Biology

20 pages, 4168 KiB

Open AccessArticle

Fgf21 Deficiency Delays Hair Follicle Cycling and Modulates miRNA–Target Gene Interactions in Mice

by Yana Li, Yue Ao, Xinru Xie, Tug Ulan, Dongjun Liu and Xudong Guo

Biology 2025, 14(5), 526; https://doi.org/10.3390/biology14050526 - 9 May 2025

Fibroblast growth factor 21 (Fgf21) is a key regulator of hair follicle development and cycling. Although microRNAs (miRNAs) are involved in this process, the specific mechanisms through which Fgf21 regulates hair follicle growth remain unclear. This study investigates the role of [...] Read more.

Fibroblast growth factor 21 (Fgf21) is a key regulator of hair follicle development and cycling. Although microRNAs (miRNAs) are involved in this process, the specific mechanisms through which Fgf21 regulates hair follicle growth remain unclear. This study investigates the role of Fgf21 and its associated miRNAs in hair follicle growth and development. Using CRISPR/Cas9, we generated Fgf21 knockout mice (Fgf21⁻/⁻), which exhibited a delayed transition from the telogen to anagen phases compared to wild-type (WT) mice. miRNA sequencing identified differentially expressed miRNAs in Fgf21⁻/⁻ mice, with dual-luciferase assays confirming that miR-134-5p directly targets vascular endothelial zinc finger 1 (Vezf1) and miR-136-5p targets mitogen-activated protein kinase kinase kinase 1 (Map3k1). Real-time qPCR analysis revealed that Vezf1 and Map3k1 expression was higher in Fgf21⁻/⁻ mice than in WT mice during catagen, but lower during telogen. These findings indicate that Fgf21 plays a critical role in regulating hair follicle growth and may modulate Vezf1 and Map3k1 expression through miRNAs. This study provides novel insights into the molecular regulation of hair follicle growth and suggests potential therapeutic strategies for hair follicle-related disorders. Full article

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

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34 pages, 4804 KiB

Open AccessArticle

High-Throughput Analysis of the Flagella FliK-Dependent Surfaceome and Secretome in Bacillus thuringiensis

by Carine Mouawad, Mireille Kallassy Awad, Carine Rodrigues-Machado, Céline Henry, Vincent Sanchis-Borja and Laure El Chamy

Biology 2025, 14(5), 525; https://doi.org/10.3390/biology14050525 - 9 May 2025

Abstract

Bacterial pathogens employ multiple strategies to invade and damage host tissues while evading immune defenses. Recent studies highlight flagella as crucial contributors to bacterial virulence, not only by facilitating motility, but also by regulating the secretion of virulence factors. However, the role of [...] Read more.

Bacterial pathogens employ multiple strategies to invade and damage host tissues while evading immune defenses. Recent studies highlight flagella as crucial contributors to bacterial virulence, not only by facilitating motility, but also by regulating the secretion of virulence factors. However, the role of the flagella-dependent secretome remains largely unexplored. We have recently shown that FliK, a key regulator that defines substrate specificity in the flagellar export apparatus, is essential for the resistance of Bacillus thuringiensis (B. thuringiensis) against antimicrobial peptides (AMPs) and its virulence in a Drosophila infection model. In this study, we used liquid chromatography–tandem mass spectrometry to conduct a large-scale comparative analysis of the proteins secreted in culture supernatant or associated with the cell wall of the ΔfliK mutant and its reference strain. Our results reveal significant differences in the secretome and surfaceome of the ΔfliK mutant compared to the reference strain. These findings emphasize the role of FliK in regulating the production and secretion of several proteins, underscoring the importance of flagella in controlling various biological processes. This work provides valuable insights into the functional characterization of potential candidate proteins involved in B. thuringiensis virulence and AMP resistance mechanisms. Overall, these results open new perspectives for understanding the molecular processes that govern bacterial resistance to AMPs. Full article

(This article belongs to the Section Microbiology)

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17 pages, 4213 KiB

Open AccessArticle

Natural Selection Shaped Codon Usage Patterns in Wheat Dwarf Virus in Triticale

by Jiuli Wang, Xinhang Lu, Jiaying Dong, Jiaqian Liu, Borui Guo, Chen Zhang, Jing Liu and Hongxia Wang

Biology 2025, 14(5), 524; https://doi.org/10.3390/biology14050524 - 9 May 2025

Abstract

Wheat dwarf virus (WDV) poses significant threats to gramineous crops, making it crucial to explore its codon usage patterns and evolutionary dynamics for effective disease control. This study analyzed ten WDV isolates, including two from triticale (WDVT_117 and WDVT_118), using metrics such as [...] Read more.

