Biology

25 pages, 2447 KB

Open AccessArticle

Niche Differentiation Characteristics of Phytoplankton Functional Groups in Arid Regions of Northwest China Based on Machine Learning

by Long Yun, Fangze Zi, Xuelian Qiu, Qi Liu, Jiaqi Zhang, Liting Yang, Yong Song and Shengao Chen

Biology 2025, 14(11), 1564; https://doi.org/10.3390/biology14111564 (registering DOI) - 7 Nov 2025

Abstract

This study investigates the distribution patterns, interspecific relationships, and community stability mechanisms of phytoplankton functional groups, aiming to elucidate the ecological processes that drive phytoplankton communities in aquatic ecosystems of arid regions. We conducted seasonal sampling from 2023 to 2024 at four auxiliary [...] Read more.

This study investigates the distribution patterns, interspecific relationships, and community stability mechanisms of phytoplankton functional groups, aiming to elucidate the ecological processes that drive phytoplankton communities in aquatic ecosystems of arid regions. We conducted seasonal sampling from 2023 to 2024 at four auxiliary reservoirs in the Tarim River Basin, namely Shangyou Reservoir (SY), Shengli Reservoir (SL), Duolang Reservoir (DL), and Xinjingzi Reservoir (XJZ). In recent years, researchers have grouped phytoplankton into functional groups based on their shared morphological, physiological, and ecological characteristics—with these three types of traits serving as the core criteria for distinguishing different functional groups. A total of 18 functional groups were identified from the phytoplankton collected across four seasons, among which eight (A, D, H1, L0, M, MP, P, and S1) are dominant. Redundancy Analysis (RDA) indicated that environmental factors such as pH, electrical conductivity (COND), and dissolved oxygen (DO) are key driving factors affecting phytoplankton functional groups. Interspecific association analysis showed that the phytoplankton communities in DL, SL, and XJZ reservoirs were dominated by positive associations, reflecting stable community structures that are less prone to drastic fluctuations under stable environmental conditions. In contrast, the SY Reservoir was dominated by negative associations, indicating that it is in the early stage of succession with an unstable community. This may be related to intense human disturbance to the reservoir and its role in replenishing the Tarim River, which leads to significant water level fluctuations. The results of the Chi-square test and Pearson correlation analysis showed consistent trends but also differences: constrained by the requirement for continuous normal distribution, Pearson correlation analysis identified more pairs of negative associations, reflecting its limitations in analysing clumped-distributed species. Random forest models further indicated that functional groups M, MP, L0, and S1 are the main positive drivers of interspecific relationships. Among them, the increase in S1 can promote the growth of functional groups dominated by Navicula sp. and Chroococcus sp. by reducing resource competition. Conversely, the expansion of functional group H1 inhibits other groups, which is related to its adaptive strategy of resisting photo-oxidation in eutrophic environments. This study reveals the patterns of interspecific interactions and stability mechanisms of phytoplankton functional groups in arid-region reservoirs, providing a scientific basis for the management and conservation of aquatic ecosystems in similar extreme environments. Full article

(This article belongs to the Special Issue Wetland Ecosystems (2nd Edition))

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17 pages, 695 KB

Open AccessArticle

Dynamics of Bacterial Diversity in Fish Farming Lagoons: Implications for the Ecosystem Trophic Status

by María Custodio and Richard Peñaloza

Biology 2025, 14(11), 1563; https://doi.org/10.3390/biology14111563 (registering DOI) - 7 Nov 2025

Abstract

Bacterial communities in lake sediments are key to ecosystem health and fish productivity, yet little is known about their composition in the high-altitude Andean lagoons of central Peru. In aquaculture systems, these microbial assemblages regulate nutrient recycling, organic matter degradation and oxygen availability, [...] Read more.

Bacterial communities in lake sediments are key to ecosystem health and fish productivity, yet little is known about their composition in the high-altitude Andean lagoons of central Peru. In aquaculture systems, these microbial assemblages regulate nutrient recycling, organic matter degradation and oxygen availability, forming a key component of the microbial loop. Intensive trout farming introduces a continuous nutrient load through uneaten feed and metabolic byproducts, which fuels eutrophication and reshapes benthic microbial structure. This study evaluated the bacterial diversity and community structure in sediments from four fish farming lagoons (Pomacocha, Habascocha, Tipicocha, and Trancagrande). Environmental variables, including dissolved oxygen (DO), inorganic nitrogen, inorganic phosphorus, and chlorophyll-a, were measured to determine trophic status. Sediment bacterial composition was analyzed using Illumina sequencing of 16S rRNA gene amplicons, and community structure differences were assessed with diversity indices and SIMPER analysis. Microbial patterns were assessed at phylum and class levels to capture changes across taxonomic scales. Pseudomonadota, Actinobacteria, Cyanobacteria and Bacteroidetes dominated across lagoons, with significant among-site variation. Richness was similar, but Tipicocha showed the highest evenness (Shannon H′ = 2.769; Simpson 1-D = 0.8969). SIMPER identified Deltaproteobacteria, Alphaproteobacteria, Actinobacteria and Gammaproteobacteria as major contributors to dissimilarity. The presence of Methanomicrobia and Bacilli in Tipicocha and Trancagrande indicated micro-oxic to anoxic conditions, characteristic of systems with high organic load and redox heterogeneity. These results show that aquaculture alters trophic status and reshapes sediment bacterial communities in high-Andean lagoons. Understanding these patterns is essential to design monitoring and management strategies that balance aquaculture productivity with the conservation of sensitive ecosystems. Full article

