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Volume 14
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Biology, Volume 14, Issue 10 (October 2025) – 18 articles

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34 pages, 28338 KB  
Article
Consensus-Guided Construction of H5N1-Specific and Universal Influenza A Multiepitope Vaccines
by Marco Palma
Biology 2025, 14(10), 1327; https://doi.org/10.3390/biology14101327 - 25 Sep 2025
Abstract
Background/Objectives: Influenza A viruses—including highly pathogenic H5N1—remain a global threat due to rapid evolution, zoonoses, and pandemic potential. Strain-specific vaccines targeting variable antigens often yield limited, short-lived immunity. The HA receptor-binding domain (RBD), a functionally constrained and immunologically relevant region, is a [...] Read more.
Background/Objectives: Influenza A viruses—including highly pathogenic H5N1—remain a global threat due to rapid evolution, zoonoses, and pandemic potential. Strain-specific vaccines targeting variable antigens often yield limited, short-lived immunity. The HA receptor-binding domain (RBD), a functionally constrained and immunologically relevant region, is a promising target for broad and subtype-focused vaccines. We aimed to design multiepitope constructs targeting conserved HA-RBD and adjacent domains to elicit robust, durable, cross-protective responses. Methods: Extensive sequence analyses (>20,000 H5N1 and >190,000 influenza A sequences) were used to derive consensus sequences. Three HA-based candidates were developed: (i) EpitoCore-HA-VX, a multi-epitope construct containing CTL, HTL, and B-cell epitopes from the H5N1 HA-RBD; (ii) StructiRBD-HA-VX, incorporating a conformationally preserved RBD segment; and (iii) FusiCon-HA-VX, targeting the conserved HA fusion peptide shared across subtypes. Two external HA comparators—a 400-aa HA fragment and the literature-reported HA-13–263-Fd-His—were analyzed under the same pipeline. The workflow predicted epitopes; evaluated antigenicity, allergenicity, toxicity, conservation, and HLA coverage; generated AlphaFold models; performed TLR2/TLR4 docking with pyDockWEB; and carried out interface analysis with PDBsum; and C-ImmSim simulations. Results: Models suggested stable, energetically favorable TLR2/TLR4 interfaces supported by substantial binding surfaces and complementary electrostatic/desolvation profiles. Distinct docking patterns indicated receptor-binding flexibility. Immune simulations predicted strong humoral responses with modeled memory formation and, for the H5N1-focused designs, cytotoxic T-cell activity. All candidates and comparators were predicted to be antigenic, non-allergenic, and non-toxic, with combined HLA coverage approaching global breadth. Conclusions: This study compares three design strategies within a harmonized framework—epitope collation, structure-preserved RBD, and fusion-peptide targeting—while benchmarking against two HA comparators. EpitoCore-HA-VX and StructiRBD-HA-VX showed promise against diverse H5N1 isolates, whereas FusiCon-HA-VX supported cross-subtype coverage. As these findings are model-based, they should be interpreted qualitatively; nonetheless, the integrated, structure-guided approach provides an adaptable path for advancing targeted H5N1 and broader influenza A vaccine concepts. Full article
(This article belongs to the Special Issue Human Leukocyte Antigen (HLA)—Antigen Interactions in Vaccine Development)
26 pages, 15140 KB  
Article
Genome-Wide Analysis and Functional Characterization of Small Heat Shock Proteins in Allium sativum L. Under Multiple Abiotic Stresses
by Na Li, Bing He and Zhenyu Cao
Biology 2025, 14(10), 1326; https://doi.org/10.3390/biology14101326 - 25 Sep 2025
Abstract
Small heat shock proteins play a pivotal role in maintaining protein homeostasis under abiotic stress conditions and are indispensable for plant viability. In the present study, a comprehensive characterization of this gene family in Allium sativum was conducted through genome-wide sequence identification, phylogenetic [...] Read more.
