Biology

15 pages, 2306 KB

Open AccessArticle

Endothelial PAI-1 Drives Lead-Induced Cerebral Amyloid Angiopathy via Activation of C3⁺ Decorin⁺ A1-like Astrocytes

by Huiying Gu, Cloria Luo and Yansheng Du

Biology 2026, 15(4), 297; https://doi.org/10.3390/biology15040297 (registering DOI) - 7 Feb 2026

Environmental lead (Pb) exposure remains a significant public health concern, and its association with cerebrovascular injury and Alzheimer’s disease (AD) is increasingly recognized. In this study, we demonstrated using an in vitro system that Pb exposure significantly increased the expression and release of [...] Read more.

Environmental lead (Pb) exposure remains a significant public health concern, and its association with cerebrovascular injury and Alzheimer’s disease (AD) is increasingly recognized. In this study, we demonstrated using an in vitro system that Pb exposure significantly increased the expression and release of endothelial plasminogen activator inhibitor-1 (PAI-1). A conditioned medium collected from Pb-treated endothelial cells induced the formation of complement component 3 (C3)⁺ decorin⁺ A1-like astrocytes, which had been shown to be specifically associated with vascular amyloid. Immunoprecipitation with the PAI-1 antibody to remove PAI-1 from the culture medium, or treatment of endothelial cells with PAI-1 inhibitors, significantly inhibited the formation of C3⁺ decorin⁺ A1-like astrocytes. Furthermore, in vivo studies further supported this finding, indicating that lead does indeed increase the number of perivascular C3⁺ decorin⁺ A1-like astrocytes, and that the PAI-1 inhibitor blocked this induction. Building upon our previous findings, we demonstrate that lead exposure may induce cerebral amyloid angiopathy (CAA) pathology through the formation of C3⁺ decorin⁺ A1-like astrocytes mediated by endothelial cell PAI-1. Our results strongly suggest that PAI-1 is a key mediator linking endothelial stress and lead-induced vascular amyloidosis pathology. Full article

(This article belongs to the Section Neuroscience)

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17 pages, 3888 KB

Open AccessArticle

Mitogenomic Phylogeny and Adaptive Evolution of Snailfishes (Liparidae) Reveal Correlation Between tRNA Rearrangements and Deep-Sea Colonization

by Ruxiang Wang, Ang Li, Shuai Che, Huan Wang and Shufang Liu

Biology 2026, 15(4), 295; https://doi.org/10.3390/biology15040295 (registering DOI) - 7 Feb 2026

Abstract

The snailfish family (Liparidae) represents one of the most rapidly speciating and ecologically diverse lineages of marine fishes, with species distributed across a broad bathymetric range from intertidal zones to the hadal depths. Despite their ecological and evolutionary significance, phylogenetic relationships and adaptive [...] Read more.

The snailfish family (Liparidae) represents one of the most rapidly speciating and ecologically diverse lineages of marine fishes, with species distributed across a broad bathymetric range from intertidal zones to the hadal depths. Despite their ecological and evolutionary significance, phylogenetic relationships and adaptive mechanisms within Liparidae remain poorly resolved due to morphological conservatism, phenotypic plasticity, and limited genomic resources due to challenges such as sampling difficulties and a reliance on partial mtDNA markers. In this study, we sequenced, assembled, and annotated the complete mitochondrial genomes of two snailfish species, Liparis chefuensis and Liparis tanakae, collected from the Yellow Sea. The mitogenome of L. chefuensis is 18,870 bp in length, encoding 13 protein-coding genes (PCGs), 2 rRNAs, and 22 tRNAs, while that of L. tanakae spans 17,485 bp and contains 13 PCGs, 2 rRNAs, and 23 tRNAs. Phylogenetic reconstruction based on the concatenated sequences of 13 mitochondrial PCGs from 15 liparid species revealed that L. chefuensis clusters within the subgenus Lyoliparis, contradicting its previous classification under Careliparis and suggesting a need for taxonomic reassessment. Notably, we identified distinct patterns of tRNA gene rearrangement in the cluster between ND2 and COI, which suggest a link to both phylogeny and habitat depth. Shallow-water species (<30 m) possess the tRNA^Trp-tRNA^Tyr-tRNA^Ala-tRNA^Asn-tRNA^Cys (WYANC) arrangement, whereas deep-water species (>100 m) display the derived tRNA^Trp-tRNA^Asn-tRNA^Cys-tRNA^Tyr-tRNA^Ala-tRNA^Cys/tRNA^Ala (WNCYAC/A) configurations. These rearrangements are hypothesized to originate from tandem duplication events followed by random gene loss, potentially reflecting adaptive evolution to deep-sea environments. Additionally, L. tanakae exhibits a markedly higher number of non-canonical G–U and A–C base pairs in its tRNA secondary structures, indicating substantial structural divergence. Our findings not only provide essential mitogenomic resources for snailfish systematics and species identification but also propose that tRNA rearrangements in mitochondrial genomes may serve as genomic innovations facilitating deep-sea colonization. This study enhances our understanding of mitochondrial genome evolution and environmental adaptation in marine fishes. Full article

(This article belongs to the Special Issue Genetics and Evolutionary Biology of Aquatic Organisms)

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18 pages, 5298 KB

Open AccessArticle

Neuroprotective Effects of Herbal Formula Yookgong-Dan on Oxidative Stress-Induced Tau Hyperphosphorylation in Rat Primary Hippocampal Neurons

by Hyunseong Kim, Jin Young Hong, Changhwan Yeo, Hyun Kim, Wan-Jin Jeon, Junseon Lee, Yoon Jae Lee and In-Hyuk Ha

Biology 2026, 15(3), 294; https://doi.org/10.3390/biology15030294 - 6 Feb 2026

Abstract

This study sought to evaluate the neuroprotective effects of YGD in an oxidative stress-induced Alzheimer’s disease (AD)-like cellular model and to elucidate the underlying molecular pathways, with a focus on tau phosphorylation, Aβ accumulation, and antioxidant defense mechanisms. Rat primary hippocampal neurons were [...] Read more.

