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12 pages, 3039 KB  
Article
Genome-Wide Analysis of Serial Passage of the Infectious Bronchitis Virus Reveals Evolutionary Dynamics Underlying Attenuation and Immunogenicity
by Joaquín Williman, Gonzalo Tomas, Ariel Vagnozzi, Claudia Techera, Sebastián Brambillasca, Ruben Pérez and Ana Marandino
Vaccines 2026, 14(6), 467; https://doi.org/10.3390/vaccines14060467 - 24 May 2026
Viewed by 453
Abstract
Background/Objectives: Serial passage in embryonated eggs is widely used to attenuate the infectious bronchitis virus (IBV) for vaccine production; however, the evolutionary processes underlying attenuation and immunogenicity remain incompletely understood. Here, we analyzed genome-wide viral evolution during serial passages to investigate how [...] Read more.
Background/Objectives: Serial passage in embryonated eggs is widely used to attenuate the infectious bronchitis virus (IBV) for vaccine production; however, the evolutionary processes underlying attenuation and immunogenicity remain incompletely understood. Here, we analyzed genome-wide viral evolution during serial passages to investigate how mutations emerge, persist, are lost, or become fixed over time and how these dynamics relate to changes in pathogenicity and immunogenicity. Methods: Deep sequencing was performed on 11 representative serial passages (P2–P79) of the UY/11/CA/18 strain, including two derivative lineages: P7 VIR (virulent) and P53 VAC (attenuated and immunogenic). Results: This study identified an early adaptive phase characterized by a limited set of mutations potentially associated with genome replication, viral RNA processing, and virion assembly, including a key change in non-structural protein 14 and variants in M and 3c (E). This phase was followed by a broader expansion of the variant spectrum across replicase genes and delayed accumulation of Spike protein variants. Most Spike changes emerged during later passages and exhibited transient dynamics, and only a subset reached a high frequency after the establishment of early replicase- and structural-associated changes. Consistent with these dynamics, P7 VIR diverged before the late accumulation of Spike variants and retained a pathogenic phenotype, whereas P53 VAC diverged after the emergence of early high-frequency variants but before the extensive late-stage Spike variation observed in P79, which was associated with reduced immunogenicity. Conclusions: These findings support a multi-step model of IBV attenuation in which progressive filtering of genome-wide variation shapes distinct evolutionary outcomes during serial passages. This evolutionary framework provides insight into the relationship between attenuation and immunogenicity and may help guide the rational design of live attenuated vaccines. Full article
(This article belongs to the Section Vaccine Design, Development, and Delivery)
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17 pages, 943 KB  
Article
Immunogenicity and Safety of Biological E’s Monovalent rDNA Hepatitis B Vaccine (BEVAC®) in Neonates and Infants: A Multicentre, Randomized, Phase IV Non-Inferiority Trial
by Subhash Thuluva, Subbareddy Gunneri, Siddalingaiah Ningaiah, Vijay Yerroju, Rammohan Reddy Mogulla, Chirag Dhar, Kamal Thammireddy, Raju Esanakarra, Pradeep Nanjappa and Niranjana S. Mahantshetti
Viruses 2026, 18(4), 472; https://doi.org/10.3390/v18040472 - 17 Apr 2026
Viewed by 795
Abstract
Biological E’s BEVAC® is a recombinant DNA hepatitis B vaccine that has been used in India for more than a decade in routine early-life immunization and has recently been prequalified by the World Health Organization (WHO). This multicentre, single-blind, parallel-group, randomized phase [...] Read more.
Biological E’s BEVAC® is a recombinant DNA hepatitis B vaccine that has been used in India for more than a decade in routine early-life immunization and has recently been prequalified by the World Health Organization (WHO). This multicentre, single-blind, parallel-group, randomized phase IV trial, conducted at seven study sites in India, compared the immunogenicity and safety of BEVAC® with a licensed comparator vaccine (GeneVac-B®, Serum Institute of India Pvt. Ltd, Pune, India.) in healthy term neonates and infants. Participants received three 0.5 mL doses administered intramuscularly at birth (within 24 h), 6 weeks of age, and 14 weeks of age. The primary endpoint was seroprotection (anti-HBs IgG ≥10 mIU/mL) at 28 days after the third dose (Day 126), compared using a non-inferiority margin of −10%. Secondary endpoints included safety and tolerability outcomes through Day 126. A total of 468 neonates were randomized (234 per group), of whom 44% were female. At Day 126, seroprotection rates were 98.2% (95% CI: 95.39, 99.50) with BEVAC® and 99.1% (95% CI: 96.78, 99.89) with the comparator; the between-group difference was −0.9% (95% CI: −3.09, 1.24), meeting the prespecified non-inferiority criterion. Solicited adverse events within 7 days after any dose occurred in 29.1% (95% CI: 23.3, 35.3) of BEVAC® recipients and 35.0% (95% CI: 28.9, 41.5) of comparator recipients, most commonly pyrexia, injection-site pain, and swelling; all were mild-to-moderate. No serious adverse events were reported. BEVAC® demonstrated non-inferior immunogenicity to the licensed comparator and a comparable safety profile. Full article
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14 pages, 3164 KB  
Article
Transcriptomic Assessment of Host Responses in Vaccinia and Venezuelan Equine Encephalitis Virus-Infected Human Dendritic Cells
by Aarti Gautam, Stacy Ann Miller, Burook Misganaw, Nicholas C. Gary, Marti Jett, Sofi Ibrahim and Rasha Hammamieh
Biomolecules 2026, 16(4), 544; https://doi.org/10.3390/biom16040544 - 8 Apr 2026
Viewed by 538
Abstract
Understanding host cell response to viral infection could lead to the identification of molecular targets that can be used for the development of diagnostics and therapeutics. In this study, we investigated human dendritic cell (DC) response to infections with Vaccinia (VAC) virus, a [...] Read more.