Small heat shock proteins play a pivotal role in maintaining protein homeostasis under abiotic stress conditions and are indispensable for plant viability. In the present study, a comprehensive characterization of this gene family in Allium sativum was conducted through genome-wide sequence identification, phylogenetic reconstruction, conserved motif analysis, promoter cis-element profiling, transcriptomic investigation, quantitative real-time PCR, subcellular localization, and yeast-based functional assays. A total of 114 small heat shock protein genes were identified across eight chromosomes and subsequently classified into ten phylogenetic subgroups. All encoded proteins conserved the α-crystallin domain, whereas their exon–intron architectures and promoter elements responsive to environmental stress or phytohormones exhibited considerable diversity. The predicted proteins range from 130 to 364 amino acids, with isoelectric points (pI) spanning 3.97 to 9.95 and GRAVY values from −1.131 to −0.014, indicating predominantly hydrophilic characteristics. Subcellular localization analysis revealed a broad distribution across the cytoplasm, chloroplasts, mitochondria, and other compartments, with the majority (74 proteins) localized in the cytoplasm. Synteny analysis uncovered two segmentally duplicated gene pairs (AsHSP20-80/31, and AsHSP20-81/32), both showing strong purifying selection (Ka/Ks = 0.0459 and 0.2545, respectively), suggesting functional conservation. Expression profiling demonstrated predominant transcript accumulation in bulbs and floral organs, with significant induction under heat, salinity, and jasmonic acid treatments. qRT–PCR validation further confirmed that several candidate genes, notably AsHSP20-94 and AsHSP20-79, were strongly and consistently upregulated across multiple stress conditions, underscoring their roles as core stress-responsive regulators. Subcellular localization experiments demonstrated that representative proteins are targeted to the cytoplasm, nucleus and chloroplasts. Furthermore, heterologous expression of AsHSP20-79 in yeast conferred marked thermotolerance. Collectively, these findings reveal extensive expansion and functional divergence of the small heat shock protein gene family in garlic and provide valuable candidate genes for improving stress resilience in this important crop species. Full article
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27 pages, 3899 KB  
Article
High Diversity and Spatiotemporal Dynamics of Silica-Scaled Chrysophytes (Class Chrysophyceae) in Reservoirs of the Angara Cascade of Hydroelectric Dams
by Anna Bessudova, Yuri Galachyants, Alena Firsova, Artyom Marchenkov, Andrey Tanichev, Darya Petrova and Yelena Likhoshway
Biology 2025, 14(10), 1325; https://doi.org/10.3390/biology14101325 - 25 Sep 2025
Abstract
The study of aquatic biodiversity in the context of ecosystem sustainability is of urgent research importance, with several existing knowledge gaps. Among the under-studied groups are silica-scaled chrysophytes. Their cells are covered with silica scales and bristles/spines, the species-specific structure of which can [...] Read more.
The study of aquatic biodiversity in the context of ecosystem sustainability is of urgent research importance, with several existing knowledge gaps. Among the under-studied groups are silica-scaled chrysophytes. Their cells are covered with silica scales and bristles/spines, the species-specific structure of which can be distinguished only by electron microscopy. In June and August 2024, samples were collected from a broad aquatic system comprising the southern part of Lake Baikal and a cascade of four reservoirs formed after the construction of hydroelectric dams on the Angara River flowing from Lake Baikal. Using electron microscopy, we identified 45 species of silica-scaled chrysophytes in phytoplankton in 2024, and the overall checklist was expanded to 57, accounting for interannual differences. Clear differences in species composition and richness were observed both between seasons and among reservoirs. Approximately a quarter of the recorded species were heterotrophs, which do not contribute to primary production, whereas 44% were phototrophs and 31% mixotrophs, both groups contributing to the Si cycle and to primary production. Continuous monitoring of reservoirs is essential for understanding the processes shaping silica-scaled chrysophytes diversity and may serve as an additional criterion for assessing the sustainability and transformation of freshwater ecosystems. Full article
(This article belongs to the Section Microbiology)
23 pages, 3210 KB  
Article
Microbial, Physicochemical, and Flavor Interactions in High-Temperature Sauce-Flavor Daqu
by Youwei Chen, Limei Zou, Luyao Wang, Weiwei Dong, Yanli Feng, Xiang Yu, Jun Liu, Yu Zhang, Yuanliang Hu and Shenxi Chen
Biology 2025, 14(10), 1324; https://doi.org/10.3390/biology14101324 - 25 Sep 2025
Abstract
Sauce-flavor Daqu is the solid-state fermentation starter for sauce-flavor Baijiu. Its microbial community influences flavor formation, yet links between community change, process conditions, and flavor development during high-temperature fermentation remain unclear. We investigated Daqu fermentation by integrating high-throughput sequencing, monitoring of physicochemical parameters, [...] Read more.
Sauce-flavor Daqu is the solid-state fermentation starter for sauce-flavor Baijiu. Its microbial community influences flavor formation, yet links between community change, process conditions, and flavor development during high-temperature fermentation remain unclear. We investigated Daqu fermentation by integrating high-throughput sequencing, monitoring of physicochemical parameters, and analysis of volatile compounds. Fermentation temperature showed three phases: rapid rise, fluctuating plateau, and gradual decline. High temperatures were associated with increased thermophilic microbes such as Bacillus and Thermoascus and with higher levels of reducing sugars and amino acid nitrogen; amylase, protease, and other hydrolase activities were detected. Bacterial composition varied more than fungal composition; Firmicutes and Ascomycota were the dominant phyla, and Bacillus and Thermoascus were abundant genera. Canonical correspondence analysis associated reducing sugars, acidity, and moisture with early community shifts, and amino acid nitrogen with later shifts; reducing sugars and moisture showed the strongest associations. Filamentous fungi and Bacillus correlated with pyrazine-type compounds. These results link microbial composition, process parameters, and flavor profiles, and may inform the standardization and mechanization of Daqu production. Full article
(This article belongs to the Section Microbiology)
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23 pages, 2800 KB  
Article
Genome-Driven Insights into Lactococcus sp. KTH0-1S Highlights Its Biotechnological Potential as a Cell Factory
by Nisit Watthanasakphuban, Hind Abibi, Nuttakan Nitayapat, Phitsanu Pinmanee, Chollachai Klaysubun, Nattarika Chaichana, Komwit Surachat and Suttipun Keawsompong
Biology 2025, 14(10), 1323; https://doi.org/10.3390/biology14101323 - 25 Sep 2025
Abstract
The safety, genetic distinctiveness, and functional capabilities of Lactococcus sp. KTH0-1S, a strain isolated from Thai fermented shrimp (Kung-Som), were investigated to assess its potential as a next-generation probiotic and microbial cell factory. Whole-genome sequencing and multilocus sequence typing (MLST) analysis revealed that [...] Read more.
