Biology

27 pages, 5349 KB

Open AccessArticle

Programmed Genome Elimination Is Evolutionarily Conserved Across Pelophylax Hybrids—As Evidenced by P. grafi Hybridogenetic Reproduction

by Anna Dudzik, Beata Rozenblut-Kościsty, Dmitrij Dedukh, Pierre-André Crochet, Lukáš Choleva, Monika Przewłocka-Kosmala, Zuzanna Stryczak, Maria Ogielska and Magdalena Chmielewska

Biology 2025, 14(11), 1526; https://doi.org/10.3390/biology14111526 (registering DOI) - 30 Oct 2025

Abstract

Gametogenesis is a fundamental biological process that ensures both genetic recombination and the continuity of successive generations. Interspecific hybrids can reproduce through modified mechanisms, such as hybridogenesis, by transmitting clonal, unrecombined genomes of only one of the parental species via their gametes. Pelophylax [...] Read more.

Gametogenesis is a fundamental biological process that ensures both genetic recombination and the continuity of successive generations. Interspecific hybrids can reproduce through modified mechanisms, such as hybridogenesis, by transmitting clonal, unrecombined genomes of only one of the parental species via their gametes. Pelophylax grafi (RP) is a natural hybrid frog composed of mixed genomes (subgenomes) of two related species, Pelophylax perezi (P) and Pelophylax ridibundus (R), and coexists in populations with P. perezi. This study tested the involvement of programmed genome elimination in gamete production of P. grafi, providing new insight into reproductive mechanisms of hybrid vertebrates. Using comparative genomic hybridization (CGH) and fluorescent in situ hybridization (FISH), we examined the genomic constitution of germline cells in tadpoles and adult male and female P. grafi. Controlled crosses between P. perezi and P. grafi produced F1 hybrid tadpoles, whose genotypes confirmed that P. grafi parents transmitted the R subgenome through their gametes. In the early germline cells (gonocytes) of these tadpoles, P chromosomes were selectively eliminated via micronuclei formation during interphase. The occasional presence of the R genome and mixed R/P genome micronuclei suggests variability and imperfect fidelity in the elimination process. In adult hybrids, the majority of diplotene oocytes, spermatogonial stem cells (SSC) and spermatocytes carried R subgenomes. We demonstrated that programmed genome rearrangement in Pelophylax hybrids is an evolutionarily conserved mechanism underlying this unique reproductive strategy. Full article

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

► Show Figures

Graphical abstract

25 pages, 5052 KB

Open AccessArticle

Comprehensive Analysis of the TaABCB Gene Family and the Role of TaABCB7 in the Phosphate Starvation Response in Wheat

by Guoqing Cui, Haigang Wang, Yanzhen Wang, Xia Liu, Menglin Lei, Huibin Qin, Rui Huang, Juan Lu, Zhixin Mu and Yanming Bai

Biology 2025, 14(11), 1525; https://doi.org/10.3390/biology14111525 (registering DOI) - 30 Oct 2025

Abstract

The ABCB subfamily, a subset transporter of the ATP-binding cassette (ABC) superfamily, is vital for various plant life processes, especially in the transport of polar auxin and brassinosteroids. Although ABCB transporters have been characterized in diverse plant species, their specific functions in wheat [...] Read more.

The ABCB subfamily, a subset transporter of the ATP-binding cassette (ABC) superfamily, is vital for various plant life processes, especially in the transport of polar auxin and brassinosteroids. Although ABCB transporters have been characterized in diverse plant species, their specific functions in wheat remain largely unexplored. In this study, we identified 99 TaABCB members in wheat and categorized them into four groups based on their conserved domains and phylogenetic relationships. These members were found to be unevenly distributed across all 21 wheat chromosomes. We conducted a comprehensive genome-wide analysis encompassing gene structure, protein motifs, gene duplication events, collinearity, and cis-acting elements. Transcriptome analysis revealed that different TaABCB members displayed distinct expression patterns under phosphate starvation stress. Notably, we discovered that TaABCB7 might play a role in regulating wheat’s phosphate starvation. Crucially, we pinpointed an elite haplotype, H001, of the candidate gene TaABCB7, which has been progressively selected and employed in wheat breeding improvement programs. Overall, this study enhances our comprehensive understanding of TaABCB members and offers a potential gene resource for molecular marker-assisted selection breeding in wheat. Full article

(This article belongs to the Section Plant Science)

► Show Figures

Figure 1

24 pages, 1408 KB

Open AccessReview

What Factors Shape the Flyability in Bats?—The Perspective from Bat’s Wing Development

by Minjie Zhang, Hui Wang, Zhongzheng Liu, Mingyue Bao, Xintong Li, Tianhui Wang, Ruixue Wang and Jiang Feng

Biology 2025, 14(11), 1524; https://doi.org/10.3390/biology14111524 (registering DOI) - 30 Oct 2025

Abstract

Among mammals, bats are the only species capable of powered flight, which is made possible by their highly evolved wings. The wings of bats are highly specialized, composed of skin membranes that extend from their forelimbs, hindlimbs, and elongated finger bones, forming the [...] Read more.

