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15 pages, 7909 KB  
Article
Chromosome-Level Genome Assembly and Annotation of the Chinese Lizard Gudgeon (Saurogobio dabryi)
by Lei Fang, Xin Liu, Yiming Huang, Kun Yang, Yongkang Jiang, Chiping Kong, Guiqin Zou, Cheng Qian, Yutong Zhou, Lie Cao, Daxian Zhao and Wanchang Zhang
Animals 2026, 16(17), 2647; https://doi.org/10.3390/ani16172647 (registering DOI) - 24 Aug 2026
Abstract
The Chinese lizard gudgeon (Saurogobio dabryi) is an economically important freshwater species within the Cyprinidae family, abundant in the middle and lower reaches of the Yangtze River and its adjacent basins. As a promising species suitable for aquaculture in China, the [...] Read more.
The Chinese lizard gudgeon (Saurogobio dabryi) is an economically important freshwater species within the Cyprinidae family, abundant in the middle and lower reaches of the Yangtze River and its adjacent basins. As a promising species suitable for aquaculture in China, the lack of genomic resources has rendered the genetic breeding and conservation research. Here, we present the first chromosome-level genome assembly of S. dabryi using PacBio HiFi long reads, short reads, and Hi-C sequencing data. The final assembly reaches a total size of 1.09 Gb and Hi-C scaffolding anchors 99.55% of the assembled contigs onto 25 chromosomes, with a scaffold N50 reaching 43.15 Mb. The final genome assembly shows a BUSCO completeness of 98.39%. We annotated 659.55 Mb repetitive sequences and 26,036 protein-coding genes, 99.47% of which are functionally annotated. Comparative phylogenomic analysis clarifies the phylogenetic position of Saurogobio within Gobioninae. This high-quality genome provides a critical genetic basis for exploring cyprinid phylogeny, benthic adaptive evolution, genetic improvement, and conservation efforts of S. dabryi. Full article
(This article belongs to the Section Animal Genetics and Genomics)
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12 pages, 7482 KB  
Article
Molecular Characterization of Infectious Laryngotracheitis Virus from Broiler Diseased Chickens in Northern Vietnam During 2023–2025
by Giang Thi Huong Tran, Vuong Trong Tran, Amonpun Rattanasrisomporn, Hieu Van Dong, Autchara Kayan and Jatuporn Rattanasrisomporn
Int. J. Mol. Sci. 2026, 27(17), 7544; https://doi.org/10.3390/ijms27177544 (registering DOI) - 23 Aug 2026
Abstract
PCR-based surveillance identified the infectious laryngotracheitis virus (ILTV) genome in 8 out of 14 (57.14%) commercial broiler farms across three Northern Vietnam provinces. Partial sequencing of the infected cell protein 4 (ICP4) and glycoprotein B, G, and J (gB, [...] Read more.
PCR-based surveillance identified the infectious laryngotracheitis virus (ILTV) genome in 8 out of 14 (57.14%) commercial broiler farms across three Northern Vietnam provinces. Partial sequencing of the infected cell protein 4 (ICP4) and glycoprotein B, G, and J (gB, gG, and gJ) genes from the ILTV isolates obtained during 2023–2025 indicated that eight Vietnamese ILTV-positive samples were field ILTV strains. Additionally, high nucleotide identity was observed among the isolates, with ranges of 99.74–100% for the gB, 99.63–100% for the gJ, 99.66–100% for the gG, and 99.34–100% for the ICP4 genes. Phylogenetic analyses based on four genes (gB, gJ, gG, and ICP4) revealed that the eight ILTV strains belonged to two distinct lineages, except for the gJ gene. Analysis of the ICP4 gene showed that the five ILTV strains (VNUA-ILTV-02, VNUA-ILTV-05 to VNUA-ILTV-08) clustered with the United States Laryno Vac, Poulvac-ILT, and ON-2462242/1987 strains, whereas the remaining strains (VNUA-ILTV-01, VNUA-ILTV-03, and VNUA-ILTV-04) were in a distinct group. Furthermore, several amino acid changes were observed in the gB, gG, and gJ proteins of the characterized ILTV strains. Full article
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27 pages, 6614 KB  
Article
Assessment of the Association of Periodontitis and Diabetes Mellitus with Alzheimer’s Disease in a Mouse Model
by Momoko Nakahara, Kota Kataoka, Takayuki Maruyama, Mohammad Nurhamim, Yixuan Zhang, Daiki Fukuhara, Yoko Uchida-Fukuhara, Md Monirul Islam, Manabu Morita, Takashi Saito and Daisuke Ekuni
Int. J. Mol. Sci. 2026, 27(17), 7542; https://doi.org/10.3390/ijms27177542 (registering DOI) - 23 Aug 2026
Abstract
The purpose of the present study was to investigate how periodontitis and diabetes mellitus (DM) are associated with Alzheimer’s disease (AD) through microRNA (miRNA) using AD model mice. The experimental period was 8 weeks. Twenty-four male knock-in mice (B6-AppNL-G-F/NL-G-F/J) were divided into four [...] Read more.
