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17 pages, 1902 KB  
Article
Nuclear Proteomics to Understand the Promotive Effect of Plant-Derived Smoke Solution on Wheat Under Salt Stress
by Sheikh Shohag, Hisateru Yamaguchi, Keisuke Hitachi, Kunihiro Tsuchida, Shafiq Ur Rehman and Setsuko Komatsu
Proteomes 2026, 14(2), 31; https://doi.org/10.3390/proteomes14020031 - 15 Jun 2026
Viewed by 215
Abstract
Background: Salinity, which hampers wheat growth and development, is one of the major abiotic stresses. Plant-derived smoke (PDS) solution alleviates salt stress and promotes wheat growth and development; however, the underlying molecular mechanisms have not been completely clarified. Methods: In this study, nuclear [...] Read more.
Background: Salinity, which hampers wheat growth and development, is one of the major abiotic stresses. Plant-derived smoke (PDS) solution alleviates salt stress and promotes wheat growth and development; however, the underlying molecular mechanisms have not been completely clarified. Methods: In this study, nuclear proteomics was employed to reveal the promotive effect of PDS solution on salt-stressed wheat. Nuclear fractions were isolated from wheat roots, and their purity was confirmed via enrichment of histone H3 and reduction of cytosolic ascorbate peroxidase. Using this nuclear purification technique, label-free nano LC–MS/MS-based nuclear proteomics was performed to identify differentially abundant nuclear proteins in salt-stressed wheat with or without PDS solution treatment. Results: Salt stress decreased histone H2A and DNA polymerase levels, whereas PDS solution treatment of salt-stressed wheat increased levels of histone variants (H2A, H2B, H3, and H4), DNA polymerase, and DNA topoisomerase II. In addition, the PDS solution increased the levels of pre-mRNA cleavage factor Im 25 kDa subunit and RNA helicase in salt-stressed wheat. Immunoblot analysis further validated the increase in histone deacetylase levels triggered by the PDS solution treatment in the salt-stressed wheat. Conclusions: These results suggest that PDS solution alters nuclear proteins in a way that contributes to chromatin remodeling and transcription during salt stress. Full article
(This article belongs to the Special Issue Plant Genomics and Proteomics)
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17 pages, 1191 KB  
Article
Unveiling the Importance of the Expression of LY6/UPAR Gene Family Members in Urothelial Carcinoma of the Urinary Bladder
by Tuba Dilay Kökenek Ünal, Keziban Korkmaz Bayram, Aida Nurul Barokah, Buse Bayazit Gözüküçük, Umut Inan, Enes Topal and Yusuf Özkul
Biomedicines 2026, 14(6), 1339; https://doi.org/10.3390/biomedicines14061339 - 12 Jun 2026
Viewed by 372
Abstract
Background/Objectives: Urothelial carcinomas are the most common tumors of the bladder. There are limited known cancer stem cell markers in these tumors. Ly6/uPAR gene family members are considered to be markers of cancer stem cells and tissue stem cells in mice, but [...] Read more.
Background/Objectives: Urothelial carcinomas are the most common tumors of the bladder. There are limited known cancer stem cell markers in these tumors. Ly6/uPAR gene family members are considered to be markers of cancer stem cells and tissue stem cells in mice, but studies on their expression or role in human cancers are limited. In this study, we aimed to investigate the expression of LY6/uPAR gene family members in human urothelial cancers. Methods: A total of 84 patients were included in the study. Patients diagnosed with urothelial carcinoma were divided into low-grade noninvasive and high-grade invasive carcinoma groups. Normal urothelial samples were used as a control group. RNA isolation was performed from paraffin blocks, and then cDNA was obtained. LY6D, LY6E, LY6H, LY6K, PSCA, LYPD2, SLURP1, GML, GPIHBP1, and LYNX1 genes were analyzed by qRT-PCR method. Results: We observed significantly higher expression of LY6E, LY6K, PSCA, GPIHBP1, and LYNX1 genes in urothelial carcinomas, but lower expression of LY6H, LYPD2, and SLURP1 genes in urothelial cancers compared to the control tissue. Decreased expression of LY6H, PSCA, LYPD2, SLURP1, and GPIHBP1 genes was significantly correlated with poor survival. Conclusions: In the present study, the expression of this gene family in bladder cancer was investigated for the first time in the literature. Given their potential prognostic role and possible relevance as therapeutic targets, this study presents preliminary observations that add to the existing literature. Full article
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16 pages, 32763 KB  
Article
Complete Mitochondrial Genome of Melophagus ovinus from Qinghai-Tibet Plateau Provides Evidence for D-Loop Length Polymorphism
by Leyi Li, Huiling Xie, Zhibing Li, Wenqiang Tang, Chunxia Zhang, Xiaoxia Qi, Runbo Luo, Wenting Chui, Jun Kui and Fuqiang Huang
Genes 2026, 17(6), 689; https://doi.org/10.3390/genes17060689 - 11 Jun 2026
Viewed by 231
Abstract
Background/Objectives: Melophagus ovinus is an economically important ectoparasite of small ruminants with a broad global distribution. Although mitochondrial genomes are widely used in population genetic studies, the D-loop region of M. ovinus remains poorly characterized because its high AT content and repetitive [...] Read more.
