Biology

21 pages, 2819 KB

Open AccessArticle

First Identification of MORF Family in Ferns: Molecular Regulation of Organellar RNA Editing in Osmunda japonica and Plenasium vachellii

by Lingling Li, Xiaolin Gu, Chuying Lu, Yingyi Liang, Jingyao Ping, Yingjuan Su and Ting Wang

Biology 2025, 14(10), 1463; https://doi.org/10.3390/biology14101463 - 21 Oct 2025

Abstract

RNA editing is a crucial mechanism regulating gene expression in plant organellar genomes, which optimizes protein structures through base substitution and plays a vital role in plant growth, development, and stress adaptation. This study revises the conventional understanding restricting MORF proteins to seed [...] Read more.

RNA editing is a crucial mechanism regulating gene expression in plant organellar genomes, which optimizes protein structures through base substitution and plays a vital role in plant growth, development, and stress adaptation. This study revises the conventional understanding restricting MORF proteins to seed plants by reporting their first identification in ferns, an early vascular plant lineage. We sequenced chloroplast genomes of O. japonica and P. vachellii, revealing one MORF9 homolog in O. japonica and three homologs (MORF1/8/9) in P. vachellii through comparative transcriptomics and structural validation. All identified MORF proteins harbor conserved MORF-box domains, suggesting structural and potentially functional conservation with angiosperms. Crucially, MORF members differentially regulate organellar RNA editing: chloroplast editing frequencies are predicted to show dose-dependent enhancement (0.7–1.0 in conserved sites), potentially influenced by MORF presence or copy number. In O. japonica, chloroplast editing exhibits tissue-specific patterns (conserved sites 0.7–1.0; tissue-specific sites lower efficiency at 0.1–0.2), while this study’s mitochondrial editing results show a balanced frequency distribution (0–1 range). Amino acid substitution analysis demonstrates MORF-mediated hydrophobic optimization (Ser→Leu > 30%, Pro→Leu > 18%), likely underpinning fern adaptability. This work provides crucial initial evidence for a conserved MORF-mediated RNA editing module shared between these early vascular plants (ferns) and angiosperms, offering fundamental insights into the evolutionary trajectory of plant organellar gene regulation. Full article

16 pages, 6472 KB

Open AccessArticle

Research on the Mechanism of Hypoxia Tolerance of a Hybrid Fish Using Transcriptomics and Metabolomics

by Yuhua Tang, Jiayi Yang, Chunchun Zhu, Hong Zhang, Li Hu, Wenting Rao, Xinxin Yu, Ming Wen, Min Tao and Shaojun Liu

Biology 2025, 14(10), 1462; https://doi.org/10.3390/biology14101462 - 21 Oct 2025

Abstract

The novel hybrid fish BTB, derived from crossing blunt snout bream (Megalobrama amblycephala, BSB) and topmouth culter (Culter alburnus, TC), exhibits markedly hypoxia tolerance in aquaculture. In this study, hypoxic treatment experiments confirmed that, comparing to its original parent [...] Read more.

The novel hybrid fish BTB, derived from crossing blunt snout bream (Megalobrama amblycephala, BSB) and topmouth culter (Culter alburnus, TC), exhibits markedly hypoxia tolerance in aquaculture. In this study, hypoxic treatment experiments confirmed that, comparing to its original parent BSB, the tolerance to low oxygen of BTB increased by 20.0%. Furthermore, a comparative analysis of the transcriptome and metabolome was performed using gill tissues from BTB exposed to normoxic and hypoxic conditions. Under hypoxic conditions, BTB displayed adaptive modifications in gill lamellae and hemocytes. Transcriptomic profiling identified 789 differentially expressed genes (DEGs), with 298 upregulated and 491 downregulated, enriched in pathways including apoptosis, NK cell-mediated cytotoxicity, MAPK/TNF/Toll-like receptor signaling, and HIF-1/FoXO signaling pathways. Twelve hypoxia-related candidate genes (egln3, im_7150988, znf395a, hif-1an, mknk2b, pck2, ero1a, igfbp-1a, vhl, bpifcl, egln1a, and ccna1) were screened and validated as potential contributors to hypoxia tolerance. Metabolomics analysis revealed a total of 108 differential metabolites (78 upregulated and 30 downregulated), predominantly linked to Arginine and proline metabolism, Ether lipid metabolism, Arachidonic acid metabolism, and Glycerophospholipid metabolism. Association analysis of transcriptomics and metabolomics revealed that the DEGs and DMs were enriched in the pathways of glycerophospholipid metabolism, ether lipid metabolism, arachidonic acid metabolism, and arginine and proline metabolism. In summary, BTB exhibited relatively high hypoxia tolerance, and 12 candidate genes related to hypoxia tolerance were identified. These findings laid a foundation for further investigation into the mechanisms of hypoxia tolerance improvement in hybrid fish. Full article

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

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19 pages, 4270 KB

Open AccessArticle

CGF-Conditioned Medium Modulates Astrocytic Differentiation and Invasiveness in U87MG Glioblastoma Cells

by Laura Giannotti, Benedetta Di Chiara Stanca, Francesco Spedicato, Christian Demitri, Eleonora Stanca, Andrea Palermo, Franco Ferrante, Fabrizio Damiano, Maria Antonietta De Sangro, Luciano Abbruzzese and Luisa Siculella

Biology 2025, 14(10), 1461; https://doi.org/10.3390/biology14101461 - 21 Oct 2025

Abstract

Background: Glioblastoma (GBM) is a highly aggressive tumor characterized by elevated plasticity and poor differentiation. Platelet-derived preparations such as Concentrated Growth Factors (CGF) are rich in bioactive molecules, but their effects on tumor biology remain underexplored. Methods: U87MG glioblastoma cells were cultured with [...] Read more.