The purpose of the present study was to investigate how periodontitis and diabetes mellitus (DM) are associated with Alzheimer’s disease (AD) through microRNA (miRNA) using AD model mice. The experimental period was 8 weeks. Twenty-four male knock-in mice (B6-AppNL-G-F/NL-G-F/J) were divided into four groups: control group fed a normal diet (C), DM group fed a high-fat/sucrose diet (DM), periodontitis (P) group, and DM + periodontitis (DM+P) group. Memory performance was compared using the Y-maze test. Next-generation sequencing was performed on brain samples, and fold changes in miRNA expression were calculated by comparing the DM+P and C groups. Integrated miRNA–mRNA analysis identified putative miRNA-targeted mRNAs, and protein expression of the top candidate gene was assessed. Memory function in the DM+P group was significantly lower than in the C group. Among the seven mRNAs identified by the integrated analysis, Neurod1 showed the greatest decrease in expression, and it was predicted to be regulated by miR-693-3p. Neurod1 protein expression in the hippocampus was significantly lower in the DM+P group than the C group. Our results suggest that the combined exposure to periodontitis and DM was associated with AD-like pathological changes and identified the miR-693-3p/Neurod1 pair as a candidate regulatory axis. Full article
(This article belongs to the Section Molecular Pathology, Diagnostics, and Therapeutics)
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29 pages, 14707 KB  
Article
Integrated Transcriptomic and Proteomic Analyses Reveal the Effects and Mechanisms of Glycyrrhiza Polysaccharides in Alleviating Immune Stress in Broilers
by Shuyan Wu, Boyi Dong, Dongying Weng, Jiaqi Chen, Hongzhu Jin, Xinrui Lin, Weize Qin, Shuyi Li, Haidong Du and Tiyu Li
Animals 2026, 16(17), 2633; https://doi.org/10.3390/ani16172633 (registering DOI) - 22 Aug 2026
Abstract
Immune stress under intensive high density production conditions impairs broiler health and performance, highlighting the need for effective nutritional strategies. This study established an immune stress model by intraperitoneal lipopolysaccharide (LPS) injection to investigate the mechanism by which Glycyrrhiza polysaccharides (GPs) alleviate LPS-induced [...] Read more.
Immune stress under intensive high density production conditions impairs broiler health and performance, highlighting the need for effective nutritional strategies. This study established an immune stress model by intraperitoneal lipopolysaccharide (LPS) injection to investigate the mechanism by which Glycyrrhiza polysaccharides (GPs) alleviate LPS-induced immune stress. A total of 240 AA broilers were randomly assigned to four groups: control (CON), GP, LPS, and GP+LPS, with six replicates per group and ten birds per replicate. During the stress phase (28 d), LPS challenge increased serum ACTH and CORT concentrations and altered several immune-related parameters; whereas, GP supplementation improved ileal morphology and reduced serum IL-1β, NF-κB, and TNF-α concentrations. Significant GP × LPS interactions were observed for IL-4, IgA, IgG, and iNOS. During the recovery phase (35 d), GP supplementation increased serum IgA and decreased iNOS, while significant GP × LPS interactions were detected for IL-1β, NF-κB, and sCD4. Notably, GP attenuated the LPS-associated increase in NF-κB. Integrated multi-omics analysis indicated coordinated regulation at transcriptional and proteomic levels. GP upregulated FOS, JUN, and CATH3 and enriched NF-κB and Wnt signaling at the transcript level, while increasing IRF1 and CATH3 and decreasing CTNNBIP1 at the protein level, primarily involving Wnt and MAPK pathways. Joint analysis identified CATH3 as a central regulatory target. Collectively, GP alleviates immune stress by restraining excessive inflammation and modulating Wnt/MAPK signaling, thereby promoting intestinal structural recovery. Full article
(This article belongs to the Section Animal Nutrition)
15 pages, 3964 KB  
Article
Engineering of a Carbonic Anhydrase from Hydrogenimonas thermophila Through Fusion Tags and Surface Mutagenesis Enhances Solubility While Revealing Stability–Function Relationships
by Colleen Varaidzo Manyumwa, Carsten Jers and Ivan Mijakovic
Int. J. Mol. Sci. 2026, 27(16), 7498; https://doi.org/10.3390/ijms27167498 - 21 Aug 2026
Viewed by 76
Abstract
Protein solubility can limit enzyme performance in industrial applications. This is the case for some carbonic anhydrases (CAs), key enzymes for CO2 capture and utilization. In this study, we investigated an α-class CA from the thermophilic bacterium Hydrogenimonas thermophila (HtCA), which was [...] Read more.
