Biology

30 pages, 2475 KiB

Open AccessReview

Trans-Scale Insights into Variability in Radiation Cancer Risk Across Tissues, Individuals, and Species

by Tatsuhiko Imaoka

Biology 2025, 14(8), 1025; https://doi.org/10.3390/biology14081025 (registering DOI) - 9 Aug 2025

Diversity is evident in various aspects of life and the human population. The current radiological protection system considers the diversity in disease susceptibility and incorporates some of it to provide a unified risk model for the human population. This paper focuses on variability [...] Read more.

Diversity is evident in various aspects of life and the human population. The current radiological protection system considers the diversity in disease susceptibility and incorporates some of it to provide a unified risk model for the human population. This paper focuses on variability in cancer risk among cells/tissues, individuals, and animal species. At the cell/tissue level, radiation cancer risk per unit dose varies among tissues, as indicated by epidemiological and animal studies. This variation is most likely due to the epigenetics of cells. At the individual level, radiation risks vary considerably depending on physiological, environmental, and genetic factors. At the species level, epidemiology is considered the most relevant source of radiological information, and limitations have been recognized in extrapolating animal data to human risks. A recent study demonstrated a fundamental relationship between cancer risk and somatic mutation rate in humans and mice. This relationship could lead to a new extrapolation method, which could be used to protect a wider range of species, including humans and other mammals. Thus, considering diversity in radiation cancer risk provides insight into the underlying aspects of radiobiology of radiological protection. Full article

(This article belongs to the Special Issue Radiation and Biology: Investigating Cellular, Organismal, and Environmental Responses)

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Graphical abstract

15 pages, 1854 KiB

Open AccessArticle

Phenotypic, Chemotaxonomic, and Genome-Based Classification of Phyllobacterium Strains: Two Proposed Novel Species, Phyllobacterium chamaecytisi sp. nov. and Phyllobacterium lublinensis sp. nov

by Sylwia Wdowiak-Wróbel, Karolina Włodarczyk-Ciekańska, Monika Marek-Kozaczuk, Marta Palusińska-Szysz, Piotr Koper and Jerzy Wielbo

Biology 2025, 14(8), 1024; https://doi.org/10.3390/biology14081024 - 8 Aug 2025

Abstract

The taxonomic status of two bacterial strains, KW56^T and 2063^T, isolated from root nodules of Chamaecytisus albus (Spanish broom), was investigated using a polyphasic approach. Both isolates belong to the genus Phyllobacterium, yet exhibit significant genotypic and phenotypic differences [...] Read more.

The taxonomic status of two bacterial strains, KW56^T and 2063^T, isolated from root nodules of Chamaecytisus albus (Spanish broom), was investigated using a polyphasic approach. Both isolates belong to the genus Phyllobacterium, yet exhibit significant genotypic and phenotypic differences from all currently described species. Whole-genome comparisons revealed that strain KW56^T is most closely related to Phyllobacterium trifolii PETP 02^T, while strain 2063^T is related to Phyllobacterium brassicacearum strains STM 196^T and 29-15. However, digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) values between the new isolates and their closest relatives were below established species delineation thresholds, supporting their recognition as novel species. Phenotypic analyses confirmed morphological and growth characteristics typical for Phyllobacterium, while also revealing several discriminatory physiological traits. Fatty acid profiling showed that cyclopropyl 19:0 was the major fatty acid in both strains, though each exhibited a unique fatty acid composition. Chemotaxonomic markers included 3-OH 14:0, a19:1, and 21:0 for strain KW56^T, and 3-OH 14:0, 3-OH 17:0, and 3-OH 18:0 for strain 2063^T. Based on the genomic, phenotypic, and chemotaxonomic data, we propose that strains KW56^T and 2063^T represent two novel species, for which the names Phyllobacterium chamaecytisi sp. nov. (DSM 113831) and Phyllobacterium lublinensis sp. nov. (DSM 113830) are proposed. Full article

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14 pages, 2527 KiB

Open AccessArticle

Herbicide-Induced Fragmentation: Regenerative Ability of Cabomba Fragments After Exposure to Flumioxazin

by Junfeng Xu, Tobias Oliver Bickel and Steve Adkins

Biology 2025, 14(8), 1023; https://doi.org/10.3390/biology14081023 - 8 Aug 2025

Abstract

Cabomba caroliniana A. Gray (cabomba) is an invasive alien aquatic plant (IAAP) posing a significant threat to aquatic ecosystems in Australia. Its ongoing spread is primarily driven by its rapid growth rate and ability to readily regenerate from stem fragments. Flumioxazin, an effective [...] Read more.