Understanding host cell response to viral infection could lead to the identification of molecular targets that can be used for the development of diagnostics and therapeutics. In this study, we investigated human dendritic cell (DC) response to infections with Vaccinia (VAC) virus, a highly immunogenic poxvirus, and Venezuelan Equine Encephalitis (VEE) virus, a single-stranded positive-strand RNA alphavirus, using human gene expression microarrays. Comparative changes in DC mRNA expression resulting from infection by the two viruses at 1, 8, and 12 h post-infection (hpi) revealed distinct temporal dynamics. VAC infection triggered early and robust activation of pathways related to chromatin organization, DNA damage, and antigen presentation, while VEE infection exhibited delayed activation of immune signaling pathways, including interferon signaling and cytokine production. Shared pathways, such as interferon signaling and inflammasome activation, highlight universal antiviral responses and potential therapeutic targets. These findings provide a molecular framework affected by VAC and VEE that need to be validated with additional experiments, such as functional assays or in vivo studies. The specific up- or downregulation of these pathways at different time points likely dictates the overall outcome of the viral infection and could potentially lead to better understanding of the temporal regulatory dynamics of virus host response. Full article
(This article belongs to the Section Bioinformatics and Systems Biology)
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19 pages, 4755 KB  
Article
Effects of Aeromonas veronii and Its Vaccine on Immune-Related Gene, Liver Transcriptomics, and Gill Microbiota in Crucian Carp
by Junbo Wang, Shiyong Huang, Yingtiao Lai, Ping Wang, Feifei Wang, Dahui Pan, Fei Zhao and Hua Gong
Vaccines 2026, 14(4), 307; https://doi.org/10.3390/vaccines14040307 - 29 Mar 2026
Cited by 1 | Viewed by 820
Abstract
Background: Aeromonas veronii is an important bacterial pathogen in crucian carp and can cause serious disease outbreaks and substantial economic losses in aquaculture. Objectives: To evaluate how A. veronii infection and its inactivated vaccine modulate immune responses in Carassius auratus. [...] Read more.
Background: Aeromonas veronii is an important bacterial pathogen in crucian carp and can cause serious disease outbreaks and substantial economic losses in aquaculture. Objectives: To evaluate how A. veronii infection and its inactivated vaccine modulate immune responses in Carassius auratus. Methods: 270 juveniles were allocated into three groups: a saline-injected control group (Ctrl), a vaccination group receiving an inactivated A. veronii vaccine (Vac), and an artificial infection group (AIG) subjected to stimulation. Liver, spleen, head kidney, gill, and intestine samples were collected from fish after anesthesia. The relative transcript levels of IgM, IgD, BAFF, MHCII, CD4, BCL6, MyD88, and NF-κB were quantified. For liver transcriptome analysis, the effective library concentration was determined. And the 16S rRNA gene resulting reads of fish gill symbiotic microbiota were processed for downstream bioinformatic analysis. Results: The results showed that the Vac achieved an RPS of 73.33%, and vaccination significantly upregulated multiple immune-related genes in different fish organs. With BAFF transcription across organs emerging as a robust sentinel readout. The Pearson correlation coefficient (r) of BAFF between other genes were all ≥0.8. GO and KEGG enrichment analyses indicated that AIG had more DEGs than Vac (5885 vs. 4008) and Ctrl (6910 vs. 6178), respectively. Some genes in AIG revealed significant over-representation of immune pathways, such as BCL6, MyD88, and NF-κB. The fish gill microbiota comprised a diverse set of low-abundance taxa, the phylum level was dominated by Proteobacteria and Fusobacteriota across all groups; whereas, the Vac group remained broadly closer to the Ctrl group in overall composition. Conclusions: These results indicated marked post-challenge immune–metabolic coupling in the liver, and suggested coordinated immunophysiological interplay between the liver and the spleen. Gill microecology of symbiotic bacteria was affected by vaccination or challenge reactions, which in turn affects the health of the gills or the organism itself. Full article
(This article belongs to the Special Issue Fish Disease Occurrence and Immune Prevention and Control)
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19 pages, 2736 KB  
Article
Rationally Engineered D-Amino Acid Peptide DT7-3 Combats Multidrug-Resistant Helicobacter pylori via a Novel “Triple-Hit” Mechanism
by Shiying Yan, Xin Yan, Jiarui Zhao, Yue Zhou, Changyi Huang, Yiping Chen, Jia Wang, Jian Zhang, Chaoyi Han, Yu Gao, Tianlan Jiang, Hansheng Zhu, Hao Shi, Fosheng Li, Jian Zhao and Mei Cao
Microorganisms 2026, 14(4), 744; https://doi.org/10.3390/microorganisms14040744 - 26 Mar 2026
Viewed by 779
Abstract
Helicobacter pylori (H. pylori) is the primary etiological agent for chronic gastritis, peptic ulcers, and gastric adenocarcinoma. The alarming rise in multidrug-resistant (MDR) strains, particularly against clarithromycin (CLR), metronidazole (MNZ), and levofloxacin (LVX), has severely compromised standard therapies. Thus, there is [...] Read more.