Protein solubility can limit enzyme performance in industrial applications. This is the case for some carbonic anhydrases (CAs), key enzymes for CO2 capture and utilization. In this study, we investigated an α-class CA from the thermophilic bacterium Hydrogenimonas thermophila (HtCA), which was predominantly expressed as an insoluble protein in Escherichia coli. Surface analysis using Molecular Operating Environment (MOE) revealed extensive hydrophobic regions, suggesting a basis for its poor solubility. To improve solubility, three C-terminal fusion tags were evaluated (Gb1, ng3-NEXT, and T7B9). All tagged variants showed markedly increased soluble expression as determined by sodium dodecyl sulfate–polyacrylamide gel electrophoresis (SDS-PAGE) analysis. To reduce surface hydrophobicity, selected residues were substituted with charged amino acids. Most variants displayed improved solubility, and V136D showed enhanced thermostability, retaining 76% activity after exposure to 90 °C for an hour. However, the F177D variant completely lost all enzymatic activity, highlighting the importance of evaluating both solubility and catalytic function during protein engineering. Molecular dynamics simulations supported the experimental findings, revealing that thermostable variants exhibited reduced structural fluctuations and favorable free-energy landscapes, while the inactive F177D mutant sampled a broader conformational space and higher-energy conformations, consistent with decreased structural stability and loss of catalytic activity. Full article
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20 pages, 10841 KB  
Article
Multiple BnaSOBIR1-Associated Receptor-like Proteins Contribute to Enhanced Resistance to Sclerotinia sclerotiorum in Brassica napus L. (Oilseed Rape)
by Chenghuizi Yang, Liying Ma, Jieying Nong and Shitou Xia
Plants 2026, 15(16), 2545; https://doi.org/10.3390/plants15162545 - 21 Aug 2026
Viewed by 122
Abstract
As a major fungal pathogen of Brassica napus, Sclerotinia sclerotiorum causes significant yield reductions worldwide. Receptor-like proteins (RLPs) are essential components of plant immunity, but the functions of many RLPs in B. napus still remain unclear. In this study, three BnaSOBIR1-interacting leucine-rich [...] Read more.
As a major fungal pathogen of Brassica napus, Sclerotinia sclerotiorum causes significant yield reductions worldwide. Receptor-like proteins (RLPs) are essential components of plant immunity, but the functions of many RLPs in B. napus still remain unclear. In this study, three BnaSOBIR1-interacting leucine-rich repeat RLPs (LRR-RLPs), named BnaRLP-G13-2, BnaRLP-G13-3, and BnaRLP-G13-4, were identified by yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays. Promoter analysis revealed diverse cis-acting elements involved in stress and phytohormone responses. Overexpression of these genes significantly improved resistance to S. sclerotiorum in both Arabidopsis thaliana and B. napus. Consistently, BnaRLP-G13-2/3/4 restored disease resistance and NLP-induced ROS production in the rlp23-1 mutant. Furthermore, BiFC assays suggested an association between BnaRLP-G13-2/3/4 and Ssnlp24SsNEP2-associated perception, although direct biochemical binding remains to be demonstrated. These findings advance the understanding of BnaSOBIR1-associated BnaRLP-G13-2/3/4-mediated immunity and provide new insights into enhancing disease resistance in oilseed crops. Full article
(This article belongs to the Special Issue Phytohormones: Methodologies, Mechanisms and Applications)
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14 pages, 6831 KB  
Article
Enhydrin Exhibits Antitumor Effects on Human Prostate Cancer Cells Associated with Reduced PI3K/AKT- and NF-κB-Related Gene and Protein Expression
by Xia Zhang, Rikiya Taoka, Dage Liu, Hirohito Naito, Yohei Abe, Akram Hossain and Mikio Sugimoto
Curr. Issues Mol. Biol. 2026, 48(8), 851; https://doi.org/10.3390/cimb48080851 - 21 Aug 2026
Viewed by 63
Abstract
Enhydrin, a melampolide-type sesquiterpene lactone abundant in the leaves of yacon (Smallanthus sonchifolius), has not previously been investigated for its anti-prostate cancer activity. This study investigated the antiproliferative effects of enhydrin in human prostate cancer cells, its regulatory effects on apoptosis-related [...] Read more.