Among mammals, bats are the only species capable of powered flight, which is made possible by their highly evolved wings. The wings of bats are highly specialized, composed of skin membranes that extend from their forelimbs, hindlimbs, and elongated finger bones, forming the structural foundation for flight. Previous research has extensively examined bat wings from various perspectives, including tissue embryology, structural morphology, and aerodynamics. These studies have focused on the origins of bat wings, their embryonic development, as well as the muscles and skeletal structures involved in flight, laying a crucial theoretical foundation for understanding the development and evolution of bat flight. In addition to structural aspects, physiological processes like the high metabolic rate, energy supply, and oxidative stress responses required for sustained bat flight have also been investigated. This review aims to explore various factors influencing the development of bat flight capabilities, with particular attention to the relationship between wing morphology and flight behavior, highlighting the importance of investigating bat flight capabilities within the context of echolocation calls development. From the perspective of bat wings, this review proposes an integrated analysis of related factors affecting the unique and intricate characteristics of bat flight capabilities, offering new perspectives and approaches for future studies in developmental and evolutionary biology. Full article

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

► Show Figures

Figure 1

11 pages, 229 KB

Open AccessArticle

HPV, EBV, CMV, and HSV in Head and Neck Cancer: Molecular Detection, Seroprevalence, and Clinical Correlations

by Mustafa Onel, Hayriye Kirkoyun Uysal, Murat Ulusan, Utkucan Ayeser, Kutay Sarsar, Yasemin Ayse Ucar, Ozlem Yoldas, Arat Hulikyan, Fulya Gurkan Kiraz, Ali Mert Uysal, Mehmet Celik, Mehmet Demirci and Ali Agacfidan

Biology 2025, 14(11), 1523; https://doi.org/10.3390/biology14111523 (registering DOI) - 30 Oct 2025

Abstract

(1) Background: This study investigated the presence of human papillomavirus (HPV), HPV genotypes, Epstein–Barr virus (EBV), cytomegalovirus (CMV) and herpes simplex virus (HSV) in patients with Head and Neck Cancer (HNC) at both molecular and serological levels. (2) Methods Fifty patients with histopathologically [...] Read more.

(1) Background: This study investigated the presence of human papillomavirus (HPV), HPV genotypes, Epstein–Barr virus (EBV), cytomegalovirus (CMV) and herpes simplex virus (HSV) in patients with Head and Neck Cancer (HNC) at both molecular and serological levels. (2) Methods Fifty patients with histopathologically confirmed HNC who were admitted to the Department of Otorhinolaryngology, Istanbul Faculty of Medicine. Viral DNA was detected using quantitative real-time PCR, and serological IgM and IgG antibodies were analyzed using the CMIA method; (3) Results: In blood samples, CMV and HSV DNA were not detected, whereas EBV DNA was identified in 2% and HPV DNA in 4% of patients. In tumor tissues, CMV DNA was detected in 8%, EBV DNA in 10%, and HPV DNA in 6%; HSV DNA is 6%. HPV genotypes 18, 45, and 69 were found in tissue samples. Serologically, IgG positivity for CMV, EBV, and HSV-1 exceeded 90%, whereas IgM positivity was low and not statistically significant; (4) Conclusions: HPV, EBV, and CMV DNA were detected at low frequencies in patients with HNC, while HSV DNA was absent. These findings underline the need for larger multi-center studies and support the consideration of routine viral screening, particularly for HPV, in specific tumor subtypes. Full article

26 pages, 1474 KB

Open AccessReview

Deciphering the Contribution of TATA Box and 5′UTR to Defense Signaling in Rice Under Blast Infection

by Xiaoru Fan, Misbah Naz, Yong Zhang and Muhammad Rahil Afzal

Biology 2025, 14(11), 1522; https://doi.org/10.3390/biology14111522 (registering DOI) - 30 Oct 2025

Abstract

The TATA box and 5′untranslated region (5′UTR) are critical regulatory elements that influence gene expression in plant defense responses. In rice (Oryza sativa), these elements modulate transcriptional and translational regulation during infection by the blast pathogen Magnaporthe oryzae. This study [...] Read more.

