Biology

24 pages, 1521 KB

Open AccessArticle

Cholinergic Transmission Dysregulation and Neurodegeneration Induced by Thyroid Signaling Disruption Following Butylparaben Single and Repeated Treatment

by Paula Moyano, Andrea Flores, Javier Sanjuan, Jose Carlos Plaza, Lucía Guerra-Menéndez, Luisa Abascal, Olga Mateo and Javier del Pino

Biology 2025, 14(10), 1380; https://doi.org/10.3390/biology14101380 - 9 Oct 2025

Abstract

Butylparaben (BP), a widely used preservative, was implicated in cognitive impairment, though its neurotoxic mechanisms remain elusive. Basal forebrain cholinergic neurons (BFCN) are selectively lost in dementias, contributing to cognitive decline. To explore different mechanisms related with BFCN loss, we employed BF SN56 [...] Read more.

Butylparaben (BP), a widely used preservative, was implicated in cognitive impairment, though its neurotoxic mechanisms remain elusive. Basal forebrain cholinergic neurons (BFCN) are selectively lost in dementias, contributing to cognitive decline. To explore different mechanisms related with BFCN loss, we employed BF SN56 cholinergic wild-type or silenced cells for Tau, amyloid-beta precursor protein (βApp), acetylcholinesterase (AChE), or glycogen synthase kinase-3 beta (GSK3β) genes, exposing them to BP (0.1–80 µM) for 1 or 14 days alongside triiodothyronine (T3; 15 nM), N-acetylcysteine (NAC; 1 mM), or recombinant heat shock protein 70 (rHSP70; 30 µM). BP disrupted cholinergic transmission by AChE inhibition and provoked cell death through thyroid hormones (THs) pathway disruption, Aβ/p-Tau protein accumulation, AChE-S overexpression, and oxidative stress (OS). Aβ/p-Tau accumulation was correlated with HSP70 downregulation, OS exacerbation, and GSK3β hyperactivation (for p-Tau). BP-induced OS was mediated by reactive oxygen species (ROS) overproduction and nuclear factor erythroid 2-related factor 2 (NRF2) pathway disruption. All observed effects were contingent upon TH signaling impairment. These findings uncover novel mechanistic links between BP exposure and BFCN neurodegeneration, providing a framework for therapeutic strategies. Full article

(This article belongs to the Section Toxicology)

19 pages, 2563 KB

Open AccessArticle

Assessing the Impacts of Climate Change on the Potential Geographical Distribution of Lycium ruthenicum in China

by Cheng Li, Yuli Gu, Bo Liu, Kwok Pan Chun, Thanti Octavianti, Mou Leong Tan, Yongping Wu and Lei Zhong

Biology 2025, 14(10), 1379; https://doi.org/10.3390/biology14101379 - 9 Oct 2025

Abstract

Understanding the climate change impacts on the geographical distribution of plant species is vital for biodiversity conservation. Lycium ruthenicum, a second-grade protected plant in China, holds considerable medicinal and ecological value; however, its potential habitat distribution under climate change remains uncertain. By [...] Read more.

Understanding the climate change impacts on the geographical distribution of plant species is vital for biodiversity conservation. Lycium ruthenicum, a second-grade protected plant in China, holds considerable medicinal and ecological value; however, its potential habitat distribution under climate change remains uncertain. By utilizing occurrence records and geographical and environmental data, we optimized a maximum entropy model and evaluated the current and future potential habitat suitability of L. ruthenicum in China. The main results were as follows: (1) The distribution of L. ruthenicum was primarily influenced by the precipitation of the warmest quarter, topsoil base saturation, precipitation seasonality, precipitation of the coldest quarter, and minimum temperature of the coldest month. (2) Under the current conditions, the potential suitable area of L. ruthenicum was approximately 2.25 × 10⁶ km² in China, predominantly distributed in Xinjiang, Qinghai, Gansu, Ningxia, and Inner Mongolia. (3) An obvious reduction in the predicted suitable area of L. ruthenicum was found under future climate scenarios, with the centroid primarily shifting northeastward. These findings highlight the potential vulnerability of this medicinally and ecologically important species and underscore the urgent need for targeted conservation strategies to ensure its long-term survival. Full article

17 pages, 2711 KB

Open AccessArticle

Homogeneous Selection and Dispersal Limitation Drive Phyllosphere Fungal Community Assembly in Constructed Wetland Ecosystems

by Nan Deng, Yuxin Tian, Qingan Song, Yandong Niu and Fengfeng Ma

Biology 2025, 14(10), 1378; https://doi.org/10.3390/biology14101378 - 9 Oct 2025

Abstract

Constructed wetlands (CWs) are widely used for ecological restoration, but their microbial assembly mechanisms and ecological functions remain poorly understood, limiting the optimization of restoration strategies. In this study, we investigated foliar fungal communities associated with dominant plant types in a CW converted [...] Read more.

