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14 pages, 2709 KB  
Article
Transcriptome Analysis of the Pathogenic Mechanism of the Novel Pathogenic Fungus Bipolaris fujianensis in Chinese Fir (Cunninghamia lanceolata) Shoot Blight
by Bin Lin, Peiwen Yang, Ruifeng Luo, Ying Lu, Zhe Li, Menglan Shang, Wangdong Xu, Zihui Huang, Guanghong Liang and Qinghua Zhang
Biology 2025, 14(11), 1488; https://doi.org/10.3390/biology14111488 (registering DOI) - 24 Oct 2025
Abstract
Bipolaris fujianensis is a novel pathogenic species causing Chinese fir (Cunninghamia lanceolata) shoot blight (CFSB), first discovered in Nanping City, Fujian Province. However, its molecular pathogenic mechanisms remain largely unknown. Elucidating theses mechanisms has the potential of aiding future developments in [...] Read more.
Bipolaris fujianensis is a novel pathogenic species causing Chinese fir (Cunninghamia lanceolata) shoot blight (CFSB), first discovered in Nanping City, Fujian Province. However, its molecular pathogenic mechanisms remain largely unknown. Elucidating theses mechanisms has the potential of aiding future developments in disease management and resistance breeding in Chinese fir. In this regard, we examined the expression pattern of B. fujianensis grown on PDA (BGPDA), and during infection of Chinese fir at 24 h (BGCF-E), 48 h (BGCF-M), and 5 d (BGCF-L) post inoculation. Comparative transcriptome analysis identified 4133 differentially expressed genes (DEGs), including 1778 upregulated and 2355 downregulated in BGCF compared with BGPDA. During the infection process, Gene ontology (GO) enrichment analysis indicated that transporters and hydrolases in the molecular function categories play essential roles. Kyoto encyclopedia of genes and genomes (KEGG) analyses showed glycolysis/gluconeogenesis, carbon metabolism, and secondary metabolite biosynthesis were the major enriched pathways. Furthermore, this pathogen could produce diterpenoid toxin ophiobolin F, with cytochrome P450 and MFS transport proteins likely involved in its biosynthesis and transport predicted by RT-qPCR. Full article
(This article belongs to the Section Microbiology)
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17 pages, 4691 KB  
Article
Vitamin B12 Protects the Exacerbated Ischemia–Reperfusion Injury-Induced Chronic Kidney Disease in Mice with Genetically Increased Elmo1
by Jiayi Zhou, Yuye Wang, John Hagaman, Qing Ma, J. Charles Jennette, Meitong Chen, Xianwen Yi, Yukako Kayashima, Nobuyo Maeda-Smithies and Feng Li
Antioxidants 2025, 14(11), 1277; https://doi.org/10.3390/antiox14111277 (registering DOI) - 24 Oct 2025
Abstract
Ischemia–reperfusion injury (IRI) is a leading cause of acute kidney injury (AKI) and a major driver of progression to chronic kidney disease (CKD). Oxidative stress is recognized as a central mediator of this transition. Engulfment and Cell Motility 1 (ELMO1) regulates cytoskeletal remodeling [...] Read more.
Ischemia–reperfusion injury (IRI) is a leading cause of acute kidney injury (AKI) and a major driver of progression to chronic kidney disease (CKD). Oxidative stress is recognized as a central mediator of this transition. Engulfment and Cell Motility 1 (ELMO1) regulates cytoskeletal remodeling and reactive oxygen species generation through Rac1 activation, but its contribution to CKD progression remains poorly defined. To investigate this, we established a unilateral renal IRI model in wild-type (WT) and Elmo1-overexpressing (Elmo1H/H) mice and evaluated kidney function one and four months post-IRI. Compared with WT, Elmo1H/H mice developed more severe kidney dysfunction, including an elevated plasma cystatin C and urinary albumin-to-creatinine ratio, reduced estimated glomerular filtration rate (eGFR), and pronounced fibrosis and glomerular injury observed by light and electron microscopy. Molecular analysis confirmed the dysregulation of redox-related pathways by RT-qPCR, with RNA sequencing showing enrichment of oxidative stress signatures. A subset of mice received chronic vitamin B12 (B12) supplementation following IRI to evaluate its therapeutic potential. Vitamin B12 supplementation improved kidney function, reduced fibrosis, preserved glomerular structure, and normalized the expression of antioxidant genes in both groups. These findings identify Elmo1 as a driver of redox-mediated kidney injury and support vitamin B12 as a promising antioxidant therapy for AKI-to-CKD progression. Full article
(This article belongs to the Special Issue Targeting Oxidative Stress in Ischemia/Reperfusion Injury)
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16 pages, 2312 KB  
Article
Association of Diarrheagenic Escherichia coli Virulence Genes and Antimicrobial Resistance Genes in an Interface Model of Swine Colonization and Human Diarrhea in Mexico
by Elsa M. Tamayo-Legorreta, Eduardo Moreno-Vazquez, Jackeline Cerón-López, Fabian Tellez-Figueroa, Rosa M. Medina-Julián, Hugo López-Gatell and Celia M. Alpuche-Aranda
Microorganisms 2025, 13(11), 2436; https://doi.org/10.3390/microorganisms13112436 - 23 Oct 2025
Abstract
The accelerated spread of antimicrobial resistance, driven by the misuse of antibiotics in the context of ‘One Health’, is a public health concern worldwide due to the increasing number of human infections associated with foodborne and/or environmental pathogens, including multidrug-resistant Escherichia coli ( [...] Read more.