Background/Objectives: Melophagus ovinus is an economically important ectoparasite of small ruminants with a broad global distribution. Although mitochondrial genomes are widely used in population genetic studies, the D-loop region of M. ovinus remains poorly characterized because its high AT content and repetitive structure complicate amplification, assembly, and sequencing. Methods: We sequenced the mitochondrial genome of M. ovinus collected from Qinghai using an integrative approach combining Illumina paired-end sequencing, targeted PCR amplification, and Nanopore long-read sequencing. Comparative genomic analysis was performed against published mitogenomes from Gansu (MH024396) and Xinjiang (NC_037368). Results: The Qinghai mitochondrial genome contained the typical 37 mitochondrial genes within a 14,728 bp conserved region. Comparative analysis revealed exceptionally high conservation (>99.6% sequence identity) among Qinghai, Gansu, and Xinjiang isolates outside the D-loop region. Notably, the D-loop exhibited length polymorphism, with different assembly strategies or samples yielding lengths ranging from 317 bp to 2385 bp. Targeted long-read sequencing of ten individuals identified a predominant D-loop variant of approximately 844 bp in nine samples and a markedly shorter variant of approximately 164 bp in one sample. The short variant was characterized by extensive deletions and a novel 45 bp insertion. Support for this variant was obtained from independent Illumina DNA-seq, RNA-seq, Nanopore sequencing, and de novo assembly analyses. Conclusions: This study provides preliminary evidence for D-loop structural heterogeneity in M. ovinus, suggesting remarkable length polymorphism and complex indel patterns that require further validation. These findings significantly expand the genomic resources available for this important veterinary parasite and establish a foundation for future population genetic and evolutionary studies. Full article
(This article belongs to the Special Issue Functional Genomics and Genetics in Insects)
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27 pages, 4613 KB  
Review
Epigenetic–Mitochondrial–Metabolic Crosstalk in Retinal Pigment Epithelium (RPE) Dysfunction in Age-Related Macular Degeneration (AMD)
by Yijing Yang, Ying Deng, Xiang Li, Pai Zhou, Qinghua Peng and J. Arjuna Ratnayaka
Antioxidants 2026, 15(6), 713; https://doi.org/10.3390/antiox15060713 - 4 Jun 2026
Viewed by 214
Abstract
Age-related macular degeneration (AMD) is a leading cause of irreversible vision loss in older adults and is characterized by progressive dysfunction of the retinal pigment epithelium (RPE). Although genetic susceptibility and environmental exposure both contribute to disease risk, the mechanisms through which chronic [...] Read more.
Age-related macular degeneration (AMD) is a leading cause of irreversible vision loss in older adults and is characterized by progressive dysfunction of the retinal pigment epithelium (RPE). Although genetic susceptibility and environmental exposure both contribute to disease risk, the mechanisms through which chronic metabolic and oxidative stress are integrated into sustained RPE dysfunction remain incompletely understood. Increasing evidence from human AMD donor tissue and experimental RPE models indicates that epigenetic regulation operates at the interface between mitochondrial dysfunction, redox imbalance, and transcriptional remodeling. This review synthesizes current findings on DNA methylation, chromatin accessibility, histone modification, and RNA-based regulation in AMD, with emphasis on their metabolic and mitochondrial context. Studies in human AMD-RPE demonstrate that epigenetic alterations are generally selective rather than global and frequently involve pathways related to mitochondrial maintenance, lipid metabolism, oxidative stress responses, and cellular homeostasis. Mechanistically, mitochondrial dysfunction and reactive oxygen species (ROS) may influence epigenetic regulation through altered Nicotinamide adenine dinucleotide (NAD+) availability, acetyl-CoA metabolism, redox-sensitive chromatin regulation, and modulation of DNA methyltransferase and histone deacetylase activity. Redox-sensitive pathways, including antioxidant signaling, further connect mitochondrial stress to adaptive or maladaptive transcriptional responses in the RPE. Importantly, while several interactions discussed are supported by findings in human AMD tissue, other components of the proposed epigenetic–mitochondrial–redox framework remain inferential or model-based and require further validation. Rather than acting as isolated disease triggers, epigenetic changes are more likely to function as stress-responsive regulatory layers that stabilize transcriptional states over time in a long-lived post-mitotic tissue. We further discuss unresolved questions regarding causality, reversibility, therapeutic feasibility, and stage-specific intervention strategies. Collectively, this framework positions the epigenetic–mitochondrial–redox axis as a unifying model for understanding RPE vulnerability and AMD progression. Full article
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15 pages, 990 KB  
Article
Standardization of an Effective Disinfection Methodology Against Microorganisms Isolated from a Pharmaceutical Industry Facility as a Contamination Control Strategy
by Amanda Silva Costa, Luciana Veloso da Costa, Rebeca Vitória da Silva Lage de Miranda, Talita Bernardo Valadão, Stephen James Forsythe and Marcelo Luiz Lima Brandão
Standards 2026, 6(2), 22; https://doi.org/10.3390/standards6020022 - 1 Jun 2026
Viewed by 177
Abstract
Inadequate surface sanitization represents a significant risk to sterility assurance and regulatory compliance. Therefore, an effective cleaning and disinfection program is a critical component of contamination control strategies in pharmaceutical facilities manufacturing sterile medicinal products. This study aimed to standardize a carrier-based methodology [...] Read more.
