Biology

19 pages, 6825 KB

Open AccessArticle

Dynamic Regulation of Gonadal Transposons and Pseudogenes via PIWI/piRNA Pathway in Gynogenetic Japanese Flounder (Paralichthys olivaceus)

by Zeyu Liu, Weigang Li, Fengchi Wang, Wei Lu, Fan Yang, Qingke Zhang and Jie Cheng

Biology 2025, 14(10), 1464; https://doi.org/10.3390/biology14101464 - 21 Oct 2025

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Abstract

PIWI-interacting RNAs (piRNAs) are small non-coding RNAs that interact with PIWI proteins and play essential roles in genome stability, gonadal development, and gametogenesis in animals. The Japanese flounder (Paralichthys olivaceus) is an important marine culture teleost in North Asia, showing pronounced [...] Read more.

PIWI-interacting RNAs (piRNAs) are small non-coding RNAs that interact with PIWI proteins and play essential roles in genome stability, gonadal development, and gametogenesis in animals. The Japanese flounder (Paralichthys olivaceus) is an important marine culture teleost in North Asia, showing pronounced sexual size dimorphism, where gynogenetic induction of all-female cohorts can markedly enhance production. However, the PIWI/piRNA pathway in gynogenetic diploid P. olivaceus, which often exhibit gonadal dysgenesis, poor gamete quality, and low fertilization rates, remains poorly understood. In this study, RNA-seq and small RNA-seq data from 11 tissues and 6 developmental stages of common P. olivaceus, as well as the gonads of gynogenetic P. olivaceus, were analyzed to characterize the PIWI/piRNA pathway and its roles in transposon and gene regulation within the germline. The results showed that PIWI/piRNA genes were predominantly expressed in gonads and early embryogenesis in common P. olivaceus, with the highest expression in testis. Clustered piRNAs were identified in the testis and early embryos of common P. olivaceus, which targeted multiple transposon and gene families. Intriguingly, gynogenetic P. olivaceus gonads harbored abundant clustered piRNAs not only in the testes but also in the ovaries, both targeting similar transposon families as that in common P. olivaceus. Notably, the DNA transposon Tc1/Mariner family and pim genes were the most heavily targeted by piRNAs in gynogenetic P. olivaceus, with testis-biased expression. Expanded pim genes were identified in P. olivaceus, overlapping with piRNA clusters, and the in vitro test in P. olivaceus testes revealed that the expanded pim genes may be pseudogenes as a piRNA cluster reference to generate piRNAs regulating the conventional pim members. These unique features of the PIWI/piRNA pathway in gynogenetic diploid P. olivaceus may underline their impaired reproductive ability, and have important theoretical and practical implications for teleost gynogenetic breeding. Full article

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20 pages, 10309 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

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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

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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

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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

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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

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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

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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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18 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

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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

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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

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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

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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

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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

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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

Viewed by 431

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

Viewed by 297

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

Viewed by 427

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

Viewed by 238

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

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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

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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

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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

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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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15 pages, 1593 KB

Open AccessArticle

Influence of Sampling Effort and Taxonomic Resolution on Benthic Macroinvertebrate Taxa Richness and Bioassessment in a Non-Wadable Hard-Bottom River (China)

by Jiaxuan Liu, Hongjia Shan, Chengxing Xia and Sen Ding

Biology 2025, 14(10), 1444; https://doi.org/10.3390/biology14101444 - 20 Oct 2025

Viewed by 281

Abstract

Benthic macroinvertebrates are widely used for river ecosystem health monitoring, yet challenges remain in non-wadable rivers, particularly regarding sampling effort. We evaluated hand-net sampling efficiency at three sites along the Danjiang River (a Yangtze River tributary) by analyzing taxa richness across taxonomic levels [...] Read more.