The safety, genetic distinctiveness, and functional capabilities of Lactococcus sp. KTH0-1S, a strain isolated from Thai fermented shrimp (Kung-Som), were investigated to assess its potential as a next-generation probiotic and microbial cell factory. Whole-genome sequencing and multilocus sequence typing (MLST) analysis revealed that Lactococcus sp. KTH0-1S is a novel, phylogenetically distinct strain within the Lactococcus genus. Comprehensive in silico safety evaluation confirmed the absence of antimicrobial resistance genes and major virulence factors, supporting its suitability for food-grade applications. The genome encodes multiple probiotic-relevant traits, including stress tolerance (e.g., dnaK, clpP), adhesion and biofilm formation (e.g., gapA, luxS, glf2), and nutrient acquisition genes, enabling adaptation to gastrointestinal and fermentation environments. Notably, Lactococcus sp. KTH0-1S harbors a chromosomally encoded nisin Z biosynthesis gene cluster with auto-induction capability, providing a self-regulated and stable alternative to conventional plasmid-based NICE systems in Lactococcus lactis. The strain also exhibits nisin immunity, allowing tolerance to high nisin concentrations, thus supporting robust protein production. Genomic evidence and phenotypic assays confirmed a functional respiration metabolism activated by heme supplementation, enhancing biomass yield and culture stability. Furthermore, the presence of diverse CAZyme families (GHs, GTs, CEs) enables utilization of various carbohydrate substrates, including lignocellulosic and starchy agro-industrial residues. These properties collectively underscore Lactococcus sp. KTH0-1S as a safe, stable, and metabolically versatile candidate for probiotic applications and as a cost-effective, food-grade expression host for biotechnological production. Full article
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22 pages, 1481 KB  
Review
Research Advances in the Synthesis and Regulation of Apple Anthocyanins
by Haidong Bu, Guangjun Gu, Yinghui Hu, Yue Yang, Ling Yang, Hui Yuan and Wenquan Yu
Biology 2025, 14(10), 1322; https://doi.org/10.3390/biology14101322 - 25 Sep 2025
Abstract
Anthocyanins are key pigments responsible for apple fruit coloration, influencing not only its appearance and marketability but also contributing significantly to its nutritional and health benefits. In their natural state, anthocyanins are chemically unstable. However, glycosylation modifies them into anthocyanin derivatives known as [...] Read more.
Anthocyanins are key pigments responsible for apple fruit coloration, influencing not only its appearance and marketability but also contributing significantly to its nutritional and health benefits. In their natural state, anthocyanins are chemically unstable. However, glycosylation modifies them into anthocyanin derivatives known as anthocyanin glycosides, which exhibit markedly enhanced stability and improved water solubility. As a result, most naturally occurring anthocyanins exist in the form of anthocyanin glycosides. The biosynthesis of anthocyanins involves a series of structural genes within the phenylpropanoid and flavonoid pathways (including PAL, C4H, 4CL, CHS, CHI, F3H, DFR, ANS/LDOX, and UFGT). The MYB–bHLH–WD40 transcriptional complex serves as the core regulatory mechanism controlling anthocyanin synthesis, with additional transcription factors also playing important roles. This review systematically summarizes recent advances in the structural characteristics, biosynthetic pathways, molecular regulatory mechanisms, and environmental factors affecting anthocyanin accumulation in apples. These insights are important both for consumer health and for breeding apple cultivars with enhanced anthocyanin content. Full article
(This article belongs to the Special Issue Feature Papers on Developmental and Reproductive Biology)
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15 pages, 3598 KB  
Article
Allelopathic Trade-Offs of Rye and Wheat Residues Versus 2-Benzoxazolinone: Impacts on Cotton Growth
by Yue Li, Vivien G. Allen, Junping Chen and David B. Wester
Biology 2025, 14(10), 1321; https://doi.org/10.3390/biology14101321 - 25 Sep 2025
Abstract
Cover crops provide soil cover benefits but can impose allelopathic risks on cotton. We evaluated the functional trade-offs of rye and wheat residues versus purified 2-benzoxazolinone (BOA) under greenhouse conditions. Four experiments applied graded residue or BOA inputs in Pullman clay loam; cotton [...] Read more.