Inadequate surface sanitization represents a significant risk to sterility assurance and regulatory compliance. Therefore, an effective cleaning and disinfection program is a critical component of contamination control strategies in pharmaceutical facilities manufacturing sterile medicinal products. This study aimed to standardize a carrier-based methodology for evaluating the efficacy of disinfectants against in-house environmental isolates recovered from a pharmaceutical industry facility. Nine representative strains were selected from five different groups—Gram-positive non-spore-forming bacteria (Micrococcus luteus and Kocuria spp.), Gram-positive spore-forming bacteria (two Bacillus spp. strains), Gram-negative bacteria (Pseudomonas aeruginosa and Acinetobacter haemolyticus), yeasts (Candida parapsilosis and Rhodotorula mucilaginosa), and filamentous fungus (Penicillium spp.)—based on historical environmental monitoring data (2012–2022), and were characterized using matrix-assisted laser desorption/ionization-time-of-flight/mass spectrometry (MALDI-TOF MS) and molecular sequencing (16S rRNA or D2 LSU rDNA). Disinfectant efficacy was assessed on stainless-steel and low-density polyethylene surfaces using NF T 72-281:2014 with adaptations, testing alcohol 70%, sodium hypochlorite 0.5%, quaternary ammonium 0.05%, peracetic acid 0.5%, and accelerated hydrogen peroxide wipes. All agents demonstrated ≥5 log10 reductions against vegetative bacteria and fungi on both surfaces. However, variable sporicidal performance was observed, particularly for one Bacillus cereus group strain (B1342/15), which showed limited viability reduction on stainless steel. These findings highlight inter-strain variability and the greater tolerance of surface-associated spores. The study reinforces the importance of carrier-based testing using in-house isolates to ensure realistic validation of disinfectants and to strengthen microbiological risk management within pharmaceutical contamination control strategies. Full article
(This article belongs to the Section Drugs Standards)
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10 pages, 1957 KB  
Article
Isolation and Genome Characterization of Escherichia Phage vB_EcoA-Sparklingdew
by Ivan M. Pchelin, Vladimir M. Shutov, T. N. Suong Nguyen, Dmitrii E. Polev, Alexander N. Suvorov and Artemiy E. Goncharov
Genes 2026, 17(6), 650; https://doi.org/10.3390/genes17060650 - 31 May 2026
Viewed by 326
Abstract
Background: Escherichia coli remains a critical multidrug-resistant nosocomial pathogen, driving interest in bacteriophage-based biocontrol. The genus Kayfunavirus (family Autotranscriptaviridae) exhibits obligately lytic replication cycles and favorable biosafety profiles, yet each new phage requires comprehensive genomic characterization to expand therapeutic candidate pools. This [...] Read more.