Benthic macroinvertebrates are widely used for river ecosystem health monitoring, yet challenges remain in non-wadable rivers, particularly regarding sampling effort. We evaluated hand-net sampling efficiency at three sites along the Danjiang River (a Yangtze River tributary) by analyzing taxa richness across taxonomic levels under varying replicate numbers. In total, 61 taxa (41 families) of benthic macroinvertebrates were identified. Non-metric multidimensional scaling analysis indicated no significant spatiotemporal variation in community composition. However, sampling effort increased, and the benthic macroinvertebrate taxa richness at both genus/species and family levels also increased. At eight sample replicates, the taxa accumulation curve at the genus/species level did not show an asymptote, with the observed richness reaching 67–80% of the predicted values calculated by Jackknife 1. In contrast, the family-level curve exhibited a clear asymptotic trend, with the observed richness reaching 82–100% of the predicted values. As sampling effort increased, bias decreased and accuracy improved, particularly for family-level taxa. Additionally, the BMWP scores also increased with the sampling effort. When the replicate number was no less than six, the BMWP reached stable assessment grades for all cases. From the perspective of bioassessment in non-wadable rivers, the hand net is suitable for collecting benthic macroinvertebrates. However, there is a risk of underestimating taxa richness due to insufficient sampling effort. Using family-level taxa can partially mitigate the impacts caused by insufficient sampling efforts to a certain extent, but further validation is needed for other non-wadable rivers (e.g., those with soft substrates). In conclusion, our research results indicate that six replicate hand-net samplings in non-wadable hard-bottom rivers can be regarded as a cost-effective and reliable sampling method for benthic macroinvertebrate BMWP assessment. This strategy provides a relatively practical reference for the monitoring of benthic macroinvertebrate in the same type of rivers in China. Full article

(This article belongs to the Special Issue Evolution, Genetics, and Conservation of Wildlife Respond to Environmental Changes)

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19 pages, 4601 KB

Open AccessArticle

Carvacrol as a Therapeutic Candidate in Breast Cancer: Insights into Subtype-Specific Cellular Modulation

by Asmaa Abuaisha, Emir Nekay, Ozgur Yilmaz, Baris Yildiz, Tarik Mecit, Cuneyd Yavas, Berrin Papila, Halil Ibrahim Arslan, Aybuke Hilal Gumus, Esra Nazligul, Sadiye Akbas and Selman Emiroglu

Biology 2025, 14(10), 1443; https://doi.org/10.3390/biology14101443 - 19 Oct 2025

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Abstract

Background: Carvacrol, a natural phenolic monoterpenoid, has been suggested to exert anticancer effects; however, its underlying mechanisms in breast cancer (BC) remain incompletely defined. Methods: MCF-7 (HR⁺) and MDA-MB-231 (TNBC) BC cell lines were treated with carvacrol at various concentrations. Cell [...] Read more.

Background: Carvacrol, a natural phenolic monoterpenoid, has been suggested to exert anticancer effects; however, its underlying mechanisms in breast cancer (BC) remain incompletely defined. Methods: MCF-7 (HR⁺) and MDA-MB-231 (TNBC) BC cell lines were treated with carvacrol at various concentrations. Cell viability was assessed using CVDK8 kit, while migration was evaluated by wound healing assays. Apoptosis was determined using Annexin V-FITC Kit, and ROS levels were measured by DCFH-DA assay. Flow cytometry was used for CD44/CD133 cancer stem cells markers analysis, and genes expression were quantified using qPCR. Results: Carvacrol significantly inhibited cell proliferation, and migration in both HR⁺ and TNBC cells. Additionally, carvacrol increased the BAX/BCL2 ratio, induced apoptosis, and decreased ROS levels, with greater antioxidant activity observed in MCF-7 cells. Moreover, carvacrol suppressed CD44⁺ levels, whereas CD133⁺ levels were not affected. Gene expression analysis revealed subtype-specific effects where ABCG2 was upregulated in MCF-7 cells but downregulated in MDA-MB-231 cells, while NF_KB1 expression increased in both lines. Conclusions: Carvacrol exerts multitargeted anticancer effects in BC by promoting apoptosis, reducing ROS, and suppressing CD44⁺, with distinct subtype-specific responses. These findings highlight carvacrol as a promising natural therapeutic compound for BC treatment; however, further in vivo studies and clinical investigations are required to validate its translational potential. Full article

(This article belongs to the Special Issue Advances in Biological Breast Cancer Research (2nd Edition))

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21 pages, 2846 KB

Open AccessArticle

Identification and Characterization of Olfactory Genes in the Cochineal Scale Insect, Porphyrophora sophorae (Hemiptera: Margarodidae)

by Yan Wang, Xiao-Li Liu, Youssef Dewer, Cai-Ge Jiang, Shuang Song and Hong-Hao Chen

Biology 2025, 14(10), 1442; https://doi.org/10.3390/biology14101442 - 18 Oct 2025

Viewed by 414

Abstract

Chemosensory systems are essential in insect behavior, with several key genes associated with these systems emerging as potential targets for pest control. Porphyrophora sophorae (Archangelskaya, 1935), a destructive pest of Chinese licorice (Glycyrrhiza uralensis, Fabaceae), poses a significant threat to the [...] Read more.