The TATA box and 5′untranslated region (5′UTR) are critical regulatory elements that influence gene expression in plant defense responses. In rice (Oryza sativa), these elements modulate transcriptional and translational regulation during infection by the blast pathogen Magnaporthe oryzae. This study investigates the functional significance of the TATA box and 5′UTR in rice defense signaling by analyzing promoter and 5′UTR variations in key defense-related genes. Through comparative genomics, expression profiling, and mutagenesis assays, we show that 60% of defense genes with specific TATA box motifs exhibit enhanced transcription, while 5′UTR variants increase translational efficiency by up to 2-fold, contributing to blast resistance. These regulatory mechanisms provide a framework for targeted breeding and biotechnological interventions to enhance disease resistance in rice. Our findings highlight the importance of these elements in fine-tuning rice immune responses and suggest potential targets for improving disease resistance in rice cultivars. Full article

(This article belongs to the Special Issue Molecular Mechanisms of Plant Stress Adaptation)

► Show Figures

Figure 1

15 pages, 1005 KB

Open AccessArticle

Spatial and Temporal Variations in the Trophic Structure of Fish Assemblages in the Eastern Region of the Yellow Sea Determined by C- and N-Stable Isotope Ratios

by Dong-Young Lee, Jae Mook Jeong, Dongyoung Kim, Donghoon Shin, Chung Il Lee, Jeong-Hoon Lee, Hawsun Sohn and Hyun Je Park

Biology 2025, 14(11), 1521; https://doi.org/10.3390/biology14111521 (registering DOI) - 30 Oct 2025

Abstract

This study aimed to determine how spatial and seasonal variations influence the trophic structure of fish assemblages in the eastern Yellow Sea during 2023. Carbon and nitrogen stable isotope analyses revealed significant but spatially variable differences in δ¹³C and δ¹⁵ [...] Read more.

This study aimed to determine how spatial and seasonal variations influence the trophic structure of fish assemblages in the eastern Yellow Sea during 2023. Carbon and nitrogen stable isotope analyses revealed significant but spatially variable differences in δ¹³C and δ¹⁵N values among seasons and sites, without consistent overarching trends. These results suggest that phytoplankton-derived organic matter predominantly supports the regional food web, with isotopic niche shifts reflecting local differences in prey availability and hydrographic conditions. The findings contribute to the development of adaptive, ecosystem-based fishery management strategies amid increasing anthropogenic and climatic pressures. Full article

(This article belongs to the Section Marine Biology)

► Show Figures

Figure 1

18 pages, 2944 KB

Open AccessArticle

Epicatechin-Loaded Nanocapsules: Development, Physicochemical Characterization, and NLRP3 Inflammasome-Targeting Anti-Inflammatory Activity

by Carolina Bordin Davidson, Éricles Forrati Machado, Amanda Kolinski Machado, Diulie Valente de Souza, Lauren Pappis, Giovana Kolinski Cossettin Bonazza, Djenifer Letícia Ulrich Bick, Taíse Regina Schuster Montagner, André Gündel, Ivana Zanella da Silva, Aline Ferreira Ourique and Alencar Kolinski Machado

Biology 2025, 14(11), 1520; https://doi.org/10.3390/biology14111520 (registering DOI) - 30 Oct 2025

Abstract

Epicatechin is a flavonoid of the catechin subclass, found in fruits and medicinal plants such as açaí and green tea, widely studied for its anti-inflammatory properties. However, flavonoids often present chemical instability, low aqueous solubility, and poor bioavailability, limiting their therapeutic potential. This [...] Read more.

Epicatechin is a flavonoid of the catechin subclass, found in fruits and medicinal plants such as açaí and green tea, widely studied for its anti-inflammatory properties. However, flavonoids often present chemical instability, low aqueous solubility, and poor bioavailability, limiting their therapeutic potential. This study aimed to incorporate epicatechin into nanocapsules to improve its applicability and evaluate whether the formulation maintains its anti-inflammatory effects via modulation of the NLRP3 inflammasome. Nanocapsules containing 0.25 mg/mL of epicatechin (NC-ECs) were prepared with Eudragit L-100 using interfacial deposition of a preformed polymer. The formulations were characterized for particle size, polydispersity index, zeta potential, and pH, as well as thermal stability over 45 days. Encapsulation efficiency and drug content were determined by high-performance liquid chromatography (HPLC), and morphology analyzed by atomic force microscopy (AFM). Cytocompatibility was assessed in VERO cells, and anti-inflammatory activity was investigated in THP-1-derived macrophages stimulated with LPS + nigericin. The NC-ECs displayed suitable physicochemical properties, high encapsulation efficiency (96%), and full drug loading. The formulation also showed good cytocompatibility and preserved anti-inflammatory activity through NLRP3 inflammasome modulation at low concentrations. These findings indicate NC-ECs as a promising nanotechnological strategy for treating inflammatory diseases involving NLRP3, highlighting its potential contribution to nanomedicine. Full article

(This article belongs to the Special Issue Biology and Function of Inflammasomes)

► Show Figures

Figure 1

21 pages, 3585 KB

Open AccessArticle

Combined Transcriptome and Metabolome Analyses of Oxidative Stress Regulatory Mechanism in Porcine Follicular Granulosa Cells

by Xilin Bi, Shu Niu, Yu Zhang, Qiang Liu, Qihang Zhang and Ruirong Hao

Biology 2025, 14(11), 1519; https://doi.org/10.3390/biology14111519 (registering DOI) - 30 Oct 2025

Abstract

Follicular atresia is mainly driven by the oxidative stress-induced apoptosis of granulosa cells (GCs). Oxidative stress mediated by H₂O₂ is the predominant form of stress in cells and plays a key role in the death of porcine GCs. In the [...] Read more.