This study sought to evaluate the neuroprotective effects of YGD in an oxidative stress-induced Alzheimer’s disease (AD)-like cellular model and to elucidate the underlying molecular pathways, with a focus on tau phosphorylation, Aβ accumulation, and antioxidant defense mechanisms. Rat primary hippocampal neurons were exposed to hydrogen peroxide to induce oxidative stress. The effects of YGD on neuronal viability, neurite outgrowth, and synaptic integrity were assessed using the immunodetection of microtubule-associated protein 2 (MAP2), postsynaptic density protein 95 (PSD-95), and synapsin-1. Levels of phosphorylated tau and Aβ were quantified, and the involvement of extracellular signal-regulated kinase (ERK), glycogen synthase kinase 3β (GSK3β), and nuclear factor-erythroid 2-related factor-2 (Nrf2) pathways was examined. Additionally, in silico molecular docking studies targeting the ATP-binding site of GSK3β were conducted to screen major phytochemicals from the ten medicinal herbs constituting YGD. YGD markedly enhanced neuronal viability under oxidative stress, promoted neurite extension, and increased synaptic marker expression (MAP2, PSD-95, and synapsin-1). Treatment reduced phosphorylated tau by suppressing ERK and GSK3β activation and significantly decreased Aβ accumulation. YGD also upregulated antioxidant defenses via the activation of the Nrf2 pathway. Docking simulations identified oleanolic acid (from Cornus officinalis) as the most potent GSK3β binder (−9.86 ± 0.40 kcal/mol), forming stable interactions with ARG96, ASN95, and GLU97. Additional compounds, including alisol C, drypemolundein B, and friedelin, demonstrated favorable binding energies and engaged key ATP-binding site residues. YGD confers neuroprotection through the integrated modulation of tau phosphorylation, Aβ pathology, and oxidative stress, partly via the multi-target engagement of GSK3β by its constituent phytochemicals. These findings support that YGD attenuates oxidative stress-induced AD-like cellular alterations. Full article

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19 pages, 5356 KB

Open AccessArticle

Transcriptome Sequencing Analysis Reveals the Mechanisms of Poly-γ-Glutamic Acid Enhanced the Chilling and Freezing Tolerance in Wheat

by Yuqi Niu, Jiang Liu, Bin Bu, Zhaohui Tang, Yongkang Ren and Haizhen Ma

Biology 2026, 15(3), 293; https://doi.org/10.3390/biology15030293 - 6 Feb 2026

Abstract

Low-temperature stress significantly limits wheat growth and productivity. Poly-γ-glutamic acid (γ-PGA) is an environmentally friendly green molecular material that plays an important role in plant growth and regulation; however, its protective mechanisms against cold stress in wheat remain poorly understood. In this study, [...] Read more.

Low-temperature stress significantly limits wheat growth and productivity. Poly-γ-glutamic acid (γ-PGA) is an environmentally friendly green molecular material that plays an important role in plant growth and regulation; however, its protective mechanisms against cold stress in wheat remain poorly understood. In this study, the effect of γ-PGA on both chilling (4 °C) and freezing (−18 °C) resistance in wheat seedlings and its underlying mechanisms were comparatively studied. The results showed that the γ-PGA-treated seedlings exhibited a 128.81% higher survival rate after freezing stress and maintained significantly greater biomass accumulation under both stress conditions (62.44% and 26.56% higher dry weight under chilling and freezing stress, respectively). A physiological analysis revealed that γ-PGA enhanced osmoprotectant (proline and soluble sugars) accumulation and activated key antioxidant enzymes (SOD, POD, and APX). Then, an RNA-seq analysis identified 11,401 and 7721 differentially expressed genes under chilling and freezing stress, respectively, with 3598 common genes constituting a core cold-response network. KEGG and GO analyses demonstrated significant enrichment in pathways related to carbon metabolism, glutathione metabolism, phenylpropanoid–flavonoid biosynthesis, fatty acid metabolism, and cell wall organization. Notably, γ-PGA strongly upregulated key genes in phenylpropanoid–flavonoid metabolism (TraesCS2B02G615000 and TraesCS2B02G624400), glutathione metabolism (TraesCS1B02G127900), and lipid metabolism (TraesCS1B02G018700). These results provide comprehensive molecular insights into γ-PGA-mediated cold tolerance and support its potential application in sustainable wheat production under low-temperature stress conditions. Full article

(This article belongs to the Collection Abiotic Stress in Plants and Resilience: Recent Advances)

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16 pages, 1250 KB

Open AccessArticle

Involvement of Nitric Oxide in TRPV4-Induced Relaxations of Mouse and Human Pulmonary Arteries

by Vytis Bajoriūnas, Agilė Tunaitytė, Augusta Volkevičiūtė, Silvijus Abramavičius, Ieva Bajoriūnienė, Edgaras Stankevičius and Ulf Simonsen

Biology 2026, 15(3), 292; https://doi.org/10.3390/biology15030292 - 6 Feb 2026

Abstract

The transient receptor potential vanilloid 4 channel (TRPV4) is thought to play a pivotal role in pulmonary arterial circulation. The present study hypothesizes that TRPV4 activation increases nitric oxide (NO) release and activates calcium-activated potassium of intermediate conductance (KCa3.1) in pulmonary arteries. Pulmonary [...] Read more.