Constructed wetlands (CWs) are widely used for ecological restoration, but their microbial assembly mechanisms and ecological functions remain poorly understood, limiting the optimization of restoration strategies. In this study, we investigated foliar fungal communities associated with dominant plant types in a CW converted from farmland by employing high-throughput sequencing. We analyzed community composition, diversity, assembly processes, and co-occurrence network structure to identify potential keystone taxa. Our results showed that plant type significantly influenced fungal community diversity and composition (α < 0.05). Assembly processes were jointly driven by heterogeneous selection (36.48%), dispersal-related processes (35.49%), and drift (24.70%), indicating comparable contributions of deterministic and stochastic processes. Co-occurrence network analysis revealed a modular structure and identified several hub taxa based on topological indices, suggesting their potential importance for network stability. This study provides an integrated perspective that links community diversity, assembly mechanisms, and network structure, providing insights for improving CW vegetation management and microbial regulation strategies. Future studies should explore and validate the functional roles of hub taxa and test the generalizability of these patterns across multiple regions and seasons. Full article

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16 pages, 1937 KB

Open AccessArticle

eDNA- and eRNA-Based Detection of 2-Methylisoborneol-Producing Cyanobacteria and Intracellular Synthesis Dynamics in Freshwater Ecosystem

by Keonhee Kim, Chaehong Park, Nan-Young Kim and Soon-Jin Hwnag

Biology 2025, 14(10), 1377; https://doi.org/10.3390/biology14101377 - 9 Oct 2025

Abstract

Taste and odor (T&O) compounds in freshwater are frequently produced by certain cyanobacteria; however, their occurrence remains difficult to predict. This study examined the temporal and spatial variations in the mibC gene, which encodes a critical enzyme in the biosynthesis of 2-methylisoborneol (2-MIB), [...] Read more.

Taste and odor (T&O) compounds in freshwater are frequently produced by certain cyanobacteria; however, their occurrence remains difficult to predict. This study examined the temporal and spatial variations in the mibC gene, which encodes a critical enzyme in the biosynthesis of 2-methylisoborneol (2-MIB), by analyzing environmental DNA (eDNA) and RNA (eRNA) in the North Han River, Republic of Korea, from July 2019 to October 2021. Surface water was sampled at twelve sites and analyzed for mibC DNA copy number, RNA expression, cyanobacterial cell density, and 2-MIB concentration using quantitative PCR (qPCR), microscopy, and gas chromatography–mass spectrometry (GC–MS). The mibC gene was present throughout the year, exhibiting peaks from late summer to early winter; higher concentrations typically initiated upstream and subsequently moved downstream. RNA expression was elevated from summer to autumn, rapidly declined following heavy rainfall, and reliably preceded increases in 2-MIB concentrations by 2–4 weeks. RNA levels were strongly correlated with 2-MIB concentrations (r = 0.879, p < 0.001) but showed only a moderate association with Pseudanabaena cell density, whereas DNA demonstrated weaker correlations. More than 95% of total 2-MIB was dissolved, limiting the ability to directly estimate concentrations from eRNA data alone. The results indicate that eRNA monitoring is an effective early warning tool for T&O events. In addition, combining eDNA and eRNA analyses enables a more accurate evaluation of T&O-producing cyanobacteria, presenting practical benefits for proactive management of drinking water. Full article

(This article belongs to the Special Issue Biology, Ecology and Management of Harmful Algae)

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25 pages, 3602 KB

Open AccessArticle

Rulers of the Open Sky at Risk: Climate-Driven Habitat Shifts of Three Conservation-Priority Raptors in the Eastern Himalayas

by Pranjal Mahananda, Imon Abedin, Anubhav Bhuyan, Malabika Kakati Saikia, Prasanta Kumar Saikia, Hilloljyoti Singha and Shantanu Kundu

Biology 2025, 14(10), 1376; https://doi.org/10.3390/biology14101376 - 8 Oct 2025

Abstract

Raptors, being at top of the food chain, serve as important models to study the impact of changing climate, as they are more vulnerable due to their unique ecology. They are vulnerable to extinction, with 52% species declining population and 18% are threatened [...] Read more.