Cover crops provide soil cover benefits but can impose allelopathic risks on cotton. We evaluated the functional trade-offs of rye and wheat residues versus purified 2-benzoxazolinone (BOA) under greenhouse conditions. Four experiments applied graded residue or BOA inputs in Pullman clay loam; cotton germination, height, chlorophyll (SPAD), and biomass were measured, and soil BOA, DIBOA, and DIMBOA were quantified by HPLC at designated sampling dates. Responses were dose dependent: BOA reduced germination linearly (−16.5% at 1000 nmol g−1 versus control) and shortened plants, and biomass and SPAD were directionally lower, most evident at 500 nmol g−1, but not statistically significant. Rye showed hormesis at 6400 kg ha−1 (+7.3% germination) and strong inhibition at 12,800 kg ha−1 (−31% germination; biomass up to −45%). Wheat produced intermediate inhibition (biomass −23.7%) and did not affect germination. In soil, benzoxazinoids exhibited significant rate effects at specific sampling dates followed by rapid decline. After storage, BOA showed no residual effects, whereas prior rye still reduced height, SPAD, and biomass. Framed at the agroecosystem scale, maintaining residue biomass below inhibitory thresholds and adjusting termination-to-planting intervals to avoid the early post-termination period, together with species or cultivar choice, can reconcile soil cover services with reliable cotton establishment. Full article
(This article belongs to the Topic Evaluating the Functional Value of Agroecosystems under Different Management Scenarios)
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15 pages, 2948 KB  
Article
Pan-Cancer Analysis of Mutations Affecting Protein Liquid–Liquid Phase Separation Revealing Clinical Implications
by Xiaoping Cen, Lulu Wang, Kai Yu, Huanming Yang, Roland Eils, Wei Dong, Huan Lin and Zexian Liu
Biology 2025, 14(10), 1320; https://doi.org/10.3390/biology14101320 - 25 Sep 2025
Abstract
Phase separation is one of the mechanisms critical for protein function, and its aberrances are associated with cancer development. However, mutations that affect protein phase separation and cancer development have not been systematically identified and analyzed. In this study, we systematically identified the [...] Read more.
Phase separation is one of the mechanisms critical for protein function, and its aberrances are associated with cancer development. However, mutations that affect protein phase separation and cancer development have not been systematically identified and analyzed. In this study, we systematically identified the mutations affecting protein liquid–liquid phase separation in multiple cancers. We calculated the phase separation scores alterations for over 1,200,000 mutations across 16 cancer types using the TCGA dataset. We then performed pathway enrichment, kinase, TF enrichment, and survival analysis to identify related biological processes and clinical implications. Nearly 10% of the mutations were defined to affect phase separation in pan-cancer. These mutations occupied a consistent percentage in each cancer type. Extremely influencing mutations accumulate on stomach adenocarcinoma (STAD), uterine corpus endometrial carcinoma (UCEC), and skin cutaneous melanoma (SKCM). Moreover, proteins carrying these mutations are enriched in cancer-related pathways, including TGF-beta signaling pathways and polycomb repressive complex. Phase separation of these proteins would be regulated by kinases, including CDK1, CDK2, and EGFR, and transcription factors, including ZNF407, ZNF318, and MGA proteins, to play functions in cancer. Protein–Protein Interaction Network revealed that these phase separation proteins are highly interconnected. Finally, patients carrying mutations that positively affect the protein phase separation are associated with poor prognosis in skin cutaneous melanoma (SKCM) and lung squamous cell carcinoma (LUSC), which could be partially explained by the pathogenicity of these mutations. The study provided a pan-cancer landscape for depicting the association of phase separation and cancer mutations, which would be a rich data resource for understanding the association of cancer mutations and phase separation. Full article
(This article belongs to the Section Bioinformatics)
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24 pages, 921 KB  
Review
The Pathophysiology of Alcohol-Associated Liver Disease: Focusing on Superoxide Dismutase 1 as a Therapeutic Target
by Thiyagarajan Gopal, Arul Daniel John Kathiravan, Alexander V. Kabanov, Carol A. Casey and Viswanathan Saraswathi
Biology 2025, 14(10), 1319; https://doi.org/10.3390/biology14101319 - 24 Sep 2025
Abstract
Alcohol-associated liver disease (ALD) is a major health problem of global importance, caused by chronic alcohol consumption, leading to the accumulation of reactive oxygen species (ROS) and subsequent oxidative stress—a central mechanism in liver injury. Superoxide dismutase 1 (SOD1), a Cu-Zn containing antioxidant [...] Read more.