The accelerated spread of antimicrobial resistance, driven by the misuse of antibiotics in the context of ‘One Health’, is a public health concern worldwide due to the increasing number of human infections associated with foodborne and/or environmental pathogens, including multidrug-resistant Escherichia coli (E. coli). Monitoring pathogenic and multidrug-resistant E. coli isolates is essential for sustainable disease management in swine and human diarrhea cases. This study was designed to assess the multidrug resistance (MDR) profiles and virulence-associated gene (pathotypes) frequency of pathogenic and commensal E. coli strains by antimicrobial susceptibility testing and endpoint PCR among 983 E. coli isolates from swine fecal material and 425 stool isolates from human diarrhea cases, obtained from a closely monitored population between March 2015 and April 2016. Our results reveal that >50% of E. coli strains isolated from swine were resistant to nalidixic acid (78.94%), tetracycline (72%), ampicillin (55.54%), and co-trimoxazole (53.91%), and that, in humans, the highest resistance was observed in tetracycline (71.77%), nalidixic acid (65.41%), ampicillin (57.88%), and co-trimoxazole (53.88%). A lower frequency of resistance to ciprofloxacin was demonstrated in both swine (23.4%) and humans (15.3%), and minimal resistance to third-generation cephalosporins, ceftazidime (2.54%), and cefotaxime (2.44%) was observed in swine; however, resistance to these cephalosporins is much higher at 14.6% and 11.53% in humans. Among the pathotypes, EPEC was the most predominant (70.97%) in swine and DAEC (40%) in humans. In addition, pulsed-field gel electrophoresis separates the E. coli isolates into 22 patterns. Pathotypes such as EPEC and EHEC in swine highlight the need for surveillance and control in animal production to prevent zoonotic transmission. These results suggest that swine could act as a reservoir in human infection and that antimicrobial resistance could be transferred to humans from swine. Although we did not find clonal dissemination between the human and swine strains, the spread of similar multi-resistance profiles was observed, thus suggesting that multidrug resistance has been widely selected in this closed environment and may pose a public health risk. Full article
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27 pages, 825 KB  
Article
miRNA-146-a, miRNA-21, miRNA-143, miRNA-29-b and miRNA-223 as Potential Biomarkers for Atopic Dermatitis
by Sanja Jakovljevic, Iva Barjaktarovic, Dunja Jakovljevic, Olivera Levakov and Ljuba Vujanovic
Clin. Pract. 2025, 15(11), 192; https://doi.org/10.3390/clinpract15110192 - 23 Oct 2025
Abstract
Background/Objectives: Recently, epigenetic mechanisms have been recognized as crucial in atopic dermatitis development. The emphasis of this research was on expanding existing knowledge about the epigenetic aspects of atopic dermatitis, as well as identifying new molecules that could serve as disease biomarkers. [...] Read more.
Background/Objectives: Recently, epigenetic mechanisms have been recognized as crucial in atopic dermatitis development. The emphasis of this research was on expanding existing knowledge about the epigenetic aspects of atopic dermatitis, as well as identifying new molecules that could serve as disease biomarkers. Methods: The research was conducted as a cross-sectional study examining two groups: the group with atopic dermatitis (50 patients) and the control group (50 healthy adults). The serum levels of total immunoglobulin E (IgE) and eosinophil count (Eos%) were performed in routine laboratory analyses, and the detection of microRNAs from peripheral blood was performed using RT-PCR. Results: Analysis of selected miRNA expressions in patients with atopic dermatitis and controls revealed that only the expression and the relative expression of miRNA-146a were statistically significantly higher in patients with atopic dermatitis than in the control group (p = 0.042 and p = 0.021, respectively). There was a weak positive correlation between miRNA-146a expression and the eosinophilia/IgE level (r = 0.22 and r = 0.25, respectively). MiRNA-21, miRNA-29b, miRNA-143 and miRNA-223 were significantly upregulated in patients with higher SCORAD (p < 0.001, p < 0.001, p < 0.001 and p = 0.015, respectively). ROC curve analysis revealed the specificity of miRNA-146a as 82% and the sensitivity as 62%. The area under the ROC curve (AUC) was 0.7, indicating its diagnostic potential. Conclusions: Our findings imply that miRNA-146a might serve as a biomarker of atopic dermatitis, suggesting its relevance in the development of the disease, while miRNA-21, miRNA-29b, miRNA-143 and miRNA-223 may have an impact on disease progression. Our findings provide a preliminary basis that should precede validation through larger, multicentric studies and use in diagnostics, targeted personalized treatments and monitoring of treatment efficacy in atopic dermatitis. Full article
15 pages, 748 KB  
Article
City or Suburb, Resistance Flows: Wastewater-Borne ESKAPE and AMR Genes in Malaysian Hospitals
by Sophia Karen Bakon, Nur Fatihah Sholehah Zakaria, Mohd Azerulazree Jamilan, Hazimah Hashim and Zuraifah Asrah Mohamad
Antibiotics 2025, 14(11), 1058; https://doi.org/10.3390/antibiotics14111058 - 23 Oct 2025
Abstract
Background/Objectives: Hospital wastewater has become a major hotspot for the spread of antimicrobial resistance and the accumulation of antibiotic-resistant genes. We focused on ESKAPE pathogens isolated from hospital wastewater and their antibiotic profiles, which are known to cause nosocomial infections in hospitals. Screening [...] Read more.
