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15 pages, 3099 KB  
Article
Integrated Bioinformatics Analysis Reveals the Impact of SHEV ORF3-Related LncRNA Network on Bile Secretion Pathway (ko 04976) in HepG2 Cells
by Hanwei Jiao, Jiya Li, Shengping Wu, Lingjie Wang, Yu Zhao, Yulong Yin, Xin Cao and Leli Wang
Vet. Sci. 2026, 13(3), 276; https://doi.org/10.3390/vetsci13030276 - 16 Mar 2026
Abstract
(1) Background: Swine hepatitis E (SHE) is an emerging zoonotic disease caused by the swine hepatitis E virus (SHEV). The open reading frame 3 (ORF3) protein is a recognized virulence factor of SHEV. Jaundice, the typical clinical sign of SHE, primarily results from [...] Read more.
(1) Background: Swine hepatitis E (SHE) is an emerging zoonotic disease caused by the swine hepatitis E virus (SHEV). The open reading frame 3 (ORF3) protein is a recognized virulence factor of SHEV. Jaundice, the typical clinical sign of SHE, primarily results from disruptions in bile production, secretion, and excretion. However, the mechanism by which SHEV ORF3 influences bile metabolism remains unclear. (2) Methods: Building on our previous work involving adenovirus-mediated overexpression of genotype IV SHEV ORF3 in HepG2 cells and subsequent high-throughput lncRNA/transcriptome sequencing, this study performed KEGG enrichment analysis on differentially expressed lncRNAs. Candidate lncRNAs were validated via qRT-PCR. Cis-regulated target genes were predicted by integrating differentially expressed mRNA data. Furthermore, AlphaFold 3.0 was employed to analyze the molecular binding sites between lncRNA UBC (MSTRG.6881.4) and its target, UBC protein. (3) Results: We identified three lncRNAs associated with the bile secretion pathway (ko 04976) in HepG2 cells expressing genotype IV SHEV ORF3, which were further confirmed by qRT-PCR: lncRNA UBC (MSTRG.6881.4), lncRNA UBC (MSTRG.6881.9), and lncRNA UBC (MSTRG.6881.12). Bioinformatics prediction suggested six lncRNA-mRNA regulatory networks involved these lncRNAs and two downregulated UBC mRNA transcripts (ENST00000540700 and ENST00000536769). Molecular docking indicated that nucleotides 395U and 41C of lncRNA UBC (MSTRG.6881.4) could potentially bind to residues 82Lys, 88Thr, and 90Thr of the UBC protein, with predicted binding energies ranging from −4.73 to −0.75 kcal/mol. (4) Conclusions: The successful identification of bile secretion-related lncRNAs, coupled with the prediction of their regulatory networks and molecular interaction sites, has advanced our understanding of SHEV ORF3 function and the pathogenesis of SHEV infection. Full article
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32 pages, 5477 KB  
Article
Novel Adenine–Hydrazone Hybrids Against Human Lung Adenocarcinoma (A549): Design, Synthesis, Cellular Mechanistic Investigation and Molecular Docking Studies
by Emre Menteşe, Nedime Çalışkan, Didem Aksu, Mustafa Emirik, Adem Güner and Fatih Yılmaz
Pharmaceuticals 2026, 19(3), 474; https://doi.org/10.3390/ph19030474 - 13 Mar 2026
Viewed by 64
Abstract
Background/Objectives: Adenine derivatives are promising anticancer scaffolds, but their cellular mechanisms remain unclear. This study aimed to synthesize adenine–hydrazone hybrids and evaluate their cytotoxic effects in human lung adenocarcinoma (A549) cells. Methods: A series of adenine–hydrazone compounds (3ar [...] Read more.