Cabomba caroliniana A. Gray (cabomba) is an invasive alien aquatic plant (IAAP) posing a significant threat to aquatic ecosystems in Australia. Its ongoing spread is primarily driven by its rapid growth rate and ability to readily regenerate from stem fragments. Flumioxazin, an effective herbicide for controlling cabomba, has been registered for use in Australia since 2021. However, exposing cabomba to flumioxazin can induce stem fragmentation, potentially facilitating further spread. This study aims to determine whether stem fragments of cabomba following treatment at different flumioxazin doses (i.e., 25, 50, 100, or 200 ppb a.i.) can regenerate new healthy shoots that could contribute to its future spread in a new environment, in either summer or winter. This study also aims to investigate how this regrowth potential changes over time after herbicide application. Results show that flumioxazin suppressed the regeneration of replanted stem fragments in a dose-dependent manner in both winter and summer. In winter, complete regeneration was suppressed at the highest concentration tested (200 ppb a.i.), while low concentrations (25 and 50 ppb a.i.) resulted in an average 45% lower regeneration rate and 93% lower regenerated biomass than the control. In summer, suppression of regeneration was lower; at 200 ppb a.i., partial regeneration (18%) occurred with a 97% biomass reduction. At lower concentrations (25 and 50 ppb a.i.), more stem fragments regenerated (66%) and biomass reduction was lower (69%) compared to winter. Furthermore, in summer, the plants gradually regained their ability to regenerate over time after herbicide exposure, regardless of flumioxazin concentration, while no such recovery occurred in winter at any concentration. The findings show that the highest tested dose (200 ppb a.i.) can effectively suppress cabomba regenerative ability, which will greatly reduce the risk of new infestations caused by dispersed fragments, particularly in winter, when cooler temperatures and lower light are suboptimal for cabomba growth. This suggests that winter may be a more effective season for flumioxazin application. However, since some regeneration still occurred in summer, even at the highest tested dose, the highest registered label rate (400 ppb a.i.) may be necessary to ensure effective suppression under warmer conditions. Further studies are needed to evaluate this higher dose and its long-term efficacy. Full article

15 pages, 9995 KiB

Open AccessArticle

Unveiling Genetic Variation in the Seed Bug Spilostethus pandurus (Scopoli, 1763) (Hemiptera: Lygaeidae) in Thailand Using Mitochondrial CO1 Sequence

by Warayutt Pilap, Nakorn Pradit, Chavanut Jaroenchaiwattanachote, Jatupon Saijuntha, Watee Kongbuntad, Wittaya Tawong, Chairat Tantrawatpan and Weerachai Saijuntha

Biology 2025, 14(8), 1022; https://doi.org/10.3390/biology14081022 - 8 Aug 2025

Abstract

Spilostethus pandurus is a phytophagous insect widely distributed across Asia, Europe, and Africa, yet its genetic variation remains poorly understood. This study presents the first comprehensive analysis of the genetic diversity and structure of S. pandurus in Thailand using mitochondrial cytochrome c oxidase [...] Read more.

Spilostethus pandurus is a phytophagous insect widely distributed across Asia, Europe, and Africa, yet its genetic variation remains poorly understood. This study presents the first comprehensive analysis of the genetic diversity and structure of S. pandurus in Thailand using mitochondrial cytochrome c oxidase subunit 1 (CO1) sequences from 202 individuals across 27 localities. A total of 58 haplotypes were identified, with high haplotype and nucleotide diversity observed, suggesting substantial genetic variation. The haplotype network revealed a star-like topology, indicating recent population expansion or ongoing gene flow. Neutrality tests and mismatch distribution analyses showed no strong signal of recent demographic expansion. Phylogenetic analysis confirmed that all Thai specimens clustered within a well-supported S. pandurus clade along with sequences from India, Namibia, and Europe. Analysis of Molecular Variance (AMOVA) revealed significant genetic differentiation among four continental groups, indicating that geographic isolation and restricted gene flow have shaped genetic divergence at a broad biogeographic scale. Further research using highly polymorphic nuclear markers is recommended to better resolve the population structure and evolutionary history of S. pandurus in Thailand and beyond. Full article

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

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11 pages, 226 KiB

Open AccessArticle

Effects of Probiotic-Fermented Corn Wet Distillers Grains on the Growth Performance, Carcass Characteristics, and Heavy Metal Residue Levels of Finishing Pigs

by Wang Liao, Xudong Wu, Zaigui Wang and Shuhao Fan

Biology 2025, 14(8), 1021; https://doi.org/10.3390/biology14081021 - 8 Aug 2025

Abstract

This study evaluated the effects of dietary probiotic-fermented corn wet distillers grains (FCWDGs) on finishing pigs. Three Bacillus subtilis strains (CGMCC21218, CCTCC2022073, and CICC10275) were used to ferment corn wet distillers grains, yielding FCWDGs-1, FCWDGs-2, and FCWDGs-3. A total of 128 130-day-old Anqing [...] Read more.

This study evaluated the effects of dietary probiotic-fermented corn wet distillers grains (FCWDGs) on finishing pigs. Three Bacillus subtilis strains (CGMCC21218, CCTCC2022073, and CICC10275) were used to ferment corn wet distillers grains, yielding FCWDGs-1, FCWDGs-2, and FCWDGs-3. A total of 128 130-day-old Anqing six white pigs were randomly assigned to four groups: a control group and groups supplemented with 6% FCWDGs-1 (T1), FCWDGs-2 (T2), and FCWDGs-3 (T3). Over a 60-day trial, FCWDGs significantly enhanced growth performance, with T1 and T3 groups showing higher final weight and average daily gain (ADG) compared to the control (p < 0.05), and feed-to-gain ratios were reduced in all treatments (p < 0.05). Loin muscle depth (LMD) was significantly greater in all treatments (p < 0.05), and the lean meat percentage (LMP) was significantly higher in the T1 group (p < 0.05). Antioxidant activity (T-AOC, SOD, and GSH-Px) was enhanced in all treatments, with the highest values observed in the T1 group (p < 0.05). Notably, FCWDGs reduced heavy-metal residues (As, Pb, Cu) in muscle, liver, and kidney tissues, particularly in the T1 group. The results highlight the potential of Bacillus subtilis-fermented FCWDGs to enhance growth performance and carcass traits, and reduce heavy metal accumulation in pig tissues. Full article