Background: Glioblastoma (GBM) is a highly aggressive tumor characterized by elevated plasticity and poor differentiation. Platelet-derived preparations such as Concentrated Growth Factors (CGF) are rich in bioactive molecules, but their effects on tumor biology remain underexplored. Methods: U87MG glioblastoma cells were cultured with a conditioned medium obtained from CGF over 14 days (CGF-CM). We analyzed cell viability, morphology, DNA integrity, migration, proliferation, and expression of astrocytic markers. Results: CGF-CM treatment induced early enhancement of cell viability, followed by decreased proliferation and reduced migration at later time points. Morphological analyses revealed astrocyte-like features. The expression of glial fibrillary acidic protein (GFAP), an astrocytic marker, and its α/δ isoform ratio increased over time, while GBM -GBM-associated markers, such as AQP-4 and S100B, were downregulated. Conclusions: Our findings demonstrate that CGF-CM modulates the phenotypic plasticity of U87MG cells and promotes differentiation toward an astroglial-like profile. These results provide a basis for future studies on the modulation of GBM aggressiveness using bioactive autologous derivatives. Full article

(This article belongs to the Special Issue Editorial Board Members' Collection Series: Cell Signaling in Health and Disease)

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22 pages, 10621 KB

Open AccessArticle

Comprehensive Analysis of the ARF Gene Family Reveals Their Roles in Chinese Chestnut (Castanea mollissima) Seed Kernel Development

by Xili Liu, Yun Li, Manman Liang, Dongsheng Wang, Meng Wang, Yi Lu, Xia Liu, Haie Zhang, Xiangyu Wang and Liyang Yu

Biology 2025, 14(10), 1460; https://doi.org/10.3390/biology14101460 - 21 Oct 2025

Abstract

Auxin response factors (ARFs) are a class of significant transcription factors that play crucial roles in the regulation of plant growth and development. Although ARF genes have been extensively characterized in various plants, their functions in perennial woody crops, particularly their involvement in [...] Read more.

Auxin response factors (ARFs) are a class of significant transcription factors that play crucial roles in the regulation of plant growth and development. Although ARF genes have been extensively characterized in various plants, their functions in perennial woody crops, particularly their involvement in regulating starch accumulation—a key determinant of yield and quality in Castanea mollissima—remain largely unexplored. To address this knowledge gap, we conducted a comprehensive study of the ARF gene family in the C. mollissima. In this study, 18 CmARF members, exhibiting diverse physicochemical properties, were identified within the C. mollissima genome. These CmARFs were categorized into four groups. Dispersed duplication emerged as the primary mechanism driving the expansion of the CmARF gene family. As C. mollissima seed kernels developed, notable changes were observed in starch content and the activity of enzymes related to starch biosynthesis, particularly a significant decrease in GBSS activity, which corresponded with an increase in seed kernel size and starch content. Transcriptome analysis delineated the expression patterns of CmARF genes during the development of C. mollissima seed kernels. A key novel finding of our research is that CmARF5a and CmARF18 are hypothesized to act as pivotal repressors of starch accumulation. This hypothesis is based on their expression profiles, strong negative correlations with physiological indicators, and WGCNA. Notably, the lack of correlation between these CmARFs and the expression of core starch biosynthetic genes suggests a potential indirect regulatory mechanism, offering a new perspective on ARF function in storage organ development. This study not only provides the first comprehensive characterization of the CmARF family but also offers a theoretical framework and candidate genes for future functional research on C. mollissima seed kernel development and starch biosynthesis. Full article

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21 pages, 6538 KB

Open AccessArticle

Enhanced Phosphorus Removal by Iron-Carbon in Constructed Wetlands Across Salinity Gradients: Mechanisms and Microbial Insights for Aquaculture Tailwater Treatment

by Rui Yin, Boan Chen, Xinyu He, Chen Cai, Tangfang Zhai, Haoyang Shi, Na Li and Xiaona Ma

Biology 2025, 14(10), 1459; https://doi.org/10.3390/biology14101459 - 21 Oct 2025

Abstract

Saline aquaculture tailwater challenges conventional constructed wetlands (CWs) with their limited phosphorus (P) removal capacity. To address this, iron-carbon constructed wetlands (IC-CWs) were developed and operated under four salinity gradients (0, 10, 20, and 30) for 155 days to investigate the effects of [...] Read more.