Wheat dwarf virus (WDV) poses significant threats to gramineous crops, making it crucial to explore its codon usage patterns and evolutionary dynamics for effective disease control. This study analyzed ten WDV isolates, including two from triticale (WDVT_117 and WDVT_118), using metrics such as relative synonymous codon usage (RSCU), effective number of codons (ENC), codon adaptation index (CAI), and codon bias index (CBI). Neutrality plots, ENC-plots, and PR2-plots were employed to assess the role of mutation and selection. Results revealed weak codon preference in triticale-derived strains (CAI: 0.145–0.269; CBI: −0.042–0.111; ENC > 40), with hierarchical GC content. Neutrality analysis and ENC-plot distributions indicated natural selection as the dominant force, supported by T/C bias at the third codon position (PR2-plot). Shared optimal codons UUC and UAC in highly expressed genes may imply a potential significant role in virus adaptation. RSCU-based clustering and MP phylogenetic analysis revealed that WDVT strains form a distinct cluster with elevated genetic diversity, potentially driven by genomic recombination in the synthetic host. These findings demonstrate that WDVT balances mutational constraints and host adaptation through selective codon optimization. This study provides a foundation for codon-based antiviral research and the development of agricultural strategies to combat WDV infections. Full article

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19 pages, 7031 KiB

Open AccessArticle

Synergistic Toxicity of Combined Exposure to Acrylamide and Polystyrene Nanoplastics on the Gut–Liver Axis in Mice

by Yongchuang Liu, Ruiping Luo, Zhongke Sun, Yidan Zhang, Yuqi Guo, Yanjuan Chen, Lili Li and Zonghao Yue

Biology 2025, 14(5), 523; https://doi.org/10.3390/biology14050523 - 9 May 2025

Abstract

Acrylamide (AA) and nanoplastics (NPs) are common food toxicants. However, their combined toxicity and health risks call for further studies. This study aimed to investigate the combined toxicity of AA and polystyrene NPs (PS-NPs) in mice through drinking water exposure. Co-exposure to AA [...] Read more.

Acrylamide (AA) and nanoplastics (NPs) are common food toxicants. However, their combined toxicity and health risks call for further studies. This study aimed to investigate the combined toxicity of AA and polystyrene NPs (PS-NPs) in mice through drinking water exposure. Co-exposure to AA and PS-NPs aggravated colon and liver damage, including more severe inflammatory infiltration, higher levels of colonic and hepatic pro-inflammatory cytokines, and elevated serum content of lipopolysaccharide and activities of diamine oxidase, alanine aminotransferase, and aspartate aminotransferase compared to single exposures. Co-exposure also significantly downregulated the expression of colonic tight-junction genes ZO-1 and Claudin-5. Metabolomics revealed that co-exposure induced more profound metabolic disorders in the liver, particularly affecting amino acid and carbohydrate metabolism. 16S amplicon sequencing showed that co-exposure caused more drastic gut microbiota dysbiosis, characterized by a decrease in beneficial bacteria (unclassified_f__Oscillospiraceae, Roseburia, UCG-005, Ruminiclostridium, unclassified_o__Clostridia_UCG-014, Fournierella, and Acetatifactor) and an increase in pathogenic bacteria (Eubacterium_xylanophilum_group and Eubacterium_nodatum_group). Correlation analysis indicated a negative correlation between beneficial bacteria and intestinal-liver toxicity indicators and a positive correlation between pathogenic bacteria and these indicators. Overall, our findings showed that AA and PS-NPs exerted synergistic toxicity to the gut–liver axis in mammals, highlighting the higher health risks of their combined ingestion. Full article

(This article belongs to the Section Toxicology)

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21 pages, 774 KiB

Open AccessArticle

Identifying Molecular Properties of Ataxin-2 Inhibitors for Spinocerebellar Ataxia Type 2 Utilizing High-Throughput Screening and Machine Learning

by Smita Sahay, Jingran Wen, Daniel R. Scoles, Anton Simeonov, Thomas S. Dexheimer, Ajit Jadhav, Stephen C. Kales, Hongmao Sun, Stefan M. Pulst, Julio C. Facelli and David E. Jones

Biology 2025, 14(5), 522; https://doi.org/10.3390/biology14050522 - 8 May 2025

Abstract

Spinocerebellar ataxia type 2 (SCA2) is an autosomal dominant neurodegenerative disorder marked by cerebellar dysfunction, ataxic gait, and progressive motor impairments. SCA2 is caused by the pathologic expansion of CAG repeats in the ataxin-2 (ATXN2) gene, leading to a toxic gain-of-function [...] Read more.