Raptors, being at top of the food chain, serve as important models to study the impact of changing climate, as they are more vulnerable due to their unique ecology. They are vulnerable to extinction, with 52% species declining population and 18% are threatened globally. The effect of climate change on raptors is poorly studied in the Eastern Himalayan region. The present study offers a complete investigation of climate change effects on the raptors in the northeast region of the Eastern Himalayas, employing ensemble species distribution modeling. The future predictions were employed to model the climate change across two socioeconomic pathways (SSP) i.e. SSP245 and SSP585 for the periods 2041–2060 and 2061–2080. Specifically, five algorithms were employed for the ensemble model, viz. boosted regression tree (BRT), generalized linear model (GLM), multivariate adaptive regression splines (MARS), maximum entropy (MaxEnt) and random forest (RF). The study highlights worrying results, as only 10.5% area of the NE region is presently suitable for Falco severus, 11.4% for the critically endangered Gyps tenuirostris, and a mere 6.9% area is presently suitable for the endangered Haliaeetus leucoryphus. The most influential covariates were precipitation of the driest quarter, precipitation of the wettest month, and temperature seasonality. Future projection revealed reduction of 33–41% in suitable habitats for F. severus, G. tenuirostris is expected to lose 53–96% of its suitable habitats, and H. leucoryphus has lost nearly 94–99% of its suitable habitats. Such decline indicates apparent habitat fragmentation, with shrinking habitat patches. Full article

(This article belongs to the Special Issue Impacts of Climate Change on Terrestrial Carbon Cycling and Biodiversity Across Spatial and Temporal Scales)

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24 pages, 1547 KB

Open AccessReview

Integration of Light and Circadian Signaling in Plant Gene Regulatory Networks: Implications for Photomorphogenesis and Stress Adaptation

by Muhammad Mujahid, Alia Ambreen, Yusra Zarlashat, Zareen Sarfraz, Muhammad Sajid Iqbal, Abdul Waheed and Muhammad Shahid Iqbal

Biology 2025, 14(10), 1375; https://doi.org/10.3390/biology14101375 - 8 Oct 2025

Abstract

Plants, as sessile organisms, rely on sophisticated gene regulatory networks (GRNs) to adapt to dynamic environmental conditions. Among the central components of these networks are the interconnected pathways of light signaling and circadian rhythms, which together optimize growth, development, and stress resilience. While [...] Read more.

Plants, as sessile organisms, rely on sophisticated gene regulatory networks (GRNs) to adapt to dynamic environmental conditions. Among the central components of these networks are the interconnected pathways of light signaling and circadian rhythms, which together optimize growth, development, and stress resilience. While light and circadian pathways have been extensively investigated independently, their integrative coordination in mediating climate change adaptation responses remains a critical knowledge gap. Light perception via photoreceptors initiates transcriptional reprogramming, while the circadian clock generates endogenous rhythms that anticipate daily and seasonal changes. This review explores the molecular integration of light and circadian signaling, emphasizing how their crosstalk fine-tunes GRNs to balance resource allocation, photomorphogenesis, and stress adaptation. We highlight recent advances in systems biology tools, e.g., single-cell omics, CRISPR screens that unravel spatiotemporal regulation of shared hubs like phytochrome-interacting factors (PIFs), ELONGATED HYPOCOTYL 5 (HY5), and CIRCADIAN CLOCK ASSOCIATED 1 (CCA1). Here, we synthesize mechanistic insights across model and crop species to bridge fundamental molecular crosstalk with actionable strategies for enhancing cropresilience. Moreover, we have tried to discuss agricultural implications in engineering light–clock interactions for the enhancement in crop productivity under climate change scenarios. Through synthesizing mechanistic insights and translational applications, this work will help underscore the potential for manipulating light–circadian networks to promote sustainability in agriculture. Full article

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17 pages, 3992 KB

Open AccessArticle

Mitogenomic Characterization of Mining Bee Family Andrenidae (Hymenoptera: Apoidea: Anthophila) and Insights into Bee Phylogeny

by Dan Zhang

Biology 2025, 14(10), 1374; https://doi.org/10.3390/biology14101374 - 8 Oct 2025

Abstract

Andrenidae is a major pollinator lineage with considerable ecological importance, yet limited molecular resources have impeded comprehensive understanding of its evolutionary history. This study sequenced and assembled five mitogenomes of Andrenidae, which were collected from Xizang, Tibet. Analyses included sequence size, nucleotide composition, [...] Read more.

Andrenidae is a major pollinator lineage with considerable ecological importance, yet limited molecular resources have impeded comprehensive understanding of its evolutionary history. This study sequenced and assembled five mitogenomes of Andrenidae, which were collected from Xizang, Tibet. Analyses included sequence size, nucleotide composition, Ka/Ks ratios, and gene rearrangements. The assembled mitogenomes ranged from 15,631 to 18,506 bp in length. AT content (%) varied between 74.46 and 79.85. Relative synonymous codon usage analysis revealed that AUU, UUA, UUU, and UUA were the most frequently preferred codons. All 13 protein-coding genes displayed Ka/Ks values below one, with ATP8 showing the highest ratio and COX1 the lowest. Gene rearrangements occurred in all mitogenomes, and three distinct tRNA rearrangement patterns were detected. This study provided more available molecular data for future evolutionary biology studies of Andrenidae. Additionally, 24 previously published Apoidea mitogenomes (three outgroups and 26 ingroups) were incorporated to infer phylogenetic relationships using Maximum Likelihood and Bayesian Inference methods. The results supported Melittidae as the basal lineage of bees, while Andrenidae was recovered as the sister clade to Halictidae + Colletidae. Full article