Saline aquaculture tailwater challenges conventional constructed wetlands (CWs) with their limited phosphorus (P) removal capacity. To address this, iron-carbon constructed wetlands (IC-CWs) were developed and operated under four salinity gradients (0, 10, 20, and 30) for 155 days to investigate the effects of salinity on P removal and associated microbial mechanisms. The results showed that salinity critically influenced long-term P removal, with the system at salinity 20 (S20) achieving the highest total phosphorus (TP) removal efficiency (78.80 ± 6.01%). Enhanced P removal was primarily attributed to the upregulation of phosphate transport genes (pstS, 14.25-fold increase) and elevated activity of key enzymes (AKP and ACP) in phosphorus-accumulating organisms (PAOs). However, high salinity (30) suppressed microbial metabolic functions. Metagenomic analysis revealed that salinity stress reshaped microbial community structure, with Bacteroidota abundance increasing 10-fold in S20 compared to S0 (control). This phylum harbored the phnE gene, significantly promoting organic phosphorus mineralization. Additionally, iron release increased with rising salinity, and the relative abundance of the phnE gene in Bacteroidota was highest in the S20 group, indicating a close association between iron release and PAOs as well as organic P mineralization genes. The quadratic polynomial model revealed that iron release under high salinity followed nonlinear kinetics, with passivation layer rupture promoting iron-phosphorus precipitate desorption in later stages. These findings provide a theoretical basis for optimizing salinity parameters to enhance chemical-biological P removal synergy, offering a promising strategy for saline aquaculture wastewater treatment. Full article

(This article belongs to the Special Issue The Relationship Between Water Quality and Aquatic Organisms (2nd Edition))

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19 pages, 538 KB

Open AccessReview

Critical Understanding of the Influence of Cellular Aging Biomarkers on Host–Parasite Relationships Serving as a Key Platform for Malaria Eradication

by Dorathy Olo Anzaku and Israel Sunmola Afolabi

Biology 2025, 14(10), 1458; https://doi.org/10.3390/biology14101458 - 21 Oct 2025

Abstract

Plasmodium parasites are the causative agents of malaria and can infect humans and other vertebrates, impacting socioeconomic development and causing significant health issues globally. Plasmodium falciparum causes the most severe type of infection, which can lead to chronic morbidity and other severe complications [...] Read more.

Plasmodium parasites are the causative agents of malaria and can infect humans and other vertebrates, impacting socioeconomic development and causing significant health issues globally. Plasmodium falciparum causes the most severe type of infection, which can lead to chronic morbidity and other severe complications like anemia and cerebral malaria. The onset of infection is marked by the injection of sporozoites into the skin through the bite of a female Anopheles mosquito. This triggers a cascade of reactions elicited both by the host immune system in response to infection and by the parasite in a bid to evade the host immune system, survive, and replicate. The dynamics of this host–parasite relationship have prompted extensive research in an attempt to understand and exploit it in the fight against malaria. Thus, understanding the temporal and spatial dimensions of adaptation in host–parasite relationships is critical for forecasting parasite evolution and spread within and between host populations. One such relationship is the complex interplay between malaria and cellular aging processes. Understanding this dynamic will provide novel insights into the pathophysiology of the disease. This comprehensive review takes us on that journey by providing an overview of the interaction between the Plasmodium parasite and its host and the interplay between infection mechanisms, host immune response, and parasite evasion strategies, narrowing it down to how it affects cellular aging biomarkers and how this can be explored as a platform in the fight against the disease. Full article

(This article belongs to the Special Issue Young Investigators in Biochemistry and Molecular Biology)

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15 pages, 11674 KB

Open AccessArticle

Characterization of Ingested Microplastics in a Regional Endemic Lizard Apathya cappadocica (Werner, 1902) from Türkiye

by Cantekin Dursun, Nagihan Demirci, Kamil Candan, Ahmet Gökay Korkmaz, Ecem Büşra Hastürk, Elif Yıldırım Caynak, Çetin Ilgaz, Yusuf Kumlutaş and Serkan Gül

Biology 2025, 14(10), 1457; https://doi.org/10.3390/biology14101457 - 21 Oct 2025

Abstract

This study investigated the presence, characteristics, and distribution of ingested microplastics (MPs) in Apathya cappadocica, a regional endemic lizard species. A total of 93 individuals were examined, and MPs were found in 19.35% (n = 18) of them. A total of 27 [...] Read more.

This study investigated the presence, characteristics, and distribution of ingested microplastics (MPs) in Apathya cappadocica, a regional endemic lizard species. A total of 93 individuals were examined, and MPs were found in 19.35% (n = 18) of them. A total of 27 microplastic particles were detected, averaging 1.5 MPs per positive individual and 0.29 MPs per individual across the sample. MP sizes ranged from 50 to 1727 µm, with a mean size of 355.46 ± 73 µm. Most MPs (93%) were fibers, while the rest were fragments. The dominant color was navy blue (41%), followed by red and black (19% each). Polyvinyl alcohol (PVA) was the most common polymer (67%), followed by polyethylene terephthalate (PET) and polyethylene (PE). Statistical tests revealed no significant differences in MP size based on shape, color, or type, nor any correlation between MP size and gastrointestinal tract weight. However, microplastic shape was significantly associated with polymer type; fiber MPs consisted mainly of PET and PVA, while fragments were equally split between PVA and PE. These findings indicate that terrestrial reptiles are exposed to microplastic pollution and that microplastic characteristics may provide insights into their potential environmental sources. Full article