Chemosensory systems are essential in insect behavior, with several key genes associated with these systems emerging as potential targets for pest control. Porphyrophora sophorae (Archangelskaya, 1935), a destructive pest of Chinese licorice (Glycyrrhiza uralensis, Fabaceae), poses a significant threat to the healthy cultivation of licorice. However, the molecular mechanisms underlying its host detection and olfactory recognition remain poorly understood. In this study, we present the first identification of odorant-binding proteins (OBPs) and olfactory receptors (ORs) from the transcriptome of P. sophorae. The identified OBPs contain six conserved cysteine residues, while predictive analysis suggests that PsopOrco may contain six transmembrane domains. Phylogenetic analysis demonstrated that the majority of these olfactory proteins are closely related to OBPs and ORs found in other scale insects. Using RT-qPCR, we assessed the anatomical structures expression of these genes and found that PsopOBP3, PsopOBP6, and PsopOrco were predominantly expressed in the antennae. Additionally, expression levels of OBPs and ORs varied across different tissues, suggesting anatomical structure regulation. These findings expand the gene repertoire of P. sophorae and provide valuable resources for further functional analysis of these key olfactory genes. Full article

(This article belongs to the Special Issue Research on Morphology and Sensorimotor Systems of Insect Antennae)

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16 pages, 2350 KB

Open AccessArticle

Effects of Biochar and PGPR Application on the Physicochemical Properties and Humus Components of Soil Used for Planting Fruit Mulberry Seedlings Under Salt Stress

by Dawei Jing, Fangchun Liu, Binghua Liu, Lin Peng, Mingjie Sun, Hailin Ma and Zhenyu Du

Biology 2025, 14(10), 1441; https://doi.org/10.3390/biology14101441 - 18 Oct 2025

Viewed by 308

Abstract

Biochar can act as a carrier and a soil carbon source for rapid colonization by plant growth-promoting rhizobacteria (PGPR). However, the effects of a combined application of biochar and PGPR on soil physicochemical properties, humus components, and their stability in the rhizosphere around [...] Read more.

Biochar can act as a carrier and a soil carbon source for rapid colonization by plant growth-promoting rhizobacteria (PGPR). However, the effects of a combined application of biochar and PGPR on soil physicochemical properties, humus components, and their stability in the rhizosphere around fruit mulberry seedlings remain unclear. A pot experiment using 1-year-old fruit mulberry seedlings with five treatments (control (CK), salt stress (SS), salt stress + Bacillus fexus (SS+P), salt stress + biochar (SS+B), and salt stress + B. fexus + biochar (SS+P+B)) was conducted to analyze the variations in soil physicochemical properties and humic acid (HA), fulvic acid (FA), and humin (HM) contents in the soil when planting fruit mulberry seedlings. The results indicated that the SS treatment significantly reduced total soil porosity, non-capillary porosity, water stable macro-aggregates content, available potassium content, and pH value compared to CK, but increased the soil bulk density, capillary porosity, and available phosphorus content. The SS+P+B treatment significantly increased soil total porosity, non-capillary porosity, pH value, electrical conductivity, the water stable macro-aggregates, organic matter, HA and HM contents, the HA/FA and HA/HE (humus-extractable) ratios, and the activities of catalase and urease. It significantly increased the water stable macro-aggregates and the HA/HE ratio by 27.83% and 25.00%, respectively. However, it significantly decreased soil bulk density and capillary porosity by 9.93% and 20.64%, respectively, compared to the SS treatment. The results suggest that the simultaneous addition of biochar and B. fexus under salt-stress conditions improves the soil physicochemical properties and increases the humus components content and stability, which is of great significance for improving the soil quality of saline–alkali land and enhancing the productivity of fruit mulberry. Full article