Background: Escherichia coli remains a critical multidrug-resistant nosocomial pathogen, driving interest in bacteriophage-based biocontrol. The genus Kayfunavirus (family Autotranscriptaviridae) exhibits obligately lytic replication cycles and favorable biosafety profiles, yet each new phage requires comprehensive genomic characterization to expand therapeutic candidate pools. This study aimed to isolate and genomically characterize a novel Kayfunavirus from an environmental reservoir in Vietnam. Methods: Escherichia phage vB_EcoA-Sparklingdew was isolated from Can Tho River water using host E. coli AgE9. The genome was assembled using SPAdes. The termini were resolved with PhageTerm. The annotation was done via the Pharokka pipeline and HHpred. Taxonomic classification was performed using taxMyPhage, VIRIDIC intergenomic comparisons, and maximum likelihood phylogeny of concatenated structural proteins. Results: The complete genome comprises a 37,944 bp linear dsDNA molecule (49.9% GC), encoding 51 open reading frames in a predominantly unidirectional arrangement. Key features include a virion-encoded T7-like RNA polymerase, a 723-residue T7-like DNA polymerase, a canonical lysis triad, and two putative tailspike proteins. A 212 bp direct terminal repeat and coverage profiles support a headful (pac) packaging mechanism. Comprehensive screening confirmed the absence of lysogeny, virulence, and antibiotic resistance determinants. A single synonymous SNP indicated high clonal purity. Intergenomic identity peaked at 87.7% against ICTV references, confirming placement in a novel species. Conclusions: Phage Sparklingdew represents a strictly lytic Kayfunavirus with a compact genomic architecture. Its favorable safety profile and absence of temperate markers support further evaluation for targeted therapeutic applications against pathogenic E. coli. Full article
(This article belongs to the Section Viral Genomics)
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40 pages, 2203 KB  
Article
Serological and Molecular Epidemiology of Hepatitis B, C, and D Viruses in Northwest Russia: A Population-Based Cross-Sectional Study
by Anna Y. Popova, Yulia V. Ostankova, Alesia Y. Olkhovskaya, Olga A. Petrova, Alexandr N. Shchemelev, Elena N. Serikova, Svetlana A. Egorova, Diana E. Reingardt, Irina V. Drozd, Ojuna B. Zhimbaeva, Ekaterina M. Danilova, Angelica M. Milichkina, Elena B. Ezhlova, Albina A. Melnikova, Natalia S. Bashketova, Lidiya V. Buts, Edward S. Ramsay and Areg A. Totolian
Viruses 2026, 18(6), 632; https://doi.org/10.3390/v18060632 - 30 May 2026
Viewed by 394
Abstract
The hepatitis B (HBV), C (HCV), and D (HDV) viruses remain a major public health burden. Occult HBV infection (OBI) represents a hidden reservoir with clinical and epidemiological significance, yet its prevalence in Northwest Russia is unknown. We aimed to comprehensively assess the [...] Read more.
The hepatitis B (HBV), C (HCV), and D (HDV) viruses remain a major public health burden. Occult HBV infection (OBI) represents a hidden reservoir with clinical and epidemiological significance, yet its prevalence in Northwest Russia is unknown. We aimed to comprehensively assess the serological and molecular epidemiology of HBV, HCV, and HDV in St. Petersburg and the Leningrad region. Methods. In this cross-sectional study, 6773 apparently healthy volunteers were enrolled. Plasma samples were tested for hepatitis B surface antigen (HBsAg), antibodies to HBV core antigen (anti-HBc), antibodies to HBsAg (anti-HBs), antibodies to HCV (anti-HCV), and antibodies to HDV (anti-HDV) by ELISA. All anti-HCV- and anti-HDV-positive samples were tested for HCV RNA and HDV RNA by real-time PCR. All samples were tested for HBV DNA using a highly sensitive in-house nested real-time PCR assay (detection limit: 5 IU/mL). All “HBV DNA-positive, HBsAg-negative” cases confirmed by two independent extractions were classified as OBI. Vaccination status, self-reported history, and iatrogenic interventions were recorded. Results. Overall seroprevalence values were: HBsAg 1.7%; anti-HBc 11.3%; anti-HBs 43.0%; anti-HCV 1.9%; and anti-HDV 0.6%. Anti-HBc increased sharply with age (3.1% in children to 26.4% in the elderly, p < 0.0001), while anti-HBs declined (69.9% to 29.8%, p < 0.0001). HBV DNA was detected in 118 participants (1.7%). Of these, only 73 individuals (1.1%) were HBsAg-positive, while the remaining 45 participants (0.7%) had undetectable HBsAg, meeting the criteria for OBI. OBI was detected across all age groups, including children. Serological profiling of OBI cases revealed that 57.8% lacked both anti-HBc and anti-HBs, 35.6% had isolated anti-HBs, 2.2% had isolated anti-HBc, and 4.4% had both antibodies. HCV RNA was detected in 15.0% of anti-HCV-positive individuals (all adults). No