Spinocerebellar ataxia type 2 (SCA2) is an autosomal dominant neurodegenerative disorder marked by cerebellar dysfunction, ataxic gait, and progressive motor impairments. SCA2 is caused by the pathologic expansion of CAG repeats in the ataxin-2 (ATXN2) gene, leading to a toxic gain-of-function mutation of the ataxin-2 protein. Currently, SCA2 therapeutic efforts are expanding beyond symptomatic relief to include disease-modifying approaches such as antisense oligonucleotides (ASOs), high-throughput screening (HTS) for small molecule inhibitors, and gene therapy aimed at reducing ATXN2 expression. In the present study, data mining and machine learning techniques were employed to analyze HTS data and identify robust molecular properties of potential inhibitors of ATXN2. Three HTS datasets were selected for analysis: ATXN2 gene expression, CMV promoter expression, and biochemical control (luciferase) gene expression. Compounds displaying significant ATXN2 inhibition with minimal impact on control assays were deciphered based on effectiveness (E) values (n = 1321). Molecular descriptors associated with these compounds were calculated using MarvinSketch (n = 82). The molecular descriptor data (MD model) was analyzed separately from the experimentally determined screening data (S model) as well as together (MD-S model). Compounds were clustered based on structural similarity independently for the three models using the SimpleKMeans algorithm into the optimal number of clusters (n = 26). For each model, the maximum response assay values were analyzed, and E values and total rank values were applied. The S clusters were further subclustered, and the molecular properties of compounds in the top candidate subcluster were compared to those from the bottom candidate subcluster. Six compounds with high ATXN2 inhibiting potential and 16 molecular descriptors were identified as significantly unique to those compounds (p < 0.05). These results are consistent with a quantitative HTS study that identified and validated similar small-molecule compounds, like cardiac glycosides, that reduce endogenous ATXN2 in a dose-dependent manner. Overall, these findings demonstrate that the integration of HTS analysis with data mining and machine learning is a promising approach for discovering chemical properties of candidate drugs for SCA2. Full article

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23 pages, 8768 KiB

Open AccessReview

Advances in Imaging Techniques for Mammalian/Human Ciliated Cell’s Cilia: Insights into Structure, Function, and Dynamics

by Jin Li, Shiqin Huang and Hao Chen

Biology 2025, 14(5), 521; https://doi.org/10.3390/biology14050521 - 8 May 2025

Abstract

Cilia are evolutionarily conserved, microtubule-based organelles characterized by their ultrastructures and diverse functional roles, including developmental signaling, mechanosensation, and fluid propulsion. They are widely distributed across cell surfaces and play crucial roles in cell cycle regulation and tissue homeostasis. Despite advances in studying [...] Read more.

Cilia are evolutionarily conserved, microtubule-based organelles characterized by their ultrastructures and diverse functional roles, including developmental signaling, mechanosensation, and fluid propulsion. They are widely distributed across cell surfaces and play crucial roles in cell cycle regulation and tissue homeostasis. Despite advances in studying their molecular regulation and functions, demonstrating the precise ultrastructure of cilia remains a challenge. Recent novel microscopy techniques, such as super-resolution microscopy and volume electron microscopy, are revolutionizing our understanding of their architecture and mechanochemical signaling. By integrating findings from different methodologies, this review highlights how these advances bridge basic research and clinical applications and provide a comprehensive understanding of the structural organization, functional mechanisms, and dynamic changes of cilia. Full article

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41 pages, 3386 KiB

Open AccessSystematic Review

Artificial Intelligence in Aquatic Biodiversity Research: A PRISMA-Based Systematic Review

by Tymoteusz Miller, Grzegorz Michoński, Irmina Durlik, Polina Kozlovska and Paweł Biczak

Biology 2025, 14(5), 520; https://doi.org/10.3390/biology14050520 - 8 May 2025

Abstract

Freshwater ecosystems are increasingly threatened by climate change and anthropogenic activities, necessitating innovative and scalable monitoring solutions. Artificial intelligence (AI) has emerged as a transformative tool in aquatic biodiversity research, enabling automated species identification, predictive habitat modeling, and conservation planning. This systematic review [...] Read more.

Freshwater ecosystems are increasingly threatened by climate change and anthropogenic activities, necessitating innovative and scalable monitoring solutions. Artificial intelligence (AI) has emerged as a transformative tool in aquatic biodiversity research, enabling automated species identification, predictive habitat modeling, and conservation planning. This systematic review follows the PRISMA framework to analyze AI applications in freshwater biodiversity studies. Using a structured literature search across Scopus, Web of Science, and Google Scholar, we identified 312 relevant studies published between 2010 and 2024. This review categorizes AI applications into species identification, habitat assessment, ecological risk evaluation, and conservation strategies. A risk of bias assessment was conducted using QUADAS-2 and RoB 2 frameworks, highlighting methodological challenges, such as measurement bias and inconsistencies in the model validation. The citation trends demonstrate exponential growth in AI-driven biodiversity research, with leading contributions from China, the United States, and India. Despite the growing use of AI in this field, this review also reveals several persistent challenges, including limited data availability, regional imbalances, and concerns related to model generalizability and transparency. Our findings underscore AI’s potential in revolutionizing biodiversity monitoring but also emphasize the need for standardized methodologies, improved data integration, and interdisciplinary collaboration to enhance ecological insights and conservation efforts. Full article

(This article belongs to the Section Ecology)

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22 pages, 5254 KiB

Open AccessArticle

Modeling the Impact of Ecological Restoration on Waterbird Diversity and Habitat Quality in Myanmar’s Moe Yun Gyi Wetland

by Phyoe Marnn, Haider Ali, Haibo Jiang, Yang Liu, Ziqi Li, Sarfraz Ahmed, Tao Yang, Ziwei Li and Chunguang He

Biology 2025, 14(5), 519; https://doi.org/10.3390/biology14050519 - 8 May 2025

Abstract

The Moe Yun Gyi constructed wetland in Myanmar, located along the East Asian–Australian bird migration path, serves as a crucial habitat for migrating waterbirds. Protecting this biodiverse habitat is crucial in the face of ongoing threats, highlighting the need for effective conservation strategies. [...] Read more.