Helicobacter pylori (H. pylori) is the primary etiological agent for chronic gastritis, peptic ulcers, and gastric adenocarcinoma. The alarming rise in multidrug-resistant (MDR) strains, particularly against clarithromycin (CLR), metronidazole (MNZ), and levofloxacin (LVX), has severely compromised standard therapies. Thus, there is an urgent clinical need for novel antimicrobial agents that operate through distinct mechanisms to bypass resistance pathways and mitigate gastric cancer risk. We designed and synthesized a series of antimicrobial peptides, focusing on the proteolytically stable all-D-amino acid enantiomer, DT7-3, derived from a probiotic-sourced template. Minimum inhibitory concentrations (MICs) were determined against standard strains and 11 clinical MDR isolates via the broth microdilution method. Antimicrobial mechanisms were elucidated using scanning electron microscopy (SEM) for morphology, fluorescence-based assays for anti-adhesion activity, and real-time qPCR to quantify virulence gene expression (babA, ureA, and vacA). Biocompatibility was assessed using defibrinated sheep erythrocytes, gastric epithelial cells (GES-1), and representative beneficial gut microbiota. Analysis of the clinical isolates revealed resistance rates of 63.6% for CLR/LVX and 81.8% for MNZ, with 54.5% identified as MDR. DT7-3 exhibited superior potency (MIC 1–32 µg/mL) against all strains, significantly outperforming its L-enantiomer counterparts. Mechanistic studies unveiled a “triple-hit” mechanism: (1) rapid membrane disruption; (2) potent inhibition of bacterial adhesion to host cells (~60% reduction at 0.5 × MIC); (3) significant downregulation of critical virulence factors (babA, ureA, and vacA). Furthermore, DT7-3 showed an excellent safety profile, with negligible hemolysis (<5% at 32 µg/mL) and minimal cytotoxicity toward GES-1 cells, yielding a high selectivity index (SI, MHC/MIC) > 32 relative to mammalian cells. Crucially, DT7-3 showed high selectivity for the pathogen over beneficial gut microbiota (MIC > 128 µg/mL, SI > 16). Crucially, DT7-3 maintained potent bactericidal activity (MIC ≤ 16 µg/mL) even under cholesterol-enriched conditions. The engineered D-peptide DT7-3 is a potent candidate for combating MDR H. pylori. Its multifaceted mechanism, targeting bacterial viability while suppressing core virulence factors, positions it as a robust lead compound for next-generation eradication therapies aimed at reducing the burden of H. pylori-associated diseases. Full article
(This article belongs to the Section Antimicrobial Agents and Resistance)
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21 pages, 4481 KB  
Article
Genome-Wide Identification and Expression Analysis of NHX Gene Family in Ziziphus jujuba var. spinosa Under Salt and Drought Stress
by Lulu Li, Xiaojun Ma, Xinhong Wang, Congcong Liu, Xiaohan Tang, Dali Geng, Xuexiang Li, Aiqin Ding and Jing Shu
Genes 2026, 17(3), 264; https://doi.org/10.3390/genes17030264 - 26 Feb 2026
Viewed by 676
Abstract
Background/Objectives: Ziziphus jujuba var. spinosa (sour jujube) is a traditional medicinal plant with remarkable tolerance to abiotic stresses, particularly salinity. However, the regulatory mechanisms underlying its salt stress tolerance remain unclear. NHX genes play a crucial role in plant adaptation to salt stress [...] Read more.