(This article belongs to the Topic Evaluating the Functional Value of Agroecosystems under Different Management Scenarios)

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20 pages, 9405 KB

Open AccessArticle

PIWIs Regulate Spermatogonia Self-Renewal and Differentiation by Wnt/β-Catenin Signaling Pathway in Eriocheir sinensis

by Bang-Hong Wei, Zhan Zhao, Hong-Yu Qi, Zhen-Fang Li, Wan-Xi Yang and Shuang-Li Hao

Biology 2025, 14(10), 1440; https://doi.org/10.3390/biology14101440 - 18 Oct 2025

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Abstract

The roles of PIWI in mammalian spermatogenesis have been well-studied but are largely unknown in invertebrates such as the Chinese mitten crab (Eriocheir sinensis), which produces non-flagellar sperm. Here, we demonstrate that knockdown of PIWIs significantly promotes the proliferation of spermatogonia [...] Read more.

The roles of PIWI in mammalian spermatogenesis have been well-studied but are largely unknown in invertebrates such as the Chinese mitten crab (Eriocheir sinensis), which produces non-flagellar sperm. Here, we demonstrate that knockdown of PIWIs significantly promotes the proliferation of spermatogonia and the transformation into spermatocytes. Expression of PIWIs in HEK 293T significantly inhibits cell proliferation through the Wnt-signaling pathway. PIWIs suppress transcriptional activity of the Wnt pathway to down-regulate Cyclin D and Cyclin E by inhibiting β-catenin and the phosphorylation of β-catenin at Ser552. The intracellular structure of the adherens junction is destroyed by PIWIs due to downregulated α-catenin, β-catenin, and ZO1. Overall, our results suggest that PIWIs regulate spermatogonia self-renewal and differentiation through inhibiting the Wnt-signaling pathway and stabilize the structure of the adherens junction by regulating the expression and location of α-catenin, β-catenin, and ZO1 in E. sinensis, which are different from the functions in mammals. Our findings revealed novel functions and molecular mechanisms of PIWIs in regulating spermatogonia self-renewal and differentiation during the Crustacea spermatogenesis. Full article

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

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29 pages, 2816 KB

Open AccessReview

Human Blastoid: A Next-Generation Model for Reproductive Medicine?

by Anfisa S. Ryabchenko, Vepa K. Abdyev, Ekaterina A. Vorotelyak and Andrey V. Vasiliev

Biology 2025, 14(10), 1439; https://doi.org/10.3390/biology14101439 - 18 Oct 2025

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Abstract

Human early embryogenesis remains unexplored due to limited access to human embryos for research purposes. Meanwhile, the number of natural early pregnancy terminations remains significant, and solving the problem requires a deep understanding of the developmental mechanisms of this period. Although assisted reproductive [...] Read more.

Human early embryogenesis remains unexplored due to limited access to human embryos for research purposes. Meanwhile, the number of natural early pregnancy terminations remains significant, and solving the problem requires a deep understanding of the developmental mechanisms of this period. Although assisted reproductive technologies (ART) utilize up-to-date approaches in culturing human embryos in vitro, characterization of the embryos is still based on visual evaluation and subjective assessment. In addition, embryonic development in animal models, such as rodents and cattle, correlates poorly with human embryonic development. Synthetic embryology presents a promising new approach for studying human embryos involving the creation of embryos without the use of haploid germ cells. Instead, diploid pluripotent stem cells (PSCs) in a given state of pluripotency, which is maintained under conditions of induction and/or inhibition of certain signaling pathways, are used. Synthetic embryo systems (SES) may become a successful alternative model for studying fundamental processes of human early preimplantation embryogenesis, exploring new methods of objective embryo qualification, and personalized approaches in ART. However, the question of whether SES models can be considered as full-fledged mimics of the embryo remains open. This review examines human blastocyst-like structures known as blastoids. It discusses their use as models, as well as the parameters that need to be modified to more accurately simulate the human blastocyst. Full article

(This article belongs to the Special Issue Feature Papers on Developmental and Reproductive Biology)

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17 pages, 1734 KB

Open AccessReview

Why Humans Prefer Phylogenetically Closer Species: An Evolutionary, Neurocognitive, and Cultural Synthesis

by Antonio Ragusa

Biology 2025, 14(10), 1438; https://doi.org/10.3390/biology14101438 - 18 Oct 2025

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Abstract

Humans form deep attachments to some nonhuman animals, yet these attachments are unequally distributed across the tree of life. Drawing on evolutionary biology, comparative cognition, neuroscience, and cultural anthropology, this narrative review explains why empathy and affective preference are typically stronger for phylogenetically [...] Read more.