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15 pages, 3422 KB

Open AccessArticle

ITS Sequencing Reveals the Changing Characteristics of Fungal Communities in Different Rice-Growing Substrates Under Salt Stress

by Hang Zhou, Xiaole Du, Yin Lin, Liming Zhao, Naijie Feng and Dianfeng Zheng

Biology 2025, 14(10), 1456; https://doi.org/10.3390/biology14101456 - 21 Oct 2025

Abstract

The impact of substrates with different physicochemical properties on the response of rhizosphere fungi in rice to salt stress has not been fully explored. The purpose of this study is to reveal the adaptation characteristics of fungal colonies to salt stress under different [...] Read more.

The impact of substrates with different physicochemical properties on the response of rhizosphere fungi in rice to salt stress has not been fully explored. The purpose of this study is to reveal the adaptation characteristics of fungal colonies to salt stress under different substrate conditions and the relationship between different properties of substrates and fungal colonies. Four different substrates were set by adjusting the sand, peat moss, and laterite ratio, with different bulk density, total porosity, and nutrient content. The same dose of sodium chloride solution was added to each substrate, and water was used as the control. The results showed that salt stress did not cause significant changes in the diversity and richness of fungal communities in different substrates. This study found that the responses of Ascomycota and Penicillium to salt stress varied depending on the substrate. The abundance of Penicillium was significantly positively correlated with total porosity (saline or non-saline conditions), but that of Acrostalagmus was significantly negatively correlated with total porosity under non-saline conditions. In addition, Lefse multi-level species difference discrimination analysis identified biomarkers in different treatments and revealed the core communities in response to substrate changes or salt stress. The results of this study contribute to a deeper understanding of the ecological functions of fungi. Full article

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15 pages, 2260 KB

Open AccessArticle

Efficient Serum-Free Rabies Virus Propagation Using BSR and Vero Cell Lines: A Comparative Evaluation of BioNOC II^® Macrocarriers in the BelloStage™-3000 Bioreactor Versus Conventional Microcarriers

by Zhanat Amanova, Zhanna Sametova, Sholpan Turyskeldy, Alina Kurmasheva, Ruslan Abitayev, Abdurakhman Ussembay, Zhanat Kondibaeva, Dariya Toktyrova, Dana Mazbayeva, Sergazy Nurabayev, Aslan Kerimbayev and Yerbol Bulatov

Biology 2025, 14(10), 1455; https://doi.org/10.3390/biology14101455 - 21 Oct 2025

Abstract

The rabies virus remains a significant public health threat, particularly in regions with limited access to vaccination. This study shows that the BelloStage™-3000 bioreactor, operating on the “Tide Motion” principle, in combination with BioNOC^® II macrocarriers, ensures highly efficient rabies virus cultivation [...] Read more.

The rabies virus remains a significant public health threat, particularly in regions with limited access to vaccination. This study shows that the BelloStage™-3000 bioreactor, operating on the “Tide Motion” principle, in combination with BioNOC^® II macrocarriers, ensures highly efficient rabies virus cultivation in BSR and Vero cells grown in serum-free OptiPRO™ SFM medium. This system supports effective cell attachment, formation of a dense and metabolically active cell layer, and reduces microbial contamination risks associated with serum-containing media. For comparison, rabies virus cultivation was also performed on Cytodex 1 and Cytodex 3 microcarriers in spinner flasks. The use of the BelloStage™-3000 bioreactor system with BelloCell™ 500A disposable vials and BioNOC II^® macrocarriers resulted in significantly higher virus titers compared to traditional Cytodex 1 and Cytodex 3 microcarrier culture systems. Thus, in the BSR cell culture, the maximum virus titer reached 5.6 × 10⁸ FFU/mL by day 4 of cultivation, which exceeded the titers obtained on Cytodex 1 and Cytodex 3 microcarriers by about 19.3-fold and 15.3-fold, respectively. A similar trend was observed for the Vero cell line: the peak titer was 2.0 × 10⁸ FFU/mL by day 5 of culturing, which was higher than the values obtained on Cytodex 1 and Cytodex 3 by about 14.0-fold and 9.6-fold, respectively. These findings demonstrate that the integrated use of BioNOC^® II macrocarriers, the BelloStage™-3000 bioreactor, and a serum-free medium provides a scalable, reproducible, and biosafe platform for rabies virus production, offering substantial advantages over traditional microcarrier-based systems. Full article

(This article belongs to the Special Issue In Vitro 2.0—Improving the Cell Culture Environment for Biology)

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12 pages, 1395 KB

Open AccessArticle

Possible Involvement of Leptin in Pathogenesis of Periodontal Disease

by Małgorzata Kozak, Agata Poniewierska-Baran, Michał Czerewaty, Karolina Łuczkowska, Małgorzata Mazurek-Mochol, Bogusław Machaliński and Andrzej Pawlik

Biology 2025, 14(10), 1454; https://doi.org/10.3390/biology14101454 - 20 Oct 2025

Abstract

Periodontitis is a chronic inflammatory condition of the periodontal tissues, ultimately leading to their destruction. The periodontal ligament is a key structure that not only secures the teeth within the alveolus but can also act as a source of numerous mediators involved in [...] Read more.