Follicular atresia is mainly driven by the oxidative stress-induced apoptosis of granulosa cells (GCs). Oxidative stress mediated by H₂O₂ is the predominant form of stress in cells and plays a key role in the death of porcine GCs. In the present study, using integrated transcriptomic and untargeted metabolomic approaches, we explored the mechanisms underlying the regulation of oxidative stress in porcine follicular GCs. Per the transcriptomic analysis, compared with the control group, we identified 328 differentially expressed mRNAs (260 upregulated, 68 downregulated) in the H₂O₂-treatment group; these mRNAs were significantly enriched in apoptosis-related pathways, including the tumour necrosis factor (TNF) and p53 signalling pathways. Furthermore, via untargeted metabolomic analysis, we identified 150 differentially expressed metabolites (101 positive, 49 negative). The pathways associated with protein digestion and absorption, glycine, serine, and threonine metabolism, amino acid biosynthesis, and carbon metabolism were enriched with these metabolites. The integrated transcriptomic and metabolomic analyses revealed taurine, creatine, L-serine, and hypoxanthine as the key metabolites under H₂O₂-induced oxidative stress. Both the differential genes and metabolites were notably enriched in the FOXO and mineral absorption pathways. In the present study, we elucidated the regulatory mechanism underlying H₂O₂-induced oxidative stress in porcine follicular GCs via transcriptomic and metabolomic analyses. Our findings offer novel insights into the alleviation of oxidative stress in GCs. Full article

► Show Figures

Graphical abstract

21 pages, 13597 KB

Open AccessArticle

Systematic Analysis of the CCoAOMT Gene Family in Isatis indigotica and the Molecular Mechanism of CCoAOMT8-Mediated Flavonoid Synthesis Under Alkaline Stress Treatment

by Bo Liu, Lingyang Kong, Junbai Ma, Shan Jiang, Lengleng Ma, Jiao Xu, Weichao Ren and Wei Ma

Biology 2025, 14(11), 1518; https://doi.org/10.3390/biology14111518 (registering DOI) - 30 Oct 2025

Abstract

Caffeoyl CoA O-methyltransferase (CCoAOMT) is one of the key regulatory enzymes in the lignin biosynthesis pathway. In addition, it participates in the modification of flavonoids, which significantly impacts plant growth, development, and antioxidant capacity, and it plays a crucial role in [...] Read more.

Caffeoyl CoA O-methyltransferase (CCoAOMT) is one of the key regulatory enzymes in the lignin biosynthesis pathway. In addition, it participates in the modification of flavonoids, which significantly impacts plant growth, development, and antioxidant capacity, and it plays a crucial role in plant responses to stress and adversity. There is a current research gap in the CCoAOMT gene family of Isatis indigotica, particularly in terms of systematic identification and functional validation. Therefore, this study employed bioinformatics techniques to determine the composition of the CCoAOMT gene family in the Isatis indigotica genome. Eight members of the IiCCoAOMT gene family were identified, and their gene structures and motifs are relatively conserved. These members of the IiCCoAOMT family are located on three different chromosomes (3, 6, and 7) and exhibit significant tandem replication. According to phylogenetic research, IiCCoAOMT is divided into four distinct groups: Ia, Ib, Ic, and II. It is worth noting that the IiCCoAOMT genes in group Ia may be candidate genes involved in flavonoid biosynthesis and indirectly affect the content of flavonoid components., Subsequently, a yeast one-hybrid experiment verified that IiWRKY48 and IiWRKY54 could activate the CCoAOMT gene promoter in Isatis indigotica. These results provide a theoretical basis for understanding the function of CCoAOMT genes. Full article

(This article belongs to the Special Issue Research Progress on Salt Stress in Plants)

► Show Figures

Figure 1

2 pages, 153 KB

Open AccessCorrection

Correction: Zhan et al. Study on the Tea Pest Classification Model Using a Convolutional and Embedded Iterative Region of Interest Encoding Transformer. Biology 2023, 12, 1017

by Baishao Zhan, Ming Li, Wei Luo, Peng Li, Xiaoli Li and Hailiang Zhang

Biology 2025, 14(11), 1517; https://doi.org/10.3390/biology14111517 (registering DOI) - 30 Oct 2025

Abstract

In the original publication [...] Full article

(This article belongs to the Section Plant Science)

18 pages, 1115 KB

Open AccessArticle

Use of Multivariate Adaptive Regression Splines (MARS) and Classification and Regression Tree (CART) Data Mining Algorithms to Predict Live Body Weight of Tswana Sheep

by Monosi Andries Bolowe, Lubabalo Bila, Ketshephaone Thutwa and Patrick Monametsi Kgwatalala

Biology 2025, 14(11), 1516; https://doi.org/10.3390/biology14111516 - 30 Oct 2025

Abstract

This study was conducted to (i) determine the association between live body weight (BW) and biometric traits, (ii) examine the effect of biometric traits on BW of Tswana sheep using MARS and CART data mining algorithms, (iii) compare the performance of the algorithms [...] Read more.