Background/Objectives: Ziziphus jujuba var. spinosa (sour jujube) is a traditional medicinal plant with remarkable tolerance to abiotic stresses, particularly salinity. However, the regulatory mechanisms underlying its salt stress tolerance remain unclear. NHX genes play a crucial role in plant adaptation to salt stress by mediating Na+/K+ transport to maintain intracellular ion homeostasis and pH balance. Although the NHX gene family has been characterized in many plant species, its functional characteristics in sour jujube have not yet been systematically investigated. Methods: In this study, using Arabidopsis thaliana as a reference, we identified NHX genes in sour jujube through genome-wide analysis and molecular approaches, and systematically analyzed their phylogenetic relationships, chromosomal locations, conserved motifs, gene structures, cis-regulatory elements in promoter regions, and expression patterns under abiotic stresses, particularly salt stress. Results: The results revealed the presence of eight NHX genes distributed across six chromosomes in sour jujube, which were classified into three subfamilies: Vac-class, Endo-class, and PM-class. Members within the same evolutionary clade exhibited high structural conservation in motif composition and gene architecture. Except for the PM-class, all other clades contained amiloride-binding sites (FF(I/L)(Y/F)LFLLPPI). Analysis of cis-regulatory elements indicated that the promoter regions of these genes were enriched with elements related to defense responses, stress adaptation, and phytohormone signaling, further supporting their role in plant environmental adaptation. Additionally, the qRT-PCR analysis showed that most of the ZjNHX genes in both roots and leaves are up-regulated by salt. Notably, ZjNHX1 expression in roots increased approximately 40-fold within 3 h, whereas ZjNHX2 and ZjNHX3 were strongly induced in leaves under prolonged salt exposure. Conclusions: Taken together, this work gives a detailed overview of the ZjNHX genes and their important roles in response to salt stress in sour jujube. Our findings also provide a foundation for further functional characterization of this gene family. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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14 pages, 975 KB  
Article
Impact of Helicobacter pylori Virulence Genotypes cagA, vacA, oipA, and babA2 on Severity of Gastropathies in Brazilian Patients
by Diogo Nery Maciel, Hellen Christina de Oliveira Santos-Dutra, Viviane Lopes Rocha, Lucas Trevizani Rasmussen and Mônica Santiago Barbosa
Int. J. Mol. Sci. 2025, 26(19), 9471; https://doi.org/10.3390/ijms26199471 - 27 Sep 2025
Cited by 1 | Viewed by 1903
Abstract
Helicobacter pylori (H. pylori) is a Gram-negative, spiral-shaped bacterium that colonizes the human stomach and is linked to various gastroduodenal diseases. The severity of different clinical outcomes may be determined by the combination of virulence genes. The aim of this study [...] Read more.
Helicobacter pylori (H. pylori) is a Gram-negative, spiral-shaped bacterium that colonizes the human stomach and is linked to various gastroduodenal diseases. The severity of different clinical outcomes may be determined by the combination of virulence genes. The aim of this study was to assess the combinations of the cytotoxin-associated gene A (cagA), the vacuolating cytotoxin A gene (vacA), the outer inflammatory protein A gene (oipA), and the blood group antigen-binding adhesin gene (babA2) genotypes in H. pylori and their associations with the clinical outcomes of infection in patients from Central Brazil. This cross-sectional study included 106 patients who underwent endoscopy or gastrectomy. The presence and genotypes of H. pylori were confirmed using Polymerase Chain Reaction (PCR). Gastropathies were classified according to established severity criteria. Multivariate logistic regression and Venn diagrams were used to evaluate gene combinations. In this study, the infection prevalence was 65.1%. The cagA/vacA/oipA/babA2 combination showed a protective effect against erosive esophagitis (p = 0.002), erosive duodenitis (p = 0.003), and general duodenitis (p < 0.001). No significant association was observed between this gene combination and severe gastric diseases, although a trend toward protection against gastric atrophy was noted (p = 0.049). These findings suggest that the coexistence of cagA/vacA/oipA/babA2 may play a protective role against inflammatory lesions. Further studies should explore the functional role of these gene combinations, also considering the immunogenetic profile of the host. Full article
(This article belongs to the Special Issue Helicobacter pylori in Gastric Diseases)
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16 pages, 12268 KB  
Article
Whole-Genome Sequencing and Antibiotic Resistance Profiling of Helicobacter pylori Isolates from a Tertiary Hospital in Southern Thailand
by Chonticha Romyasamit, Apichat Kaewdech, Pimsiri Sripongpun, Naichaya Chamroonkul, Komwit Surachat, Sirikan Suwannasin, Yosita Leepromma, Morteza Saki, Maseetoh Samaeng and Phoomjai Sornsenee
Antibiotics 2025, 14(9), 944; https://doi.org/10.3390/antibiotics14090944 - 18 Sep 2025
Viewed by 2130
Abstract
Background: Helicobacter pylori is associated with a wide range of gastroduodenal diseases, including chronic gastritis, peptic ulcer disease, and gastric cancer. Eradication efforts are challenged by increasing antimicrobial resistance rates, particularly in Southeast Asia. We sequenced the whole genomes of clinical H. [...] Read more.