The Moe Yun Gyi constructed wetland in Myanmar, located along the East Asian–Australian bird migration path, serves as a crucial habitat for migrating waterbirds. Protecting this biodiverse habitat is crucial in the face of ongoing threats, highlighting the need for effective conservation strategies. This study aims to evaluate the effects of the restoration on the populations of waterbirds from January 2014 to January 2024, by analyzing the composition and the spatiotemporal dynamics of waterbirds communities, with particular reference to changes in diversity. We measured waterbird quantity and species richness using the point count method, employing the Shannon-Wiener and D_G–F Index formulae for diversity analysis. Habitat analysis was conducted with ArcGIS 10.6 and eCognition 10.3, while data analysis utilized RStudio and Microsoft Excel. The results indicate that restoration efforts in 2016 initially led to a decline in waterbird populations. Restoration efforts after 2017 resulted in a twofold increase in both diversity and abundance. However, in 2023, flooding in Bago City caused a decline in waterbird populations, impacting habitat rehabilitation. There was a notable rise in uncommon waterbird populations, especially threatened Pelecaniformes. The community’s richness has partially recovered, but seasonal water level volatility continues to impact diversity. The application of restoration techniques directly alters the extent and depth of water bodies, which are essential parameters for supporting appropriate waterbird habitats. We propose implementing a rational system for managing water levels, optimizing wetland hydrology, and enhancing water level regulation to safeguard significant resting areas along migration paths. Full article

(This article belongs to the Special Issue Bird Biology and Conservation)

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Graphical abstract

19 pages, 13287 KiB

Open AccessArticle

Comprehensive Analysis Reveals the Molecular Features and Immune Infiltration of PANoptosis-Related Genes in Metabolic Dysfunction-Associated Steatotic Liver Disease

by Yan Huang, Jingyu Qian, Zhengyun Luan, Junling Han and Limin Tang

Biology 2025, 14(5), 518; https://doi.org/10.3390/biology14050518 - 8 May 2025

Abstract

Background: Metabolic dysfunction-associated steatotic liver disease (MASLD), a chronic inflammatory disorder characterized by alcohol-independent hepatic lipid accumulation, remains poorly understood in terms of PANoptosis involvement. Methods: We integrated high-throughput sequencing data with bioinformatics to profile differentially expressed genes (DEGs) and immune infiltration patterns [...] Read more.

Background: Metabolic dysfunction-associated steatotic liver disease (MASLD), a chronic inflammatory disorder characterized by alcohol-independent hepatic lipid accumulation, remains poorly understood in terms of PANoptosis involvement. Methods: We integrated high-throughput sequencing data with bioinformatics to profile differentially expressed genes (DEGs) and immune infiltration patterns in MASLD, identifying PANoptosis-associated DEGs (PANoDEGs). Machine learning algorithms prioritized key PANoDEGs, while ROC curves assessed their diagnostic efficacy. Cellular, animal, and clinical validations confirmed target expression. Results: Three PANoDEGs (SNHG16, Caspase-6, and Dynamin-1-like protein) exhibited strong MASLD associations and diagnostic significance. Immune profiling revealed elevated M1 macrophages, naïve B cells, and activated natural killer cells in MASLD tissues versus controls. Further experiments verified the expression of the key PANoDEGs. Conclusions: This study provides new insights for further studies on the pathogenesis and treatment strategies of PANoptosis in MASLD. Full article

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15 pages, 1835 KiB

Open AccessArticle

Genetic Variation and Gene Expression of the Antimicrobial Peptide Macins in Asian Buffalo Leech (Hirudinaria manillensis)

by Yunfei Yu, Lizhou Tang, Mingkang Xiao, Jingjing Yin, Tianyu Ye, Rujiao Sun, Rui Ai, Fang Zhao, Zuhao Huang and Gonghua Lin

Biology 2025, 14(5), 517; https://doi.org/10.3390/biology14050517 - 8 May 2025

Abstract

With the growing severity of antibiotic resistance, antimicrobial peptides demonstrate significant potential for medical applications. Here, we performed genome and transcriptome sequencing of 30 Asian buffalo leech (Hirudinaria manillensis) individuals and integrated data from three other leech species (Whitmania pigra [...] Read more.

With the growing severity of antibiotic resistance, antimicrobial peptides demonstrate significant potential for medical applications. Here, we performed genome and transcriptome sequencing of 30 Asian buffalo leech (Hirudinaria manillensis) individuals and integrated data from three other leech species (Whitmania pigra, Hirudo nipponia, and Hirudo medicinalis) to investigate genetic variation and gene expression of H. manillensis macins. Three macins (Hman1, Hman2, and Hman3), along with their encoding genes (Hman1, Hman2, and Hman3), were identified in H. manillensis. Hman1 exhibited the highest similarity (63.5 ± 12.0%) to macins from other leeches, followed by Hman2 (57.8 ± 7.4%) and Hman3 (30.0 ± 3.5%). Both amino acid and codon sequences of Hman1 were conserved within the species, whereas Hman2 and Hman3 exhibited markedly higher variability. All Hman1 sequences were translatable, while four Hman2 and 28 Hman3 sequences had degenerated into pseudogenes. Transcripts per million (TPM) values for Hman1, Hman2, and Hman3 were 2196.63, 242.35, and 1.22, respectively. Total macin expression in H. manillensis was less than 1/20 of that in W. pigra. Based on sequence variation and expression patterns, we propose that Hman1 retains functionality while Hman2 and Hman3 have lost or are losing their antibacterial functions. Full article

