Biology

45 pages, 6884 KiB

Open AccessArticle

Deciphering the Regulatory Potential of Antioxidant and Electron-Shuttling Bioactive Compounds in Oolong Tea

by Regineil A. Ferrer, Bor-Yann Chen, Jon Patrick T. Garcia, Christine Joyce F. Rejano, Po-Wei Tsai, Chung-Chuan Hsueh and Lemmuel L. Tayo

Biology 2025, 14(5), 487; https://doi.org/10.3390/biology14050487 - 28 Apr 2025

Abstract

OT has gained attention for its high polyphenol content and therapeutic potential. To elucidate this further, this study investigated the electron-shuttling bioactive compounds of OT and evaluated their effect on dysregulated breast cancer (BC) genes. OT extracts were obtained via solvent extraction (SE) [...] Read more.

OT has gained attention for its high polyphenol content and therapeutic potential. To elucidate this further, this study investigated the electron-shuttling bioactive compounds of OT and evaluated their effect on dysregulated breast cancer (BC) genes. OT extracts were obtained via solvent extraction (SE) and supercritical fluid extraction (SFE), followed by in vitro assays. Phytochemical analysis revealed that ethanol-extracted OT (OTL-E) had the highest polyphenol, flavonoid, and tannin contents, correlating with strong antioxidant activity, while water-extracted OT (OTL-W) exhibited greater bioelectricity-stimulating properties in microbial fuel cells (MFC), confirmed by cyclic voltammetry (CV). Based on phytochemical analyses, SE displayed a better extraction technique for isolating OT bioactive compounds compared to SFE. In silico approaches through network pharmacology, molecular docking and dynamics simulations revealed that polyphenols with ortho- or para-dihydroxyl groups targeted dysregulated BC proteins involved in kinase signaling, apoptosis, and hormone receptor pathways. Luteolin exhibited the highest binding affinities to MAPK1 and PIK3CA with free energy (ΔG) of −9.1 and −8.4 kcal/mol, respectively. Trajectory-based analyses confirmed enthalpy-favored ligand-induced conformational changes to these oncoproteins, altering their function in BC development. These findings suggest the potential of OT as a bioelectricity-stimulating and chemopreventive agent, warranting further in vitro and in vivo validation. Full article

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17 pages, 11651 KiB

Open AccessArticle

Integration of Single-Cell and Bulk Transcriptome to Reveal an Endothelial Transition Signature Predicting Bladder Cancer Prognosis

by Jinyu Yang, Wangxi Wu and Xiaoli Tang

Biology 2025, 14(5), 486; https://doi.org/10.3390/biology14050486 - 28 Apr 2025

Abstract

Endothelial cells (ECs) are critical drivers of tumour progression, and their angiogenic process has been widely studied. However, the post-angiogenic transition of tip endothelial cells after sprouting remains insufficiently characterised. In this study, we utilised single-cell RNA sequencing analyses to identify a novel [...] Read more.

Endothelial cells (ECs) are critical drivers of tumour progression, and their angiogenic process has been widely studied. However, the post-angiogenic transition of tip endothelial cells after sprouting remains insufficiently characterised. In this study, we utilised single-cell RNA sequencing analyses to identify a novel EC transition signature associated with endothelial permeability, migration, metabolism, and vascular maturation. Within the transition pathway, we discovered a critical EC subpopulation, termed tip-to-capillary ECs (TC-ECs), that was enriched in tumour tissues. Comparative analyses of TC-ECs with tip and capillary ECs revealed distinct differences in pathway activity, cellular communication, and transcription factor activity. The EC transition signature demonstrated substantial prognostic significance, validated across multiple cancer cohorts from TCGA data, particularly in bladder cancer. Subsequently, we constructed a robust prognostic model for bladder cancer by integrating the EC transition signature with multiple machine-learning techniques. Compared with 31 existing models across the TCGA-BLCA, GSE32894, GSE32548, and GSE70691 cohorts, our model exhibited superior predictive performance. Stratification analysis identified significant differences between different risk groups regarding pathway activity, cellular infiltration, and therapeutic sensitivity. In conclusion, our comprehensive investigation identified a novel EC transition signature and developed a prognostic model for patient stratification, offering new insights into endothelial heterogeneity, angiogenesis regulation, and precision medicine. Full article

(This article belongs to the Special Issue Latest Research in Cancer Multi-Omics)

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16 pages, 5662 KiB

Open AccessArticle

Hidden Threats: The Unnoticed Epidemic System of Pine Wilt Disease Driven by Sexually Mature Monochamus Beetles and Asymptomatic Trees

by Kazuyoshi Futai and Hideaki Ishiguro

Biology 2025, 14(5), 485; https://doi.org/10.3390/biology14050485 - 28 Apr 2025

Abstract

Pine wilt disease, caused by the nematode Bursaphelenchus xylophilus, poses a significant threat to pine forests worldwide. Understanding the dynamics of its spread is crucial for effective disease management. In this study, we investigated the involvement of asymptomatic carrier trees in the [...] Read more.