This study was conducted to (i) determine the association between live body weight (BW) and biometric traits, (ii) examine the effect of biometric traits on BW of Tswana sheep using MARS and CART data mining algorithms, (iii) compare the performance of the algorithms and, finally, select the best algorithm for predicting BW in Tswana sheep. BW and sixteen biometric traits were measured from 392 Tswana sheep (males = 85 and females = 307) aged three to four years. Pearson’s correlation coefficients were used to establish the relationship between BW and biometric traits. The goodness of fit criteria were computed to assess the predictive performance of the data mining algorithms and select the best-fit model for predicting BW. The results showed that BW had a positive and significant correlation with heart girth (HG) (r = 0.99); thus, HG was used as a sole predictor of BW. The goodness of fit results indicated that MARS has a higher predictive performance than the CART algorithm, suggesting that the MARS algorithm can be used to predict BW Tswana sheep. These findings are an important statistical tool for the selection and concurrent improvement of useful biometric traits in genetic improvement programs to improve BW in Tswana sheep. Full article

(This article belongs to the Section Zoology)

► Show Figures

Figure 1

22 pages, 6546 KB

Open AccessArticle

Birds-YOLO: A Bird Detection Model for Dongting Lake Based on Modified YOLOv11

by Shuai Fang, Yue Shen, Haojie Zou, Yerong Yin, Wei Jin and Haoyu Zhou

Biology 2025, 14(11), 1515; https://doi.org/10.3390/biology14111515 - 29 Oct 2025

Abstract

To address the challenges posed by complex background interference, varying target sizes, and high species diversity in bird detection tasks in the Dongting Lake region, this paper proposes an enhanced bird detection model named Birds-YOLO, based on the YOLOv11 framework. First, the EMA [...] Read more.

To address the challenges posed by complex background interference, varying target sizes, and high species diversity in bird detection tasks in the Dongting Lake region, this paper proposes an enhanced bird detection model named Birds-YOLO, based on the YOLOv11 framework. First, the EMA mechanism is introduced to replace the original C2PSA module. This mechanism synchronously captures global dependencies in the channel dimension and local detailed features in the spatial dimension, thereby enhancing the model’s robustness in cluttered environments. Second, the model incorporates an improved RepNCSPELAN4-ECO module, by reasonably integrating depthwise separable convolution modules and combining them with an adaptive channel compression mechanism, to strengthen feature extraction and multi-scale feature fusion, effectively enhances the detection capability for bird targets at different scales. Finally, the neck component of the network is redesigned using lightweight GSConv convolution, which integrates the principles of grouped and spatial convolutions. This design preserves the feature modeling capacity of standard convolution while incorporating the computational efficiency of depthwise separable convolution, thereby reducing model complexity without sacrificing accuracy. Experimental results show that, compared to the baseline YOLOv11n, Birds-YOLO achieves a 5.0% improvement in recall and a 3.5% increase in mAP@0.5 on the CUB200-2011 dataset. On the in-house DTH-Birds dataset, it gains 3.7% in precision, 3.7% in recall, and 2.6% in mAP@0.5, demonstrating consistent performance enhancement across both public and private benchmarks. The model’s generalization ability and robustness are further validated through extensive ablation studies and comparative experiments, indicating its strong potential for practical deployment in bird detection tasks in complex natural environments such as Dongting Lake. Full article

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

► Show Figures

Figure 1

2 pages, 152 KB

Open AccessCorrection

Correction: Luo et al. A Simple Three-Dimensional Compartmentalized Co-Culture Model for Basal Forebrain and Hippocampal Neurons. Biology 2025, 14, 1238

by Xiaoman Luo, Jing Li, Zhiyu Deng, Yali Xu, Xixi Li, Miao Ren and Xiangning Li

Biology 2025, 14(11), 1514; https://doi.org/10.3390/biology14111514 - 29 Oct 2025

Abstract

There was an error in the original publication [...] Full article

22 pages, 6580 KB

Open AccessArticle

Over-Expression of TNFRSF12A Promotes Immune Suppression and Facilitates Angiogenesis in Triple-Negative Breast Cancer

by Can Jiang, Zhengwei Zhou, Guang Shu, Gang Yin and Maonan Wang

Biology 2025, 14(11), 1513; https://doi.org/10.3390/biology14111513 - 28 Oct 2025

Abstract

The urgent need for novel therapeutic strategies in triple-negative breast cancer (TNBC)—characterized by absent ER, PR, and HER2 expression—stems from its association with a paucity of effective treatments and an adverse prognosis. This study identifies TNFRSF12A as a key gene specifically overexpressed in [...] Read more.