(This article belongs to the Section Zoology)

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24 pages, 3004 KiB

Open AccessArticle

Growth Process and Mortality of Sasa borealis Seedlings over Six Years Following Mass Flowering and Factors Influencing Them

by Hanami Suzuki and Hisashi Kajimura

Biology 2025, 14(5), 516; https://doi.org/10.3390/biology14050516 - 7 May 2025

Abstract

The sexual reproduction of Sasa borealis, a species of dwarf bamboo, occurred in central Japan from 2016 to 2017. S. borealis grows on the forest floor and serves as an important source of habitat and food for various animals. Sexual reproduction occurs [...] Read more.

The sexual reproduction of Sasa borealis, a species of dwarf bamboo, occurred in central Japan from 2016 to 2017. S. borealis grows on the forest floor and serves as an important source of habitat and food for various animals. Sexual reproduction occurs in synchrony among individuals in a given area, leading to a decline in population and causing substantial disturbances to the forest ecosystem; however, the subsequent regeneration process remains unclear. In this study, we investigated S. borealis seedling regeneration over six years. Fixed plots were established in the forest in the year following the sexual reproductive event, and the growth of seedlings was monitored from seed emergence to seedling growth at the individual level. We considered biotic and abiotic factors to evaluate their influence on regeneration. We examined mammalian and arthropod foraging as biotic factors. Conversely, abiotic factors included temperature and humidity near the ground surface, solar radiation, soil conditions, and snow cover. Seedling growth was characterized by a slow rate and affected by morphological changes resulting from foraging and abiotic factors. The return of S. borealis to its presexual reproductive stage requires an extended duration. Our study provides precious information for future S. borealis conservation and management strategies. Full article

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

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Graphical abstract

16 pages, 2130 KiB

Open AccessArticle

Application of Biochar on Soil Improvement and Speciation Transformation of Heavy Metal in Constructed Wetland

by Yuan Zhou, Xiaoqin Nie, Yao Zhao, Liqiu Zhang, Yatian Cheng, Cancan Jiang, Wenbin Zhao, Xiangchun Wang and Chao Yang

Biology 2025, 14(5), 515; https://doi.org/10.3390/biology14050515 - 7 May 2025

Abstract

The pyrolysis of sewage sludge into biochar, enhanced by incorporating agriculture waste rich in inorganic minerals and lignocellulosic compounds, provides an effective approach for achieving sludge-harmless treatment and resourceful utilization. In this study, sewage sludge and maize straw-based biochar (SMB) was prepared using [...] Read more.

The pyrolysis of sewage sludge into biochar, enhanced by incorporating agriculture waste rich in inorganic minerals and lignocellulosic compounds, provides an effective approach for achieving sludge-harmless treatment and resourceful utilization. In this study, sewage sludge and maize straw-based biochar (SMB) was prepared using the co-pyrolysis method, and the effects of different application ratios (0%, 1%, 3%, and 5%, w/w) of SMB on soil properties, ryegrass growth, microbial community structure, and Pb content and speciation in the contaminated soil of constructed wetlands were investigated. The results showed that SMB had a high carbon content (28.58%) and was rich in functional groups (e.g., -C-O, -C-N). The results indicated that increasing SMB dosage (0–5% w/w) in Pb-contaminated soil elevated soil pH from 6.40 to 7.93, cation-exchange capacity (CEC) from 30.59 to 79.03 cmol/kg (+158%), and organic carbon content by 65% (from 176.79 mg/kg to 107.3 mg/kg), while reducing available phosphorus and potassium by 20% and 30%, respectively, resulting in a 6% decline in ryegrass leaf length. SMB application enriched Pb-resistant bacteria (e.g., Sphingomonas abundance increased from 10.3% to 11.2%) and enhanced Pb immobilization. After 55 days, the total soil Pb increased by 33%, and the residual fraction Pb significantly increased by 7.3% to 21.7%, driven by functional group complexation, ion exchange, pH, and CEC improvements. Full article

(This article belongs to the Special Issue The Application of Microorganisms and Plants in Soil Improvement)

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22 pages, 6780 KiB

Open AccessArticle

Status and Best Management Practices of Potato Early Dying Disease in New Brunswick, Canada

by Khalil I. Al-Mughrabi, Rene Poirier and Salah Eddin Khabbaz

Biology 2025, 14(5), 514; https://doi.org/10.3390/biology14050514 - 7 May 2025

Abstract

Potato early dying (PED) disease complex is often called the Verticillium wilt of potato and is considered one of the most economically devastating diseases of potato worldwide. The severity of the disease greatly increases with the association of the soil-borne pathogens Verticillium dahliae [...] Read more.