Alcohol-associated liver disease (ALD) is a major health problem of global importance, caused by chronic alcohol consumption, leading to the accumulation of reactive oxygen species (ROS) and subsequent oxidative stress—a central mechanism in liver injury. Superoxide dismutase 1 (SOD1), a Cu-Zn containing antioxidant enzyme, plays a crucial role in attenuating ALD-induced oxidative stress triggered by ethanol metabolism. However, alcohol exposure, whether chronic, acute or binge, differentially affects SOD1 levels, either diminishing its expression or temporarily compensating for alcohol-induced oxidative damage. Regardless, overexpression of SOD1 reverses early stages of ethanol-induced liver inflammation and injury in animal models, highlighting the protective role of SOD1. Current therapies, including alcohol abstinence, corticosteroids, and pentoxifylline, have limited long-term efficacy. Antioxidant-based treatments, such as N-acetylcysteine (NAC) and S-adenosyl-L-methionine (SAM), have demonstrated moderate benefits. While combination therapies like NAC with prednisolone yield more promising outcomes, these benefits are often limited in duration. The use of natural compounds including nutraceuticals and probiotics provide liver protection by enhancing antioxidant defenses, reducing inflammation, and mitigating alcohol-induced liver damage. In particular, these compounds upregulate antioxidant enzymes like SOD1. Recent research suggests that enhancing the activity of SOD1, particularly through nanoformulated SOD1 (NanoSOD1), which had direct effect on the oxidative stress at the cellular level, could offer a promising therapeutic option for ALD. NanoSOD1 aims to improve the bioavailability and stability of SOD1, offering a targeted approach to reduce oxidative stress and protect against liver damage. The effectiveness of NanoSOD1 to improve antioxidant defenses suggests a valuable therapeutic arsenal in ALD treatment. Taken together, given the limited treatment options for ALD, increasing SOD1 activity is essential for managing the progression of the disease. Full article
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13 pages, 4680 KB  
Article
Gestation Regulates Growth Hormone and Its Receptor Expression in Sheep Immune Organs
by Zhouyuan Li, Xiaoxin Ma, Ziwang Du, Jingjing Li, Leying Zhang and Ling Yang
Biology 2025, 14(10), 1318; https://doi.org/10.3390/biology14101318 - 24 Sep 2025
Abstract
There are multiple adaptations in maternal physiology, hormones, and immunology during pregnancy. Growth hormone (GH) is not only produced by the pituitary but also secreted by extra-pituitary tissues. In this study, 24 ewes were randomly divided into four groups and mated with either [...] Read more.
There are multiple adaptations in maternal physiology, hormones, and immunology during pregnancy. Growth hormone (GH) is not only produced by the pituitary but also secreted by extra-pituitary tissues. In this study, 24 ewes were randomly divided into four groups and mated with either adult intact rams (pregnant ewes) or a vasectomized ram (nonpregnant ewes), and maternal thymus, lymph node, spleen, and liver were harvested at day 16 of nongestation and at days 13, 16, and 25 of gestation. The specified primers for GH and GH receptor (GHR) were utilized to analyze mRNA expression of GH and GHR using quantitative real-time PCR. Specified anti-GH1 antibody and anti-GHR antibody were used to detect protein expression of GH and GHR using Western blot and immunohistochemical analysis. The results revealed that there were increases in GH and GHR in the maternal spleen, GH in the liver, and GHR in the thymus and lymph nodes, but a downregulation of GH in lymph nodes during early gestation. In addition, early gestation affected GH expression in the thymus and GHR in the liver. In conclusion, it is reported for the first time that early gestation modulates GH and GHR expression in these maternal organs in a tissue-specific manner, which may regulate the function of these immune organs in ewes. Full article
(This article belongs to the Special Issue Paper Collection: Understanding Immune Systems)
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24 pages, 1093 KB  
Review
Neurobiochemical Effects of a High-Fat Diet: Implications for the Pathogenesis of Neurodegenerative Diseases
by Marta Srokowska, Wojciech Żwierełło, Agata Wszołek and Izabela Gutowska
Biology 2025, 14(10), 1317; https://doi.org/10.3390/biology14101317 - 24 Sep 2025
Abstract
The global rise in high-fat diet (HFD) consumption and obesity has raised concerns about their long-term effects on brain health. This review addresses how HFDs, including ketogenic diets (KDs), influence the central nervous system (CNS) and may contribute to neurodegenerative processes. The findings [...] Read more.
The global rise in high-fat diet (HFD) consumption and obesity has raised concerns about their long-term effects on brain health. This review addresses how HFDs, including ketogenic diets (KDs), influence the central nervous system (CNS) and may contribute to neurodegenerative processes. The findings show that prolonged HFD exposure is associated with altered brain metabolism, increased oxidative stress, neuroinflammation, and impaired synaptic plasticity, particularly in regions like the hippocampus and hypothalamus. These changes may affect cognitive function and accelerate neurodegenerative mechanisms linked to disorders such as Alzheimer’s and Parkinson’s disease. While certain types of KD appear to exert neuroprotective effects—such as improved motor outcomes in experimental Parkinson’s disease models—evidence remains inconsistent, and concerns about their long-term safety persist. This review emphasizes that the impact of high-fat nutrition on the CNS depends on fat type, exposure duration, and individual factors such as age and sex. Overall, further research is needed to distinguish between harmful and potentially therapeutic dietary fat patterns and to better understand their influence on brain health across the lifespan. Full article
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16 pages, 1507 KB  
Review
Mechanism of Melatonin in Alleviating Aluminum Toxicity in Plants: A Review
by Feige Wang, Xiaoli Li, Can Chen, Le Zhao and Yunmin Wei
Biology 2025, 14(10), 1316; https://doi.org/10.3390/biology14101316 - 23 Sep 2025
Abstract
Aluminum (Al) toxicity is a major limiting factor for plant growth and development in acidic soils. Melatonin, a plant growth regulator and signaling molecule, enhances resistance to multiple stresses. Recent studies show that melatonin alleviates Al toxicity through several complementary mechanisms. Here, we [...] Read more.