Background: Helicobacter pylori is associated with a wide range of gastroduodenal diseases, including chronic gastritis, peptic ulcer disease, and gastric cancer. Eradication efforts are challenged by increasing antimicrobial resistance rates, particularly in Southeast Asia. We sequenced the whole genomes of clinical H. pylori isolates from Southern Thailand to elucidate their resistance profiles, virulence determinants, and evolutionary relationships. Methods: Three clinical H. pylori isolates (004, 117, and 189) were subjected to whole-genome sequencing, phenotypic antimicrobial susceptibility testing, and comparative genomic analyses. Results: All strains exhibited high-level resistance to metronidazole. Additionally, H. pylori 117 was resistant to both amoxicillin and levofloxacin, classifying it as multidrug-resistant. Genomic analysis revealed mutations in rdxA, frxA, and rpoB, as well as in penicillin-binding protein genes (pbp2 and pbp3), supporting the phenotypic findings. While all isolates harboured clarithromycin resistance mutations (A2142G and A2143G in the 23S rRNA gene), they were phenotypically susceptible, highlighting a potential discordance that requires further investigation. Virulence gene profiling identified 115–118 conserved genes per strain, including cagA, vacA, oipA, babA, and flagellar, urease, and lipopolysaccharide biosynthesis genes. Phylogenetic analysis using core-genome single-nucleotide polymorphisms demonstrated that these strains formed a distinct Southern Thai monophyletic clade, suggesting localised clonal expansion driven by regional selective pressures. Conclusions: Region-specific surveillance strategies and treatment guidelines are urgently needed in Thailand. The combination of high-risk virulence genes and rising antimicrobial resistance in H. pylori strains necessitates tailored therapeutic approaches, the integration of genomic surveillance into clinical diagnostics, and expanded studies linking genotype to clinical outcomes in diverse populations. Full article
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13 pages, 315 KB  
Article
Uncommon Pathogens in Common Presentations: Genetic Profiling and Virulence Determinants of Vibrio alginolyticus Isolated from a Case of External Otitis
by Radu Ovidiu Togănel, Razvan Lucian Coșeriu, Anca Delia Mare, Camelia Vintilă, Ioan-Ovidiu Sîrbu, Aimée Rodica Chis, Cristina Elena Gîrbovan and Adrian Man
Infect. Dis. Rep. 2025, 17(5), 114; https://doi.org/10.3390/idr17050114 - 12 Sep 2025
Viewed by 1278
Abstract
Backgrunod/Objectives: Routine identification of common bacterial pathogens is typically efficient, utilizing standardized, cost-effective methods. However, the diagnostic process becomes significantly more complex when dealing with rare or unexpected microorganisms, especially as they can be considered colonizers in many cases. Methods: This [...] Read more.
Backgrunod/Objectives: Routine identification of common bacterial pathogens is typically efficient, utilizing standardized, cost-effective methods. However, the diagnostic process becomes significantly more complex when dealing with rare or unexpected microorganisms, especially as they can be considered colonizers in many cases. Methods: This study presents diagnostic details of an uncommon pathogen, Vibrio alginolyticus, isolated from auricular discharge in a patient with non-Hodgkin lymphoma diagnosed with persistent otitis externa and explores its identification through both conventional and modern laboratory approaches. Sequential ear discharge cultures resulted in phenotypically similar but genomically different Vibrio alginolyticus isolates. We complemented classical methods like conventional culture (on Columbia agar and CLED agar), Vitek2 Compact identification, and EUCAST disk diffusion antimicrobial susceptibility testing (following the EUCAST version 12.0 guidelines) with MALDI-TOF mass spectrometry and Illumina/Nanopore whole genome sequencing. Comparative analysis of the genomes was performed with the PeGAS pipeline, Unicycler, and 1928Diagnostics SNP analysis. Results: The Vitek2 analysis identified both isolates as V. alginolyticus with 99% confidence, and this was supported by the MALDI-TOF MS results. The first isolate (A) was fully susceptible to the antibiotics tested, while the second (B) showed resistance to ciprofloxacin. Whole genome sequencing revealed 99.23% and 98.60% nucleotide identity to the V. alginolyticus reference genome for isolates A and B, respectively, with a 99.8% match between them. Isolate B acquired a gyrA (c.1870C>T) mutation that correlates with the ciprofloxacin resistance (MIC > 0.5 mg/L). Both genomes carry hlyA (hemolysin), toxR (cholera toxin regulator), genes involved in biofilm formation (rpoN, relA, spoT, opp), luxS (motility), proA, vacB (virulence factors), and tet(34) (oxytetracycline resistance). A core genome SNP distance of <100 indicates clonal relatedness. Our integrated (phenotypic and genomic) diagnostic approach confirmed V. alginolyticus and documented host resistance evolution, with a virulence repertoire that could explain the clinical evolution. Conclusions: This case highlights the utility of molecular methods in confirming species identity, detecting resistance markers, characterizing virulence determinants, and differentiating a pathogen from a colonizer, supporting targeted clinical management. Full article
16 pages, 1909 KB  
Article
Vanadium Compound Treatment Modulates MC3t3-E1 Osteoblast Function
by Isabella K. Somera, Bryan Sosa and Jessica A. Cottrell
Int. J. Mol. Sci. 2025, 26(17), 8682; https://doi.org/10.3390/ijms26178682 - 5 Sep 2025
Viewed by 1727
Abstract
Osteoblastogenesis plays a critical role in bone repair. Insulin and insulin-mimetic compounds, such as vanadium (IV) oxide acetylacetonate (VAC), have been reported to enhance bone healing in various models. This study aimed to evaluate the effects of vanadium compounds, VAC and vanadium (IV) [...] Read more.