Potato early dying (PED) disease complex is often called the Verticillium wilt of potato and is considered one of the most economically devastating diseases of potato worldwide. The severity of the disease greatly increases with the association of the soil-borne pathogens Verticillium dahliae and V. albo-atrum and the root lesion nematode (Pratylenchus sp.). Recently, an increase in wilt disease symptoms and a sharp decline in marketable tuber yield were observed in New Brunswick (NB), Canada. A survey of 71 fields, along with eight fumigated and eight non-fumigated fields, was carried out to determine and quantify nematodes and Verticillium in the soil. Techniques used included plate counts for Verticillium (CFU/g soil), real-time qPCR (RT-qPCR) for V. dahliae (cell/g soil), and nematode identification and counts (# of nematodes/kg of soil). The survey results of the 71 fields revealed that 55 fields had Verticillium sp. ranging from 2 to 66 CFU/g of soil by the plate method, and 68 fields had high V. dahliae ranging from 261 to 27,471 cell/g of soil by RT-qPCR method. All fields had high numbers of root lesion nematodes ranging from 560 to 14,240 nematodes/kg of soil. There was an uneven distribution of PED incidence in potato fields at various locations of NB. Fumigation with Chloropicrin significantly reduced the numbers of root lesion nematodes by 34.1–99.0%, Verticillium sp. CFU/g of soil by 50–100%, and V. dahliae cell/g soil by 38–91% in the eight fumigated fields. The management of the PED complex with various disease management products under field conditions was also studied in a field plot trial setup. The nematicide Velum applied in-furrow at the recommended label rate decreased the numbers of root lesion nematodes by up to 66% compared to other products. The combination of both Velum + Aprovia and the application of ammonium-lignosulfonate significantly reduced V. dahliae by 190.55% and 274.24%, respectively, compared to other products. The fungicide Aprovia applied in-furrow at the recommended rate for the management of Verticillium wilt significantly reduced Verticillium sp. CFU/g of soil in treated soil by 73.3% compared to Velum, Mustgrow, Senator PSPT, Vapam, ammonium-lignosulfonate, Nimitz, and the untreated control. Disease management products increased potato marketable yield by 27.38–97.74%. The results of this study suggest that the root lesion nematode and V. dahliae have a ubiquitous distribution in the fields cultivated with potatoes in NB. The co-infection of potato by both V. dahliae and the root lesion nematode can greatly increase the severity of PED. Fumigation with Chloropicrin significantly reduced the levels of root lesion nematodes and Verticillium in all fumigated fields. Management practices of PED using the fungicide Aprovia, the nematicide Velum, and a combination of both Velum + Aprovia had the greatest effect in reducing the population density of the root lesion nematode and Verticillium dahliae in soils of commercial potato fields in New Brunswick. Full article

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12 pages, 1941 KiB

Open AccessArticle

The Identification of a Glucuronyltransferase-Related Gene, GlcAT-S, with Putative Mucus Protection and Anti-Inflammatory Effects from Gut-Damaged Drosophila by Dextran Sulfate Sodium (DSS)

by Seung Hun Lee, Dooseon Hwang, Jang-Won Lee, Tae-Won Goo and Eun-Young Yun

Biology 2025, 14(5), 513; https://doi.org/10.3390/biology14050513 - 7 May 2025

Abstract

The intestinal epithelium, which is protected by mucosal surfaces composed of mucins and other glycoproteins, functions as a selective barrier that absorbs nutrients while preventing the translocation of harmful substances. To understand the mechanisms between mucosal disruption and tissue inflammation, we orally administrated [...] Read more.

The intestinal epithelium, which is protected by mucosal surfaces composed of mucins and other glycoproteins, functions as a selective barrier that absorbs nutrients while preventing the translocation of harmful substances. To understand the mechanisms between mucosal disruption and tissue inflammation, we orally administrated a mucus-disrupting agent, dextran sodium sulfate, to Drosophila melanogaster and screened 63 differentially expressed genes (DEGs). Through a database search using bioinformatics tools (CHEA3 and WebGestalt), we identified ELK1 as a potential key transcription factor for the selected DEGs, and among the 63 DEGs, ELK1-related genes, B3GAT3, FIBP, and TENT2 (GlcAT-S, Fibp, and Wisp in Drosophila), were selected as the relevant genes that respond to mucus disruption. We confirmed that enterocyte (EC)-specific GlcAT-S knockdown by RNAi significantly reduced gut length and increased intestinal stem cell proliferation in Drosophila. Additionally, in EC-specific GlcAT-S-knockdown flies, it was observed that the mucus-production-related genes, Muc68D and Mur29B, were specifically reduced, whereas the inflammatory cytokines egr and upd3 were overexpressed. This study provides evidence that GlcAT-S is involved in the regulation of intestinal inflammation in Drosophila and plays a protective role against mucus disruption. Our findings suggest that GlcAT-S may be a potential therapeutic target for the treatment of intestinal inflammatory diseases such as IBD. Full article

(This article belongs to the Special Issue Differential Gene Expression and Coexpression (2nd Edition))