Pine wilt disease, caused by the nematode Bursaphelenchus xylophilus, poses a significant threat to pine forests worldwide. Understanding the dynamics of its spread is crucial for effective disease management. In this study, we investigated the involvement of asymptomatic carrier trees in the expansion of pine wilt disease through a series of experiments. Cage-releasing experiments revealed that sexually immature Japanese pine sawyer beetles, Monochamus alternatus, feeding on healthy pine branches drops only a minimal number of nematodes (primary infection). However, sexually mature beetles, still harboring numerous nematodes, fly to weakened trees for breeding and extend their feeding activities to healthy pines around weakened trees, infecting them with nematodes and thus spreading the disease further. Inoculation experiments on field-planted black pine seedlings demonstrated that even a small number of nematodes can lead to a high occurrence of asymptomatic carrier trees. Our findings suggest that nematode infections transmitted by sexually mature Monochamus beetles significantly contribute to the expansion of pine wilt damage and play a crucial role in the persistence of asymptomatic carrier trees. This conclusion is based on cage-release experiments demonstrating nematode transmission by mature beetles and inoculation experiments highlighting the conditions leading to asymptomatic carrier trees. Full article

(This article belongs to the Special Issue Editorial Board Members' Collection Series: “Biodiversity and Ecosystem Function under Global Change”)

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17 pages, 10504 KiB

Open AccessArticle

Construction and Influence of Induced Pluripotent Stem Cells on Early Embryo Development in Black Bone Sheep

by Daqing Wang, Yiyi Liu, Lu Li, Xin Li, Xin Cheng, Zhihui Guo, Guifang Cao and Yong Zhang

Biology 2025, 14(5), 484; https://doi.org/10.3390/biology14050484 - 28 Apr 2025

Abstract

The piggyBac+TET-on transposon induction system has a high efficiency in integrating exogenous genes in multiple cell types, can precisely integrate to reduce genomic damage, has a flexible gene expression regulation, and a strong genetic stability. When used in conjunction with somatic cell nuclear [...] Read more.

The piggyBac+TET-on transposon induction system has a high efficiency in integrating exogenous genes in multiple cell types, can precisely integrate to reduce genomic damage, has a flexible gene expression regulation, and a strong genetic stability. When used in conjunction with somatic cell nuclear transfer experiments, it can precisely and effectively reveal the intrinsic mechanisms of early biological development. This study successfully reprogrammed black-boned sheep fibroblasts (SFs) into induced pluripotent stem cells (iPSCs) using the piggyBac+TET-on transposon system and investigated their impact on early embryonic development. Seven exogenous reprogramming factors (bovine OCT4, SOX2, KLF4, cMyc, porcine NANOG, Lin-28, and SV40 Large T) were delivered into SFs, successfully inducing iPSCs. A growth performance analysis revealed that iPSC clones exhibited a raised or flat morphology with clear edges, positive alkaline phosphatase staining, and normal karyotypes. The transcriptome analysis indicated a significant enrichment of iPSCs in oxidative phosphorylation and cell proliferation pathways, with an up-regulated expression of the ATP5B, SDHB, Bcl-2, CDK1, and Cyclin D1 genes and a down-regulated expression of BAX (p < 0.05). Somatic cell nuclear transfer experiments demonstrated that the cleavage rate (85% ± 2.12) and blastocyst rate (52% ± 2.11) of the iPSCs were significantly higher than those of the SFs (p < 0.05). The detection of trilineage marker genes confirmed that the expression levels of endoderm (DCN, NANOS3, FOXA2, FOXD3, SOX17), mesoderm (KDR, CD34, NFH), and ectoderm (NEUROD) markers in iPSCs were significantly higher than in SFs (p < 0.01). The findings demonstrate that black-boned sheep iPSCs possess pluripotency and the potential to differentiate into all three germ layers, revealing the mechanisms by which reprogrammed iPSCs influence early embryonic development and providing a critical foundation for research on sheep pluripotent stem cells. Full article

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15 pages, 4461 KiB

Open AccessArticle

Turmeric Oil Interferes with Quorum Sensing as an Alternative Approach to Control Aeromonas hydrophila Infection in Aquaculture

by Jing Dong, Jian Tong, Shengping Li, Xinwei Ma, Qiuhong Yang, Yongtao Liu, Shun Zhou, Xizhi Shi and Xiaohui Ai

Biology 2025, 14(5), 483; https://doi.org/10.3390/biology14050483 - 27 Apr 2025

Abstract

Aquatic products play a crucial role in meeting the increasing global demands for high-quality proteins. However, the occurrence of bacterial diseases results in significant economic losses worldwide. Aeromonas hydrophila (A. hydrophila) is the pathogen of several fish diseases. Antibiotics were widely [...] Read more.