Background/Objectives: Adenine derivatives are promising anticancer scaffolds, but their cellular mechanisms remain unclear. This study aimed to synthesize adenine–hydrazone hybrids and evaluate their cytotoxic effects in human lung adenocarcinoma (A549) cells. Methods: A series of adenine–hydrazone compounds (3ar) was synthesized and tested for cytotoxicity in A549 and MRC-5 cells. Selected compounds were further analyzed for LDH release, oxidative stress markers, ROS production, mitochondrial membrane potential, cell-cycle distribution, apoptosis, and in silico docking against VEGFR2, ALK5, and EGFR. Results: Compounds with electron-withdrawing or donor–acceptor substituents showed the highest cytotoxicity, while halogenated and methoxy analogs were moderately active. Among the synthesized derivatives, 4F-substituted derivatives (3c) showed more activity than 2F- and 3F-substituted ones (3a and 3b). 4F- and 3Br-substituted derivatives (3f) showed more activity than only 4F-substituted ones (3c). 4-Nitro-substituted derivative (3i) showed more activity than 4F- (3c), 4Cl- (3d) and 4OMe- (3h) derivatives. Trimethoxy-substituted derivative (3l) showed more activity than di- and mono-substituted methoxy derivatives (3g, 3h, 3j and 3k). Among the salicyl aldehydederivatives (3mr), 4-N(et)2-substituted derivative (3r) showed more activity than non-substituted (3m), 5Br-(3n), 5Cl-(3o), 5Me (3p) and 3OCH3 (3q) derivatives. Treatment induced oxidative stress, mitochondrial depolarization, Sub-G1 cell-cycle accumulation, and apoptosis. Docking studies indicated strong binding to VEGFR2 and ALK5, suggesting dual inhibition as a potential mechanism. Conclusions: Adenine–hydrazone derivatives exert substituent-dependent anticancer effects by inducing redox imbalance-associated mitochondrial dysfunction and regulated cell death. These results highlight their potential as lead structures for lung cancer therapy. Full article
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20 pages, 2252 KB  
Article
Development and Evaluation of Compact Semi-Synthetic Promoters for Enhanced Antigen Expression in Adenoviral-Vectored Vaccines
by Matěj Hlaváč, Susan J. Morris, Barbara Dema, Marta Ulaszewska, Zakia Al-Hareth, Bruno Douradinha and Sarah C. Gilbert
Vaccines 2026, 14(3), 260; https://doi.org/10.3390/vaccines14030260 - 13 Mar 2026
Viewed by 94
Abstract
Background/Objectives: The large size of commonly used regulatory elements such as the cytomegalovirus (CMV) immediate-early promoter imposes a significant burden on the already restricted payload capacity of first-generation adenoviral vectors, potentially hindering the development of multi-antigen vaccine candidates. To address this limitation, we [...] Read more.
Background/Objectives: The large size of commonly used regulatory elements such as the cytomegalovirus (CMV) immediate-early promoter imposes a significant burden on the already restricted payload capacity of first-generation adenoviral vectors, potentially hindering the development of multi-antigen vaccine candidates. To address this limitation, we have engineered a panel of novel, small, semi-synthetic promoters designed to leverage the changes in transcriptomic milieu following adenoviral vector entry. Methods: Eight synthetic enhancer modules (SE1–SE8) were designed in silico, each composed of transcription factor binding sites (TFBSs) previously found in host genes that are upregulated during early adenoviral infection. These synthetic enhancers were coupled with a minimal CMV core promoter to generate a panel of compact semi-synthetic promoters (cSE1–cSE8), and their activity was evaluated in the context of ChAdOx1 viral vectors expressing GFP or a modified Plasmodium falciparum circumsporozoite (CSN) antigen. Promoter performance was characterised in vitro via flow cytometry, RT-qPCR, and Western blotting, and in vivo by quantifying antigen-specific T-cell (IFN-γ ELISpot) and IgG antibody (ELISA) responses in BALB/c mice. Results: In vitro characterisation revealed a wide range of promoter activity across the panel, with cSE3 and cSE5 driving transgene expression levels comparable to the benchmark CMV promoters despite their markedly reduced genomic footprint. In vivo, ChAdOx1 vectors incorporating cSE3 and cSE5 elicited potent antigen-specific T-cell and IgG responses that were comparable to those induced by the larger CMV control promoters. Conclusions: We have successfully developed semi-synthetic promoters that match the potency of the much larger, frequently used CMV promoters whilst simultaneously reducing genomic footprint. These novel regulatory elements will facilitate the design of next-generation vaccines, particularly those requiring large antigens or multi-antigen cassettes. Full article
(This article belongs to the Special Issue Innovations in Vaccine Technology)
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18 pages, 3433 KB  
Article
Protective Effect of Paeoniae Radix Alba Carbonisata on Hepatic Amyloidosis by Regulating Calcium Homeostasis
by Gangqiang Liu, Zerui Wang, Huihui Xu, Jinyu Jia, Zhong Xue, Wei Ge, Xueqing Ji, Lijian Cui and Yun Huang
Int. J. Mol. Sci. 2026, 27(6), 2582; https://doi.org/10.3390/ijms27062582 - 11 Mar 2026
Viewed by 180
Abstract
Paeoniae Radix Alba Carbonisata (PRAC), carbonized decoction pieces of the traditional Chinese medicine Paeoniae Radix Alba, has been used in clinical practice for hepatoprotective purposes. Hepatic amyloidosis (HA), a severe complication of systemic AA amyloidosis, is characterized by the deposition of fibrillar amyloid [...] Read more.
