oxide resulted in a significant reduction in larval weight and severely disrupted the antioxidant defense system. RNA sequencing (RNA-Seq) analysis identified 239 differentially expressed genes (DEGs), which were confirmed by qPCR, revealing up-regulated lipid synthesis gene AGPAT5, down-regulated chitin degradation gene Chi, and suppressed glycerolipid hydrolysis gene H9J6N7_BOMMO. Histopathological and ultrastructural examinations revealed severe damage to the structure of midgut epithelial cells. Structural and functional analysis of conserved domains in key DEG-encoded proteins revealed that gene dysregulation disrupted energy metabolism and compromised the physical barrier, ultimately linking molecular abnormalities to observed tissue damage. These findings elucidate the mechanisms by which antimony tin oxide induces midgut toxicity through interference with critical metabolic pathways and functional perturbations at the molecular level. Full article

(This article belongs to the Special Issue Advances in Ecotoxicology and Environmental Toxicology)

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21 pages, 1817 KB

Open AccessArticle

Physical Activity Is Associated with Gut Microbiome Features and Organic Acid Patterns in Adults Consuming Plant-Rich Diets: An Exploratory Cross-Sectional Study

by Ramona Alina Tomuța, Alexandra Caltea, Marc Cristian Ghitea, Evelin Claudia Ghitea, Maria Flavia Gîtea, Timea Claudia Ghitea and Florin Banica

Biology 2026, 15(6), 507; https://doi.org/10.3390/biology15060507 - 21 Mar 2026

Viewed by 430

Abstract

Background: Plant-rich dietary patterns are widely associated with metabolic and gastrointestinal health benefits. However, individuals consuming predominantly plant-based foods may also experience chronic low-dose exposure to dietary pesticide residues. At the same time, physical activity is recognized as an important lifestyle factor influencing [...] Read more.

Background: Plant-rich dietary patterns are widely associated with metabolic and gastrointestinal health benefits. However, individuals consuming predominantly plant-based foods may also experience chronic low-dose exposure to dietary pesticide residues. At the same time, physical activity is recognized as an important lifestyle factor influencing metabolic health and gut microbiome composition. How microbiome features and microbiome-related metabolic profiles vary according to physical activity level in adults consuming plant-rich diets and reporting gastrointestinal symptoms remains insufficiently characterized. Objective: To explore associations between physical activity level, gut microbiome characteristics, and urinary organic acid patterns in adults consuming predominantly plant-rich diets and experiencing gastrointestinal symptoms, within a cohort characterized by comparable estimated dietary pesticide exposure used as a contextual dietary background variable. Methods: This cross-sectional observational study included 93 adults consuming ≥50% plant-based foods for at least six months and reporting persistent gastrointestinal symptoms. Participants were stratified according to physical activity level using WHO-based thresholds (<150 vs. ≥150 min/week of moderate-intensity activity). Stool microbiota were assessed using a targeted quantitative PCR panel, and microbial diversity was summarized using a laboratory-derived Shannon index. A voluntary subgroup (n = 50) underwent targeted urinary organic acid analysis (LC–MS/MS). Dietary pesticide exposure was indirectly estimated using national surveillance data combined with individual dietary records and was applied uniformly across groups. Analyses were primarily descriptive and exploratory; results are presented as associations. Results: Estimated dietary pesticide exposure did not differ between physical activity groups. Participants with lower physical activity were older and exhibited lower microbial diversity and a higher prevalence of reduced abundance in selected commensal taxa. Differences were observed in selected intermediary organic acid markers, while no statistically significant difference was found for the bile acid-related indicator. Several cross-domain correlations were identified between microbial features and metabolite patterns. However, given the cross-sectional design, age imbalance between groups, and subgroup-based metabolomic analyses, the findings should be interpreted as hypothesis-generating rather than indicative of independent effects of physical activity. Conclusions: In adults consuming plant-rich diets and reporting gastrointestinal symptoms, physical activity level was associated with distinct microbiome and microbiome-related metabolic patterns under comparable estimated dietary pesticide exposure. These findings highlight the potential contribution of lifestyle factors to interindividual variability in gut microbial and metabolic profiles, while underscoring the need for age-adjusted, longitudinal, and biomarker-based studies to clarify directionality and mechanisms. Full article

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20 pages, 9428 KB

Open AccessArticle

Effect of Hydroxyapatite Nanoparticles on the Ultrastructure, Developmental Competence, and Expression of ZP3, MFN1, and NPM2 in Vitrified Bovine GV Oocytes

by Xiao-Xia Li, Shi-Yu Zhang, Jun Wang, Yi-Hang Wang, Jia-Hao Zhang, Shi-Han Zhao, Ping-Hua Cao, Yu-Mei Liu, Chen Zhou, Zhen Zhang, Qiao-Ting Shi, Waleid Mohamed EL-Sayed Shakweer, Ibrahim Mohamed EL-Sayed Shakweer and Zhi-Qian Xu

Biology 2026, 15(6), 506; https://doi.org/10.3390/biology15060506 - 21 Mar 2026

Viewed by 496

Abstract

To improve the vitrification efficiency of bovine germinal vesicle (GV) oocytes, the use of hydroxyapatite (HA) nanoparticles as a novel cryopreservation additive represents a promising approach. This study aimed to investigate the effects of HA nanoparticles and permeable cryoprotective agents (CPAs) on the [...] Read more.