The urgent need for novel therapeutic strategies in triple-negative breast cancer (TNBC)—characterized by absent ER, PR, and HER2 expression—stems from its association with a paucity of effective treatments and an adverse prognosis. This study identifies TNFRSF12A as a key gene specifically overexpressed in TNBC versus other subtypes. Validation with clinical specimens confirmed its exclusive upregulation in TNBC tissues, correlating significantly with worse patient outcomes. Functional enrichment analysis (STRING/DAVID) indicated TNFRSF12A’s primary involvement in pathways positively regulating cell migration, angiogenesis, and hypoxia response. Immune infiltration profiling (TIMER/TISCH2) revealed selective enrichment of TNFRSF12A in cancer-associated fibroblasts (CAFs). Its expression showed a significant positive correlation with the CAF marker FAP (ρ = 0.304) and CAF infiltration levels, but inverse correlations with CD8⁺ T-cell (Cor = −0.165) and B-cell (Cor = −0.164) infiltration. Regarding chemoresistance, elevated TNFRSF12A expression significantly increased sensitivity to docetaxel. Molecular docking simulations further verified direct binding between TNFRSF12A and docetaxel, mediated by hydrophobic interactions and hydrogen bonds. To elucidate the underlying molecular mechanisms, cellular experiments revealed that TNFRSF12A knockdown resulted in (1) significantly compromised angiogenic capacity in HUVEC tube formation assays (p < 0.01); (2) markedly augmented cytotoxicity of T cells against tumor cells (p < 0.05); and (3) reduced cellular sensitivity to docetaxel, as evidenced by significantly elevated IC₅₀ values in CCK-8 assays (p < 0.01). In summary, this study systematically elucidates how TNFRSF12A propels TNBC malignant progression by remodeling the tumor immune microenvironment and promoting angiogenesis. Concurrently, we reveal a TNFRSF12A-mediated chemosensitizing effect towards docetaxel. Therefore, these results are crucial for improving the targeting of TNFRSF12A and developing precise combination treatment regimens to improve outcomes for patients with TNBC. Full article

(This article belongs to the Section Cancer Biology)

► Show Figures

Figure 1

24 pages, 1627 KB

Open AccessArticle

Hypoxia Supports LPS-Driven Tolerance and Functional Activation in BV-2 Microglial Cells

by Alicia Chavero Vargas, Natascha Köstlin-Gille, Reinhard Bauer, Stefanie Dietz-Ziegler, Anita S. Lokaj, Soumya Lutterbach, Christian Gille and Trim Lajqi

Biology 2025, 14(11), 1512; https://doi.org/10.3390/biology14111512 - 28 Oct 2025

Abstract

Background: Prolonged hypoxia contributes to irreversible organ damage, particularly in the brain and heart. While chronic hypoxia is harmful, mild short-term hypoxia can trigger protective mechanisms. This study investigates how such hypoxic conditions affect BV-2 tolerant microglial cells in vitro, focusing on inflammation, [...] Read more.

Background: Prolonged hypoxia contributes to irreversible organ damage, particularly in the brain and heart. While chronic hypoxia is harmful, mild short-term hypoxia can trigger protective mechanisms. This study investigates how such hypoxic conditions affect BV-2 tolerant microglial cells in vitro, focusing on inflammation, metabolism, and functional activity. Although in vitro models provide a controlled setting, our findings may offer insights into microglial behavior in vivo under similar conditions. Methods: We used various molecular and biochemical techniques to assess the inflammatory state of BV-2 microglia under hypoxia, measuring glycolytic activity (via lactate production), and evaluating migratory and phagocytic capacities in vitro. Results: Hypoxic conditions induced a more tolerant, anti-inflammatory phenotype in BV-2 cells, with decreased pro-inflammatory mediators and reduced glycolytic activity, regulated by the MyD88/NF-κB p65 pathway. Tolerance supports increased migration and phagocytosis, but under hypoxic conditions, these effects were significantly declined compared to normoxic conditions, mediated through the ERK1/2 pathway. Conclusions: These findings suggest that short-term hypoxia may regulate microglial behavior and restore homeostasis, with implications for neuroinflammatory conditions. Full article

(This article belongs to the Section Immunology)

► Show Figures

Graphical abstract

18 pages, 5664 KB

Open AccessArticle

Identification of the YABBY Gene Family in Cerasus humilis and Analysis of Expression Patterns During Different Growth Stages

by Weichao Ren, Shan Jiang, Lingyang Kong, Chenzhuo Yue, Lengleng Ma, Junbai Ma, Wei Ma and Xiubo Liu

Biology 2025, 14(11), 1511; https://doi.org/10.3390/biology14111511 - 28 Oct 2025

Abstract

YABBY belongs to the family of plant-specific transcription factors, known for their role in plant morphology, growth, and development. Its name is derived from the first discovered member—the YABBY1 gene of Arabidopsis thaliana (named due to its mutated phenotype showing a “Y-shaped” bifurcation). [...] Read more.