13 pages, 2390 KB

Open AccessArticle

Uncovering the Regulatory Role of Proteins in EBSS-Induced Autophagy Using RNA-Seq Analysis

by Chen Ruan, Yuzhu Li and Ran Wu

Biology 2025, 14(10), 1373; https://doi.org/10.3390/biology14101373 - 8 Oct 2025

Abstract

Earle’s balanced salt solution (EBSS) is a classical autophagy inducer that provides a special culture environment lacking amino acids and serum, causing cell starvation. However, the production of relevant omics data surrounding EBSS-induced autophagy is still in the early stage. The objective of [...] Read more.

Earle’s balanced salt solution (EBSS) is a classical autophagy inducer that provides a special culture environment lacking amino acids and serum, causing cell starvation. However, the production of relevant omics data surrounding EBSS-induced autophagy is still in the early stage. The objective of this study was to identify new potential functional proteins in the autophagy process through omics analysis. We selected EBSS-induced autophagy as our research object and uncovered autophagy-regulatory proteins using RNA-seq analysis. Western blotting showed that EBSS increased LC3B-II protein levels in NRK cells, reaching the maximum amount at 2 h of culture. Then, we used next-generation sequencing to obtain quantified RNA-seq data from cells incubated with EBSS and the bowtie–tophat–cufflinks flow path to analyze the transcriptome data. Using significant differences in the FPKM values of genes in the treated group compared with those in the control group to indicate differential expression, 470 candidate genes were selected. Subsequently, GO and KEGG analyses of these genes were performed, revealing that most of these signaling pathways were closely associated with autophagy, and to better understand the potential functions and connections of these genes, protein–protein interaction networks were studied. Considering all the conclusions of the analysis, 27 candidate genes were selected for verification, where the knockdown of Txnrd1 decreased LC3B-II protein levels in NRK cells, consistent with the results of confocal experiments. In conclusion, we uncovered autophagy-regulatory proteins using RNA-seq analysis, with our results indicating that TXNRD1 may play a role in regulating EBSS-induced autophagy via an unknown pathway. We hope that our research can provide useful information for further autophagy omics research. Full article

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16 pages, 1137 KB

Open AccessReview

Deciphering the Fate of Burned Trees After a Forest Fire: A Systematic Review Focused on Conifers

by Alessandro Bizzarri, Margherita Paladini, Niccolò Frassinelli, Enrico Marchi, Raffaella Margherita Zampieri, Alessio Giovannelli and Claudia Cocozza

Biology 2025, 14(10), 1372; https://doi.org/10.3390/biology14101372 - 8 Oct 2025

Abstract

Climate change is intensifying fire regimes, thereby challenging forest ecosystems and making it more difficult to predict the fate of burned trees. The significant ecological impacts of latent tree mortality remain poorly understood. In this study, we reviewed the scientific literature on latent [...] Read more.

Climate change is intensifying fire regimes, thereby challenging forest ecosystems and making it more difficult to predict the fate of burned trees. The significant ecological impacts of latent tree mortality remain poorly understood. In this study, we reviewed the scientific literature on latent tree mortality in conifer forests following wildfires or prescribed fires. A total of 2294 papers published between 2000 and 2024 were identified from Scopus and Web of Science databases. Using the PICO selection method, we included 16 relevant studies in the final analysis. These studies are based on field assessment, excluding remote sensing and controlled laboratory conditions. Our research revealed that latent mortality results from multiple forms of damage and environmental stressors that disrupt hydraulic function and carbon allocation, increasing tree vulnerability to secondary biotic and abiotic stressors. The discussion is structured around four thematic areas: physiology, ecophysiology, dendrochronology, and silviculture. This approach contributes to a deeper, interdisciplinary understanding of latent tree mortality. However, predicting it remains difficult, reflecting persistent knowledge gaps. Despite the limited literature on this specific field, our review highlights the need for integrated physiological indicators, such as sap flow, transpiration, nonstructural carbohydrates and glucose concentration, as well as long-term monitoring along many growing seasons to better assess tree survival after fire. Full article

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

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17 pages, 1432 KB

Open AccessReview

Polarized Macrophages and Their Exosomes: Implications for Autoimmune and Immune-Mediated Diseases

by Vincent G. Yuan

Biology 2025, 14(10), 1371; https://doi.org/10.3390/biology14101371 - 8 Oct 2025

Abstract

Autoimmune diseases result from dysregulated immune responses that mistakenly attack the body’s own tissues, causing chronic inflammation and progressive damage. Macrophages, with their remarkable plasticity, play key roles in both promoting and resolving inflammation, with pro-inflammatory M1 and anti-inflammatory M2 states shaping disease [...] Read more.

