Biology

19 pages, 5397 KiB

Open AccessArticle

Qinghai Province (Tibetan Plateau): Quantifying the Influence of Climate Change and Human Activities on Vegetation Net Primary Productivity and Livestock Carrying Capacity Growth Potential

by Qian Wei, Bingrong Zhou and Wenying Wang

Biology 2025, 14(5), 494; https://doi.org/10.3390/biology14050494 (registering DOI) - 1 May 2025

Abstract

Quantitative exploration of shifts in regional vegetation net primary productivity (NPP) and their driving factors holds immense importance in unraveling the mechanisms steering vegetation alterations, comprehending the impact of climate variations and human interventions on NPP, and guiding ecological management. Despite this significance, [...] Read more.

Quantitative exploration of shifts in regional vegetation net primary productivity (NPP) and their driving factors holds immense importance in unraveling the mechanisms steering vegetation alterations, comprehending the impact of climate variations and human interventions on NPP, and guiding ecological management. Despite this significance, there is a scarcity of research reports on Qinghai Province. The aim is to dissect the influences of climate change and human activities on Qinghai’s vegetation NPP and to estimate the growth potential of livestock carrying capacity. This study addresses the gap by juxtaposing the characteristics of climate-induced potential NPP changes, computed using the Zhou Guangsheng model, with actual NPP changes, calculated via the CASA model. Our findings underscore climate factors as the predominant drivers of Qinghai’s vegetation NPP, accounting for 64.6% of the total area. Regions influenced by human activities contribute 34.3%, while unchanged areas constitute 2%. Climate emerges as the primary catalyst for increased vegetation NPP in Qinghai, encompassing 87% of the total area, with 73% attributed to climate factors across all counties. Conversely, human activities predominantly lead to decreased NPP, affecting 11% of the total area. Notably, 99% of the reduced NPP is attributable to human activities, concentrated in Golmud, Mangya, and Dulan counties in the northwest. Examining the growth potential of livestock carrying capacity from 1982 to 2018 reveals a consistent upward trajectory in Qinghai Province. The average annual growth potential per unit area escalates from 0.38 SHU/ha in 1982 to 0.56 SHU/ha in 2018. By 2018, regions exhibiting positive growth potential encompass 95% of the province, with areas exceeding 1 SHU/ha constituting 9%, primarily situated in the eastern part of Qinghai Province. Full article

(This article belongs to the Section Ecology)

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16 pages, 2377 KiB

Open AccessArticle

Complete Mitochondrial Genome of Chlorogomphus papilio (Odonata: Anisoptera: Chlorogomphidae) and Phylogenetic Analyses

by Xiaoxiao Jin, Xiaojia Lin, Simeng Wang and Jie Fang

Biology 2025, 14(5), 493; https://doi.org/10.3390/biology14050493 (registering DOI) - 1 May 2025

Abstract

This study aimed to elucidate the mitochondrial genome organization of Chlorogomphus papilio and the phylogenetic relationships of Chlorogomphidae. We used the Illumina MiSeq sequencing platform to sequence the mitochondrial genome of C. papilio, which was subsequently assembled, annotated, and analyzed. Bayesian inference, [...] Read more.