The transient receptor potential vanilloid 4 channel (TRPV4) is thought to play a pivotal role in pulmonary arterial circulation. The present study hypothesizes that TRPV4 activation increases nitric oxide (NO) release and activates calcium-activated potassium of intermediate conductance (KCa3.1) in pulmonary arteries. Pulmonary arteries were isolated from wild-type mice (wt) and mice deficient in KCa3.1 channels (Kcnn4⁻/⁻) and mounted for simultaneous NO concentration and relaxation measurements. Human small pulmonary arteries were isolated and mounted in microvascular myographs for isometric tension recordings. Acetylcholine-induced increases in NO and relaxation of pulmonary arteries were slightly decreased in pulmonary arteries from Kcnn4⁻/⁻ versus wt mice. An activator of TRPV4 channels, GSK1016790A, increased NO and relaxation to the same degree in pulmonary arteries from wt and Kcnn4⁻/⁻ mice. A blocker of TRPV4 channels, HC06704, inhibited increases in NO concentration with no effect on acetylcholine (ACh) relaxation in pulmonary arteries from wt mice, but blocked increases in NO concentration and relaxation in pulmonary arteries from Kcnn4⁻/⁻ mice and responses to GSK1016790A in pulmonary arteries from wt and Kcnn4⁻/⁻ mice. Concentration-dependent relaxations induced by an inhibitor of sarcoplasmic Ca-ATPase, cyclopiazonic acid, were blocked in the presence of an inhibitor of NO synthase and a blocker of KCa3.1 channels, TRAM-34, in pulmonary arteries from wt mice, but were unaltered in the presence of TRAM-34 in arteries from Kcnn4⁻/⁻ mice, or the presence of a blocker of TRPV4 channels. In small human pulmonary arteries, ACh and sodium nitroprusside (SNP) induced concentration-dependent relaxations, blocked by endothelial cell removal, in the presence of an inhibitor of NO synthase and the KCa3.1 channel blocker TRAM-34. GSK1016790A induced relaxation of human pulmonary arteries with endothelium, but failed to relax arteries without endothelium. The findings suggest that TRPV4 channels are involved in endothelium-dependent relaxation and likely regulate pulmonary vascular tone by modulating NO release. Full article

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

32 pages, 5252 KB

Open AccessReview

In Vitro Fish Cell Culture: From Primary Muscle Cells to Cell-Based Meat in Cyprinidae

by Piyathip Setthawong, Chanati Jantrachotechatchawan, Suppakorn Netmanee, Napat Tandikul, Chaiyaboot Ariyachet, Witchukorn Phuthong and Kornsorn Srikulnath

Biology 2026, 15(3), 291; https://doi.org/10.3390/biology15030291 - 6 Feb 2026

Abstract

Fish offer an excellent source of high-quality protein with balanced nutrients and low fat content. However, the increasing global demand for food and the impacts of climate change have led to a significant decline in wild fish stocks. Cultivated fish meat has therefore [...] Read more.

Fish offer an excellent source of high-quality protein with balanced nutrients and low fat content. However, the increasing global demand for food and the impacts of climate change have led to a significant decline in wild fish stocks. Cultivated fish meat has therefore emerged as a promising sustainable food alternative. In this review, we summarize the structural and physiological characteristics of fish muscle and highlight the methods used to establish primary muscle cell cultures, including explant outgrowth and enzymatic dissociation, alongside the optimization of environmental conditions and growth media composition. Particular attention is given to the isolation, development, and characterization of Cyprinidae muscle-derived cell lines via morphological assessments, gene expression profiling, and karyotyping. In addition, we discuss recent advances in scaffold-based and three-dimensional culture systems as well as the application of bioreactors for large-scale production. Current challenges include the limited availability of standardized muscle cell lines, dependence on serum-containing media, and the high cost of growth factors. Future progress will depend on innovations in serum-free formulations, cost-effective media, and reproducible culture protocols. Ultimately, fish muscle cell culture supports not only the development of alternative protein sources but also aquatic health research, disease modeling, and sustainable bioproduction. Full article

(This article belongs to the Topic Biotechnology and Microorganisms for Next-Generation Food Products and Processes)

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17 pages, 530 KB

Open AccessArticle

Neurogenetic Profiles of Anxiety, Impulsivity, and Personality Traits in Elite Combat Sport Athletes: A Cluster-Based Analysis

by Kinga Humińska-Lisowska, Remigiusz Recław, Aleksandra Suchanecka, Krzysztof Chmielowiec, Kinga Łosińska, Jolanta Chmielowiec and Anna Grzywacz

Biology 2026, 15(3), 290; https://doi.org/10.3390/biology15030290 - 6 Feb 2026

Abstract

Behavioral regulation in elite combat sports relies on traits such as anxiety, impulsivity, and personality, which are partly shaped by dopaminergic signaling. However, integrative approaches linking multidimensional behavioral profiles with genetic variability in athletes remain limited. This study aimed to identify distinct psychological [...] Read more.