18 pages, 4671 KiB

Open AccessArticle

Bacterial Community Changes in Early-Stage Engineering Simulation of Red Mud/Phosphogypsum-Based Artificial Soil Vegetation Restoration

by Yong Liu, Binbin Xue, Hefeng Wan, Lishuai Zhang, Zhi Yang, Jingfu Wang, Lirong Wang and Xiaohong Lin

Biology 2025, 14(8), 1020; https://doi.org/10.3390/biology14081020 - 8 Aug 2025

Abstract

Preparing red mud/phosphogypsum-based artificial soils for vegetation restoration is promising. However, how artificial soil develops during vegetation restoration is unclear, especially regarding the relationship between the bacterial community and the development of artificial soil. The bacterial community changes in the early-stage engineering simulation [...] Read more.

Preparing red mud/phosphogypsum-based artificial soils for vegetation restoration is promising. However, how artificial soil develops during vegetation restoration is unclear, especially regarding the relationship between the bacterial community and the development of artificial soil. The bacterial community changes in the early-stage engineering simulation of red mud/phosphogypsum-based artificial soil vegetation restoration were analyzed for the first time in this paper. The results showed that the structure of the bacterial community was simple at the beginning, mainly consisting of Proteobacteria, Firmicutes, and Bacteroidota, with total abundances of 74.5% and 89.3% in the two plots, respectively. The richness, diversity, and evenness of the bacterial communities all significantly increased over time (p < 0.05), indicating that the compositions of the bacterial communities in artificial soils undergo constant development, adjustment, and optimization. There were good correlations between bacterial communities and environmental factors (e.g., pH, W_H2O, OM, TN, TK, AK, TP), which generally reflected the significant synergistic development and interaction between the quality of the soil environmental and bacterial communities. There were complex dynamic changes in the functions of the bacteria during the development of artificial soils, which were mainly reflected in the decline in the abundances of chemoheterotrophy, aerobic chemoheterotrophy, and animal parasites or symbionts, but there was an increase in the abundances of phototrophy, cyanobacteria, and dark sulfide oxidation. This reflects the highly active physiological and biochemical reaction functions of bacterial communities in the development of artificial soils, which is of great significance for continuously enhancing the fertility quality and ecological attributes of artificial soils. Full article

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16 pages, 1614 KiB

Open AccessArticle

VaccineDesigner: A Web-Based Tool for Streamlined Multi-Epitope Vaccine Design

by Dimitrios Trygoniaris, Anna Korda, Anastasia Paraskeva, Esmeralda Dushku, Georgios Tzimagiorgis, Minas Yiangou, Charalampos Kotzamanidis and Andigoni Malousi

Biology 2025, 14(8), 1019; https://doi.org/10.3390/biology14081019 - 7 Aug 2025

Abstract

Background: Multi-epitope vaccines have become the preferred strategy for protection against infectious diseases by integrating multiple MHC-restricted T-cell and B-cell epitopes that elicit both humoral and cellular immune responses against pathogens. Computational methods address various aspects independently, yet their orchestration is technically challenging, [...] Read more.

Background: Multi-epitope vaccines have become the preferred strategy for protection against infectious diseases by integrating multiple MHC-restricted T-cell and B-cell epitopes that elicit both humoral and cellular immune responses against pathogens. Computational methods address various aspects independently, yet their orchestration is technically challenging, as most bioinformatics tools are accessible through heterogeneous interfaces and lack interoperability features. The present work proposes a novel framework for rationalized multi-epitope vaccine design that streamlines end-to-end analyses through an integrated web-based environment. Results: VaccineDesigner is a comprehensive web-based framework that streamlines the design of protective epitope-based vaccines by seamlessly integrating computational methods for B-cell, CTL, and HTL epitope prediction. VaccineDesigner incorporates single-epitope prediction and evaluation as well as additional analyses, such as multi-epitope vaccine generation, estimation of population coverage, molecular mimicry, and proteasome cleavage. The functionalities are transparently integrated into a modular architecture, providing a single access point for rationalized, multi-epitope vaccine generation in a time- and cost-effective manner. Conclusions: VaccineDesigner is a web-based tool that identifies and evaluates candidate B-cell, CTL, and HTL epitopes and constructs a library of multi-epitope vaccines that combine strong immunogenic responses, safety, and broad population coverage. The source code is available under the academic license and freely accessible. Full article

(This article belongs to the Section Bioinformatics)

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15 pages, 1229 KiB

Open AccessArticle

Population Dynamics of the Florida Softshell Turtle (Apalone ferox) in a Protected Spring Ecosystem

by Eric C. Munscher, Zachary A. Siders, Andrew S. Weber, Jessica Munscher, Madeleine Morrison, Wayne Osborne, Shannon Letcher, Brian P. Butterfield, Michael Skibsted and Andrew D. Walde

Biology 2025, 14(8), 1018; https://doi.org/10.3390/biology14081018 - 7 Aug 2025

Abstract

The Florida softshell turtle, Apalone ferox, is considered common and found in many different types of freshwater habitats throughout its range. However, despite its prevalence where it occurs, little is understood about the species’ life history and population dynamics due to difficulties [...] Read more.