Background/Objectives: Hospital wastewater has become a major hotspot for the spread of antimicrobial resistance and the accumulation of antibiotic-resistant genes. We focused on ESKAPE pathogens isolated from hospital wastewater and their antibiotic profiles, which are known to cause nosocomial infections in hospitals. Screening for antibiotic resistant genes in isolates and quantifying antibiotic residues in hospital wastewaters, which may reflect the amount of usage of antibiotics in Klang Valley city hospitals in Malaysia. Methods: Hospital wastewater treatment plants from Klang Valley city were selected based on the study criteria. ESKAPE pathogens were isolated and identified using 16S rRNA PCR, and antibiotic sensitivity testing was performed. Antibiotic resistant gene screenings were performed using quantitative PCR, and quantification of antibiotic residues in the effluent samples was performed using liquid chromatography-mass spectrometry (LC-MS). Results: Klebsiella pneumoniae with Multiple Antibiotics Resistance Index (MARi) ranging from low (0.29) to very high resistance (0.71) dominantly isolated among ESKAPE pathogens followed by Enterococcus faecium ranging from low (0.29) to critical resistance (1.0) from hospital wastewater in Klang Valley city. The ermB gene was the predominant antibiotic resistance gene identified in Klang Valley city hospitals and suburban hospitals, representing 45.5% of isolated E. faecium from suburban hospitals and 69% from city hospitals. Although the detection of antibiotic residues was minimal, vancomycin and ciprofloxacin were detected from the wastewater. Conclusions: These findings call for improved wastewater management and antibiotic stewardship to mitigate the spread of resistant pathogens from healthcare facilities into the environment. Full article
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15 pages, 3946 KB  
Article
Molecular Characterization and Expression Patterns of Sox3 and Sox30 Genes and Response to Exogenous Hormones in the Chinese Soft-Shelled Turtle (Pelodiscus sinensis)
by Kailin Xiao, Yue Li, Tong Ren, Ziman Wang, Junxian Zhu, Chen Chen, Liqin Ji, Xiaoli Liu, Xiaoyou Hong, Chengqing Wei, Haigang Chen, Xinping Zhu, Xiaofang Lai and Wei Li
Genes 2025, 16(11), 1249; https://doi.org/10.3390/genes16111249 - 22 Oct 2025
Abstract
Background/Objectives: The Sox transcription factor family is critical for gonadal development and sex differentiation in animals, yet its roles in chelonians, particularly in the Chinese soft-shelled turtle (Pelodiscus sinensis), have rarely been investigated. Methods: This study cloned and analyzed the cDNA [...] Read more.