Paeoniae Radix Alba Carbonisata (PRAC), carbonized decoction pieces of the traditional Chinese medicine Paeoniae Radix Alba, has been used in clinical practice for hepatoprotective purposes. Hepatic amyloidosis (HA), a severe complication of systemic AA amyloidosis, is characterized by the deposition of fibrillar amyloid proteins leading to progressive hepatic dysfunction. However, its role in HA remains unclear. Amyloid lysozyme (LYSO-6) was used to induce the NCTC1469 cell injury model and the HA mouse model. The effects of PRAC extract (PRAC-E) on liver injury were then evaluated using biochemical assays, enzyme-linked immunosorbent assay (ELISA), Congo red (CR) staining, Hematoxylin and Eosin (H&E) staining, and immunohistochemical staining. Liver transcriptomics combined with Western blotting was used to analyze the expression levels of key proteins in the cGMP/PKG/ATP2A1 signaling axis. UHPLC-Q-Exactive Orbitrap MS combined with network pharmacology was used to characterize the chemical components of PRAC-E and identify its core active constituents against HA. Quantitative analysis of core components was performed by UHPLC-QTRAP-MS/MS. Molecular docking predicted the binding stability of core components and key targets. The results showed that PRAC-E significantly alleviated HA. Collectively, PRAC-E restored calcium pump activity, corrected calcium homeostasis imbalance, reduced inflammatory factor levels, regulated Phosphodiesterase 5A (PDE5A), and activated the cGMP/PKG/ATP2A1 signaling axis. The main components of PRAC-E were phenolic acids, terpenoids, and flavonoids. Among these, six core components (SCCs) related to HA were Gallate (16.96 mg/g), Paeoniflorin (14.27 mg/g), Albiflorin (7.20 mg/g), Benzoyl paeoniflorin (5.33 mg/g), Methyl gallate (0.78 mg/g), and Catechin (0.09 mg/g). Molecular docking analysis demonstrated that SCCs formed stable complexes (∆G ≤ −6.2 kcal/mol) with ATP2A1. Full article
(This article belongs to the Section Molecular Biology)
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21 pages, 7702 KB  
Article
Genome-Wide Identification and Characterization of C3H-ZFP Genes and Their Expression Under Salt and Cadmium Stress Conditions in Soybean
by Intikhab Alam, Khadija Batool, Hui-Cong Wang and Fang Qiao
Curr. Issues Mol. Biol. 2026, 48(3), 287; https://doi.org/10.3390/cimb48030287 - 8 Mar 2026
Viewed by 168
Abstract
Zinc finger proteins (ZFPs) are a diverse group of plant transcription factors essential for regulating development, signaling, and stress responses. In this study, we performed a genome-wide identification and integrative analysis of 140 C3H-type zinc finger transcription factor genes in the soybean genome, [...] Read more.
Zinc finger proteins (ZFPs) are a diverse group of plant transcription factors essential for regulating development, signaling, and stress responses. In this study, we performed a genome-wide identification and integrative analysis of 140 C3H-type zinc finger transcription factor genes in the soybean genome, exhibiting an uneven distribution across all 20 chromosomes. These C3H-ZFPs contained one (37), two (58), three (19), four (7), five (17), or six (2) C3H domains and were classified into 14 subsets based on their domain architecture. All C3H genes encoding proteins harbored the conserved C3H-ZFP domain and displayed various physicochemical characteristics. Phylogenetic analysis grouped them into 10 clades, closely related to other species like Arabidopsis, rice and alfalfa. Promoter analysis revealed cis-elements associated with stress response (~39.1%), light response (~37.3%), phytohormones (~18.5%), and development (~4.97%). Duplication analysis revealed 78 pairs of segmental and eight tandem duplication events, with purifying selection indicated by Ka/Ks (nonsynonymous/synonymous) ratios, indicating that these C3H-ZFP duplicates were largely maintained under purifying selection. A total of 388 miRNAs from 196 gene families were predicted to target 140 C3H-ZFP genes, with most enriched miRNAs targeting C3H-ZFP genes, including the miR156, miR395, and miR396 families. Transcription factor binding sites for MYB, AP2, MIKC_MADS, BBR-BPC, ERF, C2H2, and Dof were found upstream of most C3H-ZFP genes. RNA-Seq and qRT-PCR analyses showed tissue-specific expression and stress-responsive expression patterns, with several C3H-ZFP genes, especially GmC3H1, GmC3H63, GmC3H124, and GmC3H127, being significantly upregulated under abiotic stress conditions. Together, these results provide a comprehensive overview of soybean C3H-ZFP genes and identify promising candidates for future functional studies on development and abiotic stress adaptation. Full article
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13 pages, 1357 KB  
Article
ELAVL1 Promotes Proliferation and Inhibits Apoptosis of the Marek’s Disease Virus (MDV)-Transformed Cell Line MSB1 via the COX-2/PGE2 Pathway
by Lei He, Dong-Mei Zhan, Hui Peng, Meng-Ru Gao, Jian Chen, Yan-Yan Jia, Cheng-Shui Liao, Song-Biao Chen, Ke Ding and Zu-Hua Yu
Animals 2026, 16(5), 843; https://doi.org/10.3390/ani16050843 - 7 Mar 2026
Viewed by 217
Abstract
Marek’s disease (MD), caused by the oncogenic Marek’s disease virus (MDV), is a highly contagious avian infection that induces lymphoproliferative tumors. The RNA-binding protein ELAVL1 is known to regulate tumor cell proliferation and apoptosis, but its role in MDV-induced oncogenesis remains unclear. This [...] Read more.