(This article belongs to the Section Ecology)

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14 pages, 1884 KB

Open AccessArticle

Effects of Foliar Application of Paclobutrazol on Grain Yield, Aroma, and Canopy Radiation Use Efficiency of Aromatic Rice

by Fengqin Hu, Jian Lu, Laiyuan Zhai, Xianjin Qiu, Bin Du and Jianlong Xu

Biology 2025, 14(11), 1562; https://doi.org/10.3390/biology14111562 (registering DOI) - 7 Nov 2025

Abstract

Paclobutrazol (PBZ) is extensively used to modulate plant architecture in rice. However, its comprehensive effects on grain yield and aroma in aromatic rice have not been thoroughly investigated. This study used the local aromatic rice cultivars (Meixiangzhan 2 and Xiangyaxiangzhan) as experimental materials [...] Read more.

Paclobutrazol (PBZ) is extensively used to modulate plant architecture in rice. However, its comprehensive effects on grain yield and aroma in aromatic rice have not been thoroughly investigated. This study used the local aromatic rice cultivars (Meixiangzhan 2 and Xiangyaxiangzhan) as experimental materials to evaluate the impacts of foliar-applied PBZ at three concentrations (0 (CK), 150 (T1), and 300 (T2) mg L⁻¹) on grain yield, photosynthetic characteristics, fragrance formation, and radiation use efficiency (RUE). Field experiments revealed that T1 significantly reduced the leaf area index (LAI) by 10.12% and intercepted photosynthetically active radiation (IPAR) by 10.74%, meanwhile significantly increasing SPAD values by 12.94% and net photosynthetic rate (Pn) by 9.95%, leading to improved RUE up to 25.21%. These changes contributed to a larger number of grains per panicle and increased 1000-grain weight, ultimately enhancing grain yield. In contrast, T2 resulted in a sharp reduction by 24.84% in IPAR and a significant decline in Pn by 10.07% during the late grain-filling stage, thus limiting the supply of photosynthetic assimilates, eventually reducing grain yield. PBZ application also significantly elevated 2-acetyl-1-pyrroline (2-AP) content by 28.74% under T1 and 17.51% under T2, compared to the control. The increase in 2-AP was mainly associated with elevated levels of key precursors, including proline, Δ1-pyrroline-5-carboxylic acid, and Δ1-pyrroline. In spite of differences in traits between cultivars, the traits responded to PBZ in the same pattern. These results indicate that foliar application of PBZ at 150 mg L⁻¹ can effectively improve both yield and aroma of aromatic rice, offering a promising cultivation strategy for high-quality aromatic rice production. Full article

(This article belongs to the Section Plant Science)

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20 pages, 2801 KB

Open AccessArticle

Population Dynamics and Body Size Structure of the Antarctic Krill Euphausia superba in the Bransfield Strait and South Shetland Islands

by Guoqing Zhao, Shuai Li, Jialiang Yang, Gangchen Zhang, Bo Xu, Hewei Liu, Xin Rao, Peng Lian, Hongliang Huang and Lingzhi Li

Biology 2025, 14(11), 1561; https://doi.org/10.3390/biology14111561 (registering DOI) - 7 Nov 2025

Abstract

Antarctic krill (Euphausia superba) is a keystone species in the marine ecosystem of the Antarctic Ocean, bringing about significant ecological and economic value. The spatio-temporal distribution of Antarctic krill directly affects commercial fishing; meanwhile, changes in krill population structure play a [...] Read more.

Antarctic krill (Euphausia superba) is a keystone species in the marine ecosystem of the Antarctic Ocean, bringing about significant ecological and economic value. The spatio-temporal distribution of Antarctic krill directly affects commercial fishing; meanwhile, changes in krill population structure play a crucial role in maintaining the balance of the Southern Ocean ecosystem. This study analyzed six years of midwater trawl data, including over 160,000 krill length measurements, to elucidate spatio-temporal dynamics and population composition, providing actionable insights for improved fishery management. Here, we reveal southward migration shifts in krill fishing grounds, with smaller individuals favoring ice-rich southern latitudes. Commercial krill fishing operations preferentially targeted high-density fishing grounds rather than selecting larger individuals. Among the catches, the age 1+ class accounted for the highest proportion at 42.80%, followed by the age 2+ class at 39.42%, with individuals ≥3+ accounting for 17.44%. Although the mean krill length experienced a decline in 2017, it demonstrated a sustained recovery in subsequent years, reaching peak dimensions in 2022. This maximum-growth year also exhibited the highest proportion (12.6%) of individuals within ≥4 age classes. Consequently, the sustained increase in fishing effort in recent years has not resulted in a reduction in the size of individual krill. The mean krill length showed a significant positive correlation with the depth (r = 0.36, p < 0.01) and temperature (r = 0.26, p < 0.01) of the krill cluster, and a significant negative correlation with resource density (r = −0.20, p < 0.01), year (ρ = −0.31, p < 0.01) and latitude (ρ = −0.31, p < 0.01). The length exhibited U-shaped temporal trends, and latitudinal and longitudinal nonlinearity. Body size was positively correlated with depth (p < 0.01), whereas as temperature increased, body size first increased and then remained constant. As density increased, the mean krill length increased first and then slowly decreased. Recent warming intensifies population shifts, with potential cascading effects on ecosystem structure and carbon sequestration. Full article