Periodontitis is a chronic inflammatory condition of the periodontal tissues, ultimately leading to their destruction. The periodontal ligament is a key structure that not only secures the teeth within the alveolus but can also act as a source of numerous mediators involved in the development of inflammation in periodontal tissues. The aim of this study was to investigate the effect of leptin on periodontal ligament cells and their secretion of selected pro-inflammatory mediators that may contribute to the pathogenesis of periodontal disease. The study was conducted on cultured periodontal ligament cells stimulated with leptin. The effect of leptin was assessed on the expression of selected cytokines implicated in the pathogenesis of periodontal disease (IL-1, IL-6, IL-8, IL-10, IL-17, IL-18, and tumour necrosis factor-alpha [TNF-α]) at the mRNA level, as well as on the protein concentrations of these cytokines in culture supernatants. Assessments were carried out after 12, 24, and 48 h of leptin stimulation. The results showed a statistically significant effect of leptin on IL-6 and IL-8 expression at both the mRNA and protein levels. For IL-1, a transient increase in mRNA expression and protein concentration was observed, persisting up to 24 h. A decrease in IL-10 mRNA expression was noted after 48 h of leptin stimulation, with no corresponding effect on IL-10 protein concentration. No significant effect of leptin was found on IL-17 or IL-18 protein concentrations in periodontal ligament cell cultures. These findings suggest that leptin may contribute to the pathogenesis of periodontitis by modulating the expression of certain pro-inflammatory cytokines in periodontal ligament cells. Full article

(This article belongs to the Special Issue Young Investigators in Biochemistry and Molecular Biology)

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27 pages, 1960 KB

Open AccessReview

AI and Machine Learning in Biology: From Genes to Proteins

by Zaw Myo Hein, Dhanyashri Guruparan, Blaire Okunsai, Che Mohd Nasril Che Mohd Nassir, Muhammad Danial Che Ramli and Suresh Kumar

Biology 2025, 14(10), 1453; https://doi.org/10.3390/biology14101453 - 20 Oct 2025

Abstract

Artificial intelligence (AI) and machine learning (ML), especially deep learning, have profoundly transformed biology by enabling precise interpretation of complex genomic and proteomic data. This review presents a comprehensive overview of cutting-edge AI methodologies spanning from foundational neural networks to advanced transformer architectures [...] Read more.

Artificial intelligence (AI) and machine learning (ML), especially deep learning, have profoundly transformed biology by enabling precise interpretation of complex genomic and proteomic data. This review presents a comprehensive overview of cutting-edge AI methodologies spanning from foundational neural networks to advanced transformer architectures and large language models (LLMs). These tools have revolutionized our ability to predict gene function, identify genetic variants, and accurately determine protein structures and interactions, exemplified by landmark milestones such as AlphaFold and DeepBind. We elaborate on the synergistic integration of genomics and protein structure prediction through AI, highlighting recent breakthroughs in generative models capable of designing novel proteins and genomic sequences at unprecedented scale and accuracy. Furthermore, the fusion of multi-omics data using graph neural networks and hybrid AI frameworks has provided nuanced insights into cellular heterogeneity and disease mechanisms, propelling personalized medicine and drug discovery. This review also discusses ongoing challenges including data quality, model interpretability, ethical concerns, and computational demands. By synthesizing current progress and emerging frontiers, we provide insights to guide researchers in harnessing AI’s transformative power across the biological spectrum from genes to functional proteins. Full article

(This article belongs to the Special Issue Artificial Intelligence Research for Complex Biological Systems)

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15 pages, 495 KB

Open AccessReview

Insect Odorant-Binding Proteins (OBPs) and Chemosensory Proteins (CSPs): Mechanisms and Research Perspectives in Mediating Insecticide Resistance

by Qian Wang, Xuping Shentu, Xiaoping Yu and Yipeng Liu

Biology 2025, 14(10), 1452; https://doi.org/10.3390/biology14101452 - 20 Oct 2025

Abstract

Insecticide resistance has become a critical issue threatening global agricultural production and food security. Previous studies have primarily focused on resistance mechanisms such as target-site mutations, enhanced metabolic detoxification, and reduced cuticular penetration. However, growing evidence in recent years indicates that odorant-binding proteins [...] Read more.