Aquatic products play a crucial role in meeting the increasing global demands for high-quality proteins. However, the occurrence of bacterial diseases results in significant economic losses worldwide. Aeromonas hydrophila (A. hydrophila) is the pathogen of several fish diseases. Antibiotics were widely used in combating bacterial diseases in aquaculture. The increasing occurrences of antibiotic resistance necessitate the restricted use of antibiotics. Consequently, developing drugs that avoid antibiotic resistance is important for the future of aquaculture. Quorum sensing (QS) is critical for bacterial pathogens in regulating bacterial virulence and is a promising target for developing anti-infective agents. Here, we found that turmeric oil with a MIC of 256 μg/mL could dose-dependently reduce the virulence phenotypes regulated by QS, ranging from 8 to 64 μg/mL, suggesting that sub-inhibitory concentrations of turmeric oil could inhibit bacterial virulence. Further qPCR findings demonstrated that turmeric oil could significantly inhibit the transcription of aerA, ahyI, and ahyR by a 54-fold, 36-fold, and 56-fold change reduction, respectively. Cell live/dead staining and animal study results showed that turmeric oil could inhibit the pathogenicity of A. hydrophila. Fish treated with turmeric oil showed a reduced mortality rate of 60%, whereas all fish in the positive control group died. Moreover, treatment with turmeric oil could alleviate the renal injury. Collectively, the results suggested that targeting bacterial virulence might be a useful approach to combating bacterial infections, and turmeric oil could serve as a potential agent for combating A. hydrophila infections. Full article

(This article belongs to the Special Issue Aquatic Economic Animal Breeding and Healthy Farming)

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24 pages, 3544 KiB

Open AccessArticle

Significant Changes in Low-Abundance Protein Content Detected by Proteomic Analysis of Urine from Patients with Renal Stones After Extracorporeal Shock Wave Lithotripsy

by Elena Carestia, Fabrizio Di Giuseppe, Mohammad Kazemi, Massoumeh Ramahi, Uditanshu Priyadarshi, Patricia Giuliani, Piergustavo De Francesco, Luigi Schips, Carmine Di Ilio, Renata Ciccarelli, Patrizia Di Iorio and Stefania Angelucci

Biology 2025, 14(5), 482; https://doi.org/10.3390/biology14050482 - 27 Apr 2025

Abstract

Extracorporeal shock wave lithotripsy (ESWL), although a highly effective method for the treatment of kidney stones, can cause significant kidney damage. Since urinary protein composition directly reflects kidney function, proteomic analysis of this fluid may be useful to identify changes in protein levels [...] Read more.

Extracorporeal shock wave lithotripsy (ESWL), although a highly effective method for the treatment of kidney stones, can cause significant kidney damage. Since urinary protein composition directly reflects kidney function, proteomic analysis of this fluid may be useful to identify changes in protein levels induced by patient exposure to ESWL as a sign of kidney damage. To this end, we collected urine samples from 80 patients with nephrolithiasis 2 h before and 24 h after exposure to ESWL, which were concentrated and subsequently processed with a commercially available enrichment method to extract low-abundance urinary proteins. These were then separated by 2D electrophoresis and subsequently analyzed by a proteomic approach. A large number of proteins were identified as being related to inflammatory, fibrotic, and antioxidant processes and changes in the levels of some of them were confirmed by Western blot analysis. Therefore, although further experimental confirmation is needed, our results demonstrate that ESWL significantly influences the low urinary protein profile of patients with nephrolithiasis. Notably, among the identified proteins, matrix metalloproteinase 7, alpha1-antitrypsin, and clusterin, as well as dimethyl arginine dimethyl amino hydrolase 2 and ab-hydrolase, may play an important role as putative biomarkers in the monitoring and management of ESWL-induced renal damage. Full article

(This article belongs to the Special Issue Proteomics and Human Diseases)

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23 pages, 5225 KiB

Open AccessArticle

Community Characteristics and Potential Risk of Nekton in Waters Adjacent to Ningde Nuclear Power Plant in Fujian, China

by Wen Huang, Biqi Zheng, Dong Wen, Feipeng Wang, Lijing Fan, Zefeng Yu, Wei Liu and Shuang Zhao

Biology 2025, 14(5), 481; https://doi.org/10.3390/biology14050481 - 27 Apr 2025

Abstract

The impact of bio-invasions and abnormal aggregations of marine life on the safety of cooling water systems in coastal nuclear power plants (NPPs) is significant and cannot be overlooked. In this study, we conducted 12 consecutive monthly surveys from September 2022 to August [...] Read more.

The impact of bio-invasions and abnormal aggregations of marine life on the safety of cooling water systems in coastal nuclear power plants (NPPs) is significant and cannot be overlooked. In this study, we conducted 12 consecutive monthly surveys from September 2022 to August 2023 in the waters near Ningde NPP in Fujian, China, focusing on nekton species composition, dominant species, abundance, biomass, and diversity indices. We conducted statistical analyses to examine potential correlations between the community structure of these organisms and environmental factors. We recorded 120 species of nekton that belonged to 20 orders, 57 families, and 92 genera, including 72 species of fish, 23 species of shrimp, 19 species of crabs, and 6 species of cephalopods. Pearson and redundancy analyses showed that pH, DIP, and inorganic nitrogen were the main environmental factors driving the observed temporal changes in the nekton community structure in the seawater intake area. We also found that May to October is the peak period for nekton abundance and biomass, and during this time, there is a high risk of nekton blocking the cooling water system of the NPP. These results are of practical significance for NPP managers to prevent and control the clogging of the cooling water system by marine organisms, and the diversity and abundance data provide a theoretical basis for bioecological restoration and management of the area around the Ningde NPP. Full article