To improve the vitrification efficiency of bovine germinal vesicle (GV) oocytes, the use of hydroxyapatite (HA) nanoparticles as a novel cryopreservation additive represents a promising approach. This study aimed to investigate the effects of HA nanoparticles and permeable cryoprotective agents (CPAs) on the ultrastructure, developmental competence, and gene expression of bovine GV oocytes following vitrification. Oocytes were vitrified in vitrification solutions containing HA nanoparticles of different sizes (20, 40, or 60 nm) and concentrations (0.01%, 0.05%, or 0.1%) to determine the optimal conditions based on survival rate, mitochondrial membrane potential (MMP) level, and developmental competence. Subsequently, the synergistic effects of HA nanoparticles and permeable CPAs (VS: 20% EG + 20% DMSO; VS1: 17.5% EG + 17.5% DMSO) were further evaluated. The optimal treatment (40 nm 0.05% HA nanoparticles) significantly increased MMP level, and improved developmental competence compared with the vitrified control group (p < 0.05). Among the vitrified groups, vitrified oocytes in the VS1-HA group (combining HA nanoparticles with reduced concentrations of permeable CPAs) exhibited the highest MMP level (1.89), maturation rate (50.39%), cleavage rate (27.07%), and blastocyst rate (10.53%) (p < 0.05). Ultrastructural analysis further revealed that the VS1-HA group maintained more intact zona pellucida structures and showed reduced mitochondrial swelling compared with the vitrified control group. Moreover, the expression levels of genes associated with zona pellucida formation (ZP3), mitochondrial fusion (MFN1), and chromatin remodeling (NPM2) were significantly upregulated in the VS1-HA group relative to the vitrified control group. Overall, these findings indicate that the combination of HA nanoparticles with lower concentrations of permeable CPAs enhances MMP level, alleviates vitrification-induced ultrastructural damage, and upregulates the expression of key developmental genes, thereby improving the developmental competence of vitrified bovine GV oocytes. Full article

(This article belongs to the Section Developmental and Reproductive Biology)

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26 pages, 7722 KB

Open AccessArticle

Transcriptome Analysis and Identification of Chemosensory Genes in Leguminivora glycinivorella

by Jiaqi Shi, Yuxin Zhou, Zhengxiao Du, Ruirui Li, Qi Wang, Yu Gao and Shusen Shi

Biology 2026, 15(6), 505; https://doi.org/10.3390/biology15060505 - 21 Mar 2026

Cited by 1 | Viewed by 441

Abstract

The soybean pod borer, Leguminivora glycinivorella, is a monophagous pest that threatens soybean production. Its larvae feed concealed within pods, which limits the efficacy of conventional insecticides. Elucidating its chemosensory system is therefore essential for developing green, behavior-based management strategies. Reference-based transcriptomics [...] Read more.

The soybean pod borer, Leguminivora glycinivorella, is a monophagous pest that threatens soybean production. Its larvae feed concealed within pods, which limits the efficacy of conventional insecticides. Elucidating its chemosensory system is therefore essential for developing green, behavior-based management strategies. Reference-based transcriptomics across multiple tissues of L. glycinivorella identified a comprehensive repertoire of chemosensory genes, including 76 odorant receptors (ORs), 15 gustatory receptors (GRs), 18 ionotropic receptors (IRs), 52 odorant-binding proteins (OBPs), 18 chemosensory proteins (CSPs), and 4 sensory neuron membrane proteins (SNMPs). Sequence and phylogenetic analyses characterized these candidates within the context of known insect chemosensory families. Notably, canonical bitter GRs and specific IR lineages (e.g., IR100/IR85a) were not detected in our dataset, potentially reflecting adaptation to the specialized soybean-feeding habit of this pest. Expression profiling further revealed pronounced sexual and tissue dimorphism: male antennae showed significant enrichment of putative pheromone receptors (PRs) and LglySNMP1, whereas several OBPs and ORs exhibited female-biased expression, suggesting roles in host location and oviposition. Additionally, the high expression of GR43a homologs points to fructose sensing, while the lack of detectable CO₂ receptor components (except LglyGR2) suggests atypical carbon dioxide perception mechanisms. Collectively, this study provides a valuable expression atlas of chemosensory genes in L. glycinivorella and identifies sex-specific candidate genes for future functional validation and behavior-based pest management. Full article

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

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19 pages, 1173 KB

Open AccessArticle

Molecular Basis of Sperm Methylome Response to Aging and Stress

by Olatunbosun Arowolo, Jiahui Zhu, Karolina Nowak, J. Richard Pilsner and Alexander Suvorov

Biology 2026, 15(6), 504; https://doi.org/10.3390/biology15060504 - 21 Mar 2026

Cited by 1 | Viewed by 460

Abstract

Aging and stress-related factors affect sperm DNA methylation in regions associated with genes responsible for embryonic development. The stochastic epigenetic variation hypothesis holds potential to explain these patterns, proposing that, in response to stressors, naturally variable methylation regions (VMRs) associated with morphogenetic genes [...] Read more.

Aging and stress-related factors affect sperm DNA methylation in regions associated with genes responsible for embryonic development. The stochastic epigenetic variation hypothesis holds potential to explain these patterns, proposing that, in response to stressors, naturally variable methylation regions (VMRs) associated with morphogenetic genes exhibit increased methylation variation to diversify phenotypes and improve the chances of survival of the genetic lineage. Here, we test predictions from this hypothesis using mouse and rat sperm DNA methylation data from publicly available sources. Specifically, we identify VMRs and analyze their overlap with regions differentially methylated (DMRs) in response to aging, stressors, and with various genomic elements. We demonstrate that the nature of the DNA regions, rather than the nature of the stressor, determines the response of the sperm methylome to aging and stress, and propose a model that explains shifts in methylation within VMRs through stochastic changes, whereby initially hypermethylated regions lose methylation and initially hypomethylated regions gain methylation. VMRs are depleted of open chromatin regions and histones in male germ cells and are enriched for a binding motif for ZFP42, an epigenetic remodeler. This knowledge may open opportunities for the development of interventions to control epigenetic information transfer via germ cells. Full article

(This article belongs to the Special Issue Feature Papers on Developmental and Reproductive Biology)

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12 pages, 1869 KB

Open AccessArticle

New Insights into Potential Anti-Aging Effects of a Dietary Supplement from Chlorella Growth Factor and γ-PGA in Aged SAMP8 Mice

by Ming-Yu Chou, Shih-An Yang, Po-Hsien Li, Tzu-Chien Kao, Shih-Yi Wang, Po-Hsun Cheng, Ching-Hsin Chi, Shu-Fen Cheng, Yue-Ching Wong and Ming-Fu Wang

Biology 2026, 15(6), 503; https://doi.org/10.3390/biology15060503 - 20 Mar 2026

Viewed by 748

Abstract

Aging is closely associated with oxidative stress, which contributes to functional decline and increased vulnerability to neurodegenerative diseases. Natural antioxidants, such as Chlorella Growth Factor (CGF) and γ-polyglutamic acid (γ-PGA), possess antioxidant and anti-aging properties; however, their combined effects remain unknown. This study [...] Read more.