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19 pages, 4043 KB

Open AccessArticle

LIMK1 Deficiency Disrupts Hippocampal–Cortical Memory Consolidation and Attenuates Trauma-Induced PTSD-like Behavior

by Xiangyu Yang, Zhengping Wu, Ziying Wang, Lihui Wang, Shuting Xia, Weidong Li and Guiqin He

Biology 2025, 14(11), 1560; https://doi.org/10.3390/biology14111560 - 7 Nov 2025

Abstract

Memory consolidation is the process by which newly acquired experiences are stabilized into long-term memory, involving coordinated cellular and network-level activity across brain regions such as the hippocampus and prefrontal cortex. Dysregulation of this process has been implicated in psychiatric disorders including post-traumatic [...] Read more.

Memory consolidation is the process by which newly acquired experiences are stabilized into long-term memory, involving coordinated cellular and network-level activity across brain regions such as the hippocampus and prefrontal cortex. Dysregulation of this process has been implicated in psychiatric disorders including post-traumatic stress disorder (PTSD), which is characterized by the over-consolidation of traumatic memories. LIM kinase 1 (LIMK1), a key regulator of synaptic plasticity, is believed to play an important role in memory consolidation across hippocampal–cortical circuits. In this study, we investigated the function of LIMK1 using Limk1 knockout mice. Behavioral tests such as the novel object location memory task revealed significant memory impairments in knockout animals. In vivo recordings during sleep showed disrupted communication between the hippocampus and prefrontal cortex, suggesting impaired systems-level consolidation. Furthermore, in an underwater trauma exposure model, pharmacological inhibition of LIMK1 with LIMK-i3 alleviated trauma-induced behavioral abnormalities. These findings highlight LIMK1 as a critical mediator of hippocampal–cortical memory consolidation and provide experimental evidence that LIMK1 inhibition can modulate maladaptive memory processes associated with PTSD-like symptoms. Full article

(This article belongs to the Section Neuroscience)

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15 pages, 1094 KB

Open AccessArticle

Genetic Diversity and Structure for Conservation Genetics of Goldeye Rockfish Sebastes thompsoni (Jordan and Hubbs, 1925) in South Korea

by Kang-Rae Kim, Keun-Sik Kim and Sung Jin Yoon

Biology 2025, 14(11), 1559; https://doi.org/10.3390/biology14111559 - 6 Nov 2025

Abstract

Sebastes thompsoni is a cold-water rockfish of commercial and ecological value off the coast of Korea, requiring conservation management. We analyzed seven microsatellite loci to assess genetic diversity, population structure, and historical effective population size (N_e) of five populations obtained [...] Read more.

Sebastes thompsoni is a cold-water rockfish of commercial and ecological value off the coast of Korea, requiring conservation management. We analyzed seven microsatellite loci to assess genetic diversity, population structure, and historical effective population size (N_e) of five populations obtained from the South and East Seas of Korea in 2018. The observed heterozygosity (H_O = 0.759–0.816) was higher than previously reported, and none of the STRUCTURE, DAPC, or AMOVA analyses detected geographic differentiation among samples from the South and East coasts of Korea, indicating a single population within these coasts. There was genetic flow between the five groups, with migration rates ranging from 4.1 to 19.11. However, the current N_e of all populations is estimated to be <1000, and VarEff-based reconstructions indicate a recent, severe bottleneck following an expansion approximately 600–1200 years ago (100–200 generations ago). This suggests that genetic diversity loss may persist in the future due to long-term habitat loss, fishing pressure, and ocean current fluctuations. Therefore, S. thompsoni should be established as a single management unit covering the Korean Peninsula coast, and habitat protection, overfishing control, genetic management type resource release using various mother and broodstock, and periodic genetic monitoring should be promoted. This study provides evidence to guide efforts to secure long-term genetic resilience and sustainable management of S. thompsoni in Korean coastal waters. Full article

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

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16 pages, 4226 KB

Open AccessArticle

Loss of βENaC Prevents Hepatic Steatosis but Promotes Abdominal Fat Deposition Associated with a High-Fat Diet

by Madison Hamby, Elizabeth Barr, Seth Lirette and Heather A. Drummond

Biology 2025, 14(11), 1558; https://doi.org/10.3390/biology14111558 - 6 Nov 2025

Abstract

Background: Degenerin proteins, such as Acid-Sensing Ion Channel 2 (ASIC2) and β Epithelial Na⁺ Channel (βENaC), have been implicated in cardiovascular function. We previously demonstrated that mice lacking normal levels of βENaC and ASIC2 are protected from diet-induced obesity, metabolic disruption, and [...] Read more.