HDV RNA was detected. Self-reported history underestimated true infection rates: 1.4% of those denying HBV infection were HBsAg-positive and 10.6% were anti-HBc-positive. Among those denying HCV infection, 1.4% were anti-HCV-positive. Vaccination coverage was 70.8%, declining from 90.9% in children to 39.0% in the elderly (p < 0.0001). Among vaccinated individuals, 48.0% lacked protective anti-HBs (<10.0 mIU/mL). Conclusions. This comprehensive serological and molecular study in Northwest Russia is the first to combine population-level serology with molecular detection of HBV, HCV, and HDV, including OBI in this region, and reveals that OBI accounts for a substantial proportion (38%) of all active HBV infections and is strongly associated with a history of iatrogenic interventions. The presence of OBI across all age groups, including children, shows that HBsAg screening alone substantially underestimates the true HBV burden. High rates of unrecognized infection and waning vaccine-induced immunity, highlight critical gaps in current surveillance. These findings provide an evidence-based rationale for integrating molecular testing into screening algorithms and for considering booster vaccination strategies to achieve viral hepatitis elimination goals. Full article
(This article belongs to the Section Human Virology and Viral Diseases)
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17 pages, 6843 KB  
Article
Peripartum-Associated Heart Failure Develops Independently of RHOT Proteins
by Natali Froese, Eluiesa Sina, Paolo Galuppo, Christopher Werlein, Anna Gigina, Jan Hegermann, Robert Geffers, Tim Scholz, Jan C. Kamp, Lavinia Neubert, Johanna Schneider, Melanie Ricke-Hoch, Alexander Dietl, Johann Bauersachs and Christian Riehle
Int. J. Mol. Sci. 2026, 27(11), 4991; https://doi.org/10.3390/ijms27114991 - 30 May 2026
Viewed by 504
Abstract
Pregnancy-associated hemodynamic overload and hormonal changes induce hypertrophy and metabolic remodeling of the maternal heart. Mitochondrial motility, mediated by ras homolog family member T (RHOT) 1 and RHOT2, is essential for cardiac adaptation to increased workload, cardiomyocyte hypertrophy, and sarcomere maturation. To test [...] Read more.
Pregnancy-associated hemodynamic overload and hormonal changes induce hypertrophy and metabolic remodeling of the maternal heart. Mitochondrial motility, mediated by ras homolog family member T (RHOT) 1 and RHOT2, is essential for cardiac adaptation to increased workload, cardiomyocyte hypertrophy, and sarcomere maturation. To test the hypothesis that Rhot1/2 expression is required for pregnancy- and postpartum-associated adaptations of the maternal heart, female mice with tamoxifen-inducible, cardiomyocyte-selective deletion of Rhot1 and Rhot2 (iRhot1/2-KO) were mated. Following gene deletion in adult mice, cardiac tissue and function were analyzed after three to five successive pregnancies and postpartum nursing periods. Age-matched nulliparous iRhot1/2-KO mice and age-matched mice expressing Rhot1 and Rhot2 served as controls. Motility of mitochondria isolated from iRhot1/2-KO hearts was impaired, as determined by the number of mobile mitochondria in an in vitro motor protein-driven single mitochondrion motility assay performed on surface-immobilized microtubules. Despite loss of Rhot1/2 expression, contractile function assessed by transthoracic echocardiography, mRNA expression of peripartum-associated heart failure markers, cardiac structure, mitochondrial morphology, mitochondrial enzymatic activity, and mitochondrial DNA content were all comparable to controls expressing Rhot1/2 at the investigated time points. RNA sequencing-based gene profiling identified a transcriptional program through which RHOT proteins preserve cardiac energetic and contraction gene expression during pregnancy and postpartum. Together, cardiomyocyte-selective loss of Rhot1/2 expression in the adult heart does not cause peripartum-associated heart failure, despite reduced cardiac energetic and contraction gene expression. Full article
(This article belongs to the Special Issue Mitochondrial Functions and Dynamics)
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19 pages, 4217 KB  
Article
Comparison of Methods for the Isolation of Salivary Extracellular Vesicles
by Ulrike Kegler, Anja Buhmann, Heinz-Peter Friedl, Manuela Hofner and Christa Noehammer
Int. J. Mol. Sci. 2026, 27(11), 4899; https://doi.org/10.3390/ijms27114899 - 28 May 2026
Viewed by 239
Abstract
Extracellular vesicles (EVs) have attracted growing attention for their diagnostic and prognostic potential as they carry molecular cargo such as DNA, RNA, proteins and lipids derived from their cells of origin. While EV research has traditionally focused on blood, this study explicitly explored [...] Read more.