(This article belongs to the Special Issue Advances in Aquatic Ecological Disasters and Toxicology)

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24 pages, 4689 KiB

Open AccessArticle

Moving Northwards: Life-History Traits of the Invasive Green Crab (Carcinus maenas) Expanding into the Southwestern Atlantic

by Micaela Müller Baigorria, Maite Narvarte and Leandro A. Hünicken

Biology 2025, 14(5), 480; https://doi.org/10.3390/biology14050480 - 26 Apr 2025

Abstract

The invasive European green crab (Carcinus maenas) poses a significant ecological threat due to its rapid global spread and disruptive impact on coastal ecosystems. In the southwestern Atlantic, the northernmost population was recently recorded in the San Matías Gulf, offering a unique [...] Read more.

The invasive European green crab (Carcinus maenas) poses a significant ecological threat due to its rapid global spread and disruptive impact on coastal ecosystems. In the southwestern Atlantic, the northernmost population was recently recorded in the San Matías Gulf, offering a unique opportunity to study its demographic and life-history traits at the leading edge of its range. We assessed the sex ratio, population density, size distribution, and size at which 50% of females were ovigerous (SM₅₀) in the intertidal zone. Our findings revealed a male-biased sex ratio (1.50 males per female) and low population density (0.42 crabs m⁻²), suggesting early-stage establishment. A size-structure analysis showed a well-structured population with clear cohort separation in both sexes and evidence of two recruitment events. The carapace width at which 50% of females were ovigerous was estimated at 61.48 mm. Although egg-bearing females exhibited a well-marked seasonality, with the highest prevalence from May to July, their presence nearly year-round suggests an extended reproductive period and adaptability to local conditions, which may be advantageous in recently established populations, facilitating invasion success. These traits, combined with the species’ ongoing range expansion, highlight the invasive potential of C. maenas and its possible ecological impacts on the San Matías Gulf. Full article

(This article belongs to the Special Issue 2nd Edition: Aquatic Alien Invasions and Their Impact on Biodiversity and Ecosystem Services )

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19 pages, 5990 KiB

Open AccessArticle

FPCAM: A Weighted Dictionary-Driven Model for Single-Cell Annotation in Pulmonary Fibrosis

by Guojun Liu, Yan Shi, Hongxu Huang, Ningkun Xiao, Chuncheng Liu, Hongyu Zhao, Yongqiang Xing and Lu Cai

Biology 2025, 14(5), 479; https://doi.org/10.3390/biology14050479 - 26 Apr 2025

Abstract

The groundbreaking development of scRNA-seq has significantly improved cellular resolution. However, accurate cell-type annotation remains a major challenge. Existing annotation tools are often limited by their reliance on reference datasets, the heterogeneity of marker genes, and subjective biases introduced through manual intervention, all [...] Read more.

The groundbreaking development of scRNA-seq has significantly improved cellular resolution. However, accurate cell-type annotation remains a major challenge. Existing annotation tools are often limited by their reliance on reference datasets, the heterogeneity of marker genes, and subjective biases introduced through manual intervention, all of which impact annotation accuracy and reliability. To address these limitations, we developed FPCAM, a fully automated pulmonary fibrosis cell-type annotation model. Built on the R Shiny platform, FPCAM utilizes a matrix of up-regulated marker genes and a manually curated gene–cell association dictionary specific to pulmonary fibrosis. It achieves accurate and efficient cell-type annotation through similarity matrix construction and optimized matching algorithms. To evaluate its performance, we compared FPCAM with state-of-the-art annotation models, including SCSA, SingleR, and SciBet. The results showed that FPCAM and SCSA both achieved an accuracy of 89.7%, outperforming SingleR and SciBet. Furthermore, FPCAM demonstrated high accuracy in annotating the external validation dataset GSE135893, successfully identifying multiple cell subtypes. In summary, FPCAM provides an efficient, flexible, and accurate solution for cell-type identification and serves as a powerful tool for scRNA-seq research in pulmonary fibrosis and other related diseases. Full article

(This article belongs to the Special Issue Computational Discovery Tools in Genomics and Precision Medicine)

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18 pages, 3993 KiB

Open AccessArticle

New Insights into the Geometry and Topology of DNA Replication Intermediates

by Victor Martínez, Edith Ruiz-Díaz, Delia Cardozo, Cristian Cappo, Christian E. Schaerer, Jorge Cebrián, Dora B. Krimer and María José Fernández-Nestosa

Biology 2025, 14(5), 478; https://doi.org/10.3390/biology14050478 - 26 Apr 2025

Abstract

The regulation of superhelical stress, mediated by the combined action of topoisomerases and fork rotation, is crucial for DNA replication. The conformational changes during DNA replication are still experimentally challenging, mainly due to the rapid kinetics of the replication process. Here, we present [...] Read more.