Background: Degenerin proteins, such as Acid-Sensing Ion Channel 2 (ASIC2) and β Epithelial Na⁺ Channel (βENaC), have been implicated in cardiovascular function. We previously demonstrated that mice lacking normal levels of βENaC and ASIC2 are protected from diet-induced obesity, metabolic disruption, and hepatic steatosis. Methods: To investigate the specific role of βENaC proteins in the progression of metabolic disease, we examined the impact of a high-fat diet (HFD) in the βENaC hypomorph mouse model (βMUT). Body composition and metabolic and behavioral phenotypes were examined in male and female and βMUT and WT mice (n = 6–14/group) fed a normal chow diet (NFD) from weaning until 16 weeks of age, then a 60% kcal-fat diet for 5 weeks. Results: Compared to WT mice, βMUT male mice have reduced lean and total body mass. No remarkable differences in energy expenditure, motor activity, or food consumption patterns were detected. HFD-fed male βMUT mice exhibited reduced liver fat content (mass and Oil Red O staining) yet increased abdominal fat depots. HFD-fed female βMUT mice exhibited lower heart mass. Conclusions: These novel findings suggest a role for βENaC in the maintenance of metabolic homeostasis and adipose tissue distribution. Full article

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

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21 pages, 2122 KB

Open AccessArticle

Characterization of the Signaling Pathways Activated by KCl-Induced RTK Stimulation in Guinea Pig Airways

by Eva Herrera-Alcibar, Edgar Flores-Soto, Ruth M. López, Enrique F. Castillo, Patricia Campos-Bedolla, Verónica Carbajal and Bettina Sommer

Biology 2025, 14(11), 1557; https://doi.org/10.3390/biology14111557 - 6 Nov 2025

Abstract

We found that, in guinea pig airway smooth muscle, the pharmacological inhibition of RTKs significantly decreased the contraction induced by 20 mM KCl. We observed that MEK pharmacological inhibitors diminished the contraction induced by 20 mM KCl, but not that induced by 60 [...] Read more.

We found that, in guinea pig airway smooth muscle, the pharmacological inhibition of RTKs significantly decreased the contraction induced by 20 mM KCl. We observed that MEK pharmacological inhibitors diminished the contraction induced by 20 mM KCl, but not that induced by 60 mM. On the other hand, ERK inhibitors also altered the contraction generated by 20 mM KCl. When a ROCK inhibitor was tested, we found that it significantly inhibited the KCl-induced contraction. These results were complemented with Western blot experiments, and a decrease in ERK phosphorylation was noticed when the RTKs were inhibited. When MEK and ERK inhibitors were used, we also observed a decrease in ERK phosphorylation. In the case of MYPT1, its phosphorylation decreased when RTK, MEK, and ROCK inhibitors were used. In conclusion, we found that, in guinea pig airway smooth muscle, the contraction induced by 20 mM KCl includes the activation of RTKs and, in turn, MEK-ERK and ROCK. Full article

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

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34 pages, 1750 KB

Open AccessReview

Histone Post-Translational Modifications and DNA Double-Strand Break Repair in Neurodegenerative Diseases: An Epigenetic Perspective

by Arefa Yeasmin and Mariana P. Torrente

Biology 2025, 14(11), 1556; https://doi.org/10.3390/biology14111556 - 6 Nov 2025

Abstract

DNA damage is a hallmark of the fatal process of neurodegeneration in the central nervous system (CNS). As neurons are terminally differentiated, they accumulate metabolic and oxidative burdens over their whole life span. Unrepaired DNA develops into DNA double-strand breaks (DSBs), which are [...] Read more.

DNA damage is a hallmark of the fatal process of neurodegeneration in the central nervous system (CNS). As neurons are terminally differentiated, they accumulate metabolic and oxidative burdens over their whole life span. Unrepaired DNA develops into DNA double-strand breaks (DSBs), which are repaired through homologous recombination (HR) or non-homologous end joining (NHEJ). Being post-mitotic and unable to normally undergo HR, damage and defective repair is especially burdensome to CNS neurons. Current research has not produced treatment to prevent and halt progression of neurodegeneration. Hence, novel targeting strategies are desperately needed. Recent investigations in histone post-translational modifications (PTMs) reveal new mechanistic insight and highlight unexplored targets to ameliorate neurodegeneration. As various histone PTMs dictate and facilitate DSB repair, they represent an underexploited area in investigating DNA damage and incorrect repair aiding neurodegeneration. Here, we review the histone PTM alterations in several neurodegenerative diseases: Amyotrophic Lateral Sclerosis/Frontotemporal Dementia, Parkinson’s Disease, Alzheimer’s Diseases, Multiple Sclerosis, and Huntington’s Disease. These findings emphasize that histone PTM alterations can enable an aberrant DNA damage response (DDR) leading to neurodegeneration. Further research into the connections between histone PTMs and DNA damage in decaying neurons will illuminate novel targets to dampen the aberrant DDR and promote neuronal survival. Full article

(This article belongs to the Special Issue How Epigenetics Shapes the Nervous System)

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21 pages, 2280 KB

Open AccessReview

Sustainable Cultivation and Functional Bioactive Compounds of Auricularia Mushrooms: Advances, Challenges, and Future Prospects

by Miao Liu, Wenxin Jiang, Kai Huang, Ling Li, Qingzhong Meng, Xiaoxuan You, Kunlun Pu, Meijing Cheng, Zhenpeng Gao, Jianzhao Qi and Minglei Li

Biology 2025, 14(11), 1555; https://doi.org/10.3390/biology14111555 - 6 Nov 2025

Abstract

The genus Auricularia, and specifically the species A. auricula, is a globally significant edible fungus with a long history of cultivation and notable nutritional and medicinal properties. This review systematically examines the taxonomic classification, morphological and physiological characteristics, and bioactive components [...] Read more.