Insecticide resistance has become a critical issue threatening global agricultural production and food security. Previous studies have primarily focused on resistance mechanisms such as target-site mutations, enhanced metabolic detoxification, and reduced cuticular penetration. However, growing evidence in recent years indicates that odorant-binding proteins (OBPs) and chemosensory proteins (CSPs)—beyond their roles in chemoreception—also play key roles in the development of insecticide resistance. Research has revealed that these proteins significantly modulate insect susceptibility to insecticides through various mechanisms, including direct binding to insecticides, regulation of detoxification metabolic pathways, and influence on behavioral adaptations in pests. This review also systematically summarizes modern research strategies employed to investigate OBPs/CSPs functions, including high-throughput omics technologies, RNA interference, CRISPR-Cas9 gene editing, and molecular docking, while discussing the potential of targeting these proteins for developing novel insecticides and resistance management strategies. Although significant progress has been made in laboratory studies, the practical application of OBPs/CSPs-mediated resistance mechanisms still faces multiple challenges. Future research should prioritize multi-gene targeting strategies, cross-species functional validation, and field trial implementation to facilitate the development of green and precise pest control approaches based on OBPs and CSPs, thereby offering new pathways for sustainable agriculture. Full article

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14 pages, 5408 KB

Open AccessArticle

Comprehensive Genome-Wide Analysis of Dmrt Transcription Factors Reveals Their Roles in Sexual Dimorphism in Scolopendra mutilans

by Zhiqiang Li, Jingjing Guo, Ghulam Nabi, Zheng Wang, Buddhi Dayananda and Lin Zhang

Biology 2025, 14(10), 1451; https://doi.org/10.3390/biology14101451 - 20 Oct 2025

Abstract

The double-sex and mab-3-related transcription factors (Dmrt) are widely distributed in the animal kingdom and play a crucial role in sex determination and differentiation. In this study, we identified eight Dmrt transcription factors in the genome of the centipede Scolopendra mutilans, including [...] Read more.

The double-sex and mab-3-related transcription factors (Dmrt) are widely distributed in the animal kingdom and play a crucial role in sex determination and differentiation. In this study, we identified eight Dmrt transcription factors in the genome of the centipede Scolopendra mutilans, including five Dsx-related genes (as Dsx1, Dsx2 (five splice variants), Dsx3, Dsx4 and Dsx5) and three Dmrt-related genes (as Dmrt11E, Dmrt99B, and Dmrt93B). Phylogenetic analysis revealed evolutionary conservation across arthropods, with Dsx genes clustered into class-specific clades (Chilopoda, Insecta, Crustacea, Arachnida). Structural analysis confirmed conserved DM domains and sex-specific motifs, with tandem duplication of Dsx2 on chromosome 4. Expression profiling demonstrated significant sexual dimorphism: Dsx5 was female-biased, whereas Dsx2, Dsx3, and Dsx4 were male-biased, suggesting their functional divergence in sexual differentiation. Correlation analysis linked the expression of Sxl and Fem-1C to the regulation of Dsx isoforms, suggesting the presence of a conserved upstream regulatory cascade for sex-specific splicing. These findings elucidate the structural and functional landscape of Dmrts in S. mutilans, and provide insights into how sex-determination mechanisms evolved in Myriapoda. Full article

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14 pages, 420 KB

Open AccessReview

Catalyzing Protein Folding by Chaperones

by Zijue Huang and Scott Horowitz

Biology 2025, 14(10), 1450; https://doi.org/10.3390/biology14101450 - 20 Oct 2025

Abstract

Protein folding is a fundamental process essential for cellular growth and health, yet it is also susceptible to errors that can result in misfolding and disease. This literature review explores the current knowledge of the roles of different factors on protein folding in [...] Read more.

Protein folding is a fundamental process essential for cellular growth and health, yet it is also susceptible to errors that can result in misfolding and disease. This literature review explores the current knowledge of the roles of different factors on protein folding in the cell. We examine the cellular proteostasis network, with a focus on the catalytic actions of prolyl isomerases and molecular chaperones (including RNA G-quadruplexes), which collaborate to guide newly synthesized polypeptides toward their native structures and prevent aggregation. By integrating structural and biochemical insights, this review highlights the current understanding and ongoing questions regarding how chaperones can improve folding times of proteins to physiological pertinent rates. Full article

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

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11 pages, 2177 KB

Open AccessArticle

Warning Before a Fight: The Role of Distance and Ritualized Agonistic Behaviors in Minimizing Aggression in the Jamaican Fruit Bat

by Orlando R. Vivanco-Montané, Jorge E. Morales-Mávil, Laura T. Hernández-Salazar, Jairo Pérez-Torres and Edgar Ahmed Bello-Sánchez

Biology 2025, 14(10), 1449; https://doi.org/10.3390/biology14101449 - 20 Oct 2025

Abstract

In many vertebrates, ritualized behaviors serve to settle conflicts while minimizing the risk of injury. The Jamaican fruit bat (Artibeus jamaicensis) is a polygynous species that roosts in caves, where dominant males form and defend harems by displaying agonistic behaviors against [...] Read more.