Behavioral regulation in elite combat sports relies on traits such as anxiety, impulsivity, and personality, which are partly shaped by dopaminergic signaling. However, integrative approaches linking multidimensional behavioral profiles with genetic variability in athletes remain limited. This study aimed to identify distinct psychological profiles in elite combat athletes and examine whether these profiles differ in selected dopaminergic gene polymorphisms. A total of 200 male Polish elite combat athletes completed validated questionnaires assessing personality, anxiety, impulsivity, attention-related symptoms, and hedonic capacity. Standardized psychological variables were analyzed using a two-step clustering procedure. Genotype distributions were compared across clusters using chi-square tests. The clusters showed clear behavioral differentiation. Cluster 1 demonstrated higher anxiety, impulsivity, neuroticism, and attention-related symptoms. Cluster 2 showed lower anxiety and impulsivity alongside higher extraversion and conscientiousness. Cluster 3 displayed intermediate behavioral characteristics but the most distinctive genotype pattern. These findings suggest that combining behavioral clustering with genetic data may help characterize meaningful neurogenetic profiles in elite athletes and provide hypothesis-generating insights into genotype–phenotype relationships. Full article

(This article belongs to the Special Issue Neurogenetics of Behaviour—2nd Edition)

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18 pages, 2826 KB

Open AccessArticle

Comprehensive Proteomics and β-Hydroxybutyrylation Profiling in Starvation-Induced Gastrocnemius Muscle Remodeling

by Leilei Cui, Chunping Huang, Yu Su, Shiqi Xu, Liang Zha, Qiuyuan Zhao, Wu Quan, Xinqiang Lan, Yang Xiang and Qiquan Wang

Biology 2026, 15(3), 289; https://doi.org/10.3390/biology15030289 - 6 Feb 2026

Abstract

Starvation elicits profound metabolic adaptations in skeletal muscle, enabling survival during nutrient scarcity. While global proteomic changes underpinning muscle atrophy have been studied, the role of lysine β-hydroxybutyrylation (Kbhb), a novel metabolite-derived post-translational modification linked to ketone metabolism, remains largely unexplored. In this [...] Read more.

Starvation elicits profound metabolic adaptations in skeletal muscle, enabling survival during nutrient scarcity. While global proteomic changes underpinning muscle atrophy have been studied, the role of lysine β-hydroxybutyrylation (Kbhb), a novel metabolite-derived post-translational modification linked to ketone metabolism, remains largely unexplored. In this study, we subjected mice to 72 h of food deprivation and performed integrative quantitative proteomics and Kbhb-modified peptide profiling on gastrocnemius muscle. Starvation induced significant body weight and muscle mass loss, accompanied by increased systemic β-hydroxybutyrate levels and widespread Kbhb modification of muscle proteins. Proteomic analysis revealed extensive downregulation of ribosomal and translation-associated proteins, coupled with upregulation of autophagy and lipid catabolism pathways, highlighting a coordinated shift from anabolic processes to catabolic and oxidative metabolism. Deep Kbhb profiling identified over 7500 modified lysine sites across 2000 proteins, with starvation triggering a global increase in Kbhb on key metabolic enzymes involved in glycolysis, TCA cycle, fatty acid β-oxidation, and amino acid metabolism. Notably, starvation-enhanced Kbhb preferentially targeted evolutionarily conserved lysines proximal to catalytic or cofactor-binding domains, implicating a regulatory role in enzymatic activity modulation. Conversely, Kbhb on structural and contractile proteins was downregulated, suggesting functional reprioritization of muscle physiology during fasting. Our findings uncover lysine β-hydroxybutyrylation as a dynamic, metabolically responsive PTM mediating gastrocnemius muscle adaptation to energy deficiency, expanding the paradigm of potentially metabolite-driven epigenetic and non-epigenetic regulatory mechanisms in muscle metabolism. Full article

(This article belongs to the Special Issue New Insights into Skeletal Muscle Metabolism in Pathological and Physiological Conditions)

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18 pages, 2436 KB

Open AccessArticle

Induction of Autoimmune Myocarditis in Diversity Outbred Mice

by Meghna Sur, Kiruthiga Mone, Shraddha Singh, Mahima T. Rasquinha, Jean-Jack M. Riethoven, Indranil Mukhopadhyay, Raymond A. Sobel and Jay Reddy

Biology 2026, 15(3), 288; https://doi.org/10.3390/biology15030288 - 6 Feb 2026

Abstract

Background. Inbred mouse models of autoimmune myocarditis are routinely used to investigate the immune mechanisms underlying dilated cardiomyopathy. However, their translational relevance is limited because observations made in a single inbred strain may not reflect those of outbred human populations. This limitation can [...] Read more.

Background. Inbred mouse models of autoimmune myocarditis are routinely used to investigate the immune mechanisms underlying dilated cardiomyopathy. However, their translational relevance is limited because observations made in a single inbred strain may not reflect those of outbred human populations. This limitation can be overcome by using Diversity Outbred (DO) mice, whose genetic variability is comparable to that of humans. Methods. To investigate the utility of DO mice, we characterized their immune cell distributions and induced myocarditis by immunization with porcine cardiac myosin (PCM) emulsified in complete Freund’s adjuvant. Antigen-specific T cell and antibody responses were evaluated using lymphocytes and serum samples, respectively, and hearts were examined histologically for inflammatory changes. Results. First, we noted no significant variations in the majority of immune cell populations, which include T cells and B cells. However, NK cells, double positive for CD49b and NK1.1, were lacking in both sexes. While we noted sex differences in the expression of major histocompatibility complex class II molecules in antigen-presenting cells, expression of costimulatory molecules was similar in both sexes. Second, upon immunization, we demonstrated that the PCM was immunogenic, and the PCM-reactive T cell responses were generated in both males and females, as measured by a proliferation assay. Third, cytokine analysis revealed marginal detection of Th1 (IFN-γ) and Th17 (IL-17 and IL-22) cytokines, mainly with three doses of immunization. Fourth, determination of PCM-reactive antibody responses revealed significant amounts of IgG1 and IgG2b isotypes. Finally, histological analysis revealed varying degrees of myocarditis in individual mice of both sexes. Conclusions. Our data suggest that mild autoimmune myocarditis can be induced in DO mice. However, to capture the heterogeneity in disease susceptibility, large sample cohorts are required. Full article

(This article belongs to the Special Issue Advances in Cardiac and Vascular Biology: From Mechanisms to Pathophysiology)

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12 pages, 1201 KB

Open AccessArticle

Low Testosterone and Sperm Quality Alterations: A Prospective Study of Sperm DNA Fragmentation and Chromatin Condensation in Infertile Men

by Asmaa Serbouti, Kenza Berrada, Samy Housbane, Noureddine Louanjli and Rachid Aboutaieb

Biology 2026, 15(3), 287; https://doi.org/10.3390/biology15030287 - 6 Feb 2026

Abstract

(1) Background: Testosterone plays a key role in spermatogenesis and in maintaining semen quality and sperm DNA integrity. Consequently, reduced testosterone levels may disrupt these processes and contribute to male infertility. This study aimed to evaluate the impact of low testosterone levels on [...] Read more.