This study aimed to elucidate the mitochondrial genome organization of Chlorogomphus papilio and the phylogenetic relationships of Chlorogomphidae. We used the Illumina MiSeq sequencing platform to sequence the mitochondrial genome of C. papilio, which was subsequently assembled, annotated, and analyzed. Bayesian inference, maximum likelihood, and maximum parsimony methods were employed to construct the mitochondrial phylogenetic tree of 25 species of Chlorogomphidae based on 16S rRNA and cox1 genes. We observed that the mitochondrial genome of C. papilio is 15,251 bp in length and includes 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and a non-coding control region. All PCGs start with a typical ATN codon. While cox1, cox2, cox3, and nad5 end with an incomplete termination codon (T), the remaining PCGs terminate with TAG. The secondary structure of the 22 tRNAs showed that only the trnS1 gene lacked the dihydrouracil arm (DHU arm), whereas the rest formed a typical cloverleaf structure. Additionally, 32 G-U mismatches were observed in the secondary structure. Phylogenetic analyses indicated that C. papilio and C. magnificus are sister species. Divergence time analyses indicated that Chlorogomphidae originated around 111.04 Ma, with C. papilio diverging from the common ancestor shared with C. magnificus approximately 58.51 Ma. This divergence is likely linked to the Paleocene–Eocene Thermal Maximum (PETM) and the tectonic uplift of the Himalayas, which created warm, humid habitats and contributed to geographic isolation. This study contributes to a better understanding of the mitochondrial genome and phylogeny of C. papilio, providing valuable molecular markers for further genetic studies. Full article

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19 pages, 2546 KiB

Open AccessArticle

Physical Modification of Whey Protein by Interacting with Methyl Hesperidin: Impacts on Antioxidant Activity and Underlying Mechanism

by Songbo Ma, Shuang Yang, Suqi Yang, Lili Chen, Meilan Yuan, Yong Jiang, Li Zhao and Chunqing Bai

Biology 2025, 14(5), 492; https://doi.org/10.3390/biology14050492 (registering DOI) - 1 May 2025

Abstract

In this work, the possibility of enhancing the antioxidant capacity of whey protein (WP) through non-covalent interaction with methyl hesperidin (MH, a hesperidin derivative) was assessed. The underlying mechanism was analyzed in terms of multi-spectroscopy methods, thermodynamic analysis, and molecular docking simulation. The [...] Read more.

In this work, the possibility of enhancing the antioxidant capacity of whey protein (WP) through non-covalent interaction with methyl hesperidin (MH, a hesperidin derivative) was assessed. The underlying mechanism was analyzed in terms of multi-spectroscopy methods, thermodynamic analysis, and molecular docking simulation. The data indicated that MH could spontaneously bind to WP and form a non-fluorescent complex when physically mixed together. The presence of MH statically quenched the intrinsic fluorescence of WP, changed the microenvironment of amino acid residue, and altered the secondary and tertiary structure of WP, which in turn enhanced the antioxidant capacity of WP. The underlying mechanism may be assigned to hydrophobic interactions, which promoted MH inserting itself into the hydrophobic cavity in WP. The methoxy group on the B ring of MH may form hydrogen bonds with amino acids, which enhances the freedom of the phenyl hydroxyl group, resulting in higher antioxidant capacity than other hesperidin structural analogs. This research would enrich the theoretical basis about the interaction between protein and hesperidin-based derivatives, and it may supply valuable information for its application in the food and medicine fields. Full article

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29 pages, 3900 KiB

Open AccessArticle

Efficacy and Safety of Visible and Near-Infrared Photobiomodulation Therapy on Astenospermic Human Sperm: Wavelength-Dependent Regulation of Nitric Oxide Levels and Mitochondrial Energetics

by Matilde Balbi, Rachele Lai, Sara Stigliani, Claudia Massarotti, Matteo Bozzo, Paola Scaruffi, Silvia Ravera and Andrea Amaroli

Biology 2025, 14(5), 491; https://doi.org/10.3390/biology14050491 (registering DOI) - 1 May 2025

Abstract

Male infertility is a growing global concern, with asthenozoospermia being an important contributing factor. Mitochondrial dysfunction and changes in the metabolism of nitric oxide (NO) are key determinants of reduced sperm motility. This study investigates the effects of photobiomodulation (PBM) with visible and [...] Read more.