In many vertebrates, ritualized behaviors serve to settle conflicts while minimizing the risk of injury. The Jamaican fruit bat (Artibeus jamaicensis) is a polygynous species that roosts in caves, where dominant males form and defend harems by displaying agonistic behaviors against satellite males attempting to mate with females. We examined how the distance of satellite males from the harem and the number of females influenced the latency of approach by dominant males during agonistic encounters, and whether these encounters follow a defined behavioral sequence. We analyzed 50 agonistic interactions from video recordings of A. jamaicensis harems collected between May and October 2021 in “Cantil Blanco” cave, Veracruz, Mexico. We quantified the number of females per harem and measured the distance of satellite males to the nearest female just before the dominant male initiated an approach. Our results show that satellite male distance determined dominant male approach latency, reflecting a minimum tolerable distance, whereas harem size had no effect. Furthermore, the succession of behaviors observed indicates that these encounters are sequential, escalating from ritualized displays to physical aggression. Full article

(This article belongs to the Special Issue Advances in Biological Research of Chiroptera)

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24 pages, 8375 KB

Open AccessArticle

Analysis of the Transcriptome Response to Low Nitrogen in Populus ussuriensis

by He Feng, Yue Chang, Runze Liu, Wenlong Li, Zhiwei Liu, Ming Wei, Zhibin Luo and Chenghao Li

Biology 2025, 14(10), 1448; https://doi.org/10.3390/biology14101448 - 20 Oct 2025

Abstract

(1) Background: Nitrogen is a key element that is essential for plant growth, and it is absorbed by roots from the soil. Nitrogen stress severely limits forest tree productivity; therefore, elucidating the molecular mechanisms underlying nitrogen stress tolerance in forest trees is critical [...] Read more.

(1) Background: Nitrogen is a key element that is essential for plant growth, and it is absorbed by roots from the soil. Nitrogen stress severely limits forest tree productivity; therefore, elucidating the molecular mechanisms underlying nitrogen stress tolerance in forest trees is critical for sustainable forestry. (2) Methods: Phenotypic analyses of wild-type (WT) Populus ussuriensis (P. ussuriensis) plantlets grown in vitro were carried out at different time points under both normal and low-nitrogen conditions. Transcriptome analyses of roots were performed at 0, 12, 24, 48, 96, and 336 h under low-nitrogen stress via RNA-seq. A gene regulatory network (GRN) for nitrogen-metabolism-associated DEGs was constructed using a three-gene module framework and a bottom-up Gaussian Graphical Model algorithm. (3) Results: WT P. ussuriensis plantlets grown in vitro exhibited a synergistic response characterized by increased root biomass and suppressed shoot growth. Transcriptome analyses identified 8289 DEGs enriched in nitrogen metabolism, ROS scavenging, root development, and phytohormone signaling. A total of 443 differentially expressed transcription factors (TFs) (mainly MYB, AP2/ERF, and bHLH) were detected. A nitrogen-metabolism-associated GRN comprising 60 nodes was established. (4) Conclusions: Transcriptomic data and nitrogen metabolism pathway predictions from this study establish a systematic foundation for investigating molecular adaptation mechanisms in P. ussuriensis roots under nitrogen stress. Full article

(This article belongs to the Special Issue Adaptation Mechanisms of Forest Trees to Abiotic Stress)

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21 pages, 2311 KB

Open AccessArticle

Impacts of Harvesting Activities on the Structure of the Intertidal Macrobenthic Community on Lvhua Island, China

by Shuhan Wang, Yuqing Wang, Jiaming Ou, Jianing Sun, Kaiyi Wang, Qiao Zou, Jianqu Chen, Li Li, Kai Wang and Shouyu Zhang

Biology 2025, 14(10), 1447; https://doi.org/10.3390/biology14101447 - 20 Oct 2025

Abstract

Human harvesting exerts significant pressure on intertidal ecosystems, yet its impact on community structure remains insufficiently understood. To assess these effects, we investigated macrobenthic communities on Lvhua Island and adjacent islets by integrating ecological surveys, questionnaire data, and Remote Sensing Ecological Indices (RSEI). [...] Read more.

Human harvesting exerts significant pressure on intertidal ecosystems, yet its impact on community structure remains insufficiently understood. To assess these effects, we investigated macrobenthic communities on Lvhua Island and adjacent islets by integrating ecological surveys, questionnaire data, and Remote Sensing Ecological Indices (RSEI). We analyzed species composition, biomass, density, and diversity indices across seven sampling sites. Results showed distinct spatial variation: the eastern Lvhua Island exhibited higher biomass and density than the west, with the remote Manduishan islet highest and the South of West Lvhua near the pier the lowest. Harvesting hotspots were dominated by Chlorostoma rusticum and Cantharus cecillei, while less-disturbed islets were characterized by Chl. rusticum, Thais luteostoma, and Turbinidae. Economically valuable gastropods showed signs of miniaturization under intensive harvesting. Biodiversity indices correlated with RSEI, and ABC curve analysis indicated moderate disturbance overall, with the greatest impact at the Donglvhua Bridge site. These findings indicate that a daily subsistence harvest of 100–150 kg resulted in a 31.82% decline in the Shannon-Wiener index, altering the community structure. RSEI provides a cost-effective complement to field monitoring and should be integrated into management frameworks to support both ecological conservation and community livelihoods. Full article

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22 pages, 4448 KB

Open AccessArticle

Genome-Wide Association Study Revealed Candidate Genes Associated with Litter Size, Weight, and Body Size Traits in Tianmu Polytocous Sheep (Ovis aries)

by Wenna Liu, Shengchao Ma, Qingwei Lu, Sen Tang, Nuramina Mamat, Yaqian Wang, Wei Hong, Xiangrong Hu, Cuiling Wu and Xuefeng Fu

Biology 2025, 14(10), 1446; https://doi.org/10.3390/biology14101446 - 20 Oct 2025

Abstract

Reproductive and growth traits are key economic traits in sheep. This study aims to identify key single nucleotide polymorphisms (SNPs) and candidate genes associated with reproductive and growth traits in Tianmu polytocous sheep through a genome-wide association study (GWAS). The findings are expected [...] Read more.