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15 pages, 12488 KiB

Open AccessArticle

Molecular and Morphological Characterization of the Entomopathogenic Nematode Oscheius cyrus (Nematoda: Rhabditidae) and Molecular Variability of Heterorhabditis bacteriophora from Georgia (Caucasus)

by Oleg Gorgadze, Elena Fanelli, Alessio Vovlas, Alberto Troccoli, Eustachio Tarasco and Francesca De Luca

Biology 2025, 14(5), 512; https://doi.org/10.3390/biology14050512 - 7 May 2025

Abstract

Surveys were conducted in the village of Shamgona in the Samegrelo Region of West Georgia, and two nematode species belonging to the Oscheius genus and a population of Heterorhabditis bacteriophora were isolated. Integrative diagnosis, combining morphology, PCA, sequencing and phylogeny, was carried for [...] Read more.

Surveys were conducted in the village of Shamgona in the Samegrelo Region of West Georgia, and two nematode species belonging to the Oscheius genus and a population of Heterorhabditis bacteriophora were isolated. Integrative diagnosis, combining morphology, PCA, sequencing and phylogeny, was carried for Oscheius sp. from the soil of hazelnut orchard. This population shows high similarity at morphological and morphometrical levels with O. cyrus from Iran, and the main distinctive features with O. cyrus from Iran are the presence of eight lateral lines and males. Sequence and phylogenetic analyses by using ITS, D2–D3 expansion domains of the 28S rRNA gene, the partial 18S rRNA gene, and the mitochondrial COI confirmed the identification as O. cyrus. A second population of Oscheius sp. and H. bacteriophora was characterized only at the molecular and phylogenetic level. The phylogenetic analyses, based on ITS and D2–D3 expansion domains, revealed the occurrence of O. insectivorus in Georgia grouping with O. insectivorus sequences with high support. The phylogenetic trees of H. bacteriophora, based on D2–D3 expansion domains, ITS, the partial 18S rRNA gene, and mitochondrial COI confirmed the high variability among geographical populations. The present study reports on the occurrence of two species of Oscheius in Georgia for the first time. Full article

(This article belongs to the Section Zoology)

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15 pages, 2257 KiB

Open AccessArticle

ACE- and DPP-IV-Inhibitory Peptides from Bambara Groundnut Hydrolysate: Elucidation Using Computational Tools and Molecular Docking

by Jirakrit Saetang, Thaiyawat Haewphet, Krisana Nilsuwan and Soottawat Benjakul

Biology 2025, 14(5), 511; https://doi.org/10.3390/biology14050511 - 7 May 2025

Abstract

Hypertension and type 2 diabetes are the major metabolic syndromes, often managed using synthetic ACE and DPP-IV inhibitors that may cause adverse effects on health. This study investigated Bambara groundnut protein hydrolysates as a natural source of dual ACE- and DPP-IV-inhibitory peptides. Protein [...] Read more.

Hypertension and type 2 diabetes are the major metabolic syndromes, often managed using synthetic ACE and DPP-IV inhibitors that may cause adverse effects on health. This study investigated Bambara groundnut protein hydrolysates as a natural source of dual ACE- and DPP-IV-inhibitory peptides. Protein isolates were hydrolyzed using Flavourzyme, and the resulting peptides were fractionated using membranes with different molecular weight cut-offs. Those fractions were then analyzed for enzyme inhibition. Peptides were identified by LC-MS/MS and screened using PeptideRanker and BIOPEP-UWM, followed by molecular docking against ACE (PDB: 1O8A) and DPP-IV (PDB: 1NU6). The >10 kDa and 5–10 kDa fractions showed the highest ACE- and DPP-IV-inhibitory activities, respectively. Some peptides such as YKDGLYSPHW, LPVSTPGKF, and EPWWPK displayed strong binding affinities (ΔG: −10.2 to −11.3 kcal/mol for ACE, −8.6 to −9.1 kcal/mol for DPP-IV) and interacted with key catalytic residues, including His387 and Glu411 in ACE, and Ser630, Glu205, and Phe357 in DPP-IV. These findings highlight the potential of Bambara groundnut hydrolysates or peptides as a source of natural ACE and DPP-IV inhibitors. Full article

(This article belongs to the Special Issue Nutraceutical and Bioactive Compounds in Foods)

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11 pages, 1547 KiB

Open AccessArticle

Temporal and Spatial Population Genetic Variation in Chilean Jack Mackerel (Trachurus murphyi)

by Cristian B. Canales-Aguirre, Sandra Ferrada Fuentes and Ricardo Galleguillos

Biology 2025, 14(5), 510; https://doi.org/10.3390/biology14050510 - 7 May 2025

Abstract

Trachurus murphyi have been studied for population genetic structures for decades, identifying only one large population across the South Pacific Ocean. Although all of these studies have extensively examined the spatial genetic pattern, there remains a gap in understanding the potential role of [...] Read more.