The genus Auricularia, and specifically the species A. auricula, is a globally significant edible fungus with a long history of cultivation and notable nutritional and medicinal properties. This review systematically examines the taxonomic classification, morphological and physiological characteristics, and bioactive components (such as polysaccharides, melanin, proteins and polyphenols) of A. auricula, as well as their pharmacological effects and industrial applications. Recent molecular biological advances have clarified taxonomic uncertainties, including the reclassification of ‘heimuer’ as A. cornea, and emphasized the species’ genetic diversity. A. auricula thrives in temperate and subtropical regions, with cultivation techniques evolving from traditional wood log inoculation to modern substrate-based methods. However, sustainability challenges persist, including reliance on virgin wood substrates and the need for improved spent substrate management. The fungus exhibits remarkable nutritional properties, with polysaccharides (up to 66.1% of dry weight) demonstrating hypoglycemic, antitumor, immunomodulatory, and antioxidant activities. Melanin and proteins further contribute to hepatoprotection, antimicrobial effects, and metabolic regulation. Industrial applications of Auricularia species extend beyond food into pharmaceuticals and functional materials. Polysaccharides are explored as drug carriers, while melanin shows promise in antioxidant and antibacterial formulations. Despite these advances, gaps remain in understanding the mechanistic basis of bioactive compound functions and optimizing cultivation for sustainable production. Future research should integrate multi-omics approaches to elucidate genetic regulation, enhance substrate formulations, and develop value-added products. This review underscores the potential of Auricularia species as a functional food and biotechnological resource, advocating for interdisciplinary efforts to address current challenges and unlock its full industrial potential. Full article

(This article belongs to the Section Microbiology)

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17 pages, 5860 KB

Open AccessArticle

Transcriptomics and Metabolomics Reveal Mechanisms Underlying the Adaptation of Lamiophlomis rotata to High Altitudes

by Yunzhang Xu, Sangjie Jiancuo, Xiao Luo, Yu-E Ma, Xin Wu, Zhenzhong Wu, Hengxia Yin, Shaoshan Zhang, Wenbing Li and Huachun Sheng

Biology 2025, 14(11), 1554; https://doi.org/10.3390/biology14111554 - 5 Nov 2025

Abstract

Lamiophlomis rotata (Benth.) Kudo is a typical alpine medicinal plant. However, the mechanism underlying its adaptation to high altitudes remains incompletely understood. In this study, we integrated transcriptome and metabolome analyses. Specifically, we used third-generation sequencing for building a reference transcriptome and second-generation [...] Read more.

Lamiophlomis rotata (Benth.) Kudo is a typical alpine medicinal plant. However, the mechanism underlying its adaptation to high altitudes remains incompletely understood. In this study, we integrated transcriptome and metabolome analyses. Specifically, we used third-generation sequencing for building a reference transcriptome and second-generation sequencing for differential gene expression analysis. Our findings revealed that the activation of the hydrogen sulfide signaling pathway and the reprogramming of amino acid metabolism are probable adaptation mechanisms. Different from previous reports, the hydrogen sulfide signaling may regulate the activity of cellulose synthase in addition to enhancement of antioxidant capacity and accumulation of osmolytes. By altering the agronomic traits of plants in a cell wall remodeling-dependent manner, it enables L. rotata to adapt to alpine stress. The accumulated amino acids not only store energy-efficient organic nitrogen as precursors for the synthesis of secondary metabolites but also act as signaling molecules to activate defense responses. Additionally, we propose a potential link between the hydrogen sulfide signaling pathway and amino acid metabolism. Overall, this study systematically explores the adaptation mechanism of L. rotata to high-altitude environments, offering a novel perspective for understanding the growth, development, stress responses, and secondary metabolic processes of alpine plants. Full article

(This article belongs to the Special Issue Advances in Plant Multi-Omics)

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18 pages, 1718 KB

Open AccessArticle

Combined Effects of Diazoxide and Moderate-Intensity Exercise on the Restoration of Redox Balance Post-Fatigue in Fast- and Slow-Twitch Skeletal Muscles of Hypertensive Rats

by Estefanía Bravo-Sánchez, César J. Nolasco-Ruiz, Sarai Sánchez-Duarte, Mariana Gómez-Barroso, Manuel Alejandro Vargas-Vargas, Christian Cortés-Rojo, Salvador Manzo-Ávalos, Elizabeth Sánchez-Duarte, Alain Raimundo Rodríguez-Orozco, Alfredo Saavedra-Molina and Rocío Montoya-Pérez

Biology 2025, 14(11), 1553; https://doi.org/10.3390/biology14111553 - 5 Nov 2025

Abstract

Muscle fatigue, defined as a decline in force generation, is closely linked to redox imbalance—a condition exacerbated by oxidative stress in hypertension. This study investigated the effects of diazoxide administration and moderate-intensity exercise on skeletal muscle redox status following a fatigue protocol in [...] Read more.