Reproductive and growth traits are key economic traits in sheep. This study aims to identify key single nucleotide polymorphisms (SNPs) and candidate genes associated with reproductive and growth traits in Tianmu polytocous sheep through a genome-wide association study (GWAS). The findings are expected to provide both a theoretical foundation for molecular breeding in this breed and novel insights into the genetic basis of ovine reproductive and growth performance. This study took 483 adult Tianmu polytocous ewes as the research subjects, collected their lambing records, measured their phenotypic values of growth traits (3 weight and 11 body size traits), and collected their blood samples for whole-genome resequencing to identify SNPs in the Tianmu polytocous sheep genome. The results identified a total of 9,499,019 (3× coverage) and 27,413,216 (30× coverage) high-quality SNPs in the Tianmu polytocous sheep genome. Subsequently, the association analysis between SNPs and reproductive and growth traits was conducted using a mixed linear model. A total of 92, 66, 18, 28, 6, 42, 3, 3, 6, 1, 12, 3, 22, 8, 6, and 3 SNPs were found associated with litter size at first parity, litter size at second parity, litter size at third parity, litter size at fourth parity, birth weight, weaning weight, body height, withers height, body length, head length, head width, cannon bone circumference, forelimb height, chest girth, chest depth, and withers width, respectively. Further, based on SNP annotation, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, candidate genes associated with the reproductive and growth traits were identified. Among these genes, 11 LOC, DEPTOR, GNG12, GRM7, PTH, PTH2R, WWOX, INHA, and NRG3 are candidate genes associated with litter size at first parity or litter size at third parity. These genes are involved in the G protein-coupled receptor signaling pathway, G protein-coupled receptor activity, ovarian tissue development, and hormone secretion. Additionally, TFRC and NTN1 are candidate genes associated with birth weight, while five UGT1A and CASR are candidate genes associated with weaning weight. These candidate genes are primarily involved in lipid metabolism. Finally, the following genes were identified as candidates associated with specific traits: DLG2, TMEM126A, and TMEM126B with body height; DSCAM and SCN8A with body length; BARX1 with cannon bone circumference; four LOC genes with forelimb height; EPHA4 with chest depth; and MRS2 with withers width. Full article

(This article belongs to the Section Genetics and Genomics)

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13 pages, 1887 KB

Open AccessArticle

Comparative Photosynthetic Induction Reveals Stomatal Limitation and Reduced Efficiency in Digitalis purpurea Versus Cucumis sativus

by Yunmin Wei, Xiaohong Xiang, Wei Jin, Haifeng Xiong and Lihong Tan

Biology 2025, 14(10), 1445; https://doi.org/10.3390/biology14101445 - 20 Oct 2025

Abstract

Digitalis purpurea, valued for its cardiotonic glycosides, remains an important medicinal species. Optimizing cultivation to enhance photosynthetic efficiency is critical for improving both biomass accumulation and metabolite yield. In this study, we compared the photosynthetic induction responses of D. purpurea from low [...] Read more.

Digitalis purpurea, valued for its cardiotonic glycosides, remains an important medicinal species. Optimizing cultivation to enhance photosynthetic efficiency is critical for improving both biomass accumulation and metabolite yield. In this study, we compared the photosynthetic induction responses of D. purpurea from low light to high light with those of Cucumis sativus, a high-performance reference species, to identify key physiological constraints. Compared with Cucumis, D. purpurea exhibited lower net photosynthetic rate (A) and maximum carboxylation rates (V_cmax) under both induction and steady-state conditions (A_f and V_cmax_f). The time required to reach steady-state photosynthesis was substantially longer in D. purpurea, resulting in significantly lower cumulative carbon gain (20.6 vs. 28.8 mmol m⁻²) and a higher carbon loss ratio (10.7% vs. 6.8%). In addition, the averaged WUE_i during induction in D. purpurea was 20.4% lower than in Cucumis; this reduction was exacerbated by continued stomatal opening after photosynthesis stabilized, leading to further inefficiency in water use. Limitation analysis further revealed contrasting dominant constraints: biochemical limitation accounted for 88.8% of total limitation in Cucumis, whereas stomatal limitation predominated in D. purpurea (64.3%). Together, these results highlight stomatal regulation as the primary bottleneck during photosynthetic induction in D. purpurea, leading to transient carbon losses and reduced water-use efficiency, providing a physiological basis for targeted cultivation strategies to improve both productivity and cardiotonic glycoside yield. Full article

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