Humans form deep attachments to some nonhuman animals, yet these attachments are unequally distributed across the tree of life. Drawing on evolutionary biology, comparative cognition, neuroscience, and cultural anthropology, this narrative review explains why empathy and affective preference are typically stronger for phylogenetically closer species—especially mammals—than for distant taxa such as reptiles, fish, or arthropods. We synthesize evidence that signal recognizability (faces, gaze, vocal formants, biological motion) and predictive social cognition facilitate mind attribution to mammals; conserved neuroendocrine systems (e.g., oxytocin) further amplify affiliative exchange, particularly in domesticated dyads (e.g., dog–human). Ontogenetic learning and media narratives magnify these effects, while fear modules and disgust shape responses to some distant taxa. Notwithstanding this average gradient, boundary cases—cephalopods, cetaceans, parrots—show that perceived agency, sociality, and communicative transparency can overcome phylogenetic distance. We discuss measurement (behavioral, psychophysiological, neuroimaging), computational accounts in predictive-processing terms, and implications for animal welfare and conservation. Pragmatically, calibrated anthropomorphism, hands-on education, and messaging that highlights agency, parental care, or ecological function reliably broaden concern for under-represented taxa. Recognizing both evolved priors and cultural plasticity enables more equitable and effective science communication and policy. Expanding empathy beyond its ancestral anchors is not only an ethical imperative but a One Health necessity: safeguarding all species means safeguarding the integrity of our shared planetary life. Full article

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13 pages, 2071 KB

Open AccessArticle

OmniCellX: A Versatile and Comprehensive Browser-Based Tool for Single-Cell RNA Sequencing Analysis

by Renwen Long, Tina Suoangbaji and Daniel Wai-Hung Ho

Biology 2025, 14(10), 1437; https://doi.org/10.3390/biology14101437 - 17 Oct 2025

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Abstract

Single-cell RNA sequencing (scRNA-seq) has revolutionized genomic investigations by enabling the exploration of gene expression heterogeneity at the individual cell level. However, the complexity of scRNA-seq data analysis remains a challenge for many researchers. Here, we present OmniCellX, a browser-based tool designed to [...] Read more.

Single-cell RNA sequencing (scRNA-seq) has revolutionized genomic investigations by enabling the exploration of gene expression heterogeneity at the individual cell level. However, the complexity of scRNA-seq data analysis remains a challenge for many researchers. Here, we present OmniCellX, a browser-based tool designed to simplify and streamline scRNA-seq data analysis while addressing key challenges in accessibility, scalability, and usability. OmniCellX features a Docker-based installation, minimizing technical barriers and ensuring rapid deployment on local machines or clusters. Its dual-mode operation (analysis and visualization) integrates a comprehensive suite of analytical tools for tasks such as preprocessing, dimensionality reduction, clustering, differential expression, functional enrichment, cell–cell communication, and trajectory inference on raw data while enabling alternative interactive and publication-quality visualizations on pre-analyzed data. Supporting multiple input formats and leveraging the memory-efficient data structure for scalability, OmniCellX can efficiently handle datasets spanning millions of cells. The platform emphasizes user flexibility, offering adjustable parameters for real-time fine-tuning, alongside extensive documentation to guide users at even beginner levels. OmniCellX combines an intuitive interface with robust analytical power to perform single-cell data analysis and empower researchers to uncover biological insights with ease. Its scalability and versatility make it a valuable tool for advancing discoveries in cellular heterogeneity and biomedical research. Full article

(This article belongs to the Special Issue Application of Bioinformatics to Unravel the Molecular Mechanisms of Cancer Biology)