Background/Objectives: The Sox transcription factor family is critical for gonadal development and sex differentiation in animals, yet its roles in chelonians, particularly in the Chinese soft-shelled turtle (Pelodiscus sinensis), have rarely been investigated. Methods: This study cloned and analyzed the cDNA sequences of Sox3 and Sox30 genes from P. sinensis, examining their amino acid sequences and structural properties. Real-time quantitative PCR (RT-qPCR) was used to assess the expression of these two genes in different adult tissues and at various stages of embryonic gonadal development. Additionally, the effects of exogenous hormones (17β-estradiol, E2 and 17α-Methyltestosterone, MT) on the expression of Sox3 and Sox30 were also investigated. Results: The results indicated that Sox3 showed significantly elevated expression in female gonads, kidney, brain, liver, lung, spleen, and muscle relative to male counterparts, displaying a female-biased expression pattern. In contrast, Sox30 showed a male-biased pattern, with higher expression in male gonads, spleen, muscle, brain, and liver than in females, showing expression. Both genes were expressed at low levels. Exogenous hormone treatments revealed that MT significantly downregulated Sox3 expression in female embryos, whereas E2 significantly enhanced Sox3 expression in male embryos. Furthermore, MT treatment significantly upregulated Sox30 expression in female embryos, and E2 treatment also significantly increased Sox30 expression in male embryos. Conclusions: These findings suggest that Sox3 and Sox30 play crucial roles in the gonadal development of P. sinensis, with Sox3 potentially involved in ovarian development and Sox30 in testicular maturation. Both genes are regulated by exogenous hormones, highlighting their importance in sex differentiation and gonadal development. This study provides valuable theoretical insights for further exploration of the molecular mechanisms of sex regulation in reptiles. Full article
(This article belongs to the Section Animal Genetics and Genomics)
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12 pages, 631 KB  
Article
Assessment of Migration of the Urethral Bulking Agent Zhoabex G® from the Urethral Injection Site to the Distant Organs in a Rabbit Model
by Bhagath Kumar Potu, Diaa Rizk, Muna Aljishi, Ameera Sultan, Wael Amin Nasr El-Din, Stefano Salvatore and Safa Taha
Int. J. Mol. Sci. 2025, 26(21), 10286; https://doi.org/10.3390/ijms262110286 - 22 Oct 2025
Abstract
Hyaluronic acid (HA)-based urethral bulking agents are promising for the treatment of stress urinary incontinence (SUI), but migration risks to distant organs remain a concern. This study evaluated the migration and cytotoxicity of Zhoabex G®, an HA-based bulking agent, in a [...] Read more.
Hyaluronic acid (HA)-based urethral bulking agents are promising for the treatment of stress urinary incontinence (SUI), but migration risks to distant organs remain a concern. This study evaluated the migration and cytotoxicity of Zhoabex G®, an HA-based bulking agent, in a female rabbit model. Twenty-seven female New Zealand white rabbits were randomized into control (no injection), sham (saline), and experimental (Zhoabex G®) groups (n = 9 each). After 5 months, tissues from the kidney, lung, liver, and spleen were analyzed using quantitative RT-PCR for hyaluronan synthase (HAS1, HAS2, HAS3) and hyaluronidase (HYAL2) gene expression, and ELISA for HA concentrations. No significant differences in gene expression were observed across groups (p ≥ 0.05, range: 0.166–0.997), with experimental fold change values near sham baselines (e.g., kidney HAS2: 0.987 ± 0.071, p = 0.422). Similarly, HA concentrations showed no group differences (p = 0.577; e.g., kidney: 119.2–121.8 ng/mL), reflecting organ-specific basal levels. These findings indicate that Zhoabex G® remains localized at the urethral injection site, with no evidence of migration or cytotoxicity in distant organs. The biodegradable and non-particulate nature of Zhoabex G® further supports its safety for SUI treatment, warranting further clinical investigation. Full article
(This article belongs to the Special Issue Molecular Metabolism in Human Health and Disease)
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15 pages, 1184 KB  
Article
8-Methoxypeucedanin: Evaluation of Anxiolytic Effects and Modulation of Neuronal Activity Related Genes in a Zebrafish Anxiety Mode
by Jarosław Widelski, Monika Maciąg, Natalia Kasica, Barbara Budzyńska, Piotr Podlasz, Simon Vlad Luca, Dafina Fondai and Krystyna Skalicka-Woźniak
Int. J. Mol. Sci. 2025, 26(21), 10259; https://doi.org/10.3390/ijms262110259 - 22 Oct 2025
Abstract
For thousands of years, medicinal plants and their constituents have been used, mostly empirically/ethnopharmacologically, to cure patients with central nervous system (CNS) disorders. Anxiolytics derived from natural products (NPs) often share similar mechanisms of action to synthetic ones (e.g., benzodiazepines, BDZs). Although typically [...] Read more.
For thousands of years, medicinal plants and their constituents have been used, mostly empirically/ethnopharmacologically, to cure patients with central nervous system (CNS) disorders. Anxiolytics derived from natural products (NPs) often share similar mechanisms of action to synthetic ones (e.g., benzodiazepines, BDZs). Although typically as effective as synthetic anxiolytics, NPs are considered to be devoid of the serious side effects linked to the use of BDZs. 8-Methoxypeucedanin (8-MP) is a rare furanocoumarin present in the fruits of Peucedanum luxurians Tamamsch. (Apiaceae). The primary objective of the presented study was to assess the anxiolytic activity of 8-MP using a zebrafish (Danio rerio) model of anxiety. Danio rerio larvae at 5 days post-fertilization (dpf) were used, with reversed thigmotaxis considered as an index of the anxiolytic activity. In addition to the behavioral study, qPCR analyses were performed to assess the role of 8-MP in modulating the expression of c-fos and bdnf, two key genes involved in neural activity. As evidenced by the behavioral study, 8-MP (1.5–15 µM) exhibited a significant influence on anxiety, with a U-shape dose–response effect. Moreover, the expression of c-fos and bdnf genes was significantly downregulated, providing novel insights into the mechanisms of action of the tested furanocoumarin. Full article
(This article belongs to the Special Issue The Zebrafish Model in Animal and Human Health Research, 2nd Edition)
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12 pages, 468 KB  
Article
Evaluation of the Effects of Carvacrol on Gram-Negative Bacilli Isolated from Wound Infections
by Agata Pruss, Anna Lichota, Helena Masiuk, Paweł Kwiatkowski, Mirosława Słaba, Monika Sienkiewicz and Barbara Dołęgowska
Appl. Sci. 2025, 15(21), 11309; https://doi.org/10.3390/app152111309 - 22 Oct 2025
Abstract
Wound infections pose a significant challenge in modern medicine, driven by multimorbidity, weakened immunity, microbial virulence factors, and resistance to antibiotics and antiseptics. This study aims to evaluate the antibacterial properties of carvacrol (CAR), its impact on biofilm formation, and its capacity to [...] Read more.