Autoimmune diseases result from dysregulated immune responses that mistakenly attack the body’s own tissues, causing chronic inflammation and progressive damage. Macrophages, with their remarkable plasticity, play key roles in both promoting and resolving inflammation, with pro-inflammatory M1 and anti-inflammatory M2 states shaping disease outcomes. Macrophage-derived exosomes have emerged as important mediators of intercellular communication, reflecting the functional state of their parent cells while influencing recipient cell behavior. Exosomes from M1 macrophages amplify inflammation through cytokines and microRNAs, whereas M2-derived exosomes support tissue repair and immune regulation. Studies in rheumatoid arthritis, lupus, multiple sclerosis, inflammatory bowel disease, type 1 diabetes, and psoriasis highlight their dual roles in pathology and resolution. In addition, macrophage exosomes can be engineered to deliver targeted therapeutic molecules, offering cell-free interventions with advantages in specificity, biocompatibility, and immunomodulation. This review summarizes current insights into macrophage-derived exosomes, their role in autoimmune pathogenesis, and emerging strategies to harness their therapeutic potential, highlighting their promise as precision-guided treatments for autoimmune diseases. Full article

(This article belongs to the Special Issue Pathophysiology of Chronic Inflammatory Diseases)

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30 pages, 613 KB

Open AccessReview

The Role of Protein Arginine Methylation as a Post-Translational Modification in Cellular Homeostasis and Disease

by Ke Li, Qing Xia, Kexin Li, Wenxin Yan and Changshan Wang

Biology 2025, 14(10), 1370; https://doi.org/10.3390/biology14101370 - 7 Oct 2025

Abstract

Post-translational modifications (PTMs) of proteins in eukaryotic cells are essential for regulating proteome function and maintaining cellular homeostasis. Among these, the methylation modification of arginine has received much attention in recent years. The enzymatic process of arginine methylation is catalyzed by a family [...] Read more.

Post-translational modifications (PTMs) of proteins in eukaryotic cells are essential for regulating proteome function and maintaining cellular homeostasis. Among these, the methylation modification of arginine has received much attention in recent years. The enzymatic process of arginine methylation is catalyzed by a family of approximately nine known protein arginine methyltransferases (PRMTs) in humans, which utilize S-adenosylmethionine (SAM) as the methyl group donor. PRMTs are involved in biological processes such as gene transcription, signal transduction, and DNA damage repair. Their role in normal cellular functions and pathological disease states is becoming increasingly clear with the advancement of research. This paper provides a review of the numerous roles of members of the PRMT family in normal cellular function and disease pathophysiology, with a focus on their association with the tumor immune microenvironment (TIME), and discusses their broad impact on various physiological processes and pathological conditions. Full article

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

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19 pages, 2389 KB

Open AccessArticle

Distribution Changes in Lichen: A Staple Fallback Food for Yunnan Snub-Nosed Monkey and Their Implications for the Species

by Yuan Zhang, Hanyu Zhu, Lianghua Huang, Xinming He, Sang Ge, Jiandong Lai, Duji Zhaba, Dayong Li and Wancai Xia

Biology 2025, 14(10), 1369; https://doi.org/10.3390/biology14101369 - 7 Oct 2025

Abstract

Under the background of global climate change, lichens as a staple fallback food source for the endangered Yunnan snub-nosed monkey (Rhinopithecus bieti) exert a critical influence on the survival of Yunnan snub-nosed monkey populations through their distribution dynamics. This study focused [...] Read more.

Under the background of global climate change, lichens as a staple fallback food source for the endangered Yunnan snub-nosed monkey (Rhinopithecus bieti) exert a critical influence on the survival of Yunnan snub-nosed monkey populations through their distribution dynamics. This study focused on the contiguous habitats of the Yunnan snub-nosed monkey in the southern Hengduan Mountains. By species distribution models (SDMs) and landscape pattern analysis, we investigated the changes in suitable habitats of lichens under four Representative Concentration Pathway (RCP) scenarios and their implications for the habitat utilization of the Yunnan snub-nosed monkey until 2050. The results indicate that the current suitable habitat for lichen spans approximately 16,821.96 km², with highly suitable habitats predominantly located in Deqin County and Weixi County. Altitude and vegetation type emerged as primary factors influencing lichen distribution. The overlap rate of suitable habitats between lichens and the Yunnan snub-nosed monkey is 72.24%. Furthermore, the Yunnan snub-nosed monkey exhibits a preference for selecting habitats characterized by the largest patch index (LPI) of lichen distribution. By 2050, the suitable habitat for lichen is projected to marginally increase in the southern Hengduan Mountains, particularly under the RCP 6.0 scenario, by 22.20% compared to the current expansion. However, both the suitable habitat and the LPI of lichen face potential decline within the habitat of the Yunnan snub-nosed monkey. Therefore, we recommend conducting a quantitative investigation into the correlation between the actual productivity of lichen radiata and the population dynamics of Yunnan snub-nosed monkey as a priority. This research will offer a more precise scientific foundation for conservation decision-making for Yunnan snub-nosed monkey. Full article