Marek’s disease (MD), caused by the oncogenic Marek’s disease virus (MDV), is a highly contagious avian infection that induces lymphoproliferative tumors. The RNA-binding protein ELAVL1 is known to regulate tumor cell proliferation and apoptosis, but its role in MDV-induced oncogenesis remains unclear. This study investigated whether ELAVL1 modulates proliferation and apoptosis in the MDV-transformed MSB1 cell line and whether its effects involve the cyclooxygenase-2 (COX-2)/prostaglandin E2 (PGE2) pathway. MSB1 cells were transiently transfected with ELAVL1-overexpressing plasmids (pEGFP-C-ELAVL1) or ELAVL1-specific siRNA, with expression confirmed by real-time PCR (qRT-PCR). Cell proliferation was assessed using the CCK-8 assay, while cell cycle distribution and apoptosis rates were analyzed by flow cytometry. COX-2 and PGE2 expression levels were determined by qRT-PCR, Western blotting, and ELISA. Overexpression of ELAVL1 significantly promoted the proliferation of MSB1 cells, decreased transition into the G1 phase, increased the proportions of S and G2 phase cells, and suppressed apoptosis. Correspondingly, both mRNA and protein levels of COX-2 and PGE2 were significantly elevated. Conversely, ELAVL1 knockdown significantly inhibited proliferation, induced G1 phase arrest, decreased S phase cells, and significantly decreased COX-2 and PGE2 expression. These findings indicate that ELAVL1 promotes proliferation and inhibits apoptosis in MDV-transformed MSB1 cells, potentially via the COX-2/PGE2 signaling pathway. Full article
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15 pages, 4441 KB  
Article
Genome-Wide Identification and Expression Analysis of R2R3-MYB Gene Family in Chrysanthemum indicum Under Low-Temperature Stress
by Shuheng Wang, Jiayi Yin, Xuanlu Liu, Siyu Feng, Dongyang Zhang, Yun Bai, Xue Yang and Yunwei Zhou
Agronomy 2026, 16(5), 567; https://doi.org/10.3390/agronomy16050567 - 5 Mar 2026
Viewed by 240
Abstract
Low-temperature stress is a major factor limiting the development of the chrysanthemum industry. Chrysanthemum indicum L., wild germplasm with strong cold tolerance within the genus, is an ideal material for mining cold resistance genes. Through preliminary transcriptome analysis of C. indicum under low-temperature [...] Read more.
Low-temperature stress is a major factor limiting the development of the chrysanthemum industry. Chrysanthemum indicum L., wild germplasm with strong cold tolerance within the genus, is an ideal material for mining cold resistance genes. Through preliminary transcriptome analysis of C. indicum under low-temperature stress (PRJNA1391062), we found that multiple R2R3-MYB family members were significantly differentially expressed (|log2FC| ≥ 1, p < 0.05), suggesting that this family may play important roles in cold stress responses. Within the C. indicum genome, we identified 63 R2R3-MYB members (CiMYBs) through HMMER and BLAST searches combined with domain validation. Phylogenetic analysis classified these genes into 19 subgroups, with most key nodes supported by bootstrap values > 80%. Promoter cis-element analysis revealed enrichment of elements related to light responsiveness, hormone signaling, and stress responses, including 41 low-temperature responsive elements distributed across 28 genes and 32 drought-induced MYB-binding sites present in 23 genes. Synteny analysis identified 13 duplicated gene pairs within the C. indicum genome and 41 collinear gene pairs between C. indicum and Arabidopsis thaliana L. Transcriptome data under low-temperature stress showed that 22 of the 63 CiMYB members were differentially expressed under 4 °C acclimation and −4 °C freezing stress, and they could be classified into three response patterns: acute stress-responsive (rapid upregulation upon initial stress), acclimation-induced (significant activation after 4 °C acclimation), and freezing-suppressed (downregulation after −4 °C freezing). Six differentially expressed genes were randomly selected for RT-qPCR validation, and the results showed consistent trends with the transcriptome data. This study provides a comprehensive identification of R2R3-MYB family members in C. indicum and reveals their expression divergence under low-temperature stress, offering candidate gene resources for deciphering the cold adaptation mechanisms of C. indicum and breeding new cold-resistant chrysanthemum cultivars. Full article
(This article belongs to the Section Crop Breeding and Genetics)
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17 pages, 1045 KB  
Article
New 1,2,3-Triazole and Dipyridothiazine Hybrids—Synthesis, Analysis, Cytotoxicity and Molecular Docking
by Emilia Martula, Weronika Bagrowska, Paulina Strzyga-Łach, Marta Struga, Małgorzata Latocha, Dariusz Kuśmierz, Małgorzata Jeleń and Beata Morak-Młodawska
Biomolecules 2026, 16(3), 349; https://doi.org/10.3390/biom16030349 - 26 Feb 2026
Viewed by 291
Abstract
Epigenetic and stress-response pathways play central roles in cancer progression and represent attractive therapeutic targets. In this study, a series of dipyridothiazine–1,2,3-triazole hybrids bearing p-fluorophenyl and p-trifluoromethylphenyl substituents was synthesized via efficient dipolar cycloaddition reactions. Structural characterization was performed using 1 [...] Read more.