YABBY belongs to the family of plant-specific transcription factors, known for their role in plant morphology, growth, and development. Its name is derived from the first discovered member—the YABBY1 gene of Arabidopsis thaliana (named due to its mutated phenotype showing a “Y-shaped” bifurcation). Despite extensive research across various plant species, no studies have conducted a genome-wide investigation of the YABBY gene family in Cerasus humilis. This study identified six ChYABBY (Cerasus humilis YABBY) genes distributed across five chromosomes through a comprehensive bioinformatic analysis of the C. humilis genome. The gene expression during the four growth phases was confirmed using real-time-quantitative fluorescent PCR (qPCR). ChYABBY is segmented into five distinct subfamilies. Genetic lineage analysis determined the close genetic relationship between the YABBY genes of C. humilis and Malus pumila. An examination of the gene architecture and preserved motifs revealed that ChYABBY typically comprises 5–6 introns, with motif1, motif2, and motif3 being preserved domains across all ChYABBY protein sequences. Promoter analysis suggests that ChYABBY genes play various roles in the growth and maturation of C. humilis. An examination of the homology revealed the absence of tandem replication in the ChYABBY gene family, with a single pair of fragment-replicating genes. The heat map and q-PCR results indicate that the expression of the ChYABBY gene is tissue-specific and correlates with some aspects of the fruit growth and development. This suggests a potential role for this gene family in fruit maturation. The determination of total sugar and total flavonoid content indicated that the content of the two substances was high when the fruit was green. The antioxidant capacity of the fruit at each stage was different. This research provides an important basis for further understanding the structure and function of the ChYABBY gene, and lays a foundation for the identification of YABBY genes in Rosaceae plants. Full article

(This article belongs to the Section Bioinformatics)

► Show Figures

Figure 1

32 pages, 446 KB

Open AccessReview

The Roles of Sirt1 in Breast and Gynecologic Malignancies

by Jianmin Ding, Matthew T. Ye and Songlin Zhang

Biology 2025, 14(11), 1510; https://doi.org/10.3390/biology14111510 - 28 Oct 2025

Abstract

Sirtuin 1 (SIRT1), an NAD⁺-dependent histone deacetylase, exerts complex and context-dependent effects in breast and gynecological cancers. By deacetylating histone and non-histone proteins such as p53, FOXO, and NF-κB, SIRT1 regulates essential processes including DNA repair, apoptosis, metabolism, and stress response. [...] Read more.

Sirtuin 1 (SIRT1), an NAD⁺-dependent histone deacetylase, exerts complex and context-dependent effects in breast and gynecological cancers. By deacetylating histone and non-histone proteins such as p53, FOXO, and NF-κB, SIRT1 regulates essential processes including DNA repair, apoptosis, metabolism, and stress response. In breast cancer, SIRT1 may act as a tumor suppressor in early stages by maintaining genomic stability but promotes epithelial–mesenchymal transition, metastasis, and chemoresistance in aggressive subtypes such as triple-negative breast cancer. Similarly, in gynecological cancers, SIRT1 displays dual roles: promoting proliferation via estrogen signaling and p53/FOXO1 inhibition in Type I endometrial cancer yet potentially supporting DNA repair in high-grade Type II tumors. Its overexpression in ovarian and cervical cancers is linked to enhanced survival and drug resistance. Preclinical studies show that pharmacological inhibition of SIRT1 (e.g., with EX-527 or cambinol) restores chemosensitivity and reduces tumor cell viability, suggesting potential for SIRT1 inhibitors as adjuncts in cancer therapy. However, clinical trials specifically targeting SIRT1 in these cancers remain limited. Further investigation is needed to define therapeutic windows, molecular contexts, and combination strategies that could optimize SIRT1-targeted therapies. This review summarizes the current understanding of SIRT1’s roles in breast and gynecologic malignancies. Full article

(This article belongs to the Special Issue Signalling Pathways in Cancer and Disease)

29 pages, 5404 KB

Open AccessArticle

The Human Omental Adipose Depot Mitigates Inflammation, Immune Response, and Oxidative Stress Pathways in Response to Injury via Its Secretome

by Meredith Krause-Hauch, Rekha S. Patel, Bangmei Wang, Brianna Jones, Paul Albear and Niketa A. Patel

Biology 2025, 14(11), 1509; https://doi.org/10.3390/biology14111509 - 28 Oct 2025

Abstract

Human intraperitoneal omental adipose tissue, part of the visceral adipose depots, surrounds the abdominal organs and has functions distinct from the subcutaneous adipose depots. In the clinical setting, it is observed that the omentum is beneficial to combat internal sources of inflammation, oxidative [...] Read more.