Trachurus murphyi have been studied for population genetic structures for decades, identifying only one large population across the South Pacific Ocean. Although all of these studies have extensively examined the spatial genetic pattern, there remains a gap in understanding the potential role of temporality. Our study aims to elucidate spatial and temporal genetic patterns in T. murphyi populations in the South Pacific Ocean, examining genetic composition across seasons, including feeding and spawning seasons, where the latter was not previously investigated. Using 10 microsatellite loci, our study confirms an overall consistent and stable population genetic pattern in T. murphyi across its geographic distribution observed over multiple years and seasons. The only exception was found for New Zealand in the spring–summer season. Furthermore, we identify potential genetic markers for monitoring variability in the species. Full article

(This article belongs to the Special Issue Genetic Variability within and between Populations)

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17 pages, 2639 KiB

Open AccessArticle

Inhibition of Thioredoxin Reductase Activity and Oxidation of Cellular Thiols by Antimicrobial Agent, 2-Bromo-2-nitro-1,3-propanediol, Causes Oxidative Stress and Cell Death in Cultured Noncancer and Cancer Cells

by Chao Jiang, Gary Krzyzanowski, Dinesh S. Chandel, Wesley A. Tom, Nirmalee Fernando, Appolinaire Olou and M. Rohan Fernando

Biology 2025, 14(5), 509; https://doi.org/10.3390/biology14050509 - 6 May 2025

Abstract

Background: The thioredoxin system (TrxS) is crucial for maintaining redox balance by regulating cellular thiol levels and is involved in various biological processes, including cancer progression. Thioredoxin reductase (TrxR), a key component of TrxS, reduces oxidized thioredoxin (Trx) using NADPH. This study investigates [...] Read more.

Background: The thioredoxin system (TrxS) is crucial for maintaining redox balance by regulating cellular thiol levels and is involved in various biological processes, including cancer progression. Thioredoxin reductase (TrxR), a key component of TrxS, reduces oxidized thioredoxin (Trx) using NADPH. This study investigates the inhibitory effects of 2-bromo-2-nitro-1,3-propanediol (Bronopol, BP), a preservative, on TrxR activity and its impact on cellular thiols and cell viability. Methods: Purified recombinant TrxR and noncancer and cancer cells were treated with different concentrations of BP and TrxR activity measured. BP-treated cells were examined for effects of BP on total cellular thiol level and GSH/GSSG ratio. Results: BP effectively inhibited TrxR in a dose-dependent manner, an effect that was reversible with dithiothreitol (DTT). BP treatment significantly reduced total thiol levels, decreased the GSH/GSSG ratio, and increased reactive oxygen species (ROS) in cells. Additionally, BP decreased cell viability and induced apoptosis, as indicated by morphological changes and increased c-fos mRNA expression. Conclusions: These findings highlight BP’s potential as a TrxR inhibitor and its cytotoxicity toward both noncancer and cancer cells. The observed effects—TrxR inhibition, thiol oxidation, GSH/GSSG imbalance, and ROS accumulation—may underlie BP’s cytotoxicity. Further research is needed to explore the precise molecular mechanisms by which BP exerts these effects. Full article

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

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16 pages, 3860 KiB

Open AccessArticle

Genome-Wide Identification and Cold Stress Response Mechanism of Barley Di19 Gene Family

by Wenbo Chai, Chao Yuan, Shufen Li, Hanyuan Xu, Qing Zhu, Hongtao Li, Wei Ji and Jun Wang

Biology 2025, 14(5), 508; https://doi.org/10.3390/biology14050508 - 6 May 2025

Abstract

The Di19 (Drought-induced 19) gene family encodes Cys2/His2-type zinc finger proteins that are known to be involved in plant responses to various abiotic stresses, including drought, salinity, and temperature extremes. However, little is known about their roles in barley (Hordeum vulgare), [...] Read more.

The Di19 (Drought-induced 19) gene family encodes Cys2/His2-type zinc finger proteins that are known to be involved in plant responses to various abiotic stresses, including drought, salinity, and temperature extremes. However, little is known about their roles in barley (Hordeum vulgare), particularly in cold stress adaptation. This study aimed to conduct a comprehensive genome-wide analysis of the barley genome to identify Di19 gene family members and examine their expression patterns under cold stress, providing theoretical support for stress-resistant barley breeding. By aligning Di19 gene sequences from Arabidopsis and rice and using BLASTp, seven HvDi19 genes were identified in barley. Bioinformatics analysis revealed that all members contain a conserved Cys2/His2-type zinc finger domain and nuclear localization signals. Phylogenetic analysis grouped the HvDi19 genes into four subfamilies, with three homologous gene pairs, and Ka/Ks analysis indicated strong purifying selection. Tissue-specific expression analysis showed significant variation in HvDi19 expression across barley organs. Under cold stress, different barley varieties exhibited distinct HvDi19 gene expression profiles: for instance, HvDi19-1 was downregulated in cold-tolerant varieties, whereas HvDi19-7 showed increased expression in a cold-tolerant mutant, suggesting their potential roles in modulating cold response. These findings reveal the evolutionary conservation and cold-responsive expression characteristics of the HvDi19 gene family, laying a foundation for future functional studies. The results also provide important molecular resources for the genetic improvement of cold tolerance in barley, contributing to the development of stress-resilient crop varieties under climate change. Full article

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