Epigenetic and stress-response pathways play central roles in cancer progression and represent attractive therapeutic targets. In this study, a series of dipyridothiazine–1,2,3-triazole hybrids bearing p-fluorophenyl and p-trifluoromethylphenyl substituents was synthesized via efficient dipolar cycloaddition reactions. Structural characterization was performed using 1H, 13C, and 19F NMR spectroscopy and high-resolution mass spectrometry. Anticancer activity was evaluated using WST-1 and MTT assays against human cancer cell lines SNB-19 (glioblastoma), C32 (amelanotic melanoma), A549 (lung carcinoma), and MDA-MB-231 and MCF-7 (breast cancer), as well as normal HFF-1 fibroblasts and HaCaT keratinocytes, with doxorubicin and cisplatin as reference drugs. The hybrids TDT2b and TDT3b containing a p-trifluoromethylphenyl moiety showed the highest cytotoxicity and cancer cell selectivity. RT-qPCR analysis of H3, TP53, CDKN1A, BCL-2, and BAX expression for the lead compound TDT2b revealed modulation of chromatin organization, p53-dependent stress responses, apoptosis, and cell cycle regulation. Molecular docking studies with human histone deacetylase 6 (HDAC6) demonstrated favorable binding of TDT2b and TDT3b, supporting their role as potential epigenetic anticancer agents. Full article
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23 pages, 55337 KB  
Article
UPLC-Q-TOF-MS/MS and Network Pharmacology Approaches to Explore the Active Compounds and Mechanisms of Kadsura coccinea for Treating Rheumatoid Arthritis
by Liya Qiao, Jiashui Liao, Yongchun Huang, Ping Li, Hairong Long, Lu Chen, Tingting Tong, Xiaowen Ji, Mengli Zhang, Yude Peng, Yu Pan and Xianghua Xia
Int. J. Mol. Sci. 2026, 27(5), 2097; https://doi.org/10.3390/ijms27052097 - 24 Feb 2026
Viewed by 259
Abstract
This study aimed to systematically identify the active constituents of Kadsura coccinea (Lem.) A. C. Smith (KC) and elucidate their potential mechanisms in treating rheumatoid arthritis (RA) using an integrated analytical and computational approach. Chemical profiling of KC root extract was performed by [...] Read more.
This study aimed to systematically identify the active constituents of Kadsura coccinea (Lem.) A. C. Smith (KC) and elucidate their potential mechanisms in treating rheumatoid arthritis (RA) using an integrated analytical and computational approach. Chemical profiling of KC root extract was performed by UPLC-Q-TOF-MS/MS. Active compounds and their targets were predicted using the SwissTargetPrediction database, while RA-related genes were retrieved from OMIM, GeneCards, and DisGeNET. A compound–target network was constructed and analyzed via Cytoscape. Functional enrichment analyses and protein–protein interaction (PPI) clustering were conducted to identify key pathways. Molecular docking was employed to validate interactions between core compounds and key RA targets. A total of 90 compounds were identified, primarily 36 lignans and 29 triterpenoids. Network analysis revealed 145 overlapping targets between KC and RA. These targets were further associated with 65 compounds derived from KC. Key compounds such as kadcoccinone F, kadsuralignan I and schisantherin M were linked to hub targets including MAPK14, MMPs, and JAKs, which are involved in inflammatory signaling, matrix degradation, and immune regulation. Molecular docking confirmed strong binding affinities (ΔG < −5.0 kcal/mol) between representative KC compounds and targets like MMP1, MMP2, JAK2 and JAK3, supported by analyses of hydrogen bonding, hydrophobic, and π-interactions. These results suggest that KC exerts anti-RA effects through multi-component, multi-target mechanisms, primarily modulating inflammatory signaling, immune cell recruitment, and tissue-destructive pathways. This study provides a pharmacological basis for the traditional use of KC in RA management and supports its potential as a complementary therapeutic agent. Full article
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17 pages, 3914 KB  
Article
Plasma Extracellular Vesicles from Bronchopulmonary Dysplasia Infants Initiate Inflammation and Abnormal Angiogenesis in Neonatal Murine Retinas
by Huijun Yuan, Matthew R. Duncan, Shaoyi Chen, Merline Benny, Augusto Schmidt, Karen Young, Audina M. Berrocal, M. Elizabeth Hartnett and Shu Wu
Cells 2026, 15(4), 367; https://doi.org/10.3390/cells15040367 - 19 Feb 2026
Viewed by 535
Abstract
Purpose: To investigate the mechanisms by which plasma extracellular vesicles (EVs) from preterm infants with bronchopulmonary dysplasia (BPD) elicit inflammation and abnormal angiogenesis in neonatal mouse retinas. Methods: EVs from the plasma of 7-day-old preterm infants, born between 230/7 and 296/7 [...] Read more.