The Florida softshell turtle, Apalone ferox, is considered common and found in many different types of freshwater habitats throughout its range. However, despite its prevalence where it occurs, little is understood about the species’ life history and population dynamics due to difficulties with capture and long-term marking. Building on a foundational study of the Florida softshell turtle at Wekiwa Springs State Park (WSSP) from 2007 to 2012, we present findings from an extended 16-year mark–recapture study spanning from 2007 to 2023. A total of 31 sampling events were conducted with a median of two capture events per year. Sampling events were spread over a median of 5 days each year (range, 2–11 days), with a total of 88 capture days. One hundred and twenty individual A. ferox were captured over 225 encounters. We estimated an average population size of 135.6 individuals using an annual Schumacher–Eschmeyer ratio estimator. Using a state-space Jolly–Seber model, we estimated that 204 individuals entered the population over the 16 years (the superpopulation), while the average current population size was 40 individuals. The median survival probability was 0.884 but the median detection probability was 0.10, reinforcing the perceived difficulty with capturing A. ferox. The continued influx of new juveniles, recapture of these individuals as adults, and strong female bias support the possibility that the WSSP and Rock Springs greater ecosystem functions as a potential nursery habitat for the Florida softshell. Though population estimates dropped 20% following a two-year sampling gap owing to the COVID-19 pandemic, the population is currently growing slowly and highlights the value of continued, long-term monitoring of elusive freshwater turtle species. Full article

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

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23 pages, 4484 KiB

Open AccessArticle

Mechanistic Study of NT5E in Reg3β-Induced Macrophage Polarization and Cooperation with Plasma Proteins in Myocarditis Injury and Repair

by Shichao Zhang, Peirou Zhou, Fanfan Zhu, Yingying Wang, Xuesong Wang, Jingwen Chen, Yumeng Li and Xiaoyi Shao

Biology 2025, 14(8), 1017; https://doi.org/10.3390/biology14081017 - 7 Aug 2025

Abstract

Background: We aimed to explore the mechanism by which extracellular-5′-nucleotidase (NT5E) regulates macrophage polarization via regenerating islet-derived protein 3 beta (Reg3β) and other plasma proteins that mediate immune-cell effects on myocarditis. Methods: The involvement of NT5E in Reg3β-induced macrophage polarization was first analyzed [...] Read more.

Background: We aimed to explore the mechanism by which extracellular-5′-nucleotidase (NT5E) regulates macrophage polarization via regenerating islet-derived protein 3 beta (Reg3β) and other plasma proteins that mediate immune-cell effects on myocarditis. Methods: The involvement of NT5E in Reg3β-induced macrophage polarization was first analyzed using RNA sequencing, Western blotting, and quantitative polymerase chain reaction. Mendelian randomization was employed to identify NT5E and various plasma proteins as potential therapeutic targets for myocarditis. Mediation analysis, enrichment analysis, protein–protein interaction network analysis, drug prediction, molecular docking, and single-cell RNA sequencing were integrated to further evaluate the biological functions and pharmacological potential of the identified targets. Finally, phenome-wide association studies were conducted to assess the safety of targeting these proteins. Results: NT5E expression was elevated in Reg3β-stimulated M2 macrophages. The expression of Arg-1, a marker of M2 macrophages, decreased upon NT5E knockdown, suggesting that NT5E is involved in the Reg3β-mediated polarization of macrophages to the M2 phenotype. Mendelian randomization analysis identified NT5E and 80 other plasma proteins as being causally associated with myocarditis. Mediation analysis revealed 12 immune-cell types were mediators of the effects of plasma protein on myocarditis progression. Drug prediction identified candidates such as ICN 1229 and chrysin, which showed strong binding affinities in molecular docking analyses. These findings may contribute to the development of effective treatments for myocarditis. Conclusions: NT5E plays a dual role in Reg3β-induced macrophage polarization and in interacting with plasma proteins that influence the onset and progression of myocarditis through immune-cell pathways. Full article

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14 pages, 670 KiB

Open AccessReview

Hygiene Practices Against Dermatophytic Fungi: A Review of Strategies to Combat Antifungal Resistance

by Aditya K. Gupta, Daniel Taylor, Tong Wang, Elizabeth A. Cooper and Ditte Marie L. Saunte

Biology 2025, 14(8), 1016; https://doi.org/10.3390/biology14081016 - 7 Aug 2025

Abstract

Superficial fungal infections of the feet, such as tinea pedis and onychomycosis, are highly prevalent and frequently recurrent, often due to persistent contamination of footwear, textiles, and foot care instruments. Despite growing concern over antifungal resistance, environmental sources of reinfection remain under-recognized in [...] Read more.