Aging is closely associated with oxidative stress, which contributes to functional decline and increased vulnerability to neurodegenerative diseases. Natural antioxidants, such as Chlorella Growth Factor (CGF) and γ-polyglutamic acid (γ-PGA), possess antioxidant and anti-aging properties; however, their combined effects remain unknown. This study investigated the potential synergistic effects of CGF and γ-PGA supplementation in senescence-accelerated mouse-prone 8 (SAMP8) mice, a model characterized by early cognitive decline, locomotor deficits, and elevated oxidative DNA damage. Three-month-old male SAMP8 mice (n = 40) were divided into four groups: control, CGF (49.2 mg/kg BW/day), γ-PGA (20.5 mg/kg BW/day), and combined CGF + γ-PGA (69.7 mg/kg BW/day), and were treated for 13 weeks. Behavioral and physiological assessments included locomotor activity, aging index, and cognitive function (passive and active avoidance tests). Biochemical analysis focused on brain 8-hydroxy-2′-deoxyguanosine (8-OHDG) as a biomarker of oxidative DNA damage. Supplementation with CGF and γ-PGA, particularly in combination, significantly improved locomotor activity, aging scores, and cognitive functions. Notably, the combined treatment yielded the greatest reduction in brain 8-OHDG levels. These findings indicate that CGF and γ-PGA, when administered together, exert enhanced protective effects against functional and molecular aging. In conclusion, long-term supplementation with CGF and γ-PGA protects against aging-related decline in SAMP8 mice. This study highlights the potential of CGF and γ-PGA as safe, natural candidates for the development of functional foods or nutraceuticals aimed at promoting healthy aging and reducing oxidative stress-associated disorders. Full article

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24 pages, 362 KB

Open AccessReview

Migration and Accumulation of Uranium-Associated Heavy Metals in Mining-Affected Ecosystems (Water, Soil, and Plants)

by Madina Kairullova, Meirat Bakhtin, Kuralay Ilbekova and Danara Ibrayeva

Biology 2026, 15(6), 502; https://doi.org/10.3390/biology15060502 - 20 Mar 2026

Viewed by 501

Abstract

Uranium mining generates complex multi-element contamination that affects interconnected ecosystem components, posing long-term ecological and sanitary risks; this review places these impacts in a broad environmental context and aims to synthesize current knowledge on the distribution, migration, and accumulation of uranium and associated [...] Read more.

Uranium mining generates complex multi-element contamination that affects interconnected ecosystem components, posing long-term ecological and sanitary risks; this review places these impacts in a broad environmental context and aims to synthesize current knowledge on the distribution, migration, and accumulation of uranium and associated heavy metals in water, soil, and plants. A structured analysis of international peer-reviewed literature was conducted, focusing on documented pathways of metal release from tailings and waste dumps, geochemical controls on mobility, and biological uptake by vegetation. The reviewed studies consistently show that tailings and disturbed ore-bearing strata act as persistent sources of uranium and heavy metals (e.g., Cd, Pb, Cr, Ni, Zn, Mn, As), which migrate through infiltration, acid mine drainage, and atmospheric dispersion, leading to elevated concentrations in surface and groundwater and long-term accumulation in soils. Soils function as the principal sink controlling metal bioavailability, while vegetation reflects the bioavailable fraction and exhibits pronounced species-specific accumulation patterns. These processes establish an active “soil–water–plant” transfer chain that facilitates entry of contaminants into food webs. The synthesis indicates that combined uranium and heavy metal contamination represents a sustained ecological and public health concern in uranium-mining regions and underscores the need for integrated monitoring of soils, waters, and vegetation, along with quantitative risk assessment and scientifically grounded remediation strategies. Full article

(This article belongs to the Section Ecology)

23 pages, 3134 KB

Open AccessArticle

Effects of Rice–Duck–Crayfish Integrated System on the Community Structure of Plankton and Its Relationships with Environmental Factors

by Yuchen Jing, Zhiwei Xu, Mengmeng Pan, Jiaqian Yu, Zehua Fang, Xufa Ma and Zemao Gu

Biology 2026, 15(6), 501; https://doi.org/10.3390/biology15060501 - 20 Mar 2026

Viewed by 499

Abstract

To accurately manage precise feeding and water quality regulation in the rice–duck–crayfish integrated system (RDCI), the continuous monitoring of plankton and physicochemical parameters in the water was conducted from March 2022 to January 2023 in both the RDCI and the rice–crayfish continuous culture [...] Read more.