Enhydrin, a melampolide-type sesquiterpene lactone abundant in the leaves of yacon (Smallanthus sonchifolius), has not previously been investigated for its anti-prostate cancer activity. This study investigated the antiproliferative effects of enhydrin in human prostate cancer cells, its regulatory effects on apoptosis-related molecules, and its impact on the PI3K/AKT and NF-κB signaling pathways. Three prostate cancer cell lines (PC3, DU145, and LNCaP) were treated with enhydrin, and its effects were analyzed using cell viability assays, morphological observation, flow cytometry, apoptosis-focused TaqMan qPCR array, qRT-PCR, and Western blotting. In vivo antitumor activity was assessed in a PC3 xenograft mouse model. Enhydrin reduced cell viability in a dose- and time-dependent manner, induced morphological changes associated with cytotoxicity, and caused G1 cell-cycle arrest. Gene expression analysis revealed downregulation of PI3K/AKT- and NF-κB-related genes and modulation of BCL2 family genes toward a pro-apoptotic profile, which was confirmed at both mRNA and protein levels. In vivo, enhydrin suppressed tumor growth without significant body-weight loss. These findings suggest that enhydrin exerts antitumor effects in prostate cancer by reducing the expression of PI3K/AKT and NF-κB related molecules and modulating apoptosis-related proteins. Although additional studies are required to determine pathway activity, directly confirm apoptosis, and evaluate normal-cell cytotoxicity and the therapeutic window, these findings provide preliminary biological evidence of the effects of enhydrin in prostate cancer models. Full article
(This article belongs to the Special Issue Molecular Mechanisms in Cancer Treatment and Anticancer Drugs)
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14 pages, 3292 KB  
Article
Lateral Flow Immunochromatographic Assay for Detection of Antibodies Against a Recombinant Human Adenovirus Type 3 Hexon Fragment Using Gold Nanoparticles and Quantum Dots
by Kanatbek Mukantayev, Kanat Tursunov, Laura Tokhtarova and Bisultan Abirbekov
Diagnostics 2026, 16(16), 2670; https://doi.org/10.3390/diagnostics16162670 - 21 Aug 2026
Viewed by 108
Abstract
Background/Objectives: Human adenoviruses (HAdVs) are widely used as vectors for vaccines and gene therapy; however, pre-existing immunity can reduce their efficacy. Therefore, rapid and accessible serological methods are required to assess antibody levels against adenoviruses. Lateral flow immunochromatographic assay (LFIA) sensitivity depends [...] Read more.
Background/Objectives: Human adenoviruses (HAdVs) are widely used as vectors for vaccines and gene therapy; however, pre-existing immunity can reduce their efficacy. Therefore, rapid and accessible serological methods are required to assess antibody levels against adenoviruses. Lateral flow immunochromatographic assay (LFIA) sensitivity depends on the label and antigen. In this study, we aimed to develop and evaluate LFIA systems based on gold nanoparticles (GNPs) and quantum dots (QDs) using a recombinant HAdV hexon protein. Methods: A recombinant HAdV hexon protein fragment (rhHAdV, 35 kDa; amino acids A120-R316) was expressed in Escherichia coli and purified using Ni2+ affinity chromatography. Protein identity was confirmed using sodium dodecyl sulfate–polyacrylamide gel electrophoresis, Western blotting, and liquid chromatography–tandem mass spectrometry analyses. Two LFIA formats were developed using Protein G-conjugated GNPs (GNP-G) and QDs (QD-G). Agreement with the reference ELISA was evaluated using 90 human serum samples. Results: The rhHAdV antigen demonstrated reactivity with anti-adenovirus-positive human sera in ELISA. Antibody detection was achieved at serum dilutions of up to 1:300 and 1:1000 for the GNP- and QD-based LFIA, respectively. The GNP-G and QD-G LFIA formats demonstrated positive percent agreements of 96.9% and 100%, respectively, while both assays showed a negative percent agreement of 98.2% compared with the reference ELISA. Conclusions: The findings demonstrate the feasibility of a QD-based LFIA for qualitative detection of antibodies reactive with the recombinant HAdV-B3 hexon fragment. Full article
(This article belongs to the Section Clinical Laboratory Medicine)
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18 pages, 1532 KB  
Article
Comparative Predictive Performance of Upper Gastrointestinal Bleeding Risk Scores and the CALLY Index in Geriatric Patients
by Muge Gul Gulecoglu Onem and Soner Onem
Diagnostics 2026, 16(16), 2664; https://doi.org/10.3390/diagnostics16162664 - 20 Aug 2026
Viewed by 107
Abstract
Background/Objectives: Elderly patients with acute upper gastrointestinal bleeding (UGIB) are a high-risk group with significant morbidity and mortality. Various risk scoring systems have been devised to predict clinical outcome in UGIB, but their effectiveness in geriatric patients is unclear. The purpose of [...] Read more.