Male infertility is a growing global concern, with asthenozoospermia being an important contributing factor. Mitochondrial dysfunction and changes in the metabolism of nitric oxide (NO) are key determinants of reduced sperm motility. This study investigates the effects of photobiomodulation (PBM) with visible and near-infrared (NIR) laser light on sperm of asthenozoospermic patients, focusing on mitochondrial energetic status, oxidative stress, and NO dynamics. Semen samples were irradiated at 450 nm, 635 nm, 810 nm, 940 nm, and 1064 nm at different power levels (0.25, 0.50, 1.00, and 2.00 W) for 60 s on a spot area of 1 cm². ATP and AMP levels, oxidative stress markers, and NO concentrations were assessed at 10 and 60 min after irradiation, with the ATP/AMP ratio calculated as an index of cellular energy balance. The results show that the PBM modulates the energetic status of spermatozoa in a way dependent on wavelength and dose. Irradiation at 810 nm produced the most marked improvement in energetic status, whereas 635 nm exposure led to a significant decrease in cellular energy levels. NO levels showed a biphasic response, correlated with the visible range and with energy metabolism at 810 nm. Irradiation with 635 nm induced higher NO production with respect to the other wavelengths. Our findings suggest that PBM mainly involves mitochondrial photoreceptors and potentially the heme and flavin groups of nitric oxide synthases, facilitating electron transitions, enhancing the effectiveness of oxidative phosphorylation, and optimizing enzymatic activity. At longer wavelengths (940 nm and 1064 nm), interactions with water and lipids may introduce additional variables that affect membrane fluidity and mitochondrial function differently from shorter wavelengths. Full article

(This article belongs to the Special Issue Male Disorders: Fertility Care and Support, Preservation and Restoration)

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28 pages, 3421 KiB

Open AccessArticle

The Impact of Nitrogen and Phosphorus Interaction on Growth, Nutrient Absorption, and Signal Regulation in Woody Plants

by Xiaan Tang, Yi Zhang, Panpan Meng, Yingke Yuan, Changhao Li, Xiaotan Zhi and Chunyan Wang

Biology 2025, 14(5), 490; https://doi.org/10.3390/biology14050490 (registering DOI) - 30 Apr 2025

Abstract

This article methodically reveals how, in woody plants (poplar), the interaction between N and P coordinates root structure and nutrient absorption through a complex hormone signaling network. This study bridges a significant gap in our knowledge of nutrient interaction networks. The results demonstrate [...] Read more.

This article methodically reveals how, in woody plants (poplar), the interaction between N and P coordinates root structure and nutrient absorption through a complex hormone signaling network. This study bridges a significant gap in our knowledge of nutrient interaction networks. The results demonstrate that NO₃⁻ significantly enhances the gene expression and enzymatic activity of organic acid synthases (MDH, PEPC) and APs. Furthermore, it synergizes with IAA/ABA signals to refine root structure, enhancing the surface area for P absorption. In low Pi availability environments, NO₃⁻ further promotes P recycling by simultaneously boosting the levels of Pi transport proteins (notably, the PHO family), facilitating myo-inositol phosphate metabolism (via IMP3/ITPK1-mediated PP-InsPs degradation), and augmenting IAA/SA signals. Pi induces the activity of N assimilation enzymes (GS/GOGAT/GDH), facilitating nitrogen metabolism. However, in the absence of N, it leads to a metabolic imbalance characterized by high enzymatic activity but low efficiency. Alternatively, adequate N availability allows Pi to improve root robustness and N assimilation efficiency, mediated by IAA/GA accumulation and ABA signaling (e.g., SNRK2/ABF). We propose the existence of an intricate network in poplar, orchestrated by transcriptional cascades, metabolic regulation, and hormonal synergism. Key modules such as SPX-PHR, NLA, HHO2, and MYB59 are likely central to this network’s function. These findings offer a foundational framework for the development of molecular breeding and precise fertilization strategies, enhancing the efficient use of N and P in forestry. Full article

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15 pages, 3125 KiB

Open AccessArticle

Mutagenesis Targeting the S¹⁵³ Residue Within the Transmembrane β-Hairpin of Mosquito-Larvicidal Mpp46Ab Affects Its Toxicity and the Synergistic Toxicity with Cry4Aa

by Tohru Hayakawa, Syun Yamaoka, Mami Asakura, Minako Hirano and Toru Ide

Biology 2025, 14(5), 489; https://doi.org/10.3390/biology14050489 (registering DOI) - 30 Apr 2025

Abstract

We constructed a library of Mpp46Ab mutants, in which S¹⁵³ within the transmembrane β-hairpin was randomly replaced by other amino acids. Mutagenesis and subsequent primary screening yielded 10 different Mpp46Ab mutants in addition to the wild type. Remarkably, S¹⁵³ was replaced [...] Read more.