To accurately manage precise feeding and water quality regulation in the rice–duck–crayfish integrated system (RDCI), the continuous monitoring of plankton and physicochemical parameters in the water was conducted from March 2022 to January 2023 in both the RDCI and the rice–crayfish continuous culture system (RCCC). The results showed that a total of 188 phytoplankton species and 92 zooplankton species were identified in the RDCI, whereas 152 phytoplankton species and 95 zooplankton species were detected in the RCCC. The phytoplankton community composition was similar between these two systems. For zooplankton, Rotifera was the dominant group. However, Chlorophyta and Bacillariophyta were the dominant phytoplankton groups. Compared with the RCCC, the RDCI exhibited lower plankton density during the crayfish-farming stage and overwintering stage, but higher plankton biomass during the crayfish-farming stage, overwintering stage, and rice maturity stage. The diversity indices, richness indices, and evenness indices of both phytoplankton and zooplankton in the RDCI were significantly higher than those in the RCCC. Correlation analysis indicated that water temperature, dissolved oxygen, total nitrogen, and ammonia nitrogen were the key environmental factors affecting plankton community structure. In summary, compared with the RCCC, the RDCI exhibits higher plankton diversity and better evenness, suggesting a more complex and stable community structure. The species composition of plankton and related indices indicate that the RDCI mitigates the degree of eutrophication in water during both the crayfish farming and the overwintering stages, while increasing nutrients levels during the rice planting stage. This approach is beneficial for reducing non-point-source pollution in agriculture and promoting green agricultural development. Full article

(This article belongs to the Section Marine and Freshwater Biology)

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17 pages, 313 KB

Open AccessReview

Organizational Principles of Biological Systems

by Roberto Carlos Navarro-Quiroz, Kelvin Navarro Quiroz, Victor Navarro Quiroz, Antonio Gabucio, Ricardo Fernández-Cisnal, Noelia Geribaldi-Doldán, Cecilia Fernandez-Ponce, Ismael Sánchez Gomar, Yesit Bello Lemus, Eloina Zárate Peñata, Lisandro A. Pacheco-Lugo, Leonardo C. Londoño-Pacheco, Martha Rebolledo Cobos, Antonio Acosta Hoyos, Diana Pava Garzon, José Luis Villarreal Camacho and Elkin Navarro Quiroz

Biology 2026, 15(6), 500; https://doi.org/10.3390/biology15060500 - 20 Mar 2026

Viewed by 763

Abstract

How does the complex, adaptive, and autonomous organization of life emerge from the laws of physics and information? This review argues that the answer lies in a convergent set of universal organizational principles that constitute a physical and informational grammar of the living. [...] Read more.

How does the complex, adaptive, and autonomous organization of life emerge from the laws of physics and information? This review argues that the answer lies in a convergent set of universal organizational principles that constitute a physical and informational grammar of the living. Living systems are dissipative structures that achieve organizational closure—materially and energetically open, yet causally closed—thereby attaining genuine autonomy and agency. Their architecture exhibits fractal and modular scaling laws that maximize energy flow, robustness, and evolvability under universal physical constraints. Critically, organisms operate at critical transitions—zones of controlled instability where fluctuations amplify information processing, transforming noise into adaptive signal. This self-organized criticality enables functional degeneracy, relational redundancy, and evolutionary antifragility. Cognition emerges as a distributed process of active inference, operating through a predictive–corrective cycle that integrates perception, action, and learning under the Free Energy Principle. From molecular networks to ecosystems, the same physico-informational grammars unfold recursively, revealing a deep organizational holography: the principles of organization are replicated across scales. Evolution under the Law of Increasing Functional Information is not random drift, but a directional expansion of functional complexity—a thermodynamic gradient towards greater agency. This synthesis challenges biological exceptionalism: the trajectory from thermodynamics to cognition is continuous, physically constrained, and potentially inevitable. Life does not violate physical laws—it fulfills them in regimes of high informational complexity, instantiating fundamental principles in self-organized architectures capable of prediction, memory, and purpose. The objective of this work is to articulate how the synthesis of these principles not only unifies physics and biology, but also illuminates the profound continuity between thermodynamics, chemistry, informational constraints, organization, and the mind. Full article

(This article belongs to the Section Theoretical Biology and Biomathematics)

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22 pages, 2251 KB

Open AccessArticle

Environmental Changes During the Late Glacial and Early Holocene Transition Revealed by Palaeolimnological Record from Southern Lithuania

by Gražyna Kluczynska, Neringa Gastevičienė and Vaida Šeirienė

Biology 2026, 15(6), 499; https://doi.org/10.3390/biology15060499 - 20 Mar 2026

Viewed by 434

Abstract

This study presents integrated Cladoceran, plant macrofossil and diatom-based environmental reconstruction from the Čepkeliai Bog (Southern Lithuania), covering the Late Glacial–Early Holocene transition. The objective was to assess palaeoenvironmental changes with a focus on trophic state, acidification, and water-level fluctuations and to explore [...] Read more.

This study presents integrated Cladoceran, plant macrofossil and diatom-based environmental reconstruction from the Čepkeliai Bog (Southern Lithuania), covering the Late Glacial–Early Holocene transition. The objective was to assess palaeoenvironmental changes with a focus on trophic state, acidification, and water-level fluctuations and to explore the applicability of these assemblages as temperature-sensitive indicators. The findings of our study revealed that sedimentation started at about 13,200–13,000 cal yr BP in a deep, oligotrophic and cold-water palaeobasin. Inferred palaeoenvironment changes correlate with the GI-1b event (Gertsenzee oscillation). A significant ecological shift to a shallow, warm, ecologically diverse environment occurredat about 13,000 cal yr BP and is consistent with the GI-1a (Allerød) period. The Younger Dryas (12,850–11,650 cal yr BP) is characterised by a rise in lake level and oligo-mesotrophic and high-water transparency conditions. At the end of the Younger Dryas (around 12,000 cal yr BP), climate warming and a drop in water levels were recorded. Intensive palaeobasin swamping processes began around 9700 years cal yr BP, during the Boreal period. A short-lived “9.2” cooling event was fixed at about 9200–9000 cal yr BP. The results obtained provide new insights into postglacial palaeoenvironmental dynamics in the southeastern Baltic region. Full article

(This article belongs to the Section Ecology)

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15 pages, 3656 KB

Open AccessArticle

Construction of a Candidate Differentially Expressed Transcript Profile Associated with the Hair Follicle Cycle in Jiangnan Cashmere Goats (Capra hircus)

by Cuiling Wu, Gvlnigar Amar, Sen Tang, Asma Anwar, Yaqian Wang, Wenna Liu, Qingfa Yan, Shengchao Ma and Xuefeng Fu

Biology 2026, 15(6), 498; https://doi.org/10.3390/biology15060498 - 20 Mar 2026

Viewed by 355

Abstract

Dynamic changes in gene and transcript expression represent a key factor in regulating the cyclical development of hair follicles. In this study, based on Nanopore sequencing (ONT-seq) data of skin tissue from three developmental stages (anagen (An), catagen (Cn), and telogen (Tn)) of [...] Read more.