Superficial fungal infections of the feet, such as tinea pedis and onychomycosis, are highly prevalent and frequently recurrent, often due to persistent contamination of footwear, textiles, and foot care instruments. Despite growing concern over antifungal resistance, environmental sources of reinfection remain under-recognized in clinical practice. This review critically examines historical and contemporary methods used to sanitize shoes, socks, podiatric tools, and related materials. Evidence from peer-reviewed studies published between 1938 and 2025 was analyzed across multiple disinfection categories, including chemical agents, thermal methods, laundering, ultraviolet- and ozone-based technologies, antimicrobial textiles, and sterilization protocols. Findings reveal a range of efficacies, limitations, and practical considerations across methods, with steam sterilization emerging as the most reliable for reusable instruments. A multifaceted approach combining pharmacologic treatment with consistent environmental hygiene is essential for breaking reinfection cycles and reducing antifungal resistance. This review highlights the need for clinical education and research into scalable, effective disinfection strategies. Full article

(This article belongs to the Section Microbiology)

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23 pages, 2328 KiB

Open AccessArticle

Novel Insights into T-Cell Exhaustion and Cancer Biomarkers in PDAC Using ScRNA-Seq

by Muhammad Usman Saleem, Hammad Ali Sajid, Muhammad Waqar Arshad, Alejandro Omar Rivera Torres, Muhammad Imran Shabbir and Sunil Kumar Rai

Biology 2025, 14(8), 1015; https://doi.org/10.3390/biology14081015 - 7 Aug 2025

Abstract

One of the aggressive and lethal cancers, pancreatic ductal adenocarcinoma (PDAC) is characterized by poor prognosis and resistance to conventional treatments. Moreover, the tumor immune microenvironment (TIME) plays a crucial role in the progression and therapeutic resistance of PDAC. It is associated with [...] Read more.

One of the aggressive and lethal cancers, pancreatic ductal adenocarcinoma (PDAC) is characterized by poor prognosis and resistance to conventional treatments. Moreover, the tumor immune microenvironment (TIME) plays a crucial role in the progression and therapeutic resistance of PDAC. It is associated with T-cell exhaustion, leading to the progressive loss of T-cell functions with an impaired ability to kill tumor cells. Therefore, this study employed single-cell RNA sequencing (scRNA-seq) analysis of a publicly available human PDAC dataset, with cells isolated from the primary tumor and adjacent normal tissues, identifying upregulated genes of T-cells and cancer cells in two groups (“cancer cells_vs_all-PDAC” and “cancer-PDAC_vs_all-normal”). Common and unique markers of cancer cells from both groups were identified. The Reactome pathways of cancer and T-cells were selected, while the genes implicated in those pathways were used to perform PPI analysis, revealing the hub genes of cancer and T-cells. The gene expression validation of cancer and T-cells hub-genes was performed using GEPIA2 and TISCH2, while the overall survival analysis of cancer cells hub-genes was performed using GEPIA2. Conclusively, this study unraveled 16 novel markers of cancer and T-cells, providing the groundwork for future research into the immune landscape of PDAC, particularly T-cell exhaustion. However, further clinical studies are needed to validate these novel markers as potential therapeutic targets in PDAC patients. Full article

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21 pages, 7477 KiB

Open AccessArticle

Bidirectional Hypoxic Extracellular Vesicle Signaling Between Müller Glia and Retinal Pigment Epithelium Regulates Retinal Metabolism and Barrier Function

by Alaa M. Mansour, Mohamed S. Gad, Samar Habib and Khaled Elmasry

Biology 2025, 14(8), 1014; https://doi.org/10.3390/biology14081014 - 7 Aug 2025

Abstract

The retina is highly sensitive to oxygen and blood supply, and hypoxia plays a key role in retinal diseases such as diabetic retinopathy (DR) and age-related macular degeneration (AMD). Müller glial cells, which are essential for retinal homeostasis, respond to injury and hypoxia [...] Read more.

The retina is highly sensitive to oxygen and blood supply, and hypoxia plays a key role in retinal diseases such as diabetic retinopathy (DR) and age-related macular degeneration (AMD). Müller glial cells, which are essential for retinal homeostasis, respond to injury and hypoxia with reactive gliosis, characterized by the upregulation of the glial fibrillary acidic protein (GFAP) and vimentin, cellular hypertrophy, and extracellular matrix changes, which can impair retinal function and repair. The retinal pigment epithelium (RPE) supports photoreceptors, forms part of the blood–retinal barrier, and protects against oxidative stress; its dysfunction contributes to retinal degenerative diseases such as AMD, retinitis pigmentosa (RP), and Stargardt disease (SD). Extracellular vesicles (EVs) play a crucial role in intercellular communication, protein homeostasis, and immune modulation, and have emerged as promising diagnostic and therapeutic tools. Understanding the role of extracellular vesicles’ (EVs’) signaling machinery of glial cells and the retinal pigment epithelium (RPE) is critical for developing effective treatments for retinal degeneration. In this study, we investigated the bidirectional EV-mediated crosstalk between RPE and Müller cells under hypoxic conditions and its impact on cellular metabolism and retinal cell integrity. Our findings demonstrate that RPE-derived extracellular vesicles (RPE EVs) induce time-dependent metabolic reprogramming in Müller cells. Short-term exposure (24 h) promotes pathways supporting neurotransmitter cycling, calcium and mineral absorption, and glutamate metabolism, while prolonged exposure (72 h) shifts Müller cell metabolism toward enhanced mitochondrial function and ATP production. Conversely, Müller cell-derived EVs under hypoxia influenced RPE metabolic pathways, enhancing fatty acid metabolism, intracellular vesicular trafficking, and the biosynthesis of mitochondrial co-factors such as ubiquinone. Proteomic analysis revealed significant modulation of key regulatory proteins. In Müller cells, hypoxic RPE-EV exposure led to reduced expression of Dyskerin Pseudouridine Synthase 1 (DKc1), Eukaryotic Translation Termination Factor 1 (ETF1), and Protein Ser/Thr phosphatases (PPP2R1B), suggesting alterations in RNA processing, translational fidelity, and signaling. RPE cells exposed to hypoxic Müller cell EVs exhibited elevated Ribosome-binding protein 1 (RRBP1), RAC1/2, and Guanine Nucleotide-Binding Protein G(i) Subunit Alpha-1 (GNAI1), supporting enhanced endoplasmic reticulum (ER) function and cytoskeletal remodeling. Functional assays also revealed the compromised barrier integrity of the outer blood–retinal barrier (oBRB) under hypoxic co-culture conditions. These results underscore the adaptive but time-sensitive nature of retinal cell communication via EVs in response to hypoxia. Targeting this crosstalk may offer novel therapeutic strategies to preserve retinal structure and function in ischemic retinopathies. Full article