(This article belongs to the Section Conservation Biology and Biodiversity)

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21 pages, 4743 KB

Open AccessArticle

Transcriptomic Investigation of FoxM1-Mediated Neuroprotection by hAEC-Derived Exosomes in an In Vitro Ischemic Stroke Model

by Dong Wang, Jiaxin Liu, Liang Wu, Xiubao Yang, Zhihao Fang, Zhong Sun and Dong Chen

Biology 2025, 14(10), 1368; https://doi.org/10.3390/biology14101368 - 7 Oct 2025

Abstract

Human amniotic epithelial cell-derived exosomes (hAECs-Exos) are nanoscale extracellular vesicles with neuroprotective, regenerative, and anti-inflammatory properties, presenting a promising cell-free therapeutic approach for ischemic stroke. This study investigated the protective effects of hAECs-Exos against ischemic injury and explored the underlying molecular mechanisms. An [...] Read more.

Human amniotic epithelial cell-derived exosomes (hAECs-Exos) are nanoscale extracellular vesicles with neuroprotective, regenerative, and anti-inflammatory properties, presenting a promising cell-free therapeutic approach for ischemic stroke. This study investigated the protective effects of hAECs-Exos against ischemic injury and explored the underlying molecular mechanisms. An optimized oxygen-glucose deprivation/reoxygenation (OGD/R) model was established in murine hippocampal HT22 neurons and BV2 microglial cells to simulate ischemic conditions. hAECs-Exos were successfully isolated and characterized via transmission electron microscopy, nanoparticle tracking analysis, and Western blotting. Confocal microscopy confirmed efficient exosome uptake by both cell types. Functional analyses revealed that hAECs-Exos significantly improved cell viability, suppressed pro-inflammatory cytokine release, alleviated oxidative stress, and modulated apoptosis-related proteins. RNA sequencing identified Forkhead box protein M1 (FoxM1) as a significantly upregulated transcription factor following hAECs-Exos treatment. Further experiments demonstrated that knockdown of FoxM1 in hAECs abolished the beneficial effects of exosomes on the viability of HT22 and BV2 cells and on the suppression of inflammation, oxidative stress, and apoptosis. These findings indicate that hAECs-Exos confer neuroprotection through FoxM1-dependent mechanisms. Together, our results highlight the therapeutic potential of hAECs-Exos as a safe, effective, and clinically translatable strategy for ischemic stroke treatment, warranting future validation in vivo and rescue experiments to fully elucidate FoxM1’s causal role. Full article

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

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4 pages, 180 KB

Open AccessEditorial

Beyond Powerhouses: Roles of Mitochondria, from Development to Therapeutic Potential

by Susana P. Pereira and Ludgero C. Tavares

Biology 2025, 14(10), 1367; https://doi.org/10.3390/biology14101367 - 7 Oct 2025

Abstract

Mitochondria, long recognized as the powerhouse of the cell, have emerged as master regulators of cellular fate and therapeutic potential through a broad range of signaling pathways and metabolic modulation [...] Full article

(This article belongs to the Special Issue Mitochondria: The Diseases' Cause and Cure)

0 pages, 7540 KB

Open AccessArticle

Genome-Wide Analysis of the Thiamine Biosynthesis Gene Families in Common Bean Reveals Their Crucial Roles Conferring Resistance to Fusarium Wilt

by Ming Feng, Yu Liu, Yang Zhao, Tao Li, Jian Chen, Yuning Huang, Weide Ge, Chao Zhong and Renfeng Xue

Biology 2025, 14(10), 1366; https://doi.org/10.3390/biology14101366 - 6 Oct 2025

Abstract

Fusarium wilt, caused by Fusarium oxysporum f. sp. phaseoli (Fop), is a major constraint to global common bean (Phaseolus vulgaris L.) production. Thiamine (vitamin B1), an essential coenzyme in plant metabolism, has recently emerged as a potential regulatory factor in plant defense. [...] Read more.