(1) Background: Testosterone plays a key role in spermatogenesis and in maintaining semen quality and sperm DNA integrity. Consequently, reduced testosterone levels may disrupt these processes and contribute to male infertility. This study aimed to evaluate the impact of low testosterone levels on semen parameters, sperm DNA fragmentation, and chromatin condensation; (2) Methods: This was a prospective study that included 214 men aged 25–45 years undergoing infertility evaluation. Participants were classified into two groups according to serum testosterone levels: low testosterone and normal testosterone. Total testosterone was determined using electrochemiluminescence immunoassay. Semen analysis was carried out according to the WHO 2021 guidelines. The DNA fragmentation index was assessed using the TUNEL assay. The sperm decondensation index was evaluated by aniline blue staining; (3) Results: Men with low serum total testosterone levels (<2.64 ng/mL) exhibited significantly impaired semen parameters compared with those with normal testosterone levels. Serum total testosterone was positively correlated with sperm concentration (rs = 0.43, p < 0.001), total motility (rs = 0.20, p = 0.005), normal morphology (rs = 0.25, p < 0.001), and sperm vitality (rs = 0.173, p = 0.014). In contrast, testosterone levels were negatively correlated with the DNA fragmentation index (rs = −0.221, p = 0.0017) and the chromatin decondensation index (rs = −0.19, p = 0.0086). A higher proportion of pathological DFI (>15%) was observed in the low testosterone group. (4) Conclusions: These findings support the essential role of testosterone in sustaining spermatogenesis, semen quality, and sperm DNA integrity and highlight the crucial importance of testosterone assessment in the diagnosis and pathophysiological understanding of male infertility. Full article

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

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21 pages, 5865 KB

Open AccessArticle

Species Composition and Biomass Dynamics of Filamentous Algae and Their Environmental Drivers in Eriocheir sinensis Aquaculture Ponds

by Yudi Song, Fei Fei, Dijun Luo, Jie Yang, Gaohua Ji and Xugan Wu

Biology 2026, 15(3), 286; https://doi.org/10.3390/biology15030286 - 5 Feb 2026

Abstract

Filamentous opportunistic algae, which behave as opportunistic species, are frequently observed in Eriocheir sinensis aquaculture ponds. These algae can entangle Eriocheir sinensis and release harmful substances during decomposition, thereby negatively impacting farming performance. At present, their management largely depends on non-selective herbicides, while [...] Read more.

Filamentous opportunistic algae, which behave as opportunistic species, are frequently observed in Eriocheir sinensis aquaculture ponds. These algae can entangle Eriocheir sinensis and release harmful substances during decomposition, thereby negatively impacting farming performance. At present, their management largely depends on non-selective herbicides, while fundamental research on species composition and biomass dynamics remains limited. In this study, 19 aquaculture ponds across five E. sinensis farms in Shanghai were monitored over a two-year period. Filamentous algae species were identified using both morphological and molecular techniques, and their biomass and coverage were quantified. Concurrently, physicochemical parameters of the water were measured to analyze algal occurrence patterns and key environmental drivers. A total of 19 species belonging to four genera of the phyla Chlorophyta and Charophyta were identified. Rhizoclonium was the most common genus, followed by Cladophora and Spirogyra. These genera exhibited distinct seasonal succession, with Cladophora and Spirogyra dominating in spring, while Rhizoclonium predominanted in summer and autumn. Filamentous algal biomass reached its peak in May 2024, with a dry weight of 42.92 g/m². The two-way ANOVA results indicated significant main effects of month and region, as well as a significant month × region interaction. The Spearman correlation analysis revealed a strong positive association between algal biomass and pH. This pattern is consistent with the effect where the intense algal photosynthesis raises water pH through the uptake of dissolved carbon dioxide. The total biomass was significantly correlated with the nitrogen-to-phosphorus ratio, suggesting that nitrogen and phosphorus availability influenced algal growth. Moreover, filamentous algal coverage was positively associated with maximum algal biomass. The linear regression analysis further revealed that multiple environmental factors jointly contributed to algal proliferation, with total nitrogen, nitrate nitrogen, and fluorescent dissolved organic matter (fDOM) showing relatively strong associations with maximum biomass. These findings provide a scientific basis for the ecological control and targeted management of filamentous algae in aquaculture systems. Full article

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16 pages, 1157 KB

Open AccessArticle

Fine-Grained Assignment of Unknown Marine eDNA Sequences Using Neural Networks

by Sébastien Villon, Morgan Mangeas, Véronique Berteaux-Lecellier, Laurent Vigliola and Gaël Lecellier

Biology 2026, 15(3), 285; https://doi.org/10.3390/biology15030285 - 5 Feb 2026

Abstract

Environmental DNA (eDNA) metabarcoding is an innovative tool that is transforming ecological research. It offers a simple and effective method for simultaneously detecting numerous species across a wide range of environments. The method relies on assigning DNA sequences sampled from the environment to [...] Read more.