Dynamic changes in gene and transcript expression represent a key factor in regulating the cyclical development of hair follicles. In this study, based on Nanopore sequencing (ONT-seq) data of skin tissue from three developmental stages (anagen (An), catagen (Cn), and telogen (Tn)) of Jiangnan cashmere goat hair follicles, this study presents a profile of candidate DETs implicated in cycle regulation by delineating their stage-specific expression patterns and dynamic expression trends from anagen to telogen. A large proportion of the candidate DETs were significantly enriched in functions related to fat synthesis, storage, or metabolism, with significance levels of p < 0.05 or p < 0.01. These significantly enriched DETs, which were generally upregulated from An to Cn or downregulated from Cn to Tn, support a model where accelerated intradermal fat deposition promotes the progression from An to Cn, while its subsequent decrease facilitates the transition from Cn to Tn. Concurrently, our results also suggest a potential role for dynamic changes in AS patterns in regulating the hair follicle cycle. This regulatory role of AS patterns is potentially mediated through affecting genes related to lipid synthesis/metabolism or cell structure/interaction. Notably, a broader range of fat synthesis, storage, or metabolism-related transcripts showed significant differential expression (p < 0.05) in the An vs. Cn group. Ultimately, by establishing this candidate DET profile, we aim to provide fresh perspectives for deciphering the complex molecular regulation of the hair follicle cycle and to identify new targets for genetically enhancing or molecularly breeding cashmere traits in cashmere goats. Full article

(This article belongs to the Section Genetics and Genomics)

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20 pages, 8540 KB

Open AccessReview

Ticks: Biology, Habitat, Threats and Protection Methods

by Marlena Szalata, Karolina Wielgus, Mikołaj Danielewski, Andrzej Hnatyszyn, Milena Szalata, Marzena Skrzypczak-Zielińska and Ryszard Słomski

Biology 2026, 15(6), 497; https://doi.org/10.3390/biology15060497 - 20 Mar 2026

Viewed by 922

Abstract

The most common species of tick in Europe is the castor bean tick (Ixodes ricinus), which is found in forests, parks, and gardens and is active almost all year round. Ticks are among the most important arthropods and vectors of disease, [...] Read more.

The most common species of tick in Europe is the castor bean tick (Ixodes ricinus), which is found in forests, parks, and gardens and is active almost all year round. Ticks are among the most important arthropods and vectors of disease, transmitting a wide range of parasites that sometimes lead to the death of infected organisms. The peak incidence of tick-borne diseases occurs between May and September; however, due to global warming, people are increasingly exposed to tick-borne diseases throughout the year. In order to increase the possibility of preventing the transmission of diseases by ticks, it is necessary to become thoroughly familiar with the life cycle of ticks and the environment in which they live. Vaccines are available for some diseases, such as tick-borne encephalitis, while others require a highly specific diagnosis. Another major problem is the long period between the tick bite, which often goes unnoticed or is even ignored by the patient or the doctor, and the development of tick-borne diseases. Increasing attention is being paid to the prevention of tick-borne diseases through prevention of tick bites, quick tick removal, use of repellents, appropriate land management, vaccinations, and the use of plants as natural acaricides. Full article

(This article belongs to the Section Ecology)

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13 pages, 7440 KB

Open AccessArticle

GAMMA-RAY: A Fully Automated and Rapid System for High-Dimensional Multi-Phenotype Analysis Considering Population Structure

by Taegun Kim, Jaeseung Song and Jong Wha Joanne Joo

Biology 2026, 15(6), 496; https://doi.org/10.3390/biology15060496 - 20 Mar 2026

Viewed by 396

Abstract

GWASs have successfully identified numerous genetic variants linked to complex traits, but traditional univariate approaches often fail to capture shared genetic architecture across multiple phenotypes. As the scale of genomic data continues to increase, the demand for more efficient multi-phenotype analysis methods has [...] Read more.

GWASs have successfully identified numerous genetic variants linked to complex traits, but traditional univariate approaches often fail to capture shared genetic architecture across multiple phenotypes. As the scale of genomic data continues to increase, the demand for more efficient multi-phenotype analysis methods has become particularly critical. In addition, the issue of population structure must also be properly addressed to ensure robust and unbiased results. Multivariate methods for multi-phenotype analysis, such as GAMMA, address this by combining linear mixed models with multivariate distance matrix regression to account for population structure; however, since these methods utilize computationally intensive models, developing efficient implementations is essential for practical analysis. Although GAMMA is a well-designed and effective tool, its original implementation relies on multiple programming environments and requires frequent data exchanges between components. These factors increase computational burden and complicate installation and execution for users unfamiliar with programming, making practical applications, particularly for high-dimensional datasets, challenging. Here, we present GAMMA-RAY, a high-performance C++ implementation that streamlines the computational pipeline, leverages parallel processing, and employs efficient matrix operations to achieve substantial reductions in runtime and memory usage. GAMMA-RAY provides both a user-friendly web-based interface for non-programmers and a standalone version for secure local execution. We further applied GAMMA-RAY to a yeast dataset and identified putative trans-eQTLs, in which several variants overlapped with previously reported cis- and trans-eQTLs. In addition, functional enrichment analysis revealed that the associated trans-eGenes are enriched, a conclusion consistently supported by biological annotation resources and underscoring the biological significance of these results. Full article

(This article belongs to the Section Bioinformatics)

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15 pages, 1654 KB

Open AccessArticle

Lipid Profiles and Fatty Acid Positional Distribution in Two Farmed Seahorse Species by Untargeted Lipidomics and Enzymatic Hydrolysis

by Tianxi Bi, Dandan Wang, Xiaoming Jiang, Tingting Lin, Yi Shao, Yuming Wang, Taher Abdelnaby, Lu Zhang, Chengcheng Wang and Tiantian Zhang

Biology 2026, 15(6), 495; https://doi.org/10.3390/biology15060495 - 20 Mar 2026

Viewed by 451

Abstract

Seahorses exhibit significant nutritional functions, including antioxidant and anti-tumor properties, with species like Hippocampus abdominalis and Hippocampus erectus now commercially farmed on a large scale. Notably, lipids are the key bioactive components distinguishing marine from terrestrial organisms. However, the lipidomic profiles of these [...] Read more.