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14 pages, 2183 KiB

Open AccessArticle

Interannual Variations in Soil Bacterial Community Diversity and Analysis of Influencing Factors During the Restoration Process of Scirpus Mariqueter Wetlands

by Yaru Li, Shubo Fang, Qinyi Wang, Pengling Wu, Peimin He and Wei Liu

Biology 2025, 14(8), 1013; https://doi.org/10.3390/biology14081013 - 7 Aug 2025

Abstract

Due to human activities and the invasion of Spartina alterniflora, the population of Scirpus mariqueter (S. mariqueter) in the Yangtze River Estuary has gradually declined. To address this issue, numerous restoration efforts have been undertaken. To investigate the changes and [...] Read more.

Due to human activities and the invasion of Spartina alterniflora, the population of Scirpus mariqueter (S. mariqueter) in the Yangtze River Estuary has gradually declined. To address this issue, numerous restoration efforts have been undertaken. To investigate the changes and influencing factors of soil bacterial communities during the restoration of S. mariqueter wetlands, we selected S. mariqueter populations as the research focus and divided the samples into two years, S1 and S2. High-throughput sequencing technology was employed for observation and analysis. The results revealed that from S1 to S2, soil bacterial diversity in the S. mariqueter wetland increased significantly and displayed clear seasonal patterns. The dominant bacterial phyla included Proteobacteria, Bacteroidota, Firmicutes, and Acidobacteriota. Among these, Proteobacteria had the highest relative abundance, while Acidobacteriota showed the most pronounced increase, surpassing Bacteroidota and Firmicutes to become the second most abundant group. Redundancy analysis (RDA) indicated that soil organic matter and electrical conductivity were the key factors influencing the composition and diversity of the soil bacterial community, with Acidobacteriota playing a dominant role during wetland restoration. In conclusion, during the ecological restoration of the S. mariqueter wetlands, attention should be given to environmental factors such as soil organic matter and electrical conductivity, while the regulatory role of Acidobacteriota in wetland soils should not be overlooked. This study provides a microscopic perspective on the interactions between microbial diversity and ecosystem functions in coastal wetlands, offering valuable guidance for the ecological restoration of degraded wetlands. Full article

(This article belongs to the Special Issue Biology, Ecology and Management of Aquatic Macrophytes and Algae—2nd Edition)

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21 pages, 4164 KiB

Open AccessArticle

Characterization and Functional Analysis of the FBN Gene Family in Cotton: Insights into Fiber Development

by Sunhui Yan, Liyong Hou, Liping Zhu, Zhen Feng, Guanghui Xiao and Libei Li

Biology 2025, 14(8), 1012; https://doi.org/10.3390/biology14081012 - 7 Aug 2025

Abstract

Fibrillins (FBNs) are indispensable for plant growth and development, orchestrating multiple physiological processes. However, the precise functional role of FBNs in cotton fiber development remains uncharacterized. This study reports a genome-wide characterization of the FBN gene family in cotton. A total of 28 [...] Read more.

Fibrillins (FBNs) are indispensable for plant growth and development, orchestrating multiple physiological processes. However, the precise functional role of FBNs in cotton fiber development remains uncharacterized. This study reports a genome-wide characterization of the FBN gene family in cotton. A total of 28 GhFBN genes were identified in upland cotton, with systematic analyses of their phylogenetic relationships, protein motifs, gene structures, and hormone-responsive cis-regulatory elements. Expression profiling of GhFBN1A during fiber development revealed stage-specific activity across the developmental continuum. Transcriptomic analyses following hormone treatments demonstrated upregulation of GhFBN family members, implicating their involvement in hormone-mediated regulatory networks governing fiber cell development. Collectively, this work presents a detailed molecular characterization of cotton GhFBNs and establishes a theoretical foundation for exploring their potential applications in cotton breeding programs aimed at improving fiber quality. Full article

(This article belongs to the Section Bioinformatics)