Fusarium wilt, caused by Fusarium oxysporum f. sp. phaseoli (Fop), is a major constraint to global common bean (Phaseolus vulgaris L.) production. Thiamine (vitamin B1), an essential coenzyme in plant metabolism, has recently emerged as a potential regulatory factor in plant defense. Here, we performed a comprehensive genome-wide analysis of thiamine biosynthesis-related genes in common bean and elucidated their roles in resistance to Fusarium wilt. Five key thiamine biosynthetic genes were identified and characterized, showing conserved functional domains and evolutionary conservation across species. Expression profiling revealed tissue-specific patterns, with PvTHI1-1 and PvTHIC being highly expressed in reproductive and photosynthetic organs, with their relative expression levels 0.28–0.57 higher than other members in the same tissue, while PvTPK maintained a basal expression level in the roots. Upon Fop infection, resistant genotypes exhibited significantly higher expression of thiamine biosynthetic genes and greater accumulation of endogenous thiamine and its derivatives than susceptible ones. Functional analysis using Agrobacterium rhizogenes-mediated transformation demonstrated that overexpression of PvTPK enhanced thiamine metabolism and conferred resistance in susceptible genotypes. Similarly, exogenous application of thiamine upregulated biosynthetic genes and improved disease resistance. Together, these results reveal that thiamine biosynthesis is intricately linked to Fusarium wilt resistance and that both genetic and biochemical manipulation of thiamine pathways can enhance disease tolerance. This study provides new insights into thiamine-mediated plant immunity and establishes a foundation for its application in the control of Fusarium wilt in common bean. Full article

(This article belongs to the Special Issue Mechanisms of Genetic and Epigenetic Regulation Underlying Plant Resistance)

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15 pages, 14177 KB

Open AccessArticle

Diversity of Menstrual Cycle, Formation of Decidual Cells, and Lack of Endometrial Glands in Spiny Mouse

by Roman Eremichev, Nina Nikolaeva, Mikhail Khandokhin, Roman Tsvetcov, Natalya Alexandrushkina, Alena Shilova, Vladimir Popov and Pavel Makarevich

Biology 2025, 14(10), 1365; https://doi.org/10.3390/biology14101365 - 5 Oct 2025

Abstract

Recent discovery of menstruation in the Egyptian spiny mouse (Acomys cahirinus) highlighted this species as a feasible model for the study of menstrual cycle physiology. However, reports on active menstrual bleeding in this animal were contradictory, so we set out to reproduce [...] Read more.

Recent discovery of menstruation in the Egyptian spiny mouse (Acomys cahirinus) highlighted this species as a feasible model for the study of menstrual cycle physiology. However, reports on active menstrual bleeding in this animal were contradictory, so we set out to reproduce major findings in the field. Using vaginal smear microscopy and occult blood assay, we have failed to detect menstrual bleeding in spiny mice from our colony at Lomonosov Moscow State University. Otherwise, we demonstrated appearance of well-defined decidual cells during the late secretory phase of the cycle that correlated with an increase in serum progesterone. Comparing the uteri of spiny mice from our colony vs. CD1 strain laboratory mice housed in the same animal unit, we have found several noteworthy features: (1) absence of endometrial glands, (2) higher volume of nerve fibers in the endometrium, and (3) spiral-like arteries in myometrium. Taking results of other groups into account, our results highlight putative diversity of menstrual cycles in spiny mice from different colonies and demonstrate important differences in uterus structure compared to M. musculus. Full article

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18 pages, 4307 KB

Open AccessArticle

Molecular Mechanisms Underlying Differences in Athletic Ability in Racehorses Based on Whole Transcriptome Sequencing

by Qiuping Huang, Wanlu Ren, Dehaxi Shan, Yi Su, Zexu Li, Luling Li, Ran Wang, Shikun Ma and Jianwen Wang

Biology 2025, 14(10), 1364; https://doi.org/10.3390/biology14101364 - 5 Oct 2025

Abstract

This study aimed to compare blood samples from Yili horses with outstanding and average performance in 5000 m races through transcriptome sequencing, identify key differentially expressed genes, lncRNAs, and circRNAs, as well as related enriched pathways, and elucidate their regulatory networks. This study [...] Read more.

This study aimed to compare blood samples from Yili horses with outstanding and average performance in 5000 m races through transcriptome sequencing, identify key differentially expressed genes, lncRNAs, and circRNAs, as well as related enriched pathways, and elucidate their regulatory networks. This study used six healthy four-year-old Yili stallions as subjects, divided into an excellent group (E group, n = 3) and an ordinary group (O group, n = 3) based on their 5000-m race performance. Blood RNA-Seq technology was used to analyze differentially expressed mRNAs, lncRNAs, and circRNAs. A total of 2298 mRNAs, 264 lncRNAs, and 215 circRNAs were identified as differentially expressed. Key genes such as EGR1, FOSB, MRPL1, LOC100049811, SIRPB2, and CYTB regulate athletic performance. These genes and their associated RNAs synergistically participate in energy metabolism, protein homeostasis, and muscle remodeling processes, revealing the molecular mechanisms influencing athletic performance and providing important references for identifying candidate genes associated with equine athletic performance. Full article