The regulation of superhelical stress, mediated by the combined action of topoisomerases and fork rotation, is crucial for DNA replication. The conformational changes during DNA replication are still experimentally challenging, mainly due to the rapid kinetics of the replication process. Here, we present the first molecular dynamics simulations of partially replicated circular DNA molecules, with stalled replication forks at both early and late stages of DNA replication. These simulations allowed us to map the distribution of superhelical stress after deproteinization. We propose a five-component model that determines the linking number difference of replication intermediates. At a thermodynamic equilibrium, the contribution of these five components was correlated to the progress of the replication forks. Additionally, we identified four types of segment collision events in replication intermediates, characterized by their geometric properties, including chirality and topological sign. The distribution of these collision events between the early and late stages of DNA replication provides new insights into the coordinated function of topoisomerases, warranting further discussion. Full article

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

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18 pages, 6470 KiB

Open AccessArticle

Mapping the Interactome of KRAS and Its G12C/D/V Mutants by Integrating TurboID Proximity Labeling with Quantitative Proteomics

by Jiangwei Song, Busong Wang, Mingjie Zou, Haiyuan Zhou, Yibing Ding, Wei Ren, Lei Fang and Jingzi Zhang

Biology 2025, 14(5), 477; https://doi.org/10.3390/biology14050477 - 26 Apr 2025

Abstract

KRAS mutations are major drivers of human cancers, yet how distinct mutations rewire protein interactions and metabolic pathways to promote tumorigenesis remains poorly understood. To address this, we systematically mapped the protein interaction networks of wild-type KRAS and three high-frequency oncogenic mutants (G12C, [...] Read more.

KRAS mutations are major drivers of human cancers, yet how distinct mutations rewire protein interactions and metabolic pathways to promote tumorigenesis remains poorly understood. To address this, we systematically mapped the protein interaction networks of wild-type KRAS and three high-frequency oncogenic mutants (G12C, G12D, and G12V) using TurboID proximity labeling coupled with quantitative proteomics. Bioinformatic analysis revealed mutant-specific binding partners and metabolic pathway alterations, including significant enrichment in insulin signaling, reactive oxygen species regulation, and glucose/lipid metabolism. These changes collectively drive tumor proliferation and immune evasion. Comparative analysis identified shared interactome shifts across all mutants: reduced binding to LZTR1, an adaptor for KRAS degradation, and enhanced recruitment of LAMTOR1, a regulator of mTORC1-mediated growth signaling. Our multi-dimensional profiling establishes the first comprehensive map of KRAS-mutant interactomes and links specific mutations to metabolic reprogramming. These findings provide mechanistic insights into KRAS-driven malignancy and highlight LZTR1 and LAMTOR1 as potential therapeutic targets. The study further lays a foundation for developing mutation-specific strategies to counteract KRAS oncogenic signaling. Full article

(This article belongs to the Special Issue Proteomics and Human Diseases)

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13 pages, 9040 KiB

Open AccessArticle

Vitamin D3-Coated Surfaces and Their Role in Bone Repair and Peri-Implant Biomechanics

by Letícia Pitol-Palin, Isadora Castaldi Sousa, Juliani Caroline Ribeiro de Araújo, Fábio Roberto de Souza Batista, Bruna Kaori Namba Inoue, Paulo Roberto Botacin, Luana Marotta Reis de Vasconcellos, Paulo Noronha Lisboa-Filho and Roberta Okamoto

Biology 2025, 14(5), 476; https://doi.org/10.3390/biology14050476 - 26 Apr 2025

Abstract

Dental rehabilitation with titanium implants may requires the optimization of techniques and materials when oral conditions affect the successful treatment result. Thus, this study aims to customize the surface of titanium implants with bioactive vitamin D3 molecules to increase the performance of bone [...] Read more.

Dental rehabilitation with titanium implants may requires the optimization of techniques and materials when oral conditions affect the successful treatment result. Thus, this study aims to customize the surface of titanium implants with bioactive vitamin D3 molecules to increase the performance of bone repair. The surfaces were functionalized following the “dip-coating” incorporation method with vitamin D3 in a solution of 1000 I.U./goat. The work was carried out in two stages: (I) physicochemical and biological tests (in vivo) in order to characterize and validate the vitamin D3 surface as well as its ability to affect peri-implant bone biomechanics; and (II) in vitro experiments to characterize viability responses, interaction and cell mineralization capacity. Scanning electron microscopy showed that the creation of vitamin D3 films is stable and homogeneous, while the in vivo results showed an increase in the biomechanical and microarchitectural capacity of the bone when vitamin D3 implants were used. Furthermore, the application of functionalized surfaces proved effective in promoting cell interaction and bone mineralization processes while preserving cell viability and capacity. In conclusion, the delivery of bioactive molecules based on vitamin D3 promotes changes in the surface microstructure of titanium, enabling an increase in the structural characteristics of bone tissue that result in an improvement in bone repair and peri-implant biomechanics. Full article

(This article belongs to the Special Issue Novel Insights of Bone Repair: Strategies for Improvement, Microscopic, Molecular and Ultrastrastructural Aspects)

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18 pages, 1911 KiB

Open AccessArticle

Evolutionary Origin and Genetic Diversity of the Pannonian Ecotype of Apis mellifera carnica Colonies in Hungary Based on Mitochondrial DNA and Microsatellite Markers

by Reka Balazs, Tamas Gergely Molnar, Erika Edvine Meleg, Andras Hidas, Edit Zajacz, Timea Racz and Nora Palinkas-Bodzsar

Biology 2025, 14(5), 475; https://doi.org/10.3390/biology14050475 - 25 Apr 2025

Abstract

Honey bees are crucial to both the ecosystem and the economy. However, they are subject to different influences that can lead to a loss of genetic diversity. In this study, we used mitochondrial DNA information and nuclear microsatellite markers to compare worker individuals [...] Read more.