Aluminum (Al) toxicity is a major limiting factor for plant growth and development in acidic soils. Melatonin, a plant growth regulator and signaling molecule, enhances resistance to multiple stresses. Recent studies show that melatonin alleviates Al toxicity through several complementary mechanisms. Here, we first outline the physiological and molecular impacts of Al stress and the external and internal strategies plants use to cope with it. We then summarize melatonin biosynthesis and its broader roles in stress adaptation. We focus on recent advances in melatonin-mediated mitigation of Al toxicity, highlighting four principal mechanisms: (i) the activation of antioxidant defense systems, (ii) the stimulation of organic acid anion exudation that chelates Al in the rhizosphere, (iii) the modification of cell wall composition to reduce Al binding sites, and (iv) the promotion of intracellular Al sequestration. We also discuss the crosstalk between melatonin and nitric oxide, as well as interactions with phytohormone signaling. Collectively, this review comprehensively synthesizes the current understanding regarding the role of melatonin in alleviating Al toxicity in plants, offering a promising strategy for crop production in acidic environments. Full article
(This article belongs to the Section Plant Science)
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17 pages, 3428 KB  
Article
The Gene Expression of the Transcription Factors HY5 and HFR1 Is Involved in the Response of Arabidopsis thaliana to Artificial Sun-like Lighting Systems
by Peter Beatrice, Gustavo Agosto, Alessio Miali, Donato Chiatante and Antonio Montagnoli
Biology 2025, 14(10), 1315; https://doi.org/10.3390/biology14101315 - 23 Sep 2025
Abstract
Plants can sense light signals using specific photoreceptors, activating light signaling pathways to precisely regulate photomorphogenesis and shade-avoidance responses. This study examines the molecular responses of Arabidopsis thaliana to the CoeLux® lighting system, a unique LED-based light source designed to simulate natural [...] Read more.
Plants can sense light signals using specific photoreceptors, activating light signaling pathways to precisely regulate photomorphogenesis and shade-avoidance responses. This study examines the molecular responses of Arabidopsis thaliana to the CoeLux® lighting system, a unique LED-based light source designed to simulate natural sunlight. Previous studies found that the CoeLux® light type, characterized by a higher blue-to-green ratio and reduced blue light levels, stimulates responses in plants comparable to those displayed in shade conditions. This research compared the effects of CoeLux® lighting to conventional high-pressure sodium (HPS) lamps, focusing on the expression of critical photomorphogenesis-related genes under both long- and short-term light treatments. Lower HY5 and elevated HFR1 expression levels were observed under the CoeLux® light type and low-intensity light conditions. On the contrary, the influence of the CoeLux® light type on COP1 and PIFs expression levels seems more marginal. These responses suggest a complex regulation involving both gene expression and protein-level adjustments. Additionally, mutant plants lacking these essential regulatory genes displayed altered morphologies under CoeLux® light, underscoring the functional contribution of these genes in the adaptation to light. Our findings are twofold, advancing the understanding of plant–light relationships and plant adaptation to artificial light environments. These may foster strategies for optimizing indoor plant growth under simulated sunlight conditions. Full article
(This article belongs to the Special Issue Physiological, Biochemical, and Molecular Response in Plants under Light-Emitting Diode (LED) Treatment (Volume II))
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20 pages, 1182 KB  
Review
Carcinogenesis: An Alternative Hypothesis Comparing Mutagenic Versus Metabolic Models
by Albert Alhatem, Claude E. Gagna, Muriel W. Lambert, Emily Keenan and W. Clark Lambert
Biology 2025, 14(10), 1314; https://doi.org/10.3390/biology14101314 - 23 Sep 2025
Abstract
Carcinogenesis, while traditionally attributed to the accumulation of driver mutations in genes regulating cell proliferation and apoptosis, may also be explored as a consequence of fundamental metabolic reprogramming, an idea catalyzed by the Warburg effect, where cancer cells exhibit a paradoxical preference for [...] Read more.
Carcinogenesis, while traditionally attributed to the accumulation of driver mutations in genes regulating cell proliferation and apoptosis, may also be explored as a consequence of fundamental metabolic reprogramming, an idea catalyzed by the Warburg effect, where cancer cells exhibit a paradoxical preference for glycolysis over the far more efficient oxidative phosphorylation. This implies that metabolic dysregulation may be a primary instigator of neoplastic transformation. Our hypothesis proposes that the abrupt loss of cellular energy may stimulate an atavistic response, wherein rapid proliferation and migration are triggered to enhance survival in fluctuating environments. These responses lead to pathological angiogenesis and unchecked cell growth, thereby bridging the gap between genetic and metabolic pathways of carcinogenesis. Full article
(This article belongs to the Section Cancer Biology)
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29 pages, 9358 KB  
Article
Deep Ensemble Learning and Explainable AI for Multi-Class Classification of Earthstar Fungal Species
by Eda Kumru, Aras Fahrettin Korkmaz, Fatih Ekinci, Abdullah Aydoğan, Mehmet Serdar Güzel and Ilgaz Akata
Biology 2025, 14(10), 1313; https://doi.org/10.3390/biology14101313 - 23 Sep 2025
Abstract
The current study presents a multi-class, image-based classification of eight morphologically similar macroscopic Earthstar fungal species (Astraeus hygrometricus, Geastrum coronatum, G. elegans, G. fimbriatum, G. quadrifidum, G. rufescens, G. triplex, and Myriostoma coliforme) using [...] Read more.