Background/Objectives: Elderly patients with acute upper gastrointestinal bleeding (UGIB) are a high-risk group with significant morbidity and mortality. Various risk scoring systems have been devised to predict clinical outcome in UGIB, but their effectiveness in geriatric patients is unclear. The purpose of the present study was to evaluate the predictive performance of established UGIB risk scores in older adults and to compare the predictive performance of the C-reactive protein–albumin–lymphocyte (CALLY) index with conventional UGIB risk scores. Methods: This study was a retrospective single-center analysis of a cohort of patients aged ≥65 years presenting with acute non-variceal upper gastrointestinal bleeding (UGIB) who had esophagogastroduodenoscopy from January to December 2025. Scores for Glasgow-Blatchford Score (GBS), Rockall, AIMS65, ABC, MAP(ASH), CANUKA, T-score, and CALLY index were calculated. The primary management endpoint was the requirement for endoscopic hemostatic treatment. Secondary outcomes were blood transfusion necessity, rebleeding, intensive care unit (ICU) admission, length of hospital stay, and 30-day death. The predictive performance of each scoring system was assessed by receiver operating characteristic (ROC) curve analysis. Results: We enrolled 113 patients (mean age 77.7 ± 8.3 years; 59.3% male), of whom 42 (37.2%) required endoscopic hemostatic treatment. No single risk score consistently outperformed the others across all clinical outcomes. GBS showed the highest observed AUC for predicting the need for transfusion (AUC = 0.892), whereas Rockall showed the highest observed AUC for rebleeding (AUC = 0.739) and ICU admission (AUC = 0.668). In the exploratory mortality analysis based on seven deaths, the directionally corrected AUC was 0.846 for CALLY, 0.756 for MAP(ASH), and 0.742 for CANUKA; no pairwise AUC comparisons were performed for this outcome. The CALLY index showed modest discrimination for endoscopic hemostatic therapy (AUC = 0.664). In the exploratory rebleeding analysis, CALLY yielded an AUC of 0.724; however, this estimate was based on only eight events. Lower CALLY levels were associated with increased 30-day mortality, whereas the CALLY index was not significantly associated with transfusion requirements or length of hospital stay. After correction for multiple comparisons, CALLY showed significantly lower discriminatory performance for transfusion requirement than GBS, T-score, CANUKA, and MAP(ASH), whereas no significant differences were observed for endoscopic intervention or ICU admission. Conclusions: No single risk score was able to predict all clinically important outcomes in older adults with acute UGIB. Conventional scoring systems remained useful for several established clinical outcomes, whereas the CALLY index showed modest discrimination for endoscopic hemostatic therapy. Its findings for rebleeding and 30-day mortality were exploratory because of the limited number of events and require external validation. More prospective multicenter studies are needed to confirm the clinical value of the CALLY index in older individuals with UGIB. Full article
(This article belongs to the Section Clinical Diagnosis and Prognosis)
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16 pages, 9460 KB  
Article
Disruption of Functional Membrane Microdomains Enhances Methicillin-Resistant Staphylococcus aureus Pathogenesis via Hyperexpression of Hemolysins
by Bingtian Jin, Changzhen Wang, Tiantian Liu, Pengcheng Dong, Xurong Wang, Xiao Yang, Dengwang Yuan and Feng Yang
Vet. Sci. 2026, 13(8), 839; https://doi.org/10.3390/vetsci13080839 - 20 Aug 2026
Viewed by 162
Abstract
(1) Background: methicillin‑resistant Staphylococcus aureus (MRSA) is a zoonotic pathogen, and its hemolysins serve as key virulence factors. Functional membrane microdomains (FMMs) are protein-enriching platforms and regulate diverse physiological functions by recruiting and assembling various proteins. However, whether and how FMMs regulate the [...] Read more.
(1) Background: methicillin‑resistant Staphylococcus aureus (MRSA) is a zoonotic pathogen, and its hemolysins serve as key virulence factors. Functional membrane microdomains (FMMs) are protein-enriching platforms and regulate diverse physiological functions by recruiting and assembling various proteins. However, whether and how FMMs regulate the hemolytic ability of MRSA remains unclear. This study aimed to investigate FMM-mediated regulation of MRSA hemolysins and the underlying mechanisms. (2) Methods: Homologous recombination was employed to generate FMM-disrupted (N315ΔfloA) and complemented (N315ΔfloA::floA) strains from the MRSA N315 wild-type strain (N315 WT). The three strains were compared with respect to hemolytic activity, transcript levels of key virulence and regulatory genes, and in vivo virulence. (3) Results: Disruption of FMMs significantly enhanced hemolytic activity compared with N315 WT and complemented strains. Meanwhile, FMM disruption repressed the two-component system genes (vraS and vraR), while activating the agr operon (agrB, agrD, agrC and agrA) and its effector molecule RNAIII, leading to upregulation of hemolysin genes (hla, hlb, hld). In vivo, N315ΔfloA infection markedly increased mortality in G. mellonella larvae and BALB/c mice, with significantly elevated pro-inflammatory factors (TNF-α, IL-6, and IL-1β) in mouse plasma. All these phenotypes were effectively reversed in N315ΔfloA::floA. (4) Conclusions: Disruption of FMMs potentiates both hemolytic activity and overall virulence in MRSA, with the potential underlying mechanism involving the VraS/R-Agr regulatory axis that drives transcriptional upregulation of hemolysin-encoding genes. Full article
(This article belongs to the Special Issue Advancements in Livestock Staphylococcus sp.)
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17 pages, 4286 KB  
Article
Identification of Conserved B-Cell Epitope Candidates Associated with Neutralizing Activity of Bovine Coronavirus Spike Protein
by Yunxin Ren, Hua Yue, Cheng Tang and Xi Chen
Animals 2026, 16(16), 2598; https://doi.org/10.3390/ani16162598 - 20 Aug 2026
Viewed by 174
Abstract
Bovine coronavirus (BCoV) is a major cause of respiratory and enteric diseases in cattle, resulting in substantial economic losses to the global cattle industry. Next-generation epitope-focused vaccines require conserved neutralizing determinants to achieve broad protective efficacy across circulating variants. Here, we applied a [...] Read more.