Seahorses exhibit significant nutritional functions, including antioxidant and anti-tumor properties, with species like Hippocampus abdominalis and Hippocampus erectus now commercially farmed on a large scale. Notably, lipids are the key bioactive components distinguishing marine from terrestrial organisms. However, the lipidomic profiles of these cultured species are rarely reported, limiting their targeted nutritional application. Therefore, this study aimed to characterize and compare the lipid profiles of the newly introduced H. abdominalis with the currently farmed H. erectus. Methodologically, we employed an integrated approach utilizing untargeted lipidomics coupled with enzymatic hydrolysis to evaluate the lipid content, composition, molecular species, and fatty acid positional distribution of both species. The results revealed that triglyceride (TG) was the dominant lipid class in both seahorses. Notably, H. abdominalis exhibited higher overall phospholipid (PL) levels, along with elevated docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA) in its TG fraction. Positional distribution analysis demonstrated that DHA was evenly distributed at the sn-1,3 and sn-2 positions in H. abdominalis, but concentrated at the sn-1,3 positions in H. erectus, whereas EPA was primarily localized at sn-1,3 in both species. Furthermore, H. abdominalis contained higher DHA levels in phosphatidylcholine (PC) and phosphatidylethanolamine (PE) (predominantly at the sn-1 position) and possessed abundant alkoxy ether PLs. Ultimately, this work fills crucial research gaps regarding the lipid characteristics of commercially cultured seahorses, providing a fundamental basis for species identification, nutritional evaluation, and the future development of seahorse-derived functional lipids. Full article

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19 pages, 5903 KB

Open AccessArticle

Spatial Distribution of Soil Bacterial Communities Along an Altitudinal Gradient in Alpine Meadows of the Northeastern Qinghai–Tibet Plateau and Their Relationship with Environmental Factors

by Wenfang Chen, Huichun Xie, Shuang Ji, Yue Zhang, Xunxun Qiu, Zhiqiang Dong and Jiaxiang Xu

Biology 2026, 15(6), 494; https://doi.org/10.3390/biology15060494 - 20 Mar 2026

Viewed by 406

Abstract

Despite the essential role of soil microbial communities in driving nutrient cycling within alpine meadows, their distribution patterns along elevational gradients and their responses to environmental changes remain largely unexplored. To investigate this, soil samples were collected from five elevations (3300–4500 m) in [...] Read more.

Despite the essential role of soil microbial communities in driving nutrient cycling within alpine meadows, their distribution patterns along elevational gradients and their responses to environmental changes remain largely unexplored. To investigate this, soil samples were collected from five elevations (3300–4500 m) in the northeastern Qinghai–Tibet Plateau to analyze bacterial community composition and diversity, as well as their associations with soil physicochemical properties and enzyme activities. The results showed significant variation in bacterial community composition and diversity across elevations. Actinomycetota, Pseudomonadota, and Acidobacteriota were the dominant phyla at all sampling sites. Community diversity, measured by the Shannon index, generally increased with elevation, peaking at 4500 m and lowest at 3300 m. Pearson correlation analysis and redundancy analysis (RDA) indicated that soil bacterial community structure was significantly correlated with both soil nutrient factors and enzyme activities. Among these variables, total potassium, available phosphorus, catalase, and urease were strongly correlated with bacterial community differentiation. In addition, PERMANOVA results showed that elevation was the primary factor driving community variation, explaining a substantial proportion of the variation in community composition at a statistically significant level. Overall, this study highlights the distribution of bacterial communities in alpine meadow soils along an elevational gradient and their environmental associations, providing foundational data for understanding microbial community responses to environmental changes in alpine ecosystems. Full article

(This article belongs to the Special Issue Microbial Life at the Extremes: From Environmental Diversity to Functional Insights)

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16 pages, 670 KB

Open AccessBrief Report

Comparative Effects of Dexamethasone and ASC Secretome in an Ex Vivo Osteoarthritis Co-Culture Model

by Elena Della Morte, Francesca Cadelano, Andrea Pasquini, Luigi Zagra, Alessandro Baj, Chiara Giannasi and Stefania Niada

Biology 2026, 15(6), 493; https://doi.org/10.3390/biology15060493 - 20 Mar 2026

Viewed by 450

Abstract

Osteoarthritis (OA) is a multifactorial disease characterized by inflammation, extracellular matrix remodeling, and joint degeneration, and it still lacks disease-modifying treatments. Here, we applied an ex vivo OA model based on transwell co-cultures of cartilage and synovial membrane explants harvested from OA patients [...] Read more.