Muscle fatigue, defined as a decline in force generation, is closely linked to redox imbalance—a condition exacerbated by oxidative stress in hypertension. This study investigated the effects of diazoxide administration and moderate-intensity exercise on skeletal muscle redox status following a fatigue protocol in rats with hypertension. Animals were assigned to eight groups: control (CTRL), diazoxide (DZX), exercise (EX), exercise + diazoxide (EX+DZX), hypertension (HTN), hypertension + diazoxide (HTN+DZX), hypertension + exercise (HTN+EX), and hypertension + exercise + diazoxide (HTN+ EX+DZX). Hypertension was induced by a high-salt diet. Diazoxide was administered daily for 14 days, and exercise consisted of moderate treadmill running for 8 weeks. Muscle fatigue was evoked in the extensor digitorum longus (EDL) and soleus by repetitive electrical stimulation. Post-fatigue analyses included oxidant levels, catalase activity, and glutathione status. Hypertension increased oxidants and reduced antioxidant defenses in both muscle types. Exercise and diazoxide, alone or in combination, improved redox balance, with the combined treatment providing the most robust protection and exhibiting fiber-specific adaptations. These findings suggest that diazoxide combined with moderate exercise represents a promising therapeutic approach to counteract oxidative stress-related skeletal muscle dysfunction in hypertension. Full article

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32 pages, 10076 KB

Open AccessArticle

Characterising PMP22-Proximal Partners in a Schwann Cell Model of Charcot–Marie–Tooth Disease Type1A

by Ian Holt, Nicholas Emery, Monte A. Gates, Sharon J. Brown, Sally L. Shirran and Heidi R. Fuller

Biology 2025, 14(11), 1552; https://doi.org/10.3390/biology14111552 - 5 Nov 2025

Abstract

Charcot–Marie–Tooth disease type 1A (CMT1A) is a hereditary condition caused by the duplication of the PMP22 gene. Overexpression of peripheral myelin protein 22 in Schwann cells leads to myelin sheath defects and axonal loss. We have produced a cell model to facilitate studies [...] Read more.

Charcot–Marie–Tooth disease type 1A (CMT1A) is a hereditary condition caused by the duplication of the PMP22 gene. Overexpression of peripheral myelin protein 22 in Schwann cells leads to myelin sheath defects and axonal loss. We have produced a cell model to facilitate studies of the molecular mechanisms involved in PMP22 accumulation and clearance. Our model is a stably transfected, clonal, immortalised human Schwann cell line with overexpressed levels of PMP22 fusion protein. A control-transfected cell line (vector lacking PMP22) was also produced. PMP22-transfected cells had reduced levels of mitosis, with the PMP22 fusion protein concentrated in punctate aggregates in the cytoplasm and expressed at the plasma membranes, which were often irregular and spindly. In contrast, control cells (control-transfected and parent cell lines) generally had smooth and regular plasma membrane morphology. Culturing in the presence of NRG1 and forskolin lead to upregulation of markers of myelination potential in the control cells. These markers were more variable in the cells stably transfected with PMP22, including decreased levels of transcripts of SOX10, JUN, S100B and NGFR, but increased levels of MPZ and EGR2 compared to controls. Using proximity-dependent biotin identification (BioID2), several hundred proteins were identified in the proximity of the overexpressed PMP22, of which 291 significant proteins were only detected in the proximity of PMP22 and not in that of control pull-downs. Among the most significantly enriched PMP22-interacting proteins were integrins alpha-2 (ITGA2) and alpha-7 (ITGA7), which play a role in myelination via their interactions with the extracellular matrix. The presence of ITGA2 in just the PMP22-transfected fraction was confirmed by western blot. Some of the proteins were associated with several enriched molecular pathways, including molecular transport and protein trafficking, and may represent potential therapeutic targets for CMT1A by promoting the degradation and enhanced trafficking of PMP22. Full article

(This article belongs to the Section Neuroscience)

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21 pages, 10683 KB

Open AccessArticle

Glycogen Synthase Kinase 3 Is Essential for Intestinal Cell Niche and Digestive Function

by Minggang Yang, Xiaohui Li, Jiajia Zhan, Rui Pan, Ziye Yang, Mengsha Zhou, Lei Ma and Chenfeng Liu

Biology 2025, 14(11), 1551; https://doi.org/10.3390/biology14111551 - 5 Nov 2025

Abstract

WNT/β-catenin signaling is essential for intestinal stem cell development and self-renewal, while its dysregulation can drive tumorigenesis. GSK3, a key negative regulator of β-catenin, in intestinal homeostasis remains incompletely understood. In this study, we investigated the role of GSK3 in intestinal development, niche [...] Read more.

WNT/β-catenin signaling is essential for intestinal stem cell development and self-renewal, while its dysregulation can drive tumorigenesis. GSK3, a key negative regulator of β-catenin, in intestinal homeostasis remains incompletely understood. In this study, we investigated the role of GSK3 in intestinal development, niche maintenance, and physiological function. Unlike Apc^Min/+ mice that developed intestinal polyps, neither GSK3α nor GSK3β deficiency disrupted intestinal homeostasis. However, complete GSK3 deletion (DKO) resulted in perinatal lethality, characterized by disturbed crypt–villus architecture, Paneth cell redistribution, and villus elongation. GSK3 deficiency disrupted the intestinal niche, leading to expanded and mislocalized stem cells and Paneth cells, along with reduced tuft and enteroendocrine cells. These alterations impaired nutrient absorption and gut motility. Mechanistically, β-catenin-positive cells were significantly increased following GSK3 deletion. Genetic ablation of β-catenin under GSK3-deficient conditions reduced stem and Paneth cell populations while restoring tuft and enteroendocrine cells, thereby ameliorating niche abnormalities and improving absorptive and peristaltic functions. This study indicates the essential role of GSK3/β-catenin signaling in maintaining intestinal niche integrity and digestive physiology, highlighting potential therapeutic targets for intestinal and digestive disorders. Full article

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

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14 pages, 2067 KB

Open AccessArticle

Relationship Between Sperm Parameters and Indices of Chromatin Condensation and DNA Fragmentation in Semen

by Othmane Adli, Noureddine Louanjli and Rachid Aboutaieb

Biology 2025, 14(11), 1550; https://doi.org/10.3390/biology14111550 - 5 Nov 2025

Abstract

Infertility is a major health problem affecting about 15% of couples worldwide. Male etiology is found in almost one-third of cases. This study identified the nature of the relationship between sperm DNA fragmentation (SDF), sperm chromatin condensation (SCC) and sperm parameters. In this [...] Read more.