The current study presents a multi-class, image-based classification of eight morphologically similar macroscopic Earthstar fungal species (Astraeus hygrometricus, Geastrum coronatum, G. elegans, G. fimbriatum, G. quadrifidum, G. rufescens, G. triplex, and Myriostoma coliforme) using deep learning and explainable artificial intelligence (XAI) techniques. For the first time in the literature, these species are evaluated together, providing a highly challenging dataset due to significant visual overlap. Eight different convolutional neural network (CNN) and transformer-based architectures were employed, including EfficientNetV2-M, DenseNet121, MaxViT-S, DeiT, RegNetY-8GF, MobileNetV3, EfficientNet-B3, and MnasNet. The accuracy scores of these models ranged from 86.16% to 96.23%, with EfficientNet-B3 achieving the best individual performance. To enhance interpretability, Grad-CAM and Score-CAM methods were utilised to visualise the rationale behind each classification decision. A key novelty of this study is the design of two hybrid ensemble models: EfficientNet-B3 + DeiT and DenseNet121 + MaxViT-S. These ensembles further improved classification stability, reaching 93.71% and 93.08% accuracy, respectively. Based on metric-based evaluation, the EfficientNet-B3 + DeiT model delivered the most balanced performance, with 93.83% precision, 93.72% recall, 93.73% F1-score, 99.10% specificity, a log loss of 0.2292, and an MCC of 0.9282. Moreover, this modeling approach holds potential for monitoring symbiotic fungal species in agricultural ecosystems and supporting sustainable production strategies. This research contributes to the literature by introducing a novel framework that simultaneously emphasises classification accuracy and model interpretability in fungal taxonomy. The proposed method successfully classified morphologically similar puffball species with high accuracy, while explainable AI techniques revealed biologically meaningful insights. All evaluation metrics were computed exclusively on a 10% independent test set that was entirely separate from the training and validation phases. Future work will focus on expanding the dataset with samples from diverse ecological regions and testing the method under field conditions. Full article
(This article belongs to the Section Bioinformatics)
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20 pages, 2067 KB  
Article
Advanced Multiscale Attention Network for Estrous Cycle Stage Identification from Rat Vaginal Cytology
by Qinyang Wang, Yihong Zhao and Xiaodi Pu
Biology 2025, 14(10), 1312; https://doi.org/10.3390/biology14101312 - 23 Sep 2025
Abstract
In clinical medicine, rats are commonly used as experimental subjects. However, their estrous cycle significantly impacts their biological responses, leading to differences in experimental results. Therefore, accurately determining the estrous cycle is crucial for minimizing interference. Manually identifying the estrous cycle in rats [...] Read more.
In clinical medicine, rats are commonly used as experimental subjects. However, their estrous cycle significantly impacts their biological responses, leading to differences in experimental results. Therefore, accurately determining the estrous cycle is crucial for minimizing interference. Manually identifying the estrous cycle in rats presents several challenges, including high costs, long training periods, and subjectivity. To address these issues, this paper proposes a classification network, Spatial Long-distance EfficientNet (SLENet). This network is designed based on EfficientNet, specifically modifying the Mobile Inverted Bottleneck Convolution (MBConv) module by introducing a novel Spatial Efficient Channel Attention (SECA) mechanism to replace the original Squeeze Excitation (SE) module. Additionally, a non-local attention mechanism is incorporated after the last convolutional layer to enhance the network’s ability to capture long-range dependencies. On 2655 microscopy images of rat vaginal epithelial cells (with 531 test), SLENet achieves 96.31% accuracy, surpassing EfficientNet (94.20%). This finding provides practical value for optimizing experimental design in rat-based studies such as reproductive and pharmacological research, but this study is limited to microscopy image data, without considering other factors; thus, future work could incorporate temporal pattern and multi-modal inputs to further enhance robustness. Full article
(This article belongs to the Section Bioinformatics)
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17 pages, 5123 KB  
Article
Bioinformatics-Based Analysis of the Screening and Evaluation of Potential Targets of FTY720 for the Treatment of Non-Small Cell Lung Cancer
by Mengyuan Han, Sendaer Hailati, Dilihuma Dilimulati, Alhar Baishan, Alifeiye Aikebaier and Wenting Zhou
Biology 2025, 14(10), 1311; https://doi.org/10.3390/biology14101311 - 23 Sep 2025
Abstract
Background: A range of cancer cells are significantly inhibited by FTY720. It is unknown, nevertheless, how FTY720 influences the onset of non-small cell lung cancer (NSCLC). Using bioinformatics techniques, we analyzed and the possible molecular mechanisms and targets of FTY720 for the treatment [...] Read more.