Wound infections pose a significant challenge in modern medicine, driven by multimorbidity, weakened immunity, microbial virulence factors, and resistance to antibiotics and antiseptics. This study aims to evaluate the antibacterial properties of carvacrol (CAR), its impact on biofilm formation, and its capacity to trigger oxidative stress in clinical strains of Pseudomonas aeruginosa, Klebsiella pneumoniae, and Enterobacter cloacae. Carbapenemases in the studied bacteria were detected using culture on CarbaId agar. The presence of genes encoding bacterial virulence factors and carbapenemase production was confirmed using the PCR method. The antimicrobial activity of carvacrol was evaluated using the broth microdilution method. The ability of strains to form biofilm was determined using a modified crystal violet assay. Oxidative stress levels in bacterial cells in response to carvacrol treatment were measured using 2′,7′-dichlorofluorescein diacetate. Real-TimePCR was used to confirm the presence of NDM family carbapenemase genes in K. pneumoniae strains, KPC genes in E. cloacae strains, and VIM genes in P. aeruginosa strains. CAR exhibited a broad spectrum of antibacterial activity against the tested bacteria, with MIC values ranging from 125 to 1000 μg/mL. Treatment with 1/2 MIC of CAR did not significantly influence biofilm formation, except in a K. pneumoniae isolate. At 1/2 MIC, CAR induced an increase in intracellular ROS in most tested strains, with the exception of P. aeruginosa 25521221. This study provides insights into the antimicrobial efficacy of carvacrol against carbapenemase-producing pathogens isolated from wound infections—specifically P. aeruginosa, K. pneumoniae, and E. cloacae. CAR demonstrated promising bactericidal properties, likely mediated through the induction of oxidative stress, as evidenced by increased ROS generation in most studied isolates. Full article
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16 pages, 1635 KB  
Article
Bioactive Glycosylated Flavonoids Exhibiting LXR Agonist Activity from a Lauraceae Colombian Species
by Juanita Pulido-Teuta, Fabian López-Vallejo, Adrián G. Sandoval-Hernández, Carlos-Eduardo Narváez-Cuenca and Mónica Avila-Murillo
Plants 2025, 14(21), 3240; https://doi.org/10.3390/plants14213240 - 22 Oct 2025
Abstract
Lipid metabolism is a vital biological process essential for human health, encompassing key pathways necessary for the survival and homeostasis of all organisms. Liver X Receptors (LXRs) are extensively acknowledged as pivotal regulators of lipid homeostasis and inflammatory responses. Pharmacological activation of Liver [...] Read more.
Lipid metabolism is a vital biological process essential for human health, encompassing key pathways necessary for the survival and homeostasis of all organisms. Liver X Receptors (LXRs) are extensively acknowledged as pivotal regulators of lipid homeostasis and inflammatory responses. Pharmacological activation of Liver X Receptor (LXR) has been shown to increase expression of ApoE and ABCA1 proteins, reducing neurodegeneration in murine models of Alzheimer’s disease. Because previous reports determined that Nectandra reticulata (Lauraceae) extract has agonistic LXRs activity, the objective of this study was to determine the metabolites present in this extract and to evaluate their in silico and in vitro agonistic activity. The chromatographic analysis revealed the presence of three glycosylated flavonols. The in silico study showed that isolated flavonoids generate a hydrogen bond with T302 and T316 (LXRα and LXRβ, respectively). The in vitro study showed that the flavonoids increased the expression of mRNA of both APOE and ABCA1 target genes of LXRs, as observed by qRT-PCR. The bioactive flavonoids isolated in this study possess a documented antioxidant effect; when combined with their LXR agonist activity, they become promising bioactive candidates for use in nutraceutical formulations aimed at promoting brain health and anti-inflammatory effects. Full article
(This article belongs to the Special Issue Bioactives from Plants: From Extraction to Functional Food Innovation)
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24 pages, 643 KB  
Review
Environmental DNA Metabarcoding in Marine Ecosystems: Global Advances, Methodological Challenges, and Applications in the MENA Region
by Sandy K. Sawh, Sarah Merabet, Nayla Higazy, Marwa Béji, Johan Mølgård Søresen, Pedro Range, Ahmad M. Alqudah and Mohamed Nejib Daly Yahia
Biology 2025, 14(11), 1467; https://doi.org/10.3390/biology14111467 - 22 Oct 2025
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Abstract
Environmental DNA (eDNA) metabarcoding has transformed marine biodiversity monitoring by allowing non-invasive, cost-effective detection of species with high resolution across diverse marine habitats. A systematic literature search was conducted using Google Scholar, Scopus, and the Qatar University Library databases. Relevant peer-reviewed publications were [...] Read more.