Honey bees are crucial to both the ecosystem and the economy. However, they are subject to different influences that can lead to a loss of genetic diversity. In this study, we used mitochondrial DNA information and nuclear microsatellite markers to compare worker individuals that strictly meet the morphological breed standard of the Pannonian bee in Hungary to those with morphological disorders (yellow color of the abdomen). Additionally, this study involves Carniolan colonies from two European countries and other bee subspecies as a reference group that might have crossed into the Pannonian bee. As for the mitochondrial DNA, the combined assessment of COI and 16S genes identified six haplotypes. Based on the tRNAleu-cox2 intergenic region (E2/H2), our samples belonged to the C evolutionary lineage. According to the microsatellite data, the level of inbreeding was low in all groups investigated, and only the genotypes of the Pannonian bee showed significant deviation from the Hardy–Weinberg equilibrium state. Cluster analysis and the Discriminant Analysis of Principal Components showed that bees that failed the morphological breed identification had started to diverge genetically from those meeting the breed standards, becoming more similar to the Carniolan bee. Our findings suggest that the genetic status of the Pannonian bees investigated in this study is satisfactory. However, in order to maintain an adequate level of diversity, periodic genetic monitoring of the colonies is necessary. Full article

(This article belongs to the Section Genetics and Genomics)

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17 pages, 2597 KiB

Open AccessArticle

Mutation of the Polygalacturonase Gene AcoPG3 Deferred Softening of Pineapple Fruit

by Haiyan Shu, Aiping Luan, You Wang, Junhu He, Qing Wei, Rulin Zhan and Shenghe Chang

Biology 2025, 14(5), 474; https://doi.org/10.3390/biology14050474 - 25 Apr 2025

Abstract

A large number of pineapple (Ananas comosus) fruits are discarded in China every year due to softening. However, the underlying molecular mechanism is still unknown. AcoPG3 (GenBank accession number: XM020243935), a pineapple gene of polygalacturonase, was found to be the major [...] Read more.

A large number of pineapple (Ananas comosus) fruits are discarded in China every year due to softening. However, the underlying molecular mechanism is still unknown. AcoPG3 (GenBank accession number: XM020243935), a pineapple gene of polygalacturonase, was found to be the major gene responsible for the softening of pineapple fruit. Fruit of AcoPG3-overexpressing tomato (Solanum lycopersicum var. Jingfan 101) begins to soften 9 days earlier than that transformed with a net vector. Fruit of AcoPG3-overexpressing pineapple (APG3-2) begins to soften 6 days earlier than that transformed with a net vector. Fruit of MPG3-1, a pineapple line in which AcoPG3 is mutated, begins to soften 31 days later than that transformed with a net vector. The sequence of polygalacturonase activities in fruit from the highest to the lowest was APG3-2, wild type, MPG3-1. The same sequences were also found in the liquid content of apoplast and the electrolyte leakage of pineapple pulp. The order of methyl-esterified pectin content in the pulp cell wall, from the highest to the lowest, was MPG3-1, wild type, and APG3-2. The same order was also observed for the contents of non-methyl-esterified homogalacturonan and rhamnogalacturonan-I in the pulp cell wall. The AcoPG3 mutation resulted in a decrease in polygalacturonase activity in pineapple fruit, decreasing the degradation of methyl-esterified pectin, non-methyl-esterified homogalacturonan, galactan and rhamnogalacturonan-I in the pulp cell wall. Fruit softening can be deferred, and the shelf life can be extended by mutating the AcoPG3 gene. Full article

(This article belongs to the Special Issue Advancing Crop Nutritional Quality Through Genomic Approaches)

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18 pages, 20269 KiB

Open AccessArticle

Immunomodulation by 4-Hydroxy-TEMPO (TEMPOL) and Dimethyl Fumarate (DMF) After Ventral Root Crush (VRC) in C57BL/6J Mice: A Flow Cytometry Analysis

by Maria Fernanda Vannucci Balzani, Lilian de Oliveira Coser and Alexandre Leite Rodrigues de Oliveira

Biology 2025, 14(5), 473; https://doi.org/10.3390/biology14050473 - 25 Apr 2025

Abstract

Spinal motor nerve root lesions can happen after avulsion or crush, generating acute motoneuron death and synaptic loss, consequently, causing motor and sensory dysfunctions. Local response is mediated by astroglial and microglial cells, giving rise to a pro-inflammatory profile. TEMPOL and DMF are [...] Read more.