Background: A range of cancer cells are significantly inhibited by FTY720. It is unknown, nevertheless, how FTY720 influences the onset of non-small cell lung cancer (NSCLC). Using bioinformatics techniques, we analyzed and the possible molecular mechanisms and targets of FTY720 for the treatment of NSCLC. Methods: DEGs (Differentially expressed genes) were acquired by differential analysis of the dataset GSE10072. Obtained FTY720 target genes and NSCLC disease genes from databases such as Swiss-TargetPrediction and GeneCard. Subsequently, target and disease genes, as well as DEGs, were merged for Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, gene ontology (GO), and protein interaction analysis. The overlapping genes of DEGs and target genes, and disease genes were also obtained separately and subjected to survival as well as expression analyses. We constructed the regulatory network of miRNAs and transcription factors (TFs) on hub genes. Finally, the immune cell association of hub genes was evaluated using the ssGSEA method, molecular docking of FTY720 to hub genes was carried out utilizing Autodock, and molecular dynamics simulations were conducted. Results: In this study, 444 DEGs, 232 target genes of FTY720, and 466 disease genes were obtained. Moreover, a total of 1062 genes were obtained by removing duplicate values after merging, among which PIK3R1, Akt1, and S1PR1 had the highest DEGREE values in the protein interactions network, and these genes were primarily enriched in MAPK, PI3K-Akt signaling pathways, with the PI3K-Akt signaling pathway being the most prominent. Among the overlapping genes, three potential targets of FTY720 for NSCLC treatment were found: S1PR1, ZEB2, and HBEGF. ZEB2 and S1PR1 were determined to be hub genes and to significantly affect NSCLC prognosis by survival analysis. Furthermore, hsa-miR-132-3p, hsa-miR-192-5p, and hsa-miR-6845-3p were strongly associated with FTY720 for the treatment of NSCLC; CTBP1 (carboxy-terminal binding protein 1), EZH2 (protein lysine N-methyltransferase), and ZNF610 (zinc-finger protein 610) may all influence the expression of ZEB2 and S1PR1. Hub genes had a substantial negative link with memory B cells and a significant positive correlation with memory CD8 T cells and Th17 helper T cells. The molecular docking and kinetic simulation results of FTY720 with the two hub genes indicate that the protein-ligand complex has good stability. Conclusion: Our research indicates that FTY720 may inhibit NSCLC via possible targets ZEB2 and S1PR1, further laying the theoretical foundation for the utilization of FTY720 in NSCLC treatment. Full article
(This article belongs to the Topic Advances in Anti-Cancer Drugs: 2nd Edition)
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13 pages, 1749 KB  
Article
Characteristics of Floral Volatiles and Their Effects on Attracting Pollinating Insects in Three Bidens Species with Sympatric Distribution
by Jun-Wei Ye, Jing-Lin Jia, Yong-Hong Xiao, Jia-Hui Zhou and Jian-Jun Zeng
Biology 2025, 14(10), 1310; https://doi.org/10.3390/biology14101310 - 23 Sep 2025
Abstract
The transition from outcrossing to self-pollination is an evolutionary process in angiosperms. However, the changes in floral volatile composition during this process and their impacts on the behavior of pollinators are poorly understood. Therefore, this study investigated the potential differences in the floral [...] Read more.
The transition from outcrossing to self-pollination is an evolutionary process in angiosperms. However, the changes in floral volatile composition during this process and their impacts on the behavior of pollinators are poorly understood. Therefore, this study investigated the potential differences in the floral volatile profiles and pollinator attraction capabilities of three invasive Bidens species. The results indicated that Bidens pilosa var. radiata (BH), which serves as a transitional species between facultative outcrossing and obligate outcrossing attracts a greater diversity and abundance of pollinators such as Apis cerana compared to the more self-compatible Bidens frondosa (DL) and Bidens pilosa var. pilosa (SY). Furthermore, a total of 37, 33, and 34 Volatile Organic Compounds (VOCs) were identified in the floral volatiles of BH, DL, and SY, respectively, with no discernible trend of decreased number of floral VOCs owing to increased self-pollination ability. Moreover, eleven significantly different compounds in the floral volatiles of the three Bidens species were obtained. Among these (E)-β-Ocimene (18.31 ± 1.10%) and (Z)-β-Ocimene (33.93 ± 3.49%) in the floral volatiles of BH (52.24 ± 4.59%) was significantly higher than that of DL (1.72 ± 0.50%) and SY (0.32 ± 0.19%). Additionally, Y-tube olfactometer behavioral assays indicated that (E)- and (Z)-β-Ocimene significantly attracted A. cerana. These findings suggested that (E)- and (Z)-β-Ocimene contribute to the attractiveness of BH to local pollinators. Furthermore, it can be inferred that within Bidens, stronger self-pollination ability reduces the relative content of VOCs—such as (E)- and (Z)-β-Ocimene—used to attract generalist pollinators. Full article
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