Environmental DNA (eDNA) metabarcoding has transformed marine biodiversity monitoring by allowing non-invasive, cost-effective detection of species with high resolution across diverse marine habitats. A systematic literature search was conducted using Google Scholar, Scopus, and the Qatar University Library databases. Relevant peer-reviewed publications were screened and selected based on predefined inclusion criteria to ensure comprehensive coverage of studies. This review synthesizes advances in global and regional eDNA applications, emphasizing the Middle East and North Africa (MENA) region, which faces unique environmental extremes, high endemism, and significant data gaps. eDNA metabarcoding often outperforms traditional methods under comparable sampling effort to traditional surveys in detecting rare, cryptic, and invasive taxa, but technical challenges like incomplete reference databases, primer biases, PCR inhibitors, and inconsistent methodologies limit their effectiveness, particularly in understudied areas such as MENA. Recent developments, including multi-marker approaches, autonomous samplers, and next-generation sequencing, are enhancing detection precision and enabling broader, real-time monitoring. In the MENA region, early studies have revealed eDNA’s potential for habitat distinction, biogeographic research, pollution assessment, and the early discovery of non-indigenous species, although progress is hindered by gaps in reference libraries, infrastructure, and regulation. This review underscores the urgent need for regional collaboration, standardized protocols, and capacity-building. By integrating eDNA with traditional methods and leveraging emerging technologies, the MENA region can establish itself as a leader in marine biomonitoring under extreme environmental conditions, providing actionable insights for conservation and sustainable management of its unique marine ecosystems. Full article
(This article belongs to the Section Ecology)
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16 pages, 2928 KB  
Article
Immunomodulatory Potential of a Composite Amniotic Membrane Hydrogel for Wound Healing: Effects on Macrophage Cytokine Secretion
by Tao Wang, Zhiyuan Zhu, Wei Hua and Siliang Xue
Biomedicines 2025, 13(10), 2574; https://doi.org/10.3390/biomedicines13102574 - 21 Oct 2025
Viewed by 100
Abstract
Background: The human acellular amniotic membrane (HAAM) is widely used as a decellularized bioscaffold in tissue engineering to promote wound healing, but its clinical application is limited by poor mechanical properties, rapid degradation, and handling difficulties. This study aimed to develop a modified [...] Read more.
Background: The human acellular amniotic membrane (HAAM) is widely used as a decellularized bioscaffold in tissue engineering to promote wound healing, but its clinical application is limited by poor mechanical properties, rapid degradation, and handling difficulties. This study aimed to develop a modified amniotic membrane-based composite material loaded with vascular endothelial growth factor (VEGF) and the Notch signaling inhibitor N-[N-(3,5-difluorophenacetyl)-Lalanylhydrazide]-Sphenylglycine t-butyl ester (DAPT) to enhance wound healing by modulating macrophage polarization and cytokine secretion. Methods: VEGF-loaded gellan gum-hyaluronic acid (GG-HA) hydrogels (VEGF-GG-HA) and DAPT-loaded HAAM (DAPT-HAAM) were prepared and combined to form a novel composite material (VEGF-GG-HA & DAPT-HAAM). The morphology and microstructure of the materials were characterized using scanning electron microscopy. In vitro studies were conducted using the human monocytic cell line (Tohoku Hospital Pediatrics-1, THP-1) to evaluate the effects of the materials on cell viability, cytokine secretion, and protein expression. Assessments included CCK-8 assays, ELISA, quantitative real-time PCR, Western blot analysis, and immunohistochemical staining. Results: The composite material VEGF-GG-HA & DAPT-HAAM exhibited good biocompatibility and significantly promoted THP-1 cell proliferation compared to control and single-component groups. It enhanced the secretion of IL-10, TNF-α, TGF-β, MMP1, and MMP3, while suppressing excessive TGF-β overexpression. The material also modulated macrophage polarization, showing a trend toward anti-inflammatory M2 phenotypes while maintaining pro-inflammatory signals (e.g., TNF-α) for a balanced immune response. Conclusions: The modified amniotic membrane hydrogel composite promotes wound healing through a phased immune response: it modulates macrophage polarization (balancing M1 and M2 phenotypes), enhances cytokine and matrix metalloproteinase secretion, and controls TGF-β levels. These effects contribute to improved vascular remodeling, reduced fibrosis, and prevention of scar formation, demonstrating the potential for enhanced wound management. Full article
(This article belongs to the Special Issue New Advances in Wound Healing and Skin Regeneration)
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23 pages, 1451 KB  
Article
CCNA2 and CCNB3 as Early Potential Molecular Candidates of Oocyte Maturation in Cumulus-Oophorous Complex Cells from Follicular Fluid
by Nergis Özlem Kılıç, Çağrı Öner, Duygu Kütük, Belgin Selam, İbrahim Orçun Olcay and Ertuğrul Çolak
Diagnostics 2025, 15(20), 2658; https://doi.org/10.3390/diagnostics15202658 - 21 Oct 2025
Viewed by 247
Abstract
Background/Objectives: Oocyte maturation is a process involving both nuclear and cytoplasmic development regulated by epigenetic changes in gene expression. Cyclin-B3 (CCNB3) and cyclin-A2 (CCNA2) genes are thought to be involved in oocyte maturation; however, the expression profiles and key function in Metaphase-I [...] Read more.