Osteoblastogenesis plays a critical role in bone repair. Insulin and insulin-mimetic compounds, such as vanadium (IV) oxide acetylacetonate (VAC), have been reported to enhance bone healing in various models. This study aimed to evaluate the effects of vanadium compounds, VAC and vanadium (IV) oxide sulfate (VOSO4), on osteoblast proliferation and function. MC3T3-E1 pre-osteoblast cells were treated with insulin, ascorbic acid, and varying concentrations of VAC or VOSO4, and samples were collected at multiple time points over 21 days. We assessed cell proliferation, functional markers, and gene and protein expression. Our findings demonstrate that both VAC and VOSO4 stimulate MC3T3-E1 proliferation, increase calcium and proteoglycan deposition, and enhance phosphorylation of Protein Kinase B (Akt) over time. Gene expression analysis revealed that VAC treatment upregulated RUNX2, BGLAP, and TWIST2 at Day 7 compared to controls, with sustained expression patterns observed at Day 10. These results align with existing literature, supporting that VAC and VOSO4 promote osteoblastogenesis and may serve as effective adjuvants to accelerate bone regeneration during fracture healing. Full article
(This article belongs to the Special Issue Molecular Crosstalk Between Bone and Inflammation)
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14 pages, 2710 KB  
Article
vapD Mutation Shows Impairment in the Persistence of Helicobacter pylori Within AGS Cells
by Rosario Morales-Espinosa, Gabriela Delgado, Carlos A. Santiago, Alejandro Flores-Alanis, Rafael Diaz-Mendez, Alberto Gonzalez-Pedraza, José L. Méndez and Alejandro Cravioto
Microorganisms 2025, 13(8), 1952; https://doi.org/10.3390/microorganisms13081952 - 21 Aug 2025
Cited by 2 | Viewed by 1188
Abstract
The Helicobacter pylori vapD gene is transcribed and expressed when the bacteria are within the gastric cell. In this current study, we investigated how vapD knockout affects the survival of H. pylori inside human gastric adenocarcinoma cells. We constructed an H. pylori 26695 [...] Read more.
The Helicobacter pylori vapD gene is transcribed and expressed when the bacteria are within the gastric cell. In this current study, we investigated how vapD knockout affects the survival of H. pylori inside human gastric adenocarcinoma cells. We constructed an H. pylori 26695 vapD (Hp ΔvapD) mutant strain. H. pylori 26695 wt and Hp ΔvapD strains were grown in synthetic media and were co-cultured with AGS cells. From the start, the growth curve, total protein concentration and colony-forming units (CFUs) of each strain were measured. From each co-culture, CFUs and total RNA were obtained, and transcript levels of GAPDH, vapD, vacA, ureA, and 16s Hp were measured by qRT-PCR. Hp ΔvapD did not affect the growth rate of the strain in synthetic media, showing that the vapD gene is not necessary when the bacteria grow outside eukaryote cells. However, in the intracellular environment, the number of CFUs recovered from the Hp ΔvapD strain from AGS cells decreased after 36 h. Transcription levels of the vacA gene from the Hp ΔvapD strain were 10,000-fold lower than those of H. pylori wt, to the point of being undetectable. The results suggest that the vapD gene contributed to maintaining H. pylori inside gastric cells. Full article
(This article belongs to the Special Issue Bacterial Pathogenesis and Host Immune Responses)
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21 pages, 3401 KB  
Article
Allelic Variation of Helicobacter pylori vacA Gene and Its Association with Gastric Pathologies in Clinical Samples Collected in Jordan
by Mamoon M. Al-Hyassat, Hala I. Al-Daghistani, Lubna F. Abu-Niaaj, Sima Zein and Talal Al-Qaisi
Microorganisms 2025, 13(8), 1841; https://doi.org/10.3390/microorganisms13081841 - 7 Aug 2025
Cited by 3 | Viewed by 3049
Abstract
Helicobacter pylori is a well-established causative agent of gastritis, peptic ulcers, gastric adenocarcinoma, and primary gastric lymphoma. It colonizes the human stomach and expresses numerous virulent factors that influence disease progression. Among these factors is the cytotoxin vacA gene, which encodes the vacuolating [...] Read more.