Bovine coronavirus (BCoV) is a major cause of respiratory and enteric diseases in cattle, resulting in substantial economic losses to the global cattle industry. Next-generation epitope-focused vaccines require conserved neutralizing determinants to achieve broad protective efficacy across circulating variants. Here, we applied a reverse-vaccinology and immunoinformatics-guided strategy to identify conserved linear B-cell epitope candidates on the BCoV spike protein. Using ABCPred (16 aa; threshold score 0.51), 139 putative linear B-cell epitopes were predicted, and 10 candidates (B1–B10) were selected based on antigenicity, allergenicity/toxicity filters, and Shannon-entropy-based conservation (≥95%). Each candidate was displayed on Helicobacter pylori ferritin and TEM confirmed the formation of self-assembled nanocages. BALB/c mice (n = 6 per group) were subcutaneously immunized with 50 μg of each epitope–ferritin fusion protein emulsified 1:1 with Montanide ISA 201 in a prime–boost regimen (at a 14-day interval), and sera were collected 14 days after the booster immunization. All 10 constructs induced BCoV-specific binding IgG (endpoint titers ranging from 1:2667 to 1:11,733), but only B1, B2, B4, B6, B7, and B8 elicited detectable in vitro neutralizing activity against both representative strains, whereas B3, B5, B9, and B10 remained below the detection limit (<1:8). Neutralizing titers were 1:24–1:99 for the enteric strain XHD4 and 1:27–1:88 for the respiratory strain HXD1, with no significant difference observed between the two strains (p > 0.05). Overall, these findings identify six conserved B-cell epitope candidates capable of eliciting neutralizing antibody responses against both representative enteric and respiratory field strains, providing experimental evidence to support epitope-focused BCoV vaccine design. Full article
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17 pages, 11487 KB  
Article
Integrated Analysis of Multiple Databases Identifies Tissue Inhibitor of Metalloproteinase 1 Expression and Its Association with the Immune Microenvironment in Colorectal Cancer
by Yun Xie, Jun Li, Zuwei Yan and Wenguang Zhang
Genes 2026, 17(8), 977; https://doi.org/10.3390/genes17080977 - 20 Aug 2026
Viewed by 196
Abstract
Background: In recent decades, the incidence of colorectal cancer (CRC) has been rising worldwide. CRC ranks second in cancer-related mortality. The identification of reliable biomarkers for early diagnosis and prognosis prediction, along with a deeper understanding of the underlying molecular events, holds substantial [...] Read more.
Background: In recent decades, the incidence of colorectal cancer (CRC) has been rising worldwide. CRC ranks second in cancer-related mortality. The identification of reliable biomarkers for early diagnosis and prognosis prediction, along with a deeper understanding of the underlying molecular events, holds substantial promise for improving patient outcomes. The tissue inhibitor of the metalloproteinase 1 (TIMP1) gene is overexpressed in various gastrointestinal malignancies and contributes to tumor progression. However, its role in regulating the CRC tumor immune microenvironment (TIME) and its potential as a clinically actionable prognostic biomarker remain unclear. Methods: To probe how TIMP1 acts as a prognosis-related candidate biomarker in colorectal carcinoma, TCGA-derived datasets were adopted to conduct Kaplan–Meier survival assessment. We also investigated the connection between the expression abundance of TIMP1 and the infiltration of immune populations and intratumoral lymphocytes; furthermore, immune checkpoint-related genes were systematically assessed across multiple tumor types via the TISIDB and TIMER2.0 platforms, with particular emphasis on CRC. We adopted the ESTIMATE scoring system to figure out how TIMP1 gene expression correlates with the phenotypic properties of the colorectal-cancer TIME. We relied on the limma toolkit for the screening of differential transcripts from high-TIMP1 and low-TIMP1 cohorts. Enrichment assessments covering Gene Ontology terms and Kyoto Encyclopedia of Genes and Genomes entries were then carried out to predict the potential biological pathways associated with TIMP1. We constructed the protein–protein interaction map for TIMP1-interacting partners via the STRING repository. To further explore TIMP1-correlated genes, we performed Venn diagram intersection analysis combined with Spearman’s correlation test. Finally, quantitative reverse-transcription PCR was then implemented to detect TIMP1 messenger-RNA abundance inside the RKO colorectal carcinoma cell line as well as normal colonic epithelial CCD-18Co cells, which offered in vitro experimental verification for our bioinformatic