Background/Objectives: Oocyte maturation is a process involving both nuclear and cytoplasmic development regulated by epigenetic changes in gene expression. Cyclin-B3 (CCNB3) and cyclin-A2 (CCNA2) genes are thought to be involved in oocyte maturation; however, the expression profiles and key function in Metaphase-I (MI) and Metaphase-II (MII) phases have yet to be fully elucidated. Small non-coding RNA sequences are involved in epigenetic regulation of specific transcriptional targets, whereas microRNAs (miRNAs) participate in the post-transcriptional and translational repression of target genes. This study examined the expression levels of CCNB3, CCNA2, and their associated miRNAs (miR-17, miR-106b, miR-190a, miR-1275) in cumulus oophorous complex (COC) cells derived from MI and MII oocytes of NOR and DOR IVF cases, with particular emphasis on elucidating their functions during the transition from MI to MII stage. Methods: Follicular fluid containing cumulus–oocyte complex (COC) cells obtained from oocytes of 120 cases in each group NOR MI (n = 30), NOR MII (n = 30), DOR MI (n = 30), and DOR MII (n = 30) who were admitted to the Istanbul Bahçeci Health Group Assisted Reproductive Treatment Center. Following total RNA isolation from COC cells, the gene and protein expression levels of CCNB3 and CCNA2, along with the expression of miR-17, miR-106b, miR-190a, and miR-1275, were assessed using (qPCR-based assay) and immunohistochemistry (IHC). To investigate the functional roles of COC cell populations, morphological analysis was performed using H&E staining. Additionally, metadata of the cases, including age, number of oocytes, fertilization, and embryonic development rates, were evaluated. Results: The expressions of miR-17 and miR-1275 were significantly elevated in both NOR MI and DOR MI groups compared to their respective NOR MII and DOR MII groups (p < 0.05). Additionally, miR-106b levels were higher in the NOR MII group relative to NOR MI (p < 0.05), while an increase was also observed in DOR MI compared to DOR MII (p < 0.05). No difference was observed in miR-190a expression between the NOR and DOR (p > 0.05). Based on the results of H and E staining, the NOR MI, NOR MII, DOR MI, and DOR MII groups exhibited distinct variations in cellular morphology, nuclear characteristics, cytoplasmic volume, and cell density. Conclusions: CCNB3 is predicted to be a potential candidate for determining MI between the NOR and DOR cases. On the other hand, only for the NOR MII cases could CCNA2 provide evidence of oocyte maturation. Moreover, we determined the relationship between related genes and miRNAs which target CCNA2 and CCNB3. Genetic and protein expression analysis across diverse molecular pathways and miRNAs yielded comprehensive preliminary data regarding the developmental stages of oocytes at the MI and MII phases, and their fertilization potential following maturation shows potential and warrants prospective validation with clinical performance evaluation. Full article
(This article belongs to the Special Issue Biomarker-Guided Advances in Diagnostic Medicine)
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14 pages, 1440 KB  
Article
Co-Occurrence and Molecular Characterization of ESBL-Producing and Colistin-Resistant Escherichia coli Isolates from Retail Raw Meat
by Arife Ezgi Telli, Nihat Telli, Yusuf Biçer, Gamze Turkal, Tahir Yılmaz and Gürkan Uçar
Foods 2025, 14(20), 3573; https://doi.org/10.3390/foods14203573 - 21 Oct 2025
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Abstract
Background: The emergence of extended-spectrum β-lactamase (ESBL) producing and colistin-resistant Escherichia coli in retail meat poses a significant public health risk. Method: A total of 180 retail meat samples (chicken parts, internals, processed products; lamb; beef; fish) were purchased from markets and butcher [...] Read more.