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15 pages, 2214 KB

Open AccessArticle

Isolation and Identification of Antifungal Polyketones from Bacillus velezensis DJ1 and Their Biocontrol Potential Against Corn Stalk Rot

by Meng Sun, Wanjia Du, Jialing Zhang, Yan Xu, Zixuan Wang, Lu Zhou, Gengxuan Yan and Shumei Zhang

Biology 2025, 14(10), 1436; https://doi.org/10.3390/biology14101436 - 17 Oct 2025

Viewed by 262

Abstract

Corn stalk rot, caused by Fusarium graminearum, severely threatens corn production, while chemical fungicides lead to resistance and environmental risks. Thus, exploring environmentally friendly biocontrol agents is crucial. Though Bacillus polyketones have antifungal activity, their active components, corn stalk rot biocontrol potential [...] Read more.

Corn stalk rot, caused by Fusarium graminearum, severely threatens corn production, while chemical fungicides lead to resistance and environmental risks. Thus, exploring environmentally friendly biocontrol agents is crucial. Though Bacillus polyketones have antifungal activity, their active components, corn stalk rot biocontrol potential and rhizosphere impacts remain unclear. This study isolated polyketones from Bacillus velezensis DJ1, assessed their antifungal activity and mechanism against F. graminearum, verified greenhouse efficacy, analyzed rhizosphere microbiota, and identified active components via HPLC-HDMS Q-TOF. The results showed that DJ1 polyketones showed dose-dependent inhibition by disrupting F. graminearum’s mycelium and membrane, with 44.33% greenhouse control efficacy. They did not disturb rhizosphere balance, only increasing Bacteroidota and DYGX01, and the active components were difficidin and bacillaene. These findings confirm DJ1 polyketones as promising eco-friendly biocontrol agents, providing a new strategy for sustainable corn stalk rot management. Full article

(This article belongs to the Topic Research on Natural Bioactive Product-Based Pesticidal Agents—2nd Edition)

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13 pages, 1149 KB

Open AccessArticle

Evidence of Folliculogenesis and the Potential of Oocyte Recovery from Koalas with Different Levels of Reproductive Pathology

by Stephen D. Johnston, Jackson Boyd, Patricio D. Palacios, Julien Grosmaire, Alexander Lee, Lyndal Hulse, Leslie Vega, Michael Pyne, Andres Gambini and Chiara Palmieri

Biology 2025, 14(10), 1435; https://doi.org/10.3390/biology14101435 - 17 Oct 2025

Viewed by 316

Abstract

Each year, hundreds of female koalas are presented to koala hospitals suffering from a range of morbidities, many of which require euthanasia for animal welfare reasons. These koalas represent a possible resource for genetic recovery by means of oocyte retrieval for genome banking [...] Read more.

Each year, hundreds of female koalas are presented to koala hospitals suffering from a range of morbidities, many of which require euthanasia for animal welfare reasons. These koalas represent a possible resource for genetic recovery by means of oocyte retrieval for genome banking or use in assisted reproductive technology. To examine the feasibility of koala oocyte recovery, this study conducted a preliminary survey of follicular activity and disease presence in fixed ovarian tissues from koala cadavers in South East Queensland. Ovarian activity and pathology were assessed by gross examination and histology. Bursal pathology was categorized into koalas with no, small (<10 mm diameter), moderate (10–20 mm diameter), or large (>20 mm diameter) sized bursae, whereas uterine pathology was diagnosed by an experienced reproductive pathologist. Antral follicles were observed in 94.4% of ovaries recovered from koalas with no bursal or uterine pathology (n = 18/44), 95.2% of the ovaries of koalas with bursal but no uterine pathology (n = 11/44), 100% of the ovaries of koalas showing only uterine pathology (n = 4/4) and 89.5% of ovaries from koalas with both bursal and uterine pathology (n = 11/44). Of the fixed ovarian tissue suitable for PCR Chlamydia detection (35/44), none were positive. As proof of concept, oocytes were also collected and evaluated from six koala cadavers within 2 h post-mortem. Although further studies are required to determine the quality and viability of the retrieved koala oocytes, our preliminary survey provides strong evidence that ovarian activity mostly continues unabated, irrespective of reproductive pathology, and that oocytes can be recovered successfully. Full article

(This article belongs to the Special Issue Feature Papers on Developmental and Reproductive Biology)

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Biology, Volume 14, Issue 10 (October 2025) – 155 articles

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