Osteoarthritis (OA) is a multifactorial disease characterized by inflammation, extracellular matrix remodeling, and joint degeneration, and it still lacks disease-modifying treatments. Here, we applied an ex vivo OA model based on transwell co-cultures of cartilage and synovial membrane explants harvested from OA patients to compare the effects of adipose-derived stem/stromal cell (ASC) conditioned medium (CM) with dexamethasone (DEX), a clinically used corticosteroid. Explants were treated for 48 h with 100 nM DEX, CM derived from 5 × 10⁵ ASCs, or left untreated. Outcomes included gene and protein expression of key mediators, metalloprotease and aggrecanase activities, and nitric oxide release. DEX significantly reduced inflammatory markers (e.g., PTGS, IL-1β, and IDO) and VEGF expression in both tissues, while CM did not elicit consistent anti-inflammatory effects. Regarding matrix remodeling, both treatments reduced metalloprotease activity, with DEX modulating MMP3 and MMP13 expression in both tissues and CM reducing only MMP3 expression in cartilage while presenting high levels of TIMP-1. These results confirm the robustness of the model, demonstrated by reproducible responses to DEX and its high-throughput potential, and underscore the need for mechanistic studies to optimize novel biotherapeutics. Full article

(This article belongs to the Special Issue Advancements in Mesenchymal Stem Cell-Derived Secretome)

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23 pages, 3028 KB

Open AccessArticle

SVNeoPP: A Workflow for Structural-Variant-Derived Neoantigen Prediction and Prioritization Using Multi-Omics Data

by Wanyang An, Xiaoxiu Tan, Zhenhao Liu, Li Zou, Manman Lu and Lu Xie

Biology 2026, 15(6), 492; https://doi.org/10.3390/biology15060492 - 19 Mar 2026

Viewed by 510

Abstract

Background: Tumor neoantigens are key targets for personalized vaccines and T-cell therapies, yet most pipelines focus on neoantigens derived from SNV/small indel and often yield a limited number of high-quality candidates. SVs are prevalent in tumors and can generate novel chimeric sequences and [...] Read more.

Background: Tumor neoantigens are key targets for personalized vaccines and T-cell therapies, yet most pipelines focus on neoantigens derived from SNV/small indel and often yield a limited number of high-quality candidates. SVs are prevalent in tumors and can generate novel chimeric sequences and neopeptides, making them a promising additional source of neoantigens. However, SV-derived neoantigen prediction remains challenging due to breakpoint uncertainty, isoform-dependent coding inference, and limited integration of multi-dimensional evidence and reproducibility. Methods: We developed SVNeoPP (Structural Variant Neoantigen Prediction and Prioritization), an end-to-end workflow for SV-derived neoantigen analysis. SVNeoPP takes WGS and RNA-seq as inputs, performs SV calling and annotation, and reconstructs altered transcripts and coding sequences in a traceable, isoform-aware manner to generate candidate peptides. Candidates are prescreened by integrating antigen-processing features with HLA binding prediction, and then hierarchically filtered and prioritized based on transcript expression, LC–MS/MS proteomics evidence, immunogenicity predictions, and sequence similarity to experimentally validated neoantigen databases. SVNeoPP is implemented in Snakemake to enable modular extension, checkpoint-based restarts, and end-to-end reproducibility. Results: Using a hepatocellular carcinoma (HCC) multi-omics dataset as a proof of concept, we demonstrated the performance of SVNeoPP and obtained a high-priority shortlist of candidate peptides. Compared with other methods, SVNeoPP substantially expanded the candidate search space for SV-derived neoantigens and showed more favorable distributions of antigen-processing and HLA binding features. Conclusions: SVNeoPP provides a reusable, traceable, and interpretable multi-dimensional evidence-driven framework for SV-derived neoantigens. As a complementary module to SNV/small-indel pipelines, it broadens the neoantigen candidate repertoire and generates ranked candidates with interpretable evidence to facilitate downstream prioritization and decision-making. Full article

(This article belongs to the Section Bioinformatics)

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16 pages, 4023 KB

Open AccessArticle

Does Vegetation Recovery Limit the Habitat Use of Herbivore? Decadal Evidence of a Potential Ecological Mismatch

by Zhiwei Liu, Zhangfeng Cheng, Rui Guo, Qian Lei, Liulin Guan, Xiao Song, Shanshan Zhao and Aichun Xu

Biology 2026, 15(6), 491; https://doi.org/10.3390/biology15060491 - 19 Mar 2026

Viewed by 331

Abstract

Large-scale forest ecological restoration is commonly expected to improve habitat quality and promote population growth of forest-dependent herbivores. Yet, whether vegetation recovery facilitates or constrains herbivore growth and habitat use at local scales within nature reserves remains unclear, as vegetation recovery and canopy [...] Read more.

Large-scale forest ecological restoration is commonly expected to improve habitat quality and promote population growth of forest-dependent herbivores. Yet, whether vegetation recovery facilitates or constrains herbivore growth and habitat use at local scales within nature reserves remains unclear, as vegetation recovery and canopy closure might alter forage availability and lead to ecological mismatch between vegetation features and population dynamic. Here, we used the endangered species South China sika deer as the study species, and its dominant distribution region—Qingliangfeng Biosphere Reserve—as the study area. Using decadal camera-trapping data (2015–2024) and extracted vegetation and other environmental variables, we quantified decadal trends in sika deer activity intensity and interannual variation in vegetation (leaf area index, LAI, and normalized difference vegetation index, NDVI). We incorporated topographic and anthropogenic disturbance variables and applied generalized linear mixed models and generalized linear models to analyze its habitat use. We found that: (1) Numbers of independent photographs and the relative abundance index of sika deer increased significantly and consistently from 2015 to 2024. (2) LAI exhibited substantial interannual variability without a stable trend. In contrast, segmented regression identified a clear temporal breakpoint in NDVI, with a significant increasing trend before 2021 followed by a pronounced decline thereafter. (3) In all years, distance to settlement had a significant and negative effect on activity intensity, whereas distance to road, elevation, and year had significant positive effects. LAI and NDVI showed negative and weak effects on sika deer activity intensity. In specific years, LAI had a significantly negative effect in early periods whereas NDVI became significantly negative in mid and late periods. Other environmental variables exhibited interannual heterogeneity. Our findings demonstrate that vegetation recovery within the reserve does not automatically improve habitats for forest-dependent herbivores and could lead to a potential ecological mismatch. Full article

(This article belongs to the Special Issue Advances in Wildlife Conservation and Habitat Management in the Anthropocene)

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11 pages, 1390 KB

Open AccessReview

A Systematic Review of the Relationship Between Host Personality Traits and Parasitic Infection

by Zhu-Cheng Gao, Ling-Ying Shuai, Li-Qing Wang, Meng-Yuan Xu, Dong Yu and Zhi-Tao Liu

Biology 2026, 15(6), 490; https://doi.org/10.3390/biology15060490 - 19 Mar 2026

Viewed by 402

Abstract

Parasitism plays an important role in many fundamental ecological processes and is widespread both geographically and taxonomically. Interactions between parasites and hosts are often complex, and much attention has been paid to the relationship between host traits and parasitism. However, a comprehensive review [...] Read more.