Purpose: To investigate the mechanisms by which plasma extracellular vesicles (EVs) from preterm infants with bronchopulmonary dysplasia (BPD) elicit inflammation and abnormal angiogenesis in neonatal mouse retinas. Methods: EVs from the plasma of 7-day-old preterm infants, born between 230/7 and 296/7 weeks of gestation, with BPD or without BPD (nBPD) at 36 weeks postmenstrual ages, were adoptively transferred into postnatal day 3 (P3) mice via intravenous retro-orbital sinus injection. Inflammation and pathological neovascularization in neonatal mouse retinas were examined by immunohistochemistry of retinal flat mounts for Allograft Inflammatory Factor 1 (AIF1), CD206, or Glial Fibrillary Acidic Protein (GFAP) and isolectin-B4 (IB4) staining on P17. Retinal inflammation-related transcripts were assessed by qRT-PCR. Proteomic profiles of BPD and nBPD EVs were examined by Liquid Chromatograph Mass Spectrometer/Mass Spectrometer (LC-MS/MS) and Gene Set Enrichment Analysis (GSEA). Results: Adoptively transferred EVs from BPD and nBPD infants crossed the blood–retinal barrier (BRB) in recipient mouse pups. BPD-EVs increased retinal activated microglia, Müller cells, and twisted proliferative neovascularization compared to nBPD-EVs. BPD-EVs also elevated retinal transcripts regulating inflammation and angiogenesis, including NOD-, LRR- and pyrin domain-containing protein 3 (Nlrp3), Apoptosis-associated speck-like protein containing a caspase recruitment domain (Asc), Caspase 3 (Casp3), Caspase 8 (Casp8), Gasdermin D (Gsdmd), Il1β, Il6, Aif1, and Vascular endothelial growth factor (Vegf). Proteomics analysis revealed that BPD-EVs had significantly elevated levels of inflammation and angiogenesis-related proteins compared to nBPD-EVs. Conclusions: BPD-EVs promote inflammation and abnormal neovascularization by upregulating genes related to apoptosis and inflammation in neonatal mouse retinas. EV protein profiles suggest that elevated levels of proteins such as Defensin alpha 1B (DEFA1B), Insulin-like growth factor binding protein 2 (IGFBP2), CD5 antigen-like (CD5L), von Willebrand factor (vWF), and Tenascin C (TNC) in BPD-EVs may contribute to the observed inflammation and angiogenesis. Full article
(This article belongs to the Section Cell Microenvironment)
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15 pages, 2552 KB  
Article
A Cyclic Pentapeptide Inhibits AgrC as a Quorum-Sensing Quenching Agent in Staphylococcus aureus
by Duiyuan Ai, Huanhuan Duan and Jiahao Yao
Antibiotics 2026, 15(2), 213; https://doi.org/10.3390/antibiotics15020213 - 15 Feb 2026
Viewed by 443
Abstract
Background/Objectives: Staphylococcus aureus virulence is tightly regulated by the agr (accessory gene regulator) quorum-sensing system. Targeting AgrC, the histidine kinase receptor that serves as a core regulator of agr signaling, represents a promising antivirulence strategy that circumvents conventional bactericidal pressure. Methods: In this [...] Read more.
Background/Objectives: Staphylococcus aureus virulence is tightly regulated by the agr (accessory gene regulator) quorum-sensing system. Targeting AgrC, the histidine kinase receptor that serves as a core regulator of agr signaling, represents a promising antivirulence strategy that circumvents conventional bactericidal pressure. Methods: In this study, structure-based virtual screening using AutoDock Vina was performed, followed by molecular dynamics simulations, to identify potent analogs of known AgrC inhibitors. Results: A cyclo[Ala-Phe-OLeu-Phe-D-Leu] exhibiting high binding affinity and stable receptor interaction was selected for further evaluation. Antimicrobial susceptibility testing confirmed that the compound did not inhibit bacterial growth. However, at a concentration of 16 µg/mL, it significantly inhibited hemolytic activity with high reproducibility, and the inhibition rate reached 77.60%. Quantitative reverse transcription PCR (RT-qPCR) demonstrated that the compound decreased some key AgrC-mediated genes, including agrC, agrA, saeS, hla, spa, fnbA, and lukS. Conclusions: These findings identify a promising cyclic pentapeptide inhibitor of AgrC that effectively attenuates S. aureus virulence without exerting bactericidal pressure. This work provides a valuable lead compound and offers novel insights for the development of advanced, safe, and effective antivirulence therapeutics. Full article
(This article belongs to the Section Novel Antimicrobial Agents)
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15 pages, 4761 KB  
Article
Leveraging Machine Learning for Screening Metal-Organic Frameworks with Selective CO2 Recognition for Early Thermal Runaway in Lithium-Ion Batteries
by Xian Wei, Xin Li, Xiong Wang, Xiaoyan Liu and Chen Zhu
Nanomaterials 2026, 16(4), 245; https://doi.org/10.3390/nano16040245 - 13 Feb 2026
Viewed by 375
Abstract
The escalation of thermal runaway in lithium-ion batteries presents severe safety hazards that necessitate advanced monitoring protocols to ensure early warning of potential failures. Carbon dioxide (CO2) is released during preliminary decomposition well before catastrophic failure occurs, thereby providing a strategic [...] Read more.