Extracellular vesicles (EVs) have attracted growing attention for their diagnostic and prognostic potential as they carry molecular cargo such as DNA, RNA, proteins and lipids derived from their cells of origin. While EV research has traditionally focused on blood, this study explicitly explored saliva as a promising, non-invasive sample matrix for EV isolation and biomarker discovery. Six different EV isolation methods were compared for their ability to recover salivary small EVs suitable for downstream DNA and microRNA analysis. Nanoparticle tracking analysis (NTA) revealed variation in vesicle sizes, concentrations and surface charges across all tested EV isolation approaches. In addition to being the fastest and simplest isolation method, the miRCURY Exosome Isolation kit—serum and plasma from Qiagen (ExiQ) also resulted in the highest EV yields with average particle sizes of ~130 nm. Western blot analysis further verified the presence of EV-specific markers (CD9, Alix) and no detectable signal for ApoA1 as an indicator for lipoprotein contamination, underscoring the purity of ExiQ-isolated vesicles. Always applying the same protocol for parallel DNA and RNA isolation on vesicles extracted by various methods, differences in DNA and RNA yields were observed across the evaluated isolation kits. ExiQ-isolated EVs showed the best recovery for both nucleic acid types. Notably, nuclease treatment of isolated EVs revealed that substantial amounts of DNA were present on the EV surface, whereas microRNA was predominantly localized within the vesicles. The present study, extensively comparing different EV isolation methods, demonstrates that salivary EVs are a viable source for non-invasive diagnostics and suggests the miRCURY Exosome Isolation kit—serum and plasma from Qiagen (ExiQ) to be a good choice for integration in future salivary EV-based diagnostic assays given its simplicity, speed and excellent performance. Full article
(This article belongs to the Special Issue Extracellular Vesicles—New Findings on the Block in Liquid Biopsy)
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20 pages, 8548 KB  
Article
Molecular Evolution of the Archaeal DNA-Dependent RNA Polymerase: Cooperative Changes in Subunit Composition and Specific Domains of Small Subunits
by Elena K. Shematorova and George V. Shpakovski
Int. J. Mol. Sci. 2026, 27(11), 4679; https://doi.org/10.3390/ijms27114679 - 22 May 2026
Viewed by 270
Abstract
The subunit composition and tertiary structure of DNA-dependent RNA polymerases in archaea, bacteria, and eukaryotes are currently well understood. The single RNA polymerase of archaea resembles the nuclear RNA polymerase II of eukaryotes in its composition and consists of 10–12 subunits. Perhaps the [...] Read more.
The subunit composition and tertiary structure of DNA-dependent RNA polymerases in archaea, bacteria, and eukaryotes are currently well understood. The single RNA polymerase of archaea resembles the nuclear RNA polymerase II of eukaryotes in its composition and consists of 10–12 subunits. Perhaps the only exception that seems to confirm this rule is the Rpo8 subunit (homologue of the eukaryotic Rpb8), which only some classes of archaea have. The development of metagenomic sequencing has led to a significant revision of the classification system of prokaryotes, in particular to the identification of a number of new Archaea evolutionary lineages. This makes it possible to analyze the subunit composition and structure of RNA polymerase of all currently isolated archaeal phyla. Our analysis shows that the Rpo8 subunit is present only in the RNA polymerase of Archaea species from the Thermoproteota of the Thermoproteati superphylum and from the whole superphylum Promethearchaeati, formerly known as the Asgard. After analyzing the changes in the small Rpo6 subunit (homologue of eukaryotic Rpb6), functionally interacting with Rpo8, we noticed that the largest number of changes in the primary and domain structures of this small subunit occurred in archaeal phyla that lack Rpo8. Shortened forms of Rpo6 without N- or C-terminal regions were observed only in representatives of archaea with an RNA polymerase that does not contain the Rpo8 subunit. Our analysis shows that the changes in Rpo6 are an adaptation of a multisubunit transcription complex to the disappearance of Rpo8. Most likely, the Rpo8 subunit was present in the RNA polymerase of the Last Common Ancestor of Archaea (LCAA) and, in the course of evolution, disappeared in the superphyla Euryarchaeota and Nanobdellati and two divisions of the Thermoproteati superphylum: Bathyarchaeota and Thaumarchaeota. Full article
(This article belongs to the Special Issue Cell and Molecular Biology of Archaea)
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19 pages, 1649 KB  
Article
Reduced Oxygen Condition Is Associated with Genome-Wide Expression Changes in Mastitis-Lineage Staphylococcus aureus During In Vitro Invasion into a Mammary Cell Line
by Kamaleldin B. Said, Marcus B. Jones, Rosslyn Maybank, Scott N. Peterson and Xin Zhao
Int. J. Mol. Sci. 2026, 27(10), 4591; https://doi.org/10.3390/ijms27104591 - 20 May 2026
Viewed by 251
Abstract
Staphylococcus aureus (S. aureus) bovine mastitis is a significant public health issue. Despite enormous efforts, important gaps remain regarding host–microenvironmental factors. How intramammary reduced oxygen modulates S. aureus transcription in bovine mammary epithelial cells (MECs) remains unclear. We examined oxygen-associated transcriptional [...] Read more.