Parasitism plays an important role in many fundamental ecological processes and is widespread both geographically and taxonomically. Interactions between parasites and hosts are often complex, and much attention has been paid to the relationship between host traits and parasitism. However, a comprehensive review of the association between host personality and parasitic infection is lacking. In this review, we systematically synthesized 54 studies published over the past few decades. Generally, the relationship between animal personality traits and parasitic infection is complex, and no generic pattern exists. Many biological processes may be involved, and biological factors (such as host sex and parasite type) may significantly shape the personality–infection relationship. Different personality traits may also indicate different relationships with parasitic infection. We confirmed that host personality and parasitic infection exhibit a mutually influential, multi-feedback dynamic. Finally, several research gaps were described, and we emphasized the importance of incorporating the BACI design in experiments. Full article

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15 pages, 277 KB

Open AccessArticle

TNFSF4/OX40L and IKZF1/IKAROS Genetic Variant Associations with Egyptian Juvenile Systemic Lupus Erythematosus (JSLE)

by Zeinab R. Attia, Ahmed M. Amshawee, Ahmed Flayyih Hasan, Dalia Tawfeek Hussein, Rania A. Abd El Azeem, Mohamed M. Zedan, Thuraya M. Mutawi, Nanis S. El-beltagy and Mohamed A. El Basuni

Biology 2026, 15(6), 489; https://doi.org/10.3390/biology15060489 - 19 Mar 2026

Viewed by 460

Abstract

Background: The etiopathogenesis of juvenile systemic lupus erythematosus (JSLE), a complex and complicated illness, is unknown. Genetic, environmental, and dysregulated immune system responses are all thought to contribute to the disease’s etiology. Important immunological molecules that regulate different immune cells and are associated [...] Read more.

Background: The etiopathogenesis of juvenile systemic lupus erythematosus (JSLE), a complex and complicated illness, is unknown. Genetic, environmental, and dysregulated immune system responses are all thought to contribute to the disease’s etiology. Important immunological molecules that regulate different immune cells and are associated with autoimmune disorders are TNFSF4 and IKZF1. Thus, our purpose was to discover if TNFSF4 and IKZF1 mutations left the Egyptian population genetically predisposed to SLE. Methods: Using real-time polymerase chain reaction (RT-PCR), polymorphism analysis of the TNFSF4 rs1234315 C/T and IKZF1 rs11980379 C/T genes was performed on extracted DNA from JSLE patients and healthy controls. Results: TNFSF4 frequencies (rs1234315 T allele, CT, TT genotypes, dominant and recessive models) were substantially associated with a higher incidence of JSLE (p < 0.05) compared to healthy controls. Conversely, IKZF1 frequencies (rs11980379 T allele, TC, TT genotypes, and dominant model) significantly correlated with a lower incidence of JSLE. Furthermore, the TC + CC rs11980379 genotype was identified as significantly associated with lower kidney biopsy grades and a lower incidence of lupus nephritis. Conclusions: Our findings suggest that TNFSF4 and IKZF1 polymorphisms affect vulnerability to juvenile SLE. Full article

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14 pages, 5177 KB

Open AccessArticle

Establishing Area-Specific Brain Organoids Through Transcription Factor-Mediated Patterning

by Jonghun Kim, Yoon-Sun Jang, Minseong Lee, Na Young Choi, Yooju Jung, Junho Lim and Tae Hwan Kwak

Biology 2026, 15(6), 488; https://doi.org/10.3390/biology15060488 - 19 Mar 2026

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Abstract

The human cerebral cortex is organized into distinct area-specific regions along the rostral–caudal axis, yet current human brain organoid models incompletely recapitulate this regional diversity. Here, we establish an area-specific brain organoid platform by leveraging transcription factors (TFs) identified through re-analysis of in [...] Read more.

The human cerebral cortex is organized into distinct area-specific regions along the rostral–caudal axis, yet current human brain organoid models incompletely recapitulate this regional diversity. Here, we establish an area-specific brain organoid platform by leveraging transcription factors (TFs) identified through re-analysis of in vivo human cortical transcriptomic datasets. Publicly available single-cell RNA sequencing datasets from human developing cortex were re-analyzed to identify differentially expressed genes associated with rostral and caudal cortical identities. From this analysis, we identified SP9 (rostral-enriched) and DMRTA2 (caudal-enriched) as candidate TFs governing regional specification. To model cortical area identity, these TFs were overexpressed in an inducible manner during human cerebral organoid (hCO) generation. Overexpression of SP9 resulted in hCOs exhibiting rostral cortical characteristics, whereas DMRTA2 overexpression promoted caudal cortical features. The resulting hCOs showed distinct regional identities, reflected by differential expression of area-specific markers. In addition, these regional identities were accompanied by distinct functional phenotypes, as calcium imaging revealed divergent patterns of spontaneous neural activity between rostral and caudal hCOs. Altogether, our findings demonstrate that overexpression of TFs enables the controlled generation of area-specific hCOs. This approach provides a scalable and reproducible platform for studying human cortical regionalization and offers a framework for investigating region-specific mechanisms underlying neurodevelopmental and neurological disorders. Full article

(This article belongs to the Special Issue Brain Organoids: Construction, Analysis, and Application)

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Biology, Volume 15, Issue 6 (March-2 2026) – 69 articles

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