Infertility is a major health problem affecting about 15% of couples worldwide. Male etiology is found in almost one-third of cases. This study identified the nature of the relationship between sperm DNA fragmentation (SDF), sperm chromatin condensation (SCC) and sperm parameters. In this study, 80 samples were analyzed using two methods: the TUNEL technique to assess sperm DNA quality and aniline blue coloration to determine the level of chromatic condensation of spermatozoa. In addition, to specify the standard sperm parameters, the spermogram and the spermocytogram were analyzed. The main results revealed a significant difference between SDF and motility and, similarly, between SCC, motility, and teratozoospermia macrocephaly types (p < 0.0001, p < 0.0001, respectively), but no differences between SCC, SDF, and the other sperm parameters (p > 0.99). Full article

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22 pages, 22159 KB

Open AccessArticle

Phylogeographic Insights into Pipistrellus Species from Türkiye: Diversity, Divergence, and Regional Lineage Structure

by Emin Seyfi, Şafak Bulut and Gül Olgun Karacan

Biology 2025, 14(11), 1549; https://doi.org/10.3390/biology14111549 - 4 Nov 2025

Abstract

This study investigates the phylogenetic relationships, genetic diversity, and biogeographic structure of Pipistrellus species in Türkiye using mitochondrial cytochrome b (Cytb) sequences from 156 specimens collected across 26 localities. Our primary aim was to clarify taxonomic boundaries of morphologically cryptic species [...] Read more.

This study investigates the phylogenetic relationships, genetic diversity, and biogeographic structure of Pipistrellus species in Türkiye using mitochondrial cytochrome b (Cytb) sequences from 156 specimens collected across 26 localities. Our primary aim was to clarify taxonomic boundaries of morphologically cryptic species and elucidate the evolutionary role of Anatolia in the Western Palearctic. Analyses strongly confirmed that molecular data are mandatory for defining taxonomic boundaries. Crucially, all individuals morphologically identified as P. pygmaeus were genetically determined to be P. pipistrellus, highlighting the inadequacy of external traits for cryptic species. We resolved deep intraspecific divergence across the genus. In P. pipistrellus, two major lineages (Eastern and Western) were identified, partially separated by the Anatolian Diagonal. Their co-occurrence in multiple localities confirms Anatolia’s function as a secondary contact zone. Similarly, P. kuhlii populations represent a transition zone where two distinct lineages, one of Asiatic origin (P. k. lepidus) and one Mediterranean-Levantine (P. k. kuhlii), meet. Furthermore, while P. nathusii is largely associated with migratory European lineages; a genetically distinct, potentially resident lineage was revealed in southwestern Anatolia. Divergence time estimations indicate that this diversification was shaped by major climatic events from the Miocene to the Pleistocene. This study demonstrates that Anatolia is more than just a geographic bridge; it is a dynamic center of evolution, functioning critically as both a glacial refugium and a secondary contact zone for Palearctic bat fauna. Full article

(This article belongs to the Section Zoology)

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19 pages, 14541 KB

Open AccessArticle

Pan-Mitogenome Construction, Intraspecific Variation, and Adaptive Evolution of the Plant Pathogenic Fungus Claviceps purpurea

by Mingliang Ding, Rui Hu, Jinlong Jia, Cuiyuan Wei, Yongzhen Cui, Hefa Liao, Zhuliang Yang, Jianwei Guo, Zhanhong Ma and Yuanbing Wang

Biology 2025, 14(11), 1548; https://doi.org/10.3390/biology14111548 - 4 Nov 2025

Abstract

Claviceps purpurea is a specialized phytopathogenic fungus that infects grasses and produces pharmacologically active compounds, attracting considerable interest in genomic research. In this study, we assembled and annotated the complete mitogenomes of 15 C. purpurea strains isolated from different host plants, including seven [...] Read more.

Claviceps purpurea is a specialized phytopathogenic fungus that infects grasses and produces pharmacologically active compounds, attracting considerable interest in genomic research. In this study, we assembled and annotated the complete mitogenomes of 15 C. purpurea strains isolated from different host plants, including seven newly sequenced isolates from China. Analysis of the C. purpurea pan-mitogenome demonstrated that the accessory regions, with an average proportion of 48.23%, are the main contributor to mitogenome variation. Analysis of the 14 protein-coding genes revealed Ka/Ks ratios below 1, indicating strong purifying selection. Notably, the atp9 gene was absent in all strains, suggesting a potential adaptive gene loss. Structural variations were predominantly located in the intergenic region between rns and rnl. Phylogenetic analysis based on concatenated mitochondrial genes placed Claviceps as most closely related to the genus Epichloë. The 15 C. purpurea strains grouped into five well-supported subclades, with Chinese and non-Chinese isolates forming distinct lineages. Among these, the Chinese strains ACCC 37001 and KUNCC 11030 represented the earliest diverging lineages. This study elucidates the intraspecific variation and evolutionary patterns of the mitogenome in C. purpurea and highlights the value of mitogenome in resolving phylogenetic relationships. Full article