The escalation of thermal runaway in lithium-ion batteries presents severe safety hazards that necessitate advanced monitoring protocols to ensure early warning of potential failures. Carbon dioxide (CO2) is released during preliminary decomposition well before catastrophic failure occurs, thereby providing a strategic advantage for early-stage warning. Consequently, identifying materials with high-selective CO2 recognition is an essential prerequisite for developing reliable sensing platforms. This study integrates Grand Canonical Monte Carlo simulations with Random Forest (RF) models to systematically screen 1470 MOFs from the CoRE-MOF 2019 database. The screening process evaluates selective CO2 recognition under multicomponent competitive adsorption conditions involving CO2, C2H4, and O2. The performance evaluation is based on working capacity, selectivity, and the trade-off between working capacity and selectivity (TSN). The RF model achieves high predictive accuracy, with tested R2 exceeding 0.92 on the test samples. Shapley Additive Explanations (SHAP) interpretability analysis identifies Q0st(CO2), Q0st(C2H4), WEPA, KH(C2H4), and ETR as key performance drivers. The results indicate that CO2 selectivity is constrained by the binding strength of competing C2H4. Optimal materials tend to have hard Lewis acid centers and polar inorganic clusters to minimize non-specific π-interactions with interfering species. Top-performing MOFs require balanced structural features, concentrating in moderate surface areas (965–1975 m2/g), narrow pore windows (PLD ≈ 4–7 Å, LCD ≈ 5.5–9.6 Å), high void fractions above 0.6, and low densities below 1.3 g/cm3. AJOTEY emerges as the optimal candidate with a TSN of 6.43 mol/kg, combining substantial working capacity (4.57 mol/kg) with strong selectivity (25.52). These results will accelerate the discovery of sensing materials and provide a practical pathway for MOF-based CO2 sensor development to enhance lithium-ion battery safety. Full article
(This article belongs to the Special Issue Advances of Machine Learning in Nanoscale Materials Science)
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15 pages, 4974 KB  
Article
The Peroxidase12 Gene Regulates Morphogenesis of the Daughter Root of Aconitum carmichaelii Debx. by Promoting Lignin Synthesis
by Xianglei Duan, Xuewen Yan, Xin Wen and Guangzhi Wang
Biology 2026, 15(4), 323; https://doi.org/10.3390/biology15040323 - 12 Feb 2026
Viewed by 284
Abstract
Although the diterpenoid alkaloids of Aconitum carmichaelii Debx. have long been a research focus in phytochemistry and pharmacology, systematic studies on the growth and development of its daughter roots remain limited, yet this process critically determines the yield and quality of the medicinal [...] Read more.
Although the diterpenoid alkaloids of Aconitum carmichaelii Debx. have long been a research focus in phytochemistry and pharmacology, systematic studies on the growth and development of its daughter roots remain limited, yet this process critically determines the yield and quality of the medicinal material. This study utilized the Jiangyou-derived daughter root of A. carmichaelii as experimental material. Quantitative real-time polymerase chain reaction (qRT-PCR) and total lignin quantification demonstrated that both the expression level of AcPRX12 and total lignin relative content were consistently higher in the non-swollen (PB) parts than in the swollen (P) parts of the daughter roots. The complete cDNA sequence of the AcPRX12 (with a full length of 1357 bp and encoding 350 amino acids) was obtained by rapid amplification of cDNA ends (RACE). Bioinformatics analysis identified AcPRX12 as an extracellular class III peroxidase containing a secretory peroxidase domain, and further predicted its strong binding affinity for syringaldazine, an S-type lignin monomer analog. In addition, the heterologous expression of AcPRX12 in Arabidopsis thaliana resulted in a significant increase in lignin content, which inhibited plant growth, as evidenced by shorter roots, thinner stems, smaller leaves, and shorter siliques. Collectively, these results support a model in which AcPRX12 promotes lignin biosynthesis to modulate daughter root development, ultimately shaping its distinctive tapered morphology. In conclusion, our findings propose a lignin-mediated regulatory mechanism for daughter root development controlled by AcPRX12, offering a key gene resource and a theoretical basis for understanding its morphogenesis. Full article
(This article belongs to the Section Plant Science)
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18 pages, 3248 KB  
Article
Snail1 Induced Suppression of Proliferation via EGR1, FOXO1, and CEPBγ Creates a Vulnerability for Targeting Apoptotic and Cellular Senescence Pathways
by Jack Tran, Samyukta Sundaram, Sukirti Shivpuri, Hunain Khawaja and Cynthia K. Miranti
Cancers 2026, 18(3), 510; https://doi.org/10.3390/cancers18030510 - 4 Feb 2026
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Abstract
Background/Objectives: The annual ~36,000 prostate cancer (PCa) deaths represent a large clinical unmet need and a call for deeper understanding of PCa metastasis. Epithelial–mesenchymal-transition (EMT) has been used to model metastatic behaviors in numerous cancers including PCa. One hallmark of EMT is cell [...] Read more.