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18 pages, 3441 KiB

Open AccessReview

Epidermal Growth Factor Receptor (EGFR)-Targeting Peptides and Their Applications in Tumor Imaging Probe Construction: Current Advances and Future Perspectives

by Lu Huang, Ying Dong, Jinhang Li, Xinyu Yang, Xiaoqiong Li, Jia Wu, Jinhua Huang, Qiaoxuan Zhang, Zemin Wan, Shuzhi Hu, Ruibing Feng, Guodong Li, Xianzhang Huang and Pengwei Zhang

Biology 2025, 14(8), 1011; https://doi.org/10.3390/biology14081011 - 7 Aug 2025

Abstract

The epidermal growth factor receptor (EGFR) is a key target for both cancer diagnosis and therapeutic interventions. Assessing EGFR expression before therapy has become routine in clinical practice, yet current methods like biopsy and immunohistochemistry (IHC) have significant limitations, including invasiveness, limited repeatability, [...] Read more.

The epidermal growth factor receptor (EGFR) is a key target for both cancer diagnosis and therapeutic interventions. Assessing EGFR expression before therapy has become routine in clinical practice, yet current methods like biopsy and immunohistochemistry (IHC) have significant limitations, including invasiveness, limited repeatability, and lack of real-time, whole-body data. EGFR-targeted imaging has emerged as a promising alternative. EGFR-targeting peptides, owing to their favorable physicochemical properties and versatility, are increasingly being explored for a variety of applications, including molecular imaging, drug delivery, and targeted therapy. Recent advances have demonstrated the potential of EGFR-targeting peptides conjugated to imaging probes for non-invasive, real-time in vivo tumor detection, precision therapy, and surgical guidance. Here, we provide a comprehensive overview of the latest progress in EGFR-targeting peptides development, with a particular focus on their application in the development of molecular imaging agents, including fluorescence imaging, PET/CT, magnetic resonance imaging, and multimodal imaging. Furthermore, we examine the challenges and future directions concerning the development and clinical application of EGFR-targeting peptide-based imaging probes. Finally, we highlight emerging technologies such as artificial intelligence, mutation-specific peptides, and multimodal imaging platforms, which offer significant potential for advancing the diagnosis and treatment of EGFR-targeted cancers. Full article

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15 pages, 1458 KiB

Open AccessArticle

Effect of Precipitation Change on Desert Steppe Aboveground Productivity

by Yonghong Luo, Jiming Cheng, Ziyu Cao, Haixiang Zhang, Pengcuo Danba, Jiazhi Wang, Ying Wang, Rong Zhang, Chao Zhang, Yingqun Feng and Shuhua Wei

Biology 2025, 14(8), 1010; https://doi.org/10.3390/biology14081010 - 6 Aug 2025

Abstract

Precipitation changes have significant impacts on biodiversity and ecosystem productivity. However, the effects of precipitation changes on species diversity have been the focus of most previous studies. Little is known about the contributions of different dimensions of biodiversity (species, functional, and phylogenetic diversity) [...] Read more.

Precipitation changes have significant impacts on biodiversity and ecosystem productivity. However, the effects of precipitation changes on species diversity have been the focus of most previous studies. Little is known about the contributions of different dimensions of biodiversity (species, functional, and phylogenetic diversity) in linking long-term precipitation changes to ecosystem functions. In this study, a randomized design was conducted in the desert steppes of Ningxia, which included three treatments: natural rainfall, precipitation reduced by 50%, and precipitation increased by 50%. After 4 years of treatment, the effects of precipitation changes on aboveground productivity and its underlying mechanisms were explored. The results showed that (1) reduced precipitation significantly decreased phylogenetic diversity and species diversity, but had no significant effect on functional diversity; (2) reduced precipitation significantly decreased aboveground productivity, while increased precipitation significantly enhanced aboveground productivity; and (3) changes in precipitation primarily regulated aboveground productivity by altering soil nitrogen availability and the size of dominant plant species. This study provides important theoretical and practical guidance for the protection and management of desert steppe vegetation under future climate change. Full article

(This article belongs to the Section Ecology)

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12 pages, 498 KiB

Open AccessArticle

Virulence of Metarhizium robertsii Strains Isolated from Forest Ecosystems Against Wax Moths (Galleria mellonella, Achroia grisella) and Pine Processionary (Thaumetopoea pityocampa) Larvae

by Spiridon Mantzoukas, Vasileios Papantzikos, Chrysanthi Zarmakoupi, Panagiotis A. Eliopoulos, Ioannis Lagogiannis and George Patakioutas

Biology 2025, 14(8), 1009; https://doi.org/10.3390/biology14081009 - 6 Aug 2025

Abstract

Entomopathogenic fungi (EPF) are one of the most environmentally friendly ways to control a plethora of chewing insects such as T. pityocampa, G. mellonella, and A. grisella. Bioassay of EPF on these highly damaging pests is considered important in the [...] Read more.