Environmental DNA (eDNA) metabarcoding is an innovative tool that is transforming ecological research. It offers a simple and effective method for simultaneously detecting numerous species across a wide range of environments. The method relies on assigning DNA sequences sampled from the environment to taxa, which is straightforward for species that have already been sequenced and are represented in reference databases. However, existing bioinformatics tools often fail to deliver accurate, fine-grained assignments when target species are absent from these databases. This limitation arises from handcrafted classification thresholds that do not account for nucleotide positional information. Here, we propose a deep neural architecture specifically designed to exploit both nucleotide identity and positional patterns in short TELEO sequences. Using an in-silico validation framework based on NCBI genbank sequences, we compare our approach with several state-of-the-art bioinformatics tools (Obitools, Kraken2, Lolo), as well as alternative sequence embedding methods, under controlled conditions. Our approach yields significantly higher classification accuracy at the genus and family levels, achieving average accuracies of 94.7% at the genus level and 86.5% at the family level, substantially outperforming the tested reference-based pipelines. The method remains robust with limited training data and shows improved performance when nucleotide positional information is preserved through sequence alignment. These results demonstrate the potential of AI-powered eDNA metabarcoding to complement existing taxonomic assignment tools, particularly in contexts where reference databases are incomplete or species-level resolution is not achievable, thereby supporting biodiversity monitoring and ecosystem management. Full article

(This article belongs to the Special Issue Environmental DNA (eDNA) for Assessment of Coastal Marine Biodiversity)

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16 pages, 1112 KB

Open AccessArticle

Lisosan G as a Modulator of Serum Lipid/Lipoprotein Changes, Lipid Metabolism and TGF-β1 Level in Neoplastic and Non-Neoplastic Liver Injury: A Rat Model Study

by Bartłomiej Szymczak, Luisa Pozzo, Szymon Zmorzyński, Anna Wilczyńska, Andrea Vornoli, Maria Lutnicka and Marta Wójcik

Biology 2026, 15(3), 284; https://doi.org/10.3390/biology15030284 - 5 Feb 2026

Abstract

Chronic liver injury is accompanied by coordinated disturbances in lipid trafficking and inflammatory–fibrogenic signaling. Transforming growth factor beta 1 (TGF-β1) signaling has been implicated in hepatic fibrogenesis and tumor-associated remodeling and may co-vary with disturbances in lipid trafficking. Lisosan G (LG), a fermented [...] Read more.

Chronic liver injury is accompanied by coordinated disturbances in lipid trafficking and inflammatory–fibrogenic signaling. Transforming growth factor beta 1 (TGF-β1) signaling has been implicated in hepatic fibrogenesis and tumor-associated remodeling and may co-vary with disturbances in lipid trafficking. Lisosan G (LG), a fermented wheat-derived nutraceutical, has reported antioxidant and anti-inflammatory activity and may influence these interconnected pathways. This study evaluated whether dietary LG alters the lipid composition of plasma lipoprotein fractions and hepatic TGF-β1 levels across distinct liver contexts. Seventy-two female Wistar rats were randomized into nine groups (n = 8/group) defined by liver condition, consisting of healthy control (Control), non-neoplastic liver (PH), and neoplastic liver injury (HCC; PH followed by diethylnitrosamine, DEN), and diet (standard diet, SD + 2.5% LG, or SD + 5% LG). Plasma lipoproteins (VLDL, LDL, HDL₁, HDL₂) were isolated by stepwise KBr density-gradient ultracentrifugation, and cholesterol (TC), phospholipids (PL), and triacylglycerols (TG) were quantified in each fraction. Hepatic TGF-β1 was measured by ELISA and normalized to total protein. LG effects depended strongly on baseline liver status, with significant Condition × Diet interactions for most lipid endpoints and for hepatic TGF-β1. In healthy rats, LG produced fraction-selective remodeling rather than uniform lipid lowering, including increased VLDL-TG at both doses and non-linear changes in cholesterol distribution across LDL and HDL subfractions. After PH, LG broadened lipid remodeling, including reduced VLDL-PL, increased VLDL-TG (both doses), and an increase in LDL-TC at 5% LG, accompanied by marked changes in HDL₁/HDL₂ cholesterol partitioning. In HCC, LG induced pronounced, often dose-dependent increases in LDL-associated lipids (LDL-PL, LDL-TG, LDL-TC) and increased HDL₁-TC while decreasing HDL₂-TC. Hepatic TGF-β1 was elevated in PH and further increased in HCC versus controls; LG reduced hepatic TGF-β1 in a condition-dependent manner, with the strongest reduction at 5% LG in HCC. Dietary Lisosan G remodels circulating lipoprotein lipid composition in a liver-status-dependent manner and is associated with reduced hepatic TGF-β1 abundance in injured liver, most prominently in neoplastic injury. These findings are consistent with the notion that nutraceutical interventions may show stronger phenotypic effects under perturbed metabolic–fibrogenic states than under stable physiology, while highlighting the need for mechanistic work to distinguish altered lipoprotein secretion from changes in peripheral clearance and to assess pathway-level TGF-β signaling. Full article

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21 pages, 1086 KB

Open AccessReview

Environmentally Driven Precision Neurology: A Neurogenomic Perspective

by Mia Yang Ang, Nur Azalina Suzianti Feisal, Muhammad Danial Che Ramli and Zaw Myo Hein

Biology 2026, 15(3), 283; https://doi.org/10.3390/biology15030283 - 5 Feb 2026

Abstract

The World Health Organization identifies environmental pollution as a primary global health threat, and its role in the onset and progression of neurological diseases is becoming increasingly clear. In the era of precision medicine, understanding the complex interplay between genetic predispositions and environmental [...] Read more.