Staphylococcus aureus (S. aureus) bovine mastitis is a significant public health issue. Despite enormous efforts, important gaps remain regarding host–microenvironmental factors. How intramammary reduced oxygen modulates S. aureus transcription in bovine mammary epithelial cells (MECs) remains unclear. We examined oxygen-associated transcriptional changes in a bovine-mammary adapted S. aureus clone following internalization into MECs and identified functional category enrichments under Normal-O2 and Reduced-O2 exposures. Bovine MAC-T monolayers were infected with a dominant bovine mastitis isolate under Normal-O2 or Reduced-O2 conditions. Triplicate infection experiments were performed for each oxygen condition. Each condition included matched non-reacted bacterial controls maintained under the same gas condition but without MAC-T exposure serving as the reference condition for expression calling. RNA was extracted and profiled using a high-throughput qRT-PCR platform covering genome-wide loci. Expression calls were mapped to curated BioQT roles and interpreted descriptively. Results indicated 211 loci were upregulated and 99 were downregulated under Normal-O2 conditions, versus 53 upregulated and 35 downregulated under Reduced-O2 conditions, relative to their non-reacted controls. Under Normal-O2 conditions, regulated loci covered multiple functional roles, including cellular processes, transport/binding proteins, regulatory functions, and energy metabolism with downregulated loci enriched in transport/binding and cell-envelope categories. Under Reduced-O2 conditions, upregulated loci were abundant in cellular process annotations dominated by pathogenesis/toxin-related functions, whereas downregulated loci were enriched in nucleotide biosynthetic and DNA/cell division categories. Thus, this reveals oxygen-associated shifts in the transcriptional response of intramammary S. aureus in MAC-T cells. Normal-O2 conditions were associated with broader category representation, whereas Reduced-O2 conditions yielded a narrower distribution enriched for selected toxin/pathogenesis- and iron/cation-associated annotations. These oxygen-linked transcriptional-shifts highlight candidate pathways for the intramammary adaptation of S. aureus, potential diagnostic markers, anti-virulence strategies, and targeted therapeutics. Full article
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15 pages, 18038 KB  
Article
Small Extracellular Vesicles (sEV) in Surgical Drain Fluids of Oral Squamous Cell Carcinoma Patients Carry Luminal and Surface DNA
by Alicja Gluszko, Zhongping Xu, James F. Conway, Monika Pietrowska, Adel Chaudhuri, Jose Zevallos and Theresa L. Whiteside
Int. J. Mol. Sci. 2026, 27(10), 4577; https://doi.org/10.3390/ijms27104577 - 20 May 2026
Viewed by 376
Abstract
Postoperative surgical draining fluid (SDF) in oral squamous cell carcinoma (OSCC) was reported to contain circulating free DNA and extracellular vesicles (EVs). The potential role of SDF DNA as a cancer biomarker in OSCC patients is investigated. To determine whether EVs contribute to [...] Read more.
Postoperative surgical draining fluid (SDF) in oral squamous cell carcinoma (OSCC) was reported to contain circulating free DNA and extracellular vesicles (EVs). The potential role of SDF DNA as a cancer biomarker in OSCC patients is investigated. To determine whether EVs contribute to the DNA content of SDF, small EVs (sEVs) were isolated by size exclusion chromatography and compared with those in paired plasma. sEV obtained from a cohort of HPV(+) and HPV(−) patients were evaluated for the endocytic origin, size, vesicular morphology, and the DNA content. The sEV from HPV(+) and HPV(−) SDF were similar. The sEVs from SDF were larger and contained more DNA than the sEV from plasma. Treatments of sEV with the DNase/RNase cocktail established the presence of DNA on the surface and in the sEV lumen. Furthermore, 20 to 30% of the total SDF DNA was associated with sEV. Fragmentomic analyses identified the largest DNA (>10,000 bp) on the vesicle surface. The DNA in the vesicle lumen consisted of smaller (~5000 bp) DNA fragments. Electron microscopy of the enzyme-treated vesicles indicated that surface DNA/RNA may be involved in maintaining vesicular integrity and modulating the vesicle entry into cells. The sEV-carrying surface and luminal DNA emerge as significant contributors to the total SDF DNA and, following validation, might serve as useful biomarkers of disease presence/progression in OSCC. Full article
(This article belongs to the Special Issue Extracellular Vesicles in Cancer and Tumor Microenvironment)
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14 pages, 2201 KB  
Article
Taxonomic Description and Genomic Characterization of Saccharibacillus soli sp. nov., Isolated from Copper Mine Soil, Khetri, Rajasthan, India
by Himani Darangwal, Bhawna Vyas, Munesh Kumari, Ojal Bansal, Shanmugam Mayilraj and Venkata Ramana Vemuluri
Microorganisms 2026, 14(5), 1150; https://doi.org/10.3390/microorganisms14051150 - 19 May 2026
Viewed by 306
Abstract
Gram-stain-positive, endospore-producing, mesophilic and rod-shaped strain O16T was isolated from a copper mine’s soil and characterized using a polyphasic taxonomic approach. The 16S rRNA gene-sequence analysis revealed that strain O16T belongs to the genus Saccharibacillus. It exhibited the highest sequence [...] Read more.