Entomopathogenic fungi (EPF) are one of the most environmentally friendly ways to control a plethora of chewing insects such as T. pityocampa, G. mellonella, and A. grisella. Bioassay of EPF on these highly damaging pests is considered important in the face of climate change in order to research alternative solutions that are capable of limiting chemical control, the overuse of which increases insects’ resistance to chemical compounds. In this study, the insecticidal virulence of Metarhizium robertsii isolates, retrieved from forest ecosystems, was tested on second-instar larvae of T. pityocampa, G. mellonella, and A. grisella. Bioassays were carried out in the laboratory, where experimental larvae were sprayed with 2 mL of a six-conidial suspension from each isolate. Mortality was recorded for 144 h after exposure. Mean mortality, lethal concentrations, sporulation percentage, and sporulation time were estimated for each isolate. Metarhizium isolates resulted in the highest mortality (89.2% for G. mellonella and 90.2% for A. grisella). Based on the LC₅₀ estimates determined by the concentration–mortality relationships for the tested fungal isolates, we demonstrated significant virulence on larvae of G. mellonella, A. grisella, and T. pityocampa. Our results indicate that entomopathogenic fungi have the potential to become a very useful tool in reducing chemical applications. Full article

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20 pages, 1753 KiB

Open AccessArticle

Vitamin E Enhances Immune Function and the Intestinal Histological Structure by Regulating the Nodal-Mediated Signaling Pathway: A Case Study on the Sea Cucumber Apostichopus japonicus

by Zitong Wang, Yan Wang, Xianyu Wang, Guangyao Zhao, Haiqing Zeng, Haoran Xiao, Lingshu Han, Jun Ding, Yaqing Chang and Rantao Zuo

Biology 2025, 14(8), 1008; https://doi.org/10.3390/biology14081008 - 6 Aug 2025

Abstract

The histological integrity of the intestine depends on the tight and orderly arrangement of epithelial cells within the intestinal villi. Nodal, a transforming growth factor-β (TGF-β) family member, has been reported to promote epithelial cell proliferation. Collagen not only establishes physical connections [...] Read more.

The histological integrity of the intestine depends on the tight and orderly arrangement of epithelial cells within the intestinal villi. Nodal, a transforming growth factor-β (TGF-β) family member, has been reported to promote epithelial cell proliferation. Collagen not only establishes physical connections between adjacent cells but also serves as an anchoring platform for cell adhesion and regeneration processes. Therefore, a 21-day feeding trial was conducted using RNA interference to investigate the role of the Nodal gene in regulating intestinal collagen synthesis and histological structure integrity in juvenile A. japonicus fed diets containing graded levels of vitamin E (VE) (0, 200, and 400 mg/kg). The results showed that the addition of 200 mg/kg VE significantly improved the growth rate, immune enzyme activities and related gene expression, as well as intestinal villus morphology. Additionally, the addition of 200 mg/kg VE upregulated the expression of Nodal, which activated the expression of collagen synthesis-related genes and promoted collagen deposition in the intestines of A. japonicus. After Nodal gene knockdown, A. japonicus presented a decreased growth rate, damage to the intestinal histological structure, and impaired collagen synthesis, with the most notable findings observed in A. japonicus fed diets without VE addition. However, these detrimental effects were eliminated to some extent by the addition of 200 mg/kg VE. These findings indicate that VE improves immune function and intestinal histological structure in A. japonicus through a Nodal-dependent pathway. Full article

(This article belongs to the Special Issue Current Advances in Echinoderm Research (2nd Edition))

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16 pages, 1541 KiB

Open AccessArticle

A Ubiquitous Volatile in Noctuid Larval Frass Attracts a Parasitoid Species

by Chaowei Wang, Xingzhou Liu, Sylvestre T. O. Kelehoun, Kai Dong, Yueying Wang, Maozhu Yin, Jinbu Li, Yu Gao and Hao Xu

Biology 2025, 14(8), 1007; https://doi.org/10.3390/biology14081007 - 6 Aug 2025

Abstract

Natural enemies commonly probe larval bodies and frass with their antennae for prey hunting. However, the attractants to natural enemies emitted directly from hosts and host-associated tissues remained largely unknown. Here, we used two generalist noctuid species, Helicoverpa armigera (Hübner) and Spodoptera frugiperda [...] Read more.

Natural enemies commonly probe larval bodies and frass with their antennae for prey hunting. However, the attractants to natural enemies emitted directly from hosts and host-associated tissues remained largely unknown. Here, we used two generalist noctuid species, Helicoverpa armigera (Hübner) and Spodoptera frugiperda (JE Smith), along with the larval endoparasitoid Microplitis mediator (Haliday) to address the question. Extracts of larval frass of both the noctuid species were strongly attractive to M. mediator females when hosts were fed either maize, cotton, soybean leaves, or an artificial diet without leaf tissues. By using a combination of electrophysiological measurements and behavioral tests, we found that the attractiveness of frass mainly relied on a volatile compound ethyl palmitate. The compound was likely to be a by-product of host digestion involving gut bacteria because an antibiotic supplement in diets reduced the production of the compound in frass and led to the decreased attractiveness of frass to the parasitoids. In contrast, extracts of the larval bodies of both the noctuid species appeared to be less attractive to the parasitoids than their respective fecal extracts, independently of types of food supplied to the larvae. Altogether, larval frass of the two noctuid species was likely to be more important than their bodies in attracting the endoparasitoid species, and the main attractant of frass was probably one of the common metabolites of digestion involving gut microbes, and its emission is likely to be independent of host plant species. Full article

(This article belongs to the Special Issue The Biology, Ecology, and Management of Plant Pests)

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