The World Health Organization identifies environmental pollution as a primary global health threat, and its role in the onset and progression of neurological diseases is becoming increasingly clear. In the era of precision medicine, understanding the complex interplay between genetic predispositions and environmental factors is particularly important. The global increase in neurological conditions such as Alzheimer’s disease, Parkinson’s disease, and neurodevelopmental disorders highlights the urgent need for precision neurology. Environmental factors like air pollution, pesticides, and prenatal stress can induce epigenetic changes, including DNA methylation and histone modifications, which alter gene expression and shape disease risk. Advances in neurogenomics, bioinformatics, and artificial intelligence are revolutionizing our ability to decipher these mechanisms, presenting new approaches for personalized diagnostics and interventions. However, significant challenges related to data integration, computational complexity, high implementation costs, and ethical considerations remain. Overcoming these barriers is essential to harness the full potential of environmentally informed precision neurology. This review synthesizes current knowledge on the integration of environmental and genomic data to better predict, prevent, and treat neurological diseases, aiming to alleviate their growing global burden and improve patient outcomes. Full article

(This article belongs to the Section Neuroscience)

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15 pages, 2806 KB

Open AccessArticle

The Complete Mitochondrial Genome of Portunion sinensis (Crustacea: Isopoda) and Its Phylogenies

by Teng Huang, Xiaowan Ma, Shengping Zhong, Jie Chen, Dewei Cheng, Xuyang Chen, Dong Yang, Lixing Huang, Theerakamol Pengsakul, Ying Qiao and Wenhong Li

Biology 2026, 15(3), 282; https://doi.org/10.3390/biology15030282 - 4 Feb 2026

Abstract

In this study, we conducted molecular identification and complete mitochondrial genome annotation of isopod parasites isolated from mud crabs (Scylla paramamosain) in the China Sea. The specimen was identified as Portunion sinensis, a recently described species of the family Entoniscidae. [...] Read more.

In this study, we conducted molecular identification and complete mitochondrial genome annotation of isopod parasites isolated from mud crabs (Scylla paramamosain) in the China Sea. The specimen was identified as Portunion sinensis, a recently described species of the family Entoniscidae. P. sinensis is characterized by an anterior thorax positioned vertically and posterior ventral processes directed backwards; the female’s marsupium is formed by the close adhesion of oostegites to the host membrane; the first oostegite is differentiated into three parts; the pleopoda have well-developed lamellar and pleural lamellae; and two ventral ovarian processes are present along with a pair of dorsal processes. The complete mitochondrial genome of the parasite is 14,603 bp in length, containing 35 genes (13 protein-coding genes, 20 transfer RNAs, and 2 ribosomal RNAs) as well as a putative control region (CR) located between the cob and nad1 genes. This study represents the initial characterization of the mitochondrial genome of P. sinensis. These findings provide molecular validation of its status as an independent species and lay the groundwork for the future identification of parasites within the genus Portunion. These data provide a necessary molecular reference for future research into the systematics and evolutionary history of decapod-infesting parasites. Full article

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

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14 pages, 1208 KB

Open AccessArticle

Using Sodium Thiosulfate to Heighten Copper (Cu (II)) Tolerance of the Freshwater Microalga Chlorella vulgaris

by Caihong Tian, Tongshun Si, Wenxin Chen, Menglin Liu, Zan Li, Weijun Wang, Guohua Sun, Yanwei Feng, Xiaohui Xu, Qiang Wang, Cuiju Cui and Jianmin Yang

Biology 2026, 15(3), 281; https://doi.org/10.3390/biology15030281 - 4 Feb 2026

Abstract

Heavy metals such as copper are commonly found in aquatic environments. Microalgae can effectively adsorb heavy metals, while high concentrations impair their physiological and biochemical processes. This research investigated the impact of varying concentrations of sodium thiosulfate (Na₂S₂O₃ [...] Read more.

Heavy metals such as copper are commonly found in aquatic environments. Microalgae can effectively adsorb heavy metals, while high concentrations impair their physiological and biochemical processes. This research investigated the impact of varying concentrations of sodium thiosulfate (Na₂S₂O₃) on the heavy metal tolerance of Chlorella vulgaris. Results showed that Na₂S₂O₃ and copper ions Cu(II) co-stress significantly improved the tolerance of C. vulgaris to Cu(II). To explore the mechanism, weighted gene co-expression network analysis (WGCNA) and trend analysis were applied to study the gene regulatory network under combined stress. A total of 103 significantly differentially expressed genes (DEGs) were identified. Further Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that the majority of DEGs are associated with photosynthesis, energy and liposome metabolisms. Physiological metrics, including chlorophyll content, photosynthetic activity, malondialdehyde (MDA), superoxide dismutase (SOD), and catalase (CAT), also aligned with bioinformatics results. This research offers a promising approach to reduce heavy metal pollution in water bodies. Full article

17 pages, 3309 KB

Open AccessArticle

Fusarium pseudograminearum Isolates Show Enhanced Growth and Na⁺ Uptake but Suppressed Mycotoxin Production After Exposure to NaCl at Different Temperatures

by Emiliano Delli Compagni, Mario Masiello, Miriam Haidukowski, Giulia Carmassi, Antonio Moretti, Alberto Pardossi and Susanna Pecchia

Biology 2026, 15(3), 280; https://doi.org/10.3390/biology15030280 - 4 Feb 2026

Abstract

Several Fusarium species have demonstrated the ability to thrive in saline soils and to tolerate or prefer high salt concentrations. In this context, the potential halophilic or halotolerant lifestyle of Fusarium pseudograminearum was investigated. Four isolates (3B, PVS-Fu 7, ColPat-1, and CBS 109956) [...] Read more.