Background/Objectives: The annual ~36,000 prostate cancer (PCa) deaths represent a large clinical unmet need and a call for deeper understanding of PCa metastasis. Epithelial–mesenchymal-transition (EMT) has been used to model metastatic behaviors in numerous cancers including PCa. One hallmark of EMT is cell cycle suppression, but how EMT impacts PCa proliferation remains unclear primarily due to the lack of appropriate models. Methods: We transiently induced Snail1 (SNAI1) expression, an EMT driver expressed in PCa, at physiological levels in three PCa cells lines, C4-2B, 22Rv1, and DU145. We used RNA-seq, ChIP-Seq, bioinformatics, qRT-PCR, shRNA, and immunoblotting to identify mechanisms of Snail1-driven inhibition of proliferation. Results: Snail1 suppressed proliferation and G2/M cell cycle progression, without affecting cell death. Mechanistically, Snail1 upregulated expression of CEBPγ, ERG1, FOXO1, cyclin G1, p21, stress genes SESN3 and SOD3, apoptotic programmers Puma, Bax, and Noxa, and senescence-related laminB1, and downregulated Ki67, cyclins A2 and B2. ChIP-Seq data identified Snail1 direct binding to p21, cyclin B2 and G1, EGR1, and CEPBγ promoters. EGR1 induced FOXO1, and EGR1 was required for Snail1-induced SOD3 and Puma, and suppression of Caspase 3 to prevent apoptosis. The EGR1/FOXO1 axis induced BAX, Noxa, and SESN3. CEBPγ was required for Snail1 induction of Lamin B1 to block Snail1-induced senescence. Conclusions: We identified three new major downstream targets of Snail1 that improve our understanding of the role of EMT in limiting stress signaling, apoptosis, and senescence during cell cycle suppression to create a vulnerability for therapeutic targeting. Full article
(This article belongs to the Special Issue The Impact of Treatment Resistance in Prostate Cancer)
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19 pages, 2458 KB  
Article
Maresin-1 Ameliorates Chronic Unpredictable Stress-Induced Depressive-like Behaviors Associated with Dynamic Modulation of Hippocampal Microglial Activity and TSPO PET Signals
by Anhai Zheng, Tian Qiu, Lei Shi, Lixia Wang, Zhu Xia, Zhiping Peng, Li Kuang and Jiamei Guo
Biomedicines 2026, 14(2), 335; https://doi.org/10.3390/biomedicines14020335 - 31 Jan 2026
Viewed by 441
Abstract
Background/Objectives: Maresin-1 (MaR1), a specialized pro-resolving mediator (SPM) derived from omega-3 fatty acids, has demonstrated potent anti-inflammatory and pro-resolving properties. However, its effects on depression-like behaviors and the associated dynamics of neuroinflammation, particularly in the context of chronic stress, are not yet [...] Read more.
Background/Objectives: Maresin-1 (MaR1), a specialized pro-resolving mediator (SPM) derived from omega-3 fatty acids, has demonstrated potent anti-inflammatory and pro-resolving properties. However, its effects on depression-like behaviors and the associated dynamics of neuroinflammation, particularly in the context of chronic stress, are not yet fully understood. This study aimed to investigate the therapeutic potential of MaR1 in a chronic unpredictable stress (CUS) model and to monitor its dynamic effects on neuroimmune activity using longitudinal in vivo imaging. Methods: Adolescent male C57BL/6J mice were subjected to a 5-week CUS protocol. Mice exhibiting stable anhedonia were randomized to receive intraperitoneal injections of either MaR1 (5 µg/kg) or vehicle every other day for 4 weeks. During this period, CUS procedures were maintained. Depression-like behaviors were assessed using the sucrose preference test (SPT), tail suspension test (TST), and open field test (OFT). Dynamic changes in neuroinflammation were monitored via longitudinal [18F]DPA-714 positron emission tomography (PET) scans at baseline and after 2 and 4 weeks of treatment. Ex vivo analyses included immunofluorescence quantification of hippocampal microglia (ionized calcium-binding adaptor molecule 1, Iba1), astrocytes (glial fibrillary acidic protein, GFAP), and 18 kDa translocator protein (TSPO) co-expression, alongside quantitative polymerase chain reaction (qPCR) and Western blotting for inflammatory markers (IL-1β, IL-4, TSPO). Results: MaR1 treatment selectively alleviated depression-like behaviors, significantly reversing CUS-induced anhedonia in the SPT and improving locomotor activity, while its effect on despair-like behavior (TST) was not statistically significant. Longitudinal PET imaging revealed a biphasic neuroimmune response, characterized by an initial increase in [18F]DPA-714 standardized uptake value (SUV) at 2 weeks, followed by a return toward baseline at 4 weeks. Histologically, MaR1 reversed CUS-induced hippocampal microglial loss, resulting in a rebound of microglial numbers, and normalized astrocytic activation. At the molecular level, MaR1 dynamically modulated cytokine expression, culminating in a significant upregulation of the pro-resolving marker IL-4 and TSPO at 4 weeks. Conclusions: These findings indicate that Maresin-1 treatment is associated with behavioral improvement and dynamic modulation of glial activity and TSPO PET signals in the hippocampus. This study highlights the value of TSPO PET imaging for monitoring dynamic glial changes during therapeutic intervention and provides supportive evidence for targeting neuroimmune pathways in depression. Full article
(This article belongs to the Special Issue Advanced Research on Psychiatric Disorders)
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