Helicobacter pylori is a well-established causative agent of gastritis, peptic ulcers, gastric adenocarcinoma, and primary gastric lymphoma. It colonizes the human stomach and expresses numerous virulent factors that influence disease progression. Among these factors is the cytotoxin vacA gene, which encodes the vacuolating capacity of the cytotoxin and plays a key role in the bacterium’s pathogenic potential. This study investigated the allelic diversity of the vacA among H. pylori strains infecting patients in Jordan with various gastric conditions and examined potential associations between vacA s-and m- genotypes, histopathological and endoscopic findings, and the development of gastric diseases. Gastric biopsies were collected from 106 patients at two hospitals in Jordan who underwent endoscopic examination. The collected biopsies for each patient were subjected to histopathological assessment, urease detection using the Rapid Urease Test (RUT), a diagnostic test for H. pylori, and molecular detection of the vacA gene and its s and m alleles. The histopathology reports indicated that 83 of 106 patients exhibited gastric disorders, of which 81 samples showed features associated with H. pylori infection. The RUT was positive in 76 of 106 with an accuracy of 93.8%. Real-time polymerase chain reaction (RT-PCR) targeting the 16S rRNA gene confirmed the presence of H. pylori in 79 of 81 histologically diagnosed cases as infected (97.5%), while the vacA gene was detected only in 75 samples (~95%). To explore genetic diversity, PCR-amplified fragments underwent sequence analysis of the vacA gene. The m-allele was detected in 58 samples (73%), the s-allele was detected in 45 (57%), while both alleles were not detected in 13% of samples. The predominant genotype combination among Jordanians was vacA s2/m2 (50%), significantly linked to mild chronic gastritis, followed by s1/m2 (35%) and s1/m1 (11.8%) which are linked to severe gastric conditions including malignancies. Age-and gender-related differences in vacA genotype were observed with less virulent s2m2 and s1m2 genotypes predominating in younger adults specially males, while the more virulent m1 genotypes were found exclusively in females and middle-aged patients. Genomic sequencing revealed extensive diversity within H. pylori, likely reflecting its long-standing co-evolution with human hosts in Jordan. This genetic variability plays a key role in modulating virulence and influencing clinical outcomes. Comprehensive characterization of vacA genotypic variations through whole-genome sequencing is essential to enhance diagnostic precision, strengthen epidemiological surveillance, and inform targeted therapeutic strategies. While this study highlights the significance of the vacA m and s alleles, future research is recommended in order to investigate the other vacA allelic variations, such as the i, d, and c alleles, to achieve a more comprehensive understanding of H. pylori pathogenicity and associated disease severity across different strains. These investigations will be crucial for improving diagnostic accuracy and guiding the development of targeted therapeutic strategies. Full article
(This article belongs to the Special Issue Helicobacter pylori Infection: Detection and Novel Treatment)
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21 pages, 1292 KB  
Article
Polymorphism in IFNλ Can Impact the Immune/Inflammatory Response to COVID-19 Vaccination in Older CMV-Seropositive Adults
by Ariane Nardy, Fernanda Rodrigues Monteiro, Brenda Rodrigues Silva, Jônatas Bussador do Amaral, Danielle Bruna Leal Oliveira, Érika Donizetti de Oliveira Cândido, Edison Luiz Durigon, Andressa Simões Aguiar, Guilherme Pereira Scagion, Vanessa Nascimento Chalup, Guilherme Eustáquio Furtado, Marina Tiemi Shio, Carolina Nunes França, Luiz Henrique da Silva Nali and André Luis Lacerda Bachi
Vaccines 2025, 13(8), 785; https://doi.org/10.3390/vaccines13080785 - 24 Jul 2025
Viewed by 1370
Abstract
Background: Chronic cytomegalovirus (CMV) infection may favor the development of immunosenescence and inflammation that impair vaccine responses, including COVID-19. In addition, the polymorphism of the interferon-lambda gene (IFNλ) affects COVID-19 immune responses in older adults. Objective: We aimed to investigate the impact of [...] Read more.
Background: Chronic cytomegalovirus (CMV) infection may favor the development of immunosenescence and inflammation that impair vaccine responses, including COVID-19. In addition, the polymorphism of the interferon-lambda gene (IFNλ) affects COVID-19 immune responses in older adults. Objective: We aimed to investigate the impact of IFNλ polymorphism (IL28B gene-rs12979860) on the immune/inflammatory response to vaccination with CoronaVac for COVID-19 in older adults who were CMV-seropositive. Methods: Blood samples from 42 CMV-seropositive older adults (73.7 ± 4.5 years) were collected before and 30 days after immunization with a second dose of the CoronaVac vaccine to evaluate the immune/inflammatory response. Results: At genotyping, 20 subjects were homozygous for the C/C alleles (Allele-1 group), 5 were homozygous for the T/T Alleles (Allele-2 group), and 17 were heterozygous (C/T, Alleles-1/2 group). The Allele-1 group showed higher IgG levels for COVID-19 (p = 0.0269) and intermediate monocyte percentage (p = 0.017), in contrast to a lower non-classical monocyte percentage (p = 0.0141) post-vaccination than pre-vaccination. Also, this group showed that IgG levels for CMV were positively associated with a systemic pro-inflammatory state and senescent T cells (CD4+ and CD8+). The Allele-2 group presented higher IFN-β levels at pre- (p = 0.0248) and post-vaccination (p = 0.0206) than the values in the Allele-1 and Alleles-1/2 groups, respectively. In addition, the Allele-2 and Alleles-1/2 groups showed that IgG levels for COVID-19 were positively associated with a balanced systemic inflammatory state. Conclusion: CMV-seropositivity in older adults who had Allele-1 could lead to an unbalanced systemic inflammatory state, which may impair their antibody response to COVID-19 vaccination compared to other volunteer groups. Full article
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20 pages, 1383 KB  
Article
Determination of the Roles of H. pylori Outer Membrane Virulence Factors and Pyroptosis-Associated NLRP3, ASC, Caspase-1, Gasdermin D, IL-1β, and IL-18 in Ulcer and Gastritis Pathogenesis
by Yaren Buyukcolak-Cebeci, Emel Timucin, Sumeyye Akcelik-Deveci, Nesteren Mansur-Ozen, Tuana Aydinlar, Arzu Tiftikci and Sinem Oktem-Okullu
Biology 2025, 14(6), 634; https://doi.org/10.3390/biology14060634 - 30 May 2025
Cited by 1 | Viewed by 1869
Abstract
Background: This study aims to investigate the association between pyroptosis and the outer membrane virulence factor of H. pylori in patients with gastritis and ulcers. Methods: DNA, RNA, and protein were extracted from a single tissue sample taken from the antrum region of [...] Read more.