We constructed a library of Mpp46Ab mutants, in which S¹⁵³ within the transmembrane β-hairpin was randomly replaced by other amino acids. Mutagenesis and subsequent primary screening yielded 10 different Mpp46Ab mutants in addition to the wild type. Remarkably, S¹⁵³ was replaced with a more hydrophobic amino acid in most of the mutants, and the S153I mutant in particular exhibited significantly increased toxicity. Electrophysiologic analysis using artificial lipid bilayers revealed that the single-channel conductance and P_K/P_Cl permeability ratio were significantly increased for S153I pores. This suggests that the formation of highly ion-permeable and highly cation-selective toxin pores increases the influx of cations and water into cells, thereby facilitating osmotic shock. In addition, the S153F, S153L, and S153I mutants exhibited significantly reduced synergistic toxicity with Cry4Aa. Electrophysiologic analysis showed that the S153F, S153L, and S153I mutants form toxin pores with a significantly reduced P_K/P_Na permeability ratio and a significantly increased P_K/P_Ca permeability ratio compared to wild-type pores. Thus, our results suggest that pore formation is central to the insecticidal activity of Mpp46Ab and that the ion permeability of toxin pores is a potential indicator correlated with both toxicity and synergistic toxicity with other toxins. Full article

(This article belongs to the Section Toxicology)

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15 pages, 3528 KiB

Open AccessArticle

Antiepileptic Effects of Acorus tatarinowii Schott in a Rat Model of Epilepsy: Regulation of Metabolic Axes and Gut Microbiota

by Liang Chen, Jiaxin Li, Wenhui Zhang and Jiepeng Wang

Biology 2025, 14(5), 488; https://doi.org/10.3390/biology14050488 - 29 Apr 2025

Abstract

As a phytotherapeutic agent with historical applications in epilepsy management, Acorus tatarinowii Schott (ATS) remains pharmacologically enigmatic, particularly regarding its pathophysiological mechanisms. This knowledge gap significantly hinders the clinical application of ATS-based treatments. To explore the potential of ATS in combating epileptogenesis, we [...] Read more.

As a phytotherapeutic agent with historical applications in epilepsy management, Acorus tatarinowii Schott (ATS) remains pharmacologically enigmatic, particularly regarding its pathophysiological mechanisms. This knowledge gap significantly hinders the clinical application of ATS-based treatments. To explore the potential of ATS in combating epileptogenesis, we utilized a pentylenetetrazole (PTZ)-induced chronic epilepsy rat model. Brain metabolomic analysis was performed by ultra-performance liquid chromatography coupled with mass spectrometry (UPLC/MS). Principal component analysis (PCA) and orthogonal projections to latent structures-discriminant analysis (OPLS-DA) were performed for screening differential metabolites. Gut microbiota composition was analyzed through 16S rRNA gene sequencing and examined using Spearman correlation analysis. The results show that oral ATS (50 mg/kg) significantly improved the seizure latency and pathology of rats with epilepsy. Ascorbate and aldarate metabolism, glycerophospholipid metabolism, arachidonic acid metabolism, and intestinal flora were crucial for ATS’s ability to counteract epilepsy. The therapeutic effects of ATS against epilepsy were investigated with brain metabolomics and gut microbiota analysis, providing the basis for further comprehensive research. Full article

(This article belongs to the Special Issue Animal Models of Neurodegenerative Diseases)

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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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Graphical abstract

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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