outcomes. Results: According to outcome data, TIMP1 transcripts were markedly up-regulated in CRC specimens and cell lines relative to normal samples. Elevated TIMP1 expression served as a poor-prognosis indicator for overall survival (hazard ratio [HR] = 0.43, 95% confidence interval [CI] = 0.29–0.64, p < 0.001) and disease-specific survival (HR = 0.39, 95% CI = 0.22–0.68, p = 0.001) among colorectal-carcinoma patients. TIMP1-high and TIMP1-low groups exhibited notable differences in immune cell infiltration (CD8+ T, macrophage, mast, neutrophil, B, monocyte, dendritic, and CD4+ T cells). TIMP1 expression was also significantly correlated with tumor-infiltrating lymphocytes, key immune checkpoint genes (e.g., CD274 [PD-L1] and CTLA4), and immunomodulatory chemokines (e.g., CCL3 and CCL5). Twelve TIMP1-interacting DEGs were selected: COL5A1, FN1, PRG4, and a cluster of nine MMPs (MMP1/2/3/7/8/9/11/13/14), all of which showed significant positive correlations with TIMP1 (r = 0.31–0.63, all p < 0.001). Conclusions: TIMP1 expression correlates with features of the tumor immune microenvironment and extracellular matrix remodeling in CRC, suggesting that TIMP1 shows potential as a candidate biomarker. However, its potential as a therapeutic target warrants further experimental investigation. Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
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24 pages, 1736 KB  
Article
Berberine Enhances Radiosensitivity of Head and Neck Squamous Cell Carcinoma Concurrent with the Inhibition of DNA Repair, Stemness and Tumor Growth
by Deepali Mishra, Aishwarya Jaiswal, Aleena Sinha, Navneendra Singh and Rana P. Singh
Cancers 2026, 18(16), 2690; https://doi.org/10.3390/cancers18162690 - 19 Aug 2026
Viewed by 251
Abstract
Background/Objectives: The emergence of radioresistance is a major challenge in cancer treatment. Herein, we evaluated the radiosensitizing effects and associated molecular mechanisms of a small molecule, berberine, in HNSCC. Methods: HNSCC cells were treated with berberine, ionizing radiation (IR), and their combination. Radiosensitivity [...] Read more.
Background/Objectives: The emergence of radioresistance is a major challenge in cancer treatment. Herein, we evaluated the radiosensitizing effects and associated molecular mechanisms of a small molecule, berberine, in HNSCC. Methods: HNSCC cells were treated with berberine, ionizing radiation (IR), and their combination. Radiosensitivity was assessed using methods for clonogenic survival, proliferation, cell death, apoptosis, cell cycle distribution, DNA damage, and associated mechanisms. Spheroid models were employed to examine tumor growth and stemness-related markers. Therapeutic efficacy was further evaluated using the syngeneic MOC2 tumor syngraft mouse model. Results: The combination of berberine and IR significantly decreased the colony-forming ability, cell proliferation, and survival in UM-SCC-22B and MOC2 cells. Correspondingly, a decrease in the pro-survival signaling, EGFR, ERK1/2, mTOR, and STAT-3 was noted. The combination treatment increased sub-G1 cell population and apoptotic cell death with enhanced DNA damage, which was also associated with downregulation of DNA repair proteins. Spheroids showed disintegration and altered morphology in the combination treatment. This combination also inhibited Wnt/β-catenin signaling and reduced the expression of genes associated with stemness-related pluripotency. Berberine further enhanced DNA damage and reduced stemness in EGFR-knockdown cells. The berberine-IR combination not only inhibited the growth of syngeneic MOC2 tumors but also mitigated the toxicity associated with IR. The in vitro findings of reduced expression of stemness and DNA damage repair genes were also observed in tumors. Conclusions: Our findings indicated that berberine enhances the radiation response of HNSCC through perturbation of pro-survival signaling, DDR signaling and reduction of stemness-associated features, thereby enhancing the therapeutic efficacy. Full article
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20 pages, 6212 KB  
Article
Isolation and Anti-Melanogenic Activity of Polycarpol from Ganoderma lucidum Mycelia: Expanding the Functional Potential of Cultured Mycelial Biomass
by Che-Hwon Park, Sung-Chul Lee, Rae-Won Kang and Young-Jin Park
J. Fungi 2026, 12(8), 625; https://doi.org/10.3390/jof12080625 - 19 Aug 2026
Viewed by 196
Abstract
Ganoderma lucidum is a medicinal mushroom widely recognized as a source of bioactive metabolites, particularly triterpenoids. Although most studies have focused on fruiting bodies and spores, the potential of cultured mycelial biomass as a source of functional secondary metabolites remains less explored. In [...] Read more.