Spinal motor nerve root lesions can happen after avulsion or crush, generating acute motoneuron death and synaptic loss, consequently, causing motor and sensory dysfunctions. Local response is mediated by astroglial and microglial cells, giving rise to a pro-inflammatory profile. TEMPOL and DMF are drugs that have been studied in our laboratory after spinal cord nerve root injuries and have demonstrated significant results in terms of neuroprotection and immunomodulation, decreasing the inflammation process. In the present work, a flow cytometry approach was used to evaluate cellular responses to injury and immunomodulation. For this, injured animals received TEMPOL, DMF or vehicle once a day for 7, 14 or 28 days of treatment. Flow cytometry multiparametric analysis allowed the quantification of different pro- and anti-inflammatory glial, macrophage and lymphocyte markers. Contrasting with the vehicle treated counterpart, TEMPOL and DMF led to downregulation of pro-inflammatory cytokines in astrocytes and microglia subpopulations, but did not show significant results in increasing anti-inflammatory phenotypes. As for macrophage and lymphocyte subpopulations, both treatments showed a balance between pro- and anti-inflammatory phenotypes. Therefore, it was concluded that both drugs exhibit immunomodulatory action, contributing to a pro-regenerative profile in the tissue. Full article

(This article belongs to the Special Issue Regenerative Biology: Regeneration After Spinal Cord and Peripheral Nerve Injury)

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30 pages, 442 KiB

Open AccessReview

Oxidative Stress Biomarkers in Fish Exposed to Environmental Concentrations of Pharmaceutical Pollutants: A Review

by Lăcrămioara Grădinariu, Mirela Crețu, Camelia Vizireanu and Lorena Dediu

Biology 2025, 14(5), 472; https://doi.org/10.3390/biology14050472 - 25 Apr 2025

Abstract

Pharmaceutical residues are a result of human activities and are increasingly recognized as environmental contaminants that pose significant risks to aquatic ecosystems. There are many well-known pathways (agricultural runoff, veterinary use, human excretion, etc.) for the entry of these pharmaceuticals into the aquatic [...] Read more.

Pharmaceutical residues are a result of human activities and are increasingly recognized as environmental contaminants that pose significant risks to aquatic ecosystems. There are many well-known pathways (agricultural runoff, veterinary use, human excretion, etc.) for the entry of these pharmaceuticals into the aquatic environment, and among them, the inability to remove these biologically active compounds from wastewater treatment plant (WWTP) effluents is becoming increasingly significant in the context of societal evolution. Once introduced, pharmaceuticals persist at low concentrations, exerting sub-lethal effects that disrupt the physiological processes of aquatic organisms. Among these effects, oxidative stress (OS) has gained attention as a key mechanism that is induced by pharmaceutical toxicity, serving as a sentinel indicator of homeostatic disturbance. Thus, studying OS biomarkers in fish is crucial for understanding the extent of pharmaceutical pollution, as these biomarkers provide early warning signals of environmental stress and help assess sub-lethal impacts on aquatic organisms. Their application, correlated with other eco-physiological investigations, can improve ecological risk assessments. In this context, this review explores the role of OS biomarkers by assessing the effects of pharmaceutical contaminants on fish. It highlights the utility and limitations of these biomarkers for environmental monitoring, while also identifying key research gaps—particularly regarding long-term ecological consequences. Full article

(This article belongs to the Section Toxicology)

16 pages, 2324 KiB

Open AccessReview

Recent Progress in Rice–Xanthomonas oryzae Interactions

by Yuting Qi, Qiong Rao, Chenglong Lu, Junyi Gong and Yuxuan Hou

Biology 2025, 14(5), 471; https://doi.org/10.3390/biology14050471 - 25 Apr 2025

Abstract

Rice bacterial blight (BB) and bacterial leaf streak (BLS), caused by Xanthomonas oryzae pv. oryzae (Xoo) and Xanthomonas oryzae pv. oryzicola (Xoc), respectively, are among the most devastating bacterial diseases threatening global rice production. The interactions between rice and [...] Read more.

Rice bacterial blight (BB) and bacterial leaf streak (BLS), caused by Xanthomonas oryzae pv. oryzae (Xoo) and Xanthomonas oryzae pv. oryzicola (Xoc), respectively, are among the most devastating bacterial diseases threatening global rice production. The interactions between rice and Xanthomonas oryzae are complex and dynamic, involving recognition, attack, defense, and adaptation mechanisms enacted by both the rice host and the pathogens. This review summarizes recent advances in understanding rice–Xanthomonas oryzae interactions, focusing on infection models, pathogenic mechanisms, and immune responses elicited by Xanthomonas oryzae. Special attention is devoted to the roles of transcription activator-like effectors (TALEs) and non-TALE effectors in pathogenicity, the functions of resistance (R) genes in defense, and the interconnected molecular networks of interactions derived from multi-omics approaches. Understanding these interactions is essential for developing effective disease-resistance strategies and creating elite disease-resistant rice varieties. Full article