Background: This study aims to investigate the association between pyroptosis and the outer membrane virulence factor of H. pylori in patients with gastritis and ulcers. Methods: DNA, RNA, and protein were extracted from a single tissue sample taken from the antrum region of the stomach of volunteer patients. The expression of bacterial outer membrane virulence genes was analyzed at the gene level, and the expression levels of key pyroptosis markers were compared between H. pylori-infected and uninfected gastritis and ulcer patient groups. Results: H. pylori infection induced significant alterations in the expression levels of pyroptosis markers, including ASC, NLRP3, caspase-1, GSDMD, IL-18, and IL-1β, indicating a strong association with gastritis and ulcer pathology. Statistically significant correlations were observed between elevated levels of these markers and the activation of caspase-1 across different patient cohorts, supporting effective detection of pyroptosis. Both pro and active forms of caspase-1, GSDMD, IL-18, and IL-1β were assessed, revealing pyroptotic activity in specific patient samples. The vacA m2 allele showed a distinct ASC response in gastritis versus ulcer patients and was associated with increased GSDMD expression in ulcerative cases. Along with the babB gene, this allele appears to play a critical role in the interaction between H. pylori virulence and host pyroptotic responses. A statistically significant negative association was identified between the presence of the H. pylori alpA gene and Gasdermin D expression (odds ratio = 0, p < 0.01), suggesting that Gasdermin D was absent in all alpA-positive samples. Conclusion: This study provides novel insights into the interrelation between the virulence factors of H. pylori and pyroptosis in gastritis and ulcer diseases. Our findings demonstrate that H. pylori infection significantly alters the expression levels of pyroptosis markers, including ASC, NLRP3, caspase-1, GSDMD, IL-18, and IL-1β, in gastric tissues. Notably, the vacA m2 allele was associated with a differential response in ASC expression among patients with gastritis and ulcers, correlating with increased GSDMD levels in ulcerative conditions. The presence of the H. pylori alpA gene is markedly associated with the lack of Gasdermin D activation, indicating a possible suppressive function or immune evasion tactic. These results underscore the critical role of H. pylori virulence determinants in modulating pyroptosis and suggest that understanding this relationship may pave the way for developing targeted therapeutic strategies to mitigate H. pylori-associated pathologies. Full article
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13 pages, 2729 KB  
Article
Influence of Unidirectional Vacuum Application on Bone Healing in Maxillofacial Surgery
by Tom Alexander Schröder, Athanasios Karasavvas, Maximilian Bauckloh, Matthias C. Schulz, Günter Lauer and Lysann Michaela Kroschwald
Cells 2025, 14(10), 751; https://doi.org/10.3390/cells14100751 - 21 May 2025
Viewed by 3150
Abstract
Negative-pressure wound therapy (NPWT) using vacuum-assisted closure (VAC) is a well known tissue defect bridging method that applies a vacuum pump to sterile, open-cell foam dressings via suction tubes. Although it has mostly been described for soft tissue use, there are also a [...] Read more.
Negative-pressure wound therapy (NPWT) using vacuum-assisted closure (VAC) is a well known tissue defect bridging method that applies a vacuum pump to sterile, open-cell foam dressings via suction tubes. Although it has mostly been described for soft tissue use, there are also a few studies concerning its use on hard tissue. However, as oral and maxillofacial surgery has to deal with both soft and hard tissue, which lie next to each other in these regions, there is a particular need to assess the influence of negative pressure on bone. Therefore, the effects of different negative pressure levels (530 mbar and 725 mbar) and atmospheric pressure (1013 mbar) on bone tissue cultures and osteoblast cell cultures were investigated over periods of 1, 3, and 6 weeks. During the culture period, osteoblast growth and the tissue regeneration of bone defects were studied in vitro using tissue cultures that were histologically supplemented by cytological investigations and quantitative RNA expression studies. In the bone defect model, there was a faster defect reduction using NPWT; the effect was especially strong for 530 mbar. Compared to the control group, up to 30% more newly generated bone tissue was detected. This effect on the mineralization capacity was assessed by the mRNA expression of osteogenic marker genes, as well as the receptor activator of nuclear factor κB ligand (RANKL) and osteoprotegerin (OPG), two multifaceted cytokines that regulate bone metabolism. The influence of negative pressure consequently resulted in a decreased RANKL/OPG ratio in osteoblasts. Associated with the upregulation of marker genes to up to 400%, including Col1, BMP4, OCN, and RUNX2, the decrease in the RANKL/OPG ratio to 41% indicates the stimulation of osteogenesis. Since VAC has been shown to be a safe and effective method to close wounds in general, these data suggest that patients suffering from compound bone and soft tissue defects in the maxillofacial area may benefit from an adapted therapy approach accelerating both soft and hard tissue regeneration. Full article
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