Human intraperitoneal omental adipose tissue, part of the visceral adipose depots, surrounds the abdominal organs and has functions distinct from the subcutaneous adipose depots. In the clinical setting, it is observed that the omentum is beneficial to combat internal sources of inflammation, oxidative stress, and injury-related stress. However, the molecular mechanisms involved in these functions are not fully understood. We previously demonstrated that adipose stem cells derived from human omental adipose tissue (om-hASCs) secrete exosomes (exos). We and others have extensively evaluated the subcutaneous adipose depot-derived exosomes; however, the role of adipose stem cells derived from the human omental depot (om-hASCs) remains less known. In this study, we postulated that exosomes from om-hASCs (om-hASCexos) drive the repair ability of the omentum to heal organs after internal injury and insults. First, we characterized the om-hASCexos using a proteomic analysis which identified the distinct cargo. Using in vitro injury models, we show that om-hASCexos significantly improve cell migration and proliferation, while decreasing oxidative stress and inflammation. To study acute in vivo healing, a rat wound model was evaluated. Om-hASCexos significantly improved the healing rate of injuries. RNAseq revealed that om-hASCexo treatment acts upon pathways associated with lipid and fatty acid metabolism, apoptosis, immune response, and cell differentiation. The pathway analysis indicated that om-hASCexos significantly regulate the expression of Clec5a and Trem1 in the immune response pathway. Overall, we demonstrate the singular properties of om-hASCexos that are distinct from other sources of hASC. Thus, this study provides an understanding of the unique ability of the omental adipose depot to combat internal injuries. Full article

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

► Show Figures

Figure 1

24 pages, 5039 KB

Open AccessArticle

Diet Reconstruction Under Limited Prior Information: Dietary Contributions and Isotopic Niche of Metridium senile in the North Yellow Sea

by Yongsong Zhao, Xiujuan Shan, Guangliang Teng, Shiqi Song, Yunlong Chen and Xianshi Jin

Biology 2025, 14(11), 1508; https://doi.org/10.3390/biology14111508 - 28 Oct 2025

Abstract

Biomass of the plumose anemone Metridium senile has surged in the benthic ecosystem of the North Yellow Sea in recent years. Understanding its diet and the proportional contributions of food sources is essential for assessing the ecological consequences of this expansion. The species [...] Read more.

Biomass of the plumose anemone Metridium senile has surged in the benthic ecosystem of the North Yellow Sea in recent years. Understanding its diet and the proportional contributions of food sources is essential for assessing the ecological consequences of this expansion. The species is often characterized as a passive suspension feeder, yet laboratory feeding trials have documented shrimp consumption. Because prior dietary information from the region is scarce, conventional stable isotope approaches are poorly constrained. We developed an integrative framework coupling trophic position estimation, isotopic niche metrics, spatial point pattern analysis, and a Bayesian mixing model to improve diet attribution under limited prior information and to test whether M. senile preys on small-bodied and juvenile teleosts and invertebrates under natural conditions. Our analyses showed that: (i) M. senile occupied a high trophic position (TP = 3.09 ± 0.25), exceeding those estimated for putative predators in our dataset, implying weak top-down control; (ii) in isotopic niche analyses, M. senile showed high posterior probabilities of occurring within the niches of cephalopods and medium-sized fishes (78.30% and 63.04%, respectively), consistent with shared prey and inconsistent with a strictly suspension-feeding strategy; (iii) mixing space diagnostics informed by spatial point pattern analysis indicated that including small-sized fishes and shrimps as sources was necessary to reconcile the elevated TP; and (iv) the Bayesian mixing model estimated that small-bodied and juvenile teleosts and invertebrates supplied most long-term nutrition (posterior mean ≈ 0.65), with the remainder from suspension-derived sources, consistent with an opportunistic generalist rather than a strict suspension feeder. Sustained predation on small-bodied and juvenile teleosts and invertebrates could suppress early fish recruitment, impose top-down control on forage species, and alter the local food web structure. Management should monitor M. senile (size structure, population density, and co-occurrence with juveniles and forage biota) and consider targeted removals and seafloor litter cleanups in priority habitats. The framework is applicable to diet studies with limited prior information; adding δ³⁴S, compound-specific amino-acid isotopes (CSIA-AA), and DNA-based dietary evidence should further sharpen source discrimination. Full article

(This article belongs to the Special Issue Living Resources of the Deep Sea: Biological Profiles and Environmental Linkages)

► Show Figures

Graphical abstract

Journal Description

Biology

Latest Articles

Journal Menu

Journal Browser

Highly Accessed Articles

Latest Books

E-Mail Alert

News

Topics

Conferences

Special Issues

Topical Collections

Further Information

Guidelines

MDPI Initiatives

Follow MDPI