(This article belongs to the Special Issue Advances in Animal Functional Genomics)

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17 pages, 13481 KB

Open AccessArticle

Luopan Mountain Pig Bone Marrow Mesenchymal Stem Cells Promote Liver Regeneration in D-Galactosamine-Induced Acute Liver Failure Rats by Regulating the PTEN-PI3K/Akt/mTOR Pathway

by Minjuan Li, Zhongfa Wang, Xingxing Yan, Yanchen Liu, Yunan He, Bianying Zhang and Weijun Guan

Biology 2025, 14(10), 1363; https://doi.org/10.3390/biology14101363 - 5 Oct 2025

Abstract

Treatment for acute liver failure (ALF) is constrained by shortages of liver transplant donors and immune rejection. Porcine bone marrow mesenchymal stem cells (pBMSCs) demonstrate clinical potential in xenotransplantation due to their abundant availability, low immunogenicity, and strong proliferative activity. This study is [...] Read more.

Treatment for acute liver failure (ALF) is constrained by shortages of liver transplant donors and immune rejection. Porcine bone marrow mesenchymal stem cells (pBMSCs) demonstrate clinical potential in xenotransplantation due to their abundant availability, low immunogenicity, and strong proliferative activity. This study is the first to investigate the reparative effects and mechanisms of pBMSCs derived from Luopan Mountain pigs in a D-galactosamine (D-GalN)-induced ALF rat model. The results demonstrated that tail-vein transplantation of pBMSCs significantly improved survival rates in ALF rats; reduced serum ALT, AST, and TBIL levels; enhanced hepatic glycogen metabolism; and mitigated histopathological liver damage. Additionally, pBMSC transplantation upregulated serum HGF, IGF-1, and VEGF levels while inhibiting hepatocyte apoptosis. Mechanistic studies indicate that pBMSCs promote liver function recovery and regeneration by activating the PI3K/Akt/mTOR signaling pathway and suppressing its key negative regulator, PTEN, by regulating the expression of key genes involved in inflammation, fibrosis, proliferation, and apoptosis. This study provides crucial experimental evidence for the use of pBMSCs in treating acute liver failure (ALF) and lays the groundwork for its clinical translation in the field of xenotransplantation. Full article

(This article belongs to the Section Cell Biology)

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22 pages, 3445 KB

Open AccessArticle

Decoding the Impacts of Mating Behavior on Ovarian Development in Mud Crab (Scylla paramamosain, Estampador 1949): Insights from SMRT RNA-seq

by Chenyang Wu, Sadek Md Abu, Xiyi Zhou, Yang Yu, Mhd Ikhwanuddin, Waqas Waqas and Hongyu Ma

Biology 2025, 14(10), 1362; https://doi.org/10.3390/biology14101362 - 4 Oct 2025

Abstract

Pubertal molting represents a pivotal transition in the life cycle of crustaceans, marking the shift from somatic growth to reproductive development. In mud crabs, mating is known to facilitate this process, yet the molecular mechanisms remain poorly understood. Here, we applied full-length transcriptome [...] Read more.

Pubertal molting represents a pivotal transition in the life cycle of crustaceans, marking the shift from somatic growth to reproductive development. In mud crabs, mating is known to facilitate this process, yet the molecular mechanisms remain poorly understood. Here, we applied full-length transcriptome sequencing to characterize changes in gene expression and alternative splicing (AS) across post-mating ovarian development. AS analysis revealed extensive transcript diversity, predominantly alternative first exon (AF) and alternative 5′ splice site (A5) events, enriched in genes linked to chromatin remodeling, protein regulation, and metabolism, underscoring AS as a fine-tuning mechanism in ovarian development. Comparative analyses revealed profound molecular reprogramming after mating. In the UM vs. M1 comparison, pathways related to serotonin and catecholamine signaling were enriched, suggesting early neuroendocrine regulation. Serotonin likely promoted, while dopamine inhibited, oocyte maturation, indicating a potential “inhibition–activation” switch. In the UM vs. M3 comparison, pathways associated with oxidative phosphorylation, ATP biosynthesis, and lipid metabolism were upregulated, reflecting heightened energy demands during vitellogenesis. ECM-receptor interaction, HIF-1, and IL-17 signaling pathways further pointed to structural remodeling and tissue regulation. Enhanced antioxidant defenses, including upregulation of SOD2, CAT, GPX4, and GSTO1, highlighted the importance of redox homeostasis. Together, these findings provide the first comprehensive view of transcriptional and splicing dynamics underlying post-mating ovarian maturation in Scylla paramamosain, offering novel insights into the molecular basis of crustacean reproduction. Full article

(This article belongs to the Section Marine Biology)

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