Background: The emergence of extended-spectrum β-lactamase (ESBL) producing and colistin-resistant Escherichia coli in retail meat poses a significant public health risk. Method: A total of 180 retail meat samples (chicken parts, internals, processed products; lamb; beef; fish) were purchased from markets and butcher shops across Turkiye. Presumptive ESBL-producing isolates were screened on chromogenic agar and phenotypically confirmed. Species identity was verified by uspA PCR, and resistance genes (blaCTX-M, blaTEM, blaOXA, blaSHV, mcr-1, mcr-2, mcr-3) were analyzed. Colistin MICs were determined by broth microdilution, while antimicrobial susceptibility of ESBL-positive isolates was assessed by disk diffusion. Results: Overall, ESBL-producing E. coli were detected in 21.7% (n = 39) of the 180 meat samples analyzed, with the highest prevalence observed in chicken parts (26/40, 65.0%) and giblets (6/10, 60%). All ESBL-E. coli isolates harbored blaCTX-M, with blaCTX-M-1 identified as the sole variant. The blaTEM gene was detected in 61.5% (24/39) of ESBL-positive E. coli isolates. Colistin resistance was identified in six isolates (15.4%), all of which carried the mcr-1 gene. Additionally, one lamb minced meat isolate harbored the mcr-2 gene. Co-occurrence analysis revealed that the most frequent resistance gene combination among ESBL-producing isolates was blaCTX-M1 + blaTEM, detected predominantly in chicken meat samples, while mcr-1 was observed only in isolates harboring single or limited resistance genes, suggesting a distinct acquisition pattern. Conclusions: A high prevalence of blaCTX-M-1 and the co-occurrence of mcr genes were detected in E. coli isolates from retail meat, particularly poultry. The detection of mcr-1/mcr-2 co-carriage in lamb meat, though rare, highlights the need for broader surveillance. These findings underscore the need for integrated monitoring and prudent antimicrobial use in food animals. The use of antibiotics as growth promoters is prohibited in Türkiye, and therapeutic applications require a veterinary prescription; however, stronger enforcement remains essential to limit the dissemination of multidrug-resistant bacteria in the food chain. Full article
(This article belongs to the Section Food Microbiology)
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16 pages, 2955 KB  
Article
SARS-CoV-2 Infection of Lung Epithelia Leads to an Increase in the Cleavage and Translocation of RNase-III Drosha; Loss of Drosha Is Associated with a Decrease in Viral Replication
by Michael T. Winters, Emily S. Westemeier-Rice, Travis W. Rawson, Kiran J. Patel, Gabriel M. Sankey, Maya Dixon-Gross, Olivia R. McHugh, Nasrin Hashemipour, McKenna L. Carroll, Isabella R. Wilkerson and Ivan Martinez
Genes 2025, 16(10), 1239; https://doi.org/10.3390/genes16101239 - 20 Oct 2025
Viewed by 245
Abstract
Background/Objectives: Since its emergence, COVID-19—caused by the novel coronavirus SARS-CoV-2—has affected millions globally and led to over 1.2 million deaths in the United States alone. This global impact, coupled with the emergence of five new human coronaviruses over the past two decades, underscores [...] Read more.
Background/Objectives: Since its emergence, COVID-19—caused by the novel coronavirus SARS-CoV-2—has affected millions globally and led to over 1.2 million deaths in the United States alone. This global impact, coupled with the emergence of five new human coronaviruses over the past two decades, underscores the urgency of understanding its pathogenic mechanisms at the molecular level—not only for managing the current pandemic but also preparing for future outbreaks. Small non-coding RNAs (sncRNAs) critically regulate host and viral gene expression, including antiviral responses. Among the molecular regulators implicated in antiviral defense, the microRNA-processing enzyme Drosha has emerged as a particularly intriguing factor. In addition to its canonical role, Drosha also exerts a non-canonical, interferon-independent antiviral function against several RNA viruses. Methods: To investigate this, we employed q/RT-PCR, Western blot, and immunocytochemistry/immunofluorescence in an immortalized normal human lung/bronchial epithelial cell line (NuLi-1), as well as a human colorectal carcinoma Drosha CRISPR knockout cell line. Results: In this study, we observed a striking shift in Drosha isoform expression following infection with multiple SARS-CoV-2 variants. This shift was absent following treatment with the viral mimetic poly (I:C) or infection with other RNA viruses, including the non-severe coronaviruses HCoV-OC43 and HCoV-229E. We also identified a distinct alteration in Drosha’s cellular localization post SARS-CoV-2 infection. Moreover, Drosha ablation led to reduced expression of SARS-CoV-2 genomic and sub-genomic targets. Conclusions: Together, these observations not only elucidate a novel aspect of Drosha’s antiviral role but also advance our understanding of SARS-CoV-2 host–pathogen interactions, highlighting potential therapeutic avenues for future human coronavirus infections. Full article
(This article belongs to the Section RNA)
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