(This article belongs to the Section Microbiology)

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24 pages, 13370 KB

Open AccessArticle

PLIN5 Promotes Lipid Reconstitution in Goat Intramuscular Fat via the PPARγ Signaling Pathway

by Yuhan Dai, Yuling Yang, Haiyang Li, Yinggui Wang, Yong Wang, Yaqiu Lin, Lian Huang, Zhanyu Du, Hua Xiang, Changhui Zhang and Jiangjiang Zhu

Biology 2025, 14(11), 1547; https://doi.org/10.3390/biology14111547 - 4 Nov 2025

Abstract

Intramuscular fat (IMF) content is an important factor of goat meat quality, which is related to the proliferation and differentiation of intramuscular preadipocytes. Perilipin 5 (PLIN5) is a lipid droplet-associated protein; however, the specific function and underlying mechanism of PLIN5 in goat IMF [...] Read more.

Intramuscular fat (IMF) content is an important factor of goat meat quality, which is related to the proliferation and differentiation of intramuscular preadipocytes. Perilipin 5 (PLIN5) is a lipid droplet-associated protein; however, the specific function and underlying mechanism of PLIN5 in goat IMF deposition are still unclear. In this study, overexpression of PLIN5 significantly enhanced apoptosis and reduced the proliferation of preadipocytes and also promoted cellular lipid deposition via both the upregulation of the expression of peroxisome proliferator-activated receptor gamma (PPARγ) and a significant increase in the expression of lipogenesis-related genes. The inhibition of PLIN5 then confirmed these results. Untargeted lipidomics sequencing identified a total of 34 differentially expressed lipids after PLIN5 overexpression in goat preadipocytes and analysis by KEGG pathway enrichment, which are mainly involved in the PI3K-AKT signaling pathway. The lipid omics findings also show that ceramides and lysophosphatidylinositol were significantly upregulated, e.g., Cer (d35:1), Cer (d18:2/22:1), LPI (18:0), and LPI (16:0), after overexpression of the PLIN5 gene. Higher expression of LPI (16:0) or LPI (18:0) may regulate lipid droplet accumulation by activating PPARγ. Rescue experiments with the PI3K-AKT inhibitor (LY294002) and the PPARγ inhibitor (GW9662) showed that the PI3K-AKT signaling pathway is involved in the regulation of cell proliferation, and PPARγ is involved in the regulation of lipid deposition. In conclusion, our findings demonstrate that PLIN5 regulates lipid reconstitution in goat intramuscular fat via PPARγ and PI3K-AKT signaling pathways. This regulation delivered theoretical support for improving meat quality from the aspect of IMF deposition. Full article

20 pages, 3220 KB

Open AccessArticle

Metabolome and Metagenome Signatures Underlying the Differential Resistance of Percocypris pingi, Crucian Carp, and Yellow Catfish to Ichthyophthirius multifiliis Infection

by Yi Liu, Jiang Xie, Yang He, Qingchao Shi, Quan Gong, Weihong Zhao, Chuanjie Qin and Chuang Zhou

Biology 2025, 14(11), 1546; https://doi.org/10.3390/biology14111546 - 4 Nov 2025

Abstract

Ichthyophthirius multifiliis poses a significant threat to global aquaculture, yet some fish species exhibit remarkable resistance. This study employed a combined LC-MS-based metabolomics and 16S rRNA gene sequencing approach to investigate the intrinsic mechanisms underlying the differential susceptibility of Percocypris pingi, crucian [...] Read more.

Ichthyophthirius multifiliis poses a significant threat to global aquaculture, yet some fish species exhibit remarkable resistance. This study employed a combined LC-MS-based metabolomics and 16S rRNA gene sequencing approach to investigate the intrinsic mechanisms underlying the differential susceptibility of Percocypris pingi, crucian carp, and yellow catfish. Our results revealed distinct skin molecular and microbial profiles in P. pingi associated with its enhanced resilience. Metabolomic analysis identified a significant upregulation of key antioxidants (L-Glutathione reduced, L-Glutathione oxidized, L-Cysteine-glutathione gisulfide, Uric acid, Histamine, N-Acetylhistamine, and scorbic acid) in P. pingi, most notably L-Glutathione reduced, which was 31- and 59-fold higher than in yellow catfish and crucian carp, respectively. Functional enrichment further highlighted the critical role of enhanced antioxidant capacity (centered on glutathione metabolism) and immune/inflammatory responses in the resistance to I. multifiliis of P. pingi. Concurrently, skin microbiome analysis showed that P. pingi hosted a microbial community distinct from the other two species, with significantly higher α-diversity. Notably, P. pingi skin was significantly depleted of the parasitic bacteria Candidatus_Megaira and Candidatus_Midichloria, which were highly abundant in the susceptible species. Furthermore, predicted metagenomic functions indicated that P. pingi’s microbiota was enriched in fundamental metabolic pathways, whereas the microbiota of crucian carp and yellow catfish was skewed towards disease- and immune-related pathways. In conclusion, our findings demonstrate that the superior resistance of P. pingi to I. multifiliis is likely conferred by a synergistic effect of a robust skin antioxidant capacity (primarily driven by glutathione) and a protective skin microbiome that excludes specific parasites. This study provides novel insights into the multi-faceted mechanisms of disease resistance in fish. Full article

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

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