(This article belongs to the Special Issue Regulatory Mechanisms of Plant Stress Response)

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16 pages, 9628 KiB

Open AccessArticle

Bactericidal Effect and Mechanism of Polyhexamethylene Biguanide (PHMB) on Pathogenic Bacteria in Marine Aquaculture

by Lanting Wu, Chunyuan Wang, Yingeng Wang, Yongxiang Yu, Zheng Zhang, Cuiping Ma, Xiaojun Rong, Ling Chen, Meijie Liao and Yapeng Yang

Biology 2025, 14(5), 470; https://doi.org/10.3390/biology14050470 - 25 Apr 2025

Abstract

Guanidine disinfectants are cationic polymers recognized for their effective sterilization properties and their ability to prevent bacterial resistance. As a result, they are widely utilized in medical, healthcare, household, and animal husbandry settings. However, the bactericidal effects and mechanisms of guanidine in marine [...] Read more.

Guanidine disinfectants are cationic polymers recognized for their effective sterilization properties and their ability to prevent bacterial resistance. As a result, they are widely utilized in medical, healthcare, household, and animal husbandry settings. However, the bactericidal effects and mechanisms of guanidine in marine aquaculture systems remain unclear due to the polymeric nature of guanidine ions and the complexity of marine environments. The inhibitory effects and bactericidal mechanisms of polyhexamethylene biguanide (PHMB) on key pathogens and probiotics are examined in this study. It was shown that PHMB had inhibitory effects on Vibrio parahaemolyticus (VP), Photobacterium damselae subsp. damselae (PDD), Bacillus subtilis (BS), Escherichia coli (EPEC), and Staphylococcus aureus (SAU), with minimum inhibitory concentrations (MICs) ranging from 3.91 to 125.0 µg/mL, and minimum bactericidal concentrations (MBCs) from 15.63 to 250.0 µg/mL. A stronger bactericidal effect of PHMB on marine bacteria compared to EPEC and SAU was exhibited. It was shown in ion interference experiments that the addition of calcium ions reduced the bactericidal effectiveness of PHMB against VP and PDD by 87.73% and 53.35%, respectively. At a PHMB concentration of 62.50 µg/mL, minor changes in cell surface potential energy (CSPE) were exhibited by Gram-positive bacteria (SAU and BS), while more significant alterations were shown by Gram-negative pathogens. It was revealed by propidium iodide staining and scanning electron microscopy (SEM) analysis that the bacterial cell membrane was directly disrupted by PHMB. DNA and RNA release analysis further revealed that following PHMB treatment, changes in membrane permeability were exhibited by Gram-negative pathogens, with a significant increase in extracellular DNA content as PHMB concentration increased. No such effect was observed in Gram-positive bacteria. Additional evidence was provided by the findings that PHMB effectively inhibits bacterial pathogens in mariculture systems, with a significantly stronger inhibitory effect on Gram-negative pathogens than on Gram-positive bacteria. These results indicated that PHMB could serve as a new antimicrobial agent in mariculture. Full article

(This article belongs to the Special Issue Sustainable Management of Aquatic Animal Health: Advances in Immunology, Pathogenesis, and Innovative Disease Control Strategies)

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15 pages, 4240 KiB

Open AccessArticle

The Application of Multiple Strategies to Enhance Methylparaben Synthesis Using the Engineered Saccharomyces cerevisiae

by Lu Liu, Kai Wang, Pan Liu, Limin Ba, Huan Liu and Yanhui Liu

Biology 2025, 14(5), 469; https://doi.org/10.3390/biology14050469 - 25 Apr 2025

Abstract

Methylparaben (MP) is an important member of the paraben family of aromatic compounds, which is under great demand in the industrial market as an antibacterial agent, preservative, and feed additive, and also has potential application value in the preparation of bio-based polyetherester materials. [...] Read more.

Methylparaben (MP) is an important member of the paraben family of aromatic compounds, which is under great demand in the industrial market as an antibacterial agent, preservative, and feed additive, and also has potential application value in the preparation of bio-based polyetherester materials. However, the current chemical production method of MP has various problems, such as serious environmental pollution, its dependence on petrochemical resources, and the generation of different types of waste. It is of great significance to develop an environmentally friendly MP synthesis method via synthetic biology. In this work, Saccharomyces cerevisiae was used as the host to construct the biosynthetic pathway of MP and various metabolic engineering strategies were applied to break the bottlenecks in the synthesis process, including the regulation of the rate-limiting steps in the endogenous shikimate pathway, the enhancement of central carbon flux via knocking out competitive pathways and promoting precursors synthesis, and the improvement of the exogenous enzyme expression using promoter engineering. The final engineered S. cerevisiae could produce 68.59 mg/L MP in shake flasks, which was the highest titer of MP synthesized by S. cerevisiae so far. It was indicated that the strategies applied in our work were effective in promoting the synthesis of MP, which not only laid an important foundation for the industrial production of MP, but also provided a platform for the synthesis of other aromatic compounds. Full article

(This article belongs to the Special Issue Advances in Systems Metabolic Engineering for Biochemicals Production)

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