Several Fusarium species have demonstrated the ability to thrive in saline soils and to tolerate or prefer high salt concentrations. In this context, the potential halophilic or halotolerant lifestyle of Fusarium pseudograminearum was investigated. Four isolates (3B, PVS-Fu 7, ColPat-1, and CBS 109956) were grown at different temperatures (10, 15, 20, 25, 30, and 35 °C) and NaCl concentrations (0, 7, 14, 21, and 28 g L⁻¹), and daily growth, mycotoxin production, and K⁺ and Na⁺ accumulation within hyphae were assessed. All F. pseudograminearum isolates exhibited strong adaptability to saline conditions, with significantly enhanced growth in the presence of NaCl. All isolates accumulated Na⁺ within their hyphae while retaining K⁺. The production of deoxynivalenol (DON) and zearalenone (ZEA) was generally suppressed following NaCl exposure, consistent with the known inhibitory effect of reduced water activity on mycotoxin biosynthesis. However, at 22 °C, two isolates, 3B and CBS 109956, showed no significant differences in ZEA production between the control (no salt) and the medium containing the lowest NaCl concentration tested (7 g L⁻¹). Notably, isolate 3B, obtained from the halophyte Salicornia europaea, retained the highest levels of both Na⁺ and K⁺ within hyphae and showed the greatest overall adaptation to salinity. These results confirm the hypothesis that the ability of F. pseudograminearum to colonize and infect a halophytic host is indicative of a halophilic lifestyle. In the context of increasing soil salinization, these findings help identify conditions that permit pathogen persistence without hazardous mycotoxin accumulation. Full article

(This article belongs to the Special Issue Young Researchers in Plant Sciences)

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17 pages, 948 KB

Open AccessReview

Effect of Dry–Wet Cycling on Methanotrophs in Wetland Soils

by Xi Zhu, Zhihao Zhang, Anan Du and Bingru Liu

Biology 2026, 15(3), 279; https://doi.org/10.3390/biology15030279 - 4 Feb 2026

Abstract

Wetlands occupy a mere 6% of Earth’s land surface, yet they contribute 25–45% of global natural methane (CH₄) emissions. A key contradiction emerges here: it is the soil of these wetlands that serves as the host for methane-trophic microorganisms, which can [...] Read more.

Wetlands occupy a mere 6% of Earth’s land surface, yet they contribute 25–45% of global natural methane (CH₄) emissions. A key contradiction emerges here: it is the soil of these wetlands that serves as the host for methane-trophic microorganisms, which can oxidize the vast majority of the methane they produce under specific conditions (for example, the aerobic interface). A wetland’s role as either a net source or sink for atmospheric CH₄ is therefore a primary driver of hydrological variability. This research synthesis current understandings of how wet–dry cycles regulate methanotrophic communities and their CH₄ consumption capacity. Shifts in the water table directly modulate methanotroph physiology, community structure, and metabolic activity. These hydrological effects are further amplified or attenuated by nitrogen availability, plant-derived exudates, and edaphic properties. Herein, key knowledge gaps concerning the adaptive responses of methanotrophs to hydrological change are identified, and targeted research priorities improving predictions of wetland CH₄ fluxes under contrasting moisture regimes are accordingly outlined. This review synthesizes recent advances to highlight the mechanistic understanding essential for guiding wetland management strategies. Full article

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17 pages, 7817 KB

Open AccessArticle

Spatial Analysis and Spread Monitoring of a Population of Juniperus macrocarpa Sm. Across Coastal Dune Systems in Northern Tuscany (Italy)

by Andrea Bertacchi, Diego Orazi, Stefano Bedini and Tiziana Lombardi

Biology 2026, 15(3), 278; https://doi.org/10.3390/biology15030278 - 3 Feb 2026

Abstract

Background: Juniperus macrocarpa Sm. is a key shrub species of the Mediterranean coastal dune systems. The species, considered vulnerable, often shows fragmented or declining populations due to coastal erosion and human pressure. However, along a protected stretch of the northern Tuscany coast [...] Read more.

Background: Juniperus macrocarpa Sm. is a key shrub species of the Mediterranean coastal dune systems. The species, considered vulnerable, often shows fragmented or declining populations due to coastal erosion and human pressure. However, along a protected stretch of the northern Tuscany coast it displays an opposite trend, with an apparent expansion of the species. Methods: To assess recent population dynamics, we compared high-resolution aerial imagery from 2013 with UAV orthophotos from 2023 across two dune systems of the Migliarino–San Rossore–Massaciuccoli Regional Park (Italy). The dune profile was divided into three belts (B1: shifting dune; B2: consolidated grassland dune; B3: consolidated juniper dune). A total of 368 plots (10 × 10 m) were analyzed to quantify temporal changes in individual abundance and vegetation cover. Results: Over the ten-year period, total abundance increased from 99 to 342 individuals (+245%) at Lecciona and from 117 to 324 individuals (+177%) at Marina di Vecchiano. Mean cover per plot increased significantly at both sites (overall p < 0.001), with the strongest proportional increases recorded in the seaward belts (B1: up to +1220% in abundance and +4500% in cover) revealing a clear shift from an inner-dune concentration in 2013 to a more homogeneous spatial distribution across the entire dune system in 2023. Conclusions: Under conditions of low anthropogenic disturbance, shoreline stability, or geomorphological progradation, J. macrocarpa is able to expand well beyond its recognized ecological niche. These findings demonstrate the central role of geomorphological and disturbance regimes in driving coastal dune vegetation dynamics and highlight the need for adaptive, site-specific management strategies for the long-term conservation of priority habitat 2250/EUNIS N1B. Full article

(This article belongs to the Section Plant Science)

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