Ganoderma lucidum is a medicinal mushroom widely recognized as a source of bioactive metabolites, particularly triterpenoids. Although most studies have focused on fruiting bodies and spores, the potential of cultured mycelial biomass as a source of functional secondary metabolites remains less explored. In this study, we isolated and characterized polycarpol from the mycelia of G. lucidum and evaluated its anti-melanogenic activity in B16F10 murine melanoma cells. Dried mycelia obtained after liquid culture were extracted with 70% ethanol, partitioned with ethyl acetate, and purified by repeated chromatographic separation. The isolated compound was identified as polycarpol by LC–ESI–MS, HR-MS/MS, and NMR spectroscopy, together with comparison with previously reported spectroscopic data. The anti-melanogenic activity of polycarpol was evaluated in α-MSH-stimulated B16F10 murine melanoma cells, a commonly used cellular model of melanogenesis. Polycarpol reduced α-melanocyte-stimulating hormone-induced cellular tyrosinase activity and melanin production at concentrations that did not markedly affect cell viability. Notably, 2 μg/mL (4.54 μM) polycarpol showed a melanin-inhibitory effect comparable to that of arbutin. Western blot analysis showed that polycarpol decreased the expression of microphthalmia-associated transcription factor, tyrosinase, and tyrosinase-related protein-1. In addition, polycarpol suppressed CREB phosphorylation and modulated the MAPK signaling pathways. These findings suggest that polycarpol inhibits melanogenesis through regulation of MITF-associated melanogenic signaling. Overall, this study demonstrates that cultured G. lucidum mycelia can produce anti-melanogenic triterpenoids and highlights cultured mycelial biomass as a controllable fungal material for exploring anti-melanogenic triterpenoids, although further optimization is required to improve production efficiency. Full article
(This article belongs to the Special Issue Molecular Biology of Mushroom, 2nd Edition)
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16 pages, 4728 KB  
Article
miR-27b-3p Exacerbates VCD-Induced KGN Cell Injury by Targeting PAPPA to Suppress IGF-1 Release and Inhibit the PI3K/AKT Pathway
by Manyu Zhang, Xiangyu Meng, Mengdi Shi and Pengling Ge
Genes 2026, 17(8), 966; https://doi.org/10.3390/genes17080966 - 18 Aug 2026
Viewed by 183
Abstract
Background/Objectives: While currently termed premature ovarian insufficiency (POI), premature ovarian failure (POF) remains a prominent driver of female infertility with a molecular pathogenesis that is still lacking comprehensive clarification. In in vitro studies, the pathology of POI is commonly simulated through a well-characterized [...] Read more.
Background/Objectives: While currently termed premature ovarian insufficiency (POI), premature ovarian failure (POF) remains a prominent driver of female infertility with a molecular pathogenesis that is still lacking comprehensive clarification. In in vitro studies, the pathology of POI is commonly simulated through a well-characterized model involving VCD (4-vinylcyclohexene diepoxide)-mediated cytotoxicity within KGN-derived human granulosa cells. However, the key regulatory molecular networks involved in this process are still poorly characterized. Although microRNAs (miRNAs) have emerged as critical regulators in ovarian function decline, the specific role and underlying mechanism of miR-27b-3p in POI remain elusive. Methods: A VCD-induced KGN cell injury model was established by treating cells with 1.0 mM VCD for 24 h. Cell viability, apoptosis rate, and miR-27b-3p expression were assessed by CCK-8 assay, flow cytometry, and RT-qPCR, respectively. Overexpression and targeted suppression of miR-27b-3p were achieved by introducing its specific mimics and inhibitors, respectively. Target identification was conducted via bioinformatic prediction, EdU incorporation, Western blot, and dual-luciferase reporter assays. Functional rescue experiments were carried out by co-transfection with a PAPPA-overexpressing plasmid (oe-PAPPA). IGF-1 secretion was quantified by ELISA, and phosphorylation of IGF1R and AKT was analyzed by Western blot to determine whether miR-27b-3p modulates cellular phenotypes via the PAPPA–IGF-1–PI3K/AKT axis. Exogenous IGF-1 supplementation was further applied to confirm pathway dependence. Results: VCD treatment dose-dependently restrained cellular growth and stimulated apoptotic pathways in KGN cells; paralleling these phenotypic changes, miR-27b-3p abundance was remarkably increased. Ectopic expression of miR-27b-3p exacerbated VCD-induced growth inhibition and apoptosis, whereas its inhibition conferred cytoprotective effects. Through the integration of computational predictions and dual-luciferase reporter systems, PAPPA was definitively established as a direct downstream target of miR-27b-3p. miR-27b-3p negatively regulated both PAPPA mRNA and protein levels, thereby impairing PAPPA-mediated cleavage of IGF-binding proteins (e.g., IGFBP4) and subsequent release of free IGF-1. This led to reduced IGF-1 secretion and significantly diminished phosphorylation of IGF1R and AKT. Remarkably, PAPPA overexpression effectively reversed the detrimental effects of miR-27b-3p, and exogenous IGF-1 supplementation similarly attenuated miR-27b-3p–mediated proliferation arrest and pro-apoptotic phenotypes. Conclusions: This study uncovers a novel pathogenic mechanism whereby miR-27b-3p exacerbates VCD-induced granulosa cell injury by directly targeting PAPPA, suppressing IGF-1 release, and consequently inhibiting the PI3K/AKT pro-survival signaling pathway. A novel perspective on the fundamental basis of POI is established by this research, which further posits therapeutic manipulation of the miR-27b-3p/PAPPA/IGF-1 module as a prospective treatment for disrupted ovarian function. Full article
(This article belongs to the Special Issue Targeting RNA Coding Mechanisms in Disease Molecular Pathways)
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