Gram-stain-positive, endospore-producing, mesophilic and rod-shaped strain O16T was isolated from a copper mine’s soil and characterized using a polyphasic taxonomic approach. The 16S rRNA gene-sequence analysis revealed that strain O16T belongs to the genus Saccharibacillus. It exhibited the highest sequence similarity to Saccharibacillus endophyticus JM-1350T (97.2%), followed by ‘Saccharibacillus alkalitolerans’ VR-M41T (97.1%), Saccharibacillus sacchari GR21T (96.8%), Saccharibacillus kuerlensis HR1T (96.6%), and Saccharibacillus deserti WLJ055T (95.7%). Genome-based comparisons revealed that the digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strain O16T and its closest relatives, S. endophyticus JM-1350T and ‘S. alkalitolerans’ VR-M41T, were 21.3% and 22.3%, and 76.6% and 77.6%, respectively, which are well below the recommended thresholds for species delineation. The diagnostic diamino acid of the cell wall was meso-diaminopimelic acid. Phosphatidylglycerol and diphosphatidylglycerol were the major polar lipids in strain O16T. The predominant menaquinone was MK-7. The DNA G+C content was 53.4%. The major cellular fatty acids present were anteiso-C15:0 (60.8%), iso-C16:0 (9.5%) and C16:1 ω11c (7.4%). On the basis of phenotypic, chemotaxonomic, and genotypic evidence, strain O16T is considered to represent a novel species within the genus Saccharibacillus. This data strongly supports the classification of the strain O16T as a novel species in the genus Saccharibacillus, for which we propose the name Saccharibacillus soli sp. nov. strain O16T (=CCM 8781T = KCTC 33898T). Full article
(This article belongs to the Section Environmental Microbiology)
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13 pages, 612 KB  
Article
In Vitro Effects of Amygdalin on Proliferation and Apoptosis in SH-SY5Y Neuroblastoma Cells
by Tuba Gül and Mücahit Seçme
Curr. Issues Mol. Biol. 2026, 48(5), 522; https://doi.org/10.3390/cimb48050522 - 17 May 2026
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Abstract
Background and Objectives: Neuroblastoma represents the most common extracranial solid tumor in childhood and is associated with a poor prognosis in high-risk cases. Amygdalin, a naturally occurring cyanogenic glycoside, has been reported to exhibit anti-tumor properties in various cancer models; however, its effects [...] Read more.
Background and Objectives: Neuroblastoma represents the most common extracranial solid tumor in childhood and is associated with a poor prognosis in high-risk cases. Amygdalin, a naturally occurring cyanogenic glycoside, has been reported to exhibit anti-tumor properties in various cancer models; however, its effects on neuroblastoma cells remain insufficiently characterized. The present study was conducted with the objective of investigating the effects of amygdalin on cell proliferation, apoptosis, and invasion in SH-SY5Y neuroblastoma cells in vitro. Materials and Methods: The SH-SY5Y neuroblastoma cells were cultivated under the optimal conditions for their growth. The cytotoxic effect of amygdalin was determined using the CCK8 assay, which is dose- and time-dependent. Total RNA isolation was performed using Trizol. Subsequently, a process of cDNA synthesis was initiated. The real-time PCR method was utilized to ascertain alterations in the expression levels of mRNA molecules associated with apoptosis, namely Bax, Bcl2, caspase-3, caspase-7, caspase-8, caspase-9, caspase-10, NFkB, and invasion-related genes MMP2, MMP9, TIMP1, and TIMP3. Furthermore, alterations in NFkB levels were examined through the utilization of the ELISA method. Results: The IC50 value of amygdalin in SH-SY5Y cells was determined to be 112.7 µM at 24 h. Amygdalin demonstrated a dose-dependent cytotoxic effect on neuroblastoma cells. Furthermore, the study revealed that the drug induced apoptosis through the upregulation of BAX and BID, and the downregulation of BCL-2 and NF-κB. This process led to a reduction in cell proliferation. Furthermore, the study demonstrated an anti-invasive effect through the downregulation of MMP9 and the upregulation of TIMP1 and TIMP3. In addition, a substantial decrease in NF-κB protein concentration was observed. Conclusions: These findings demonstrate that amygdalin exerts anti-proliferative, pro-apoptotic, and anti-invasive effects in SH-SY5Y neuroblastoma cells in vitro. Amygdalin may represent a promising natural compound for further investigation as a potential therapeutic agent in neuroblastoma. Full article
(This article belongs to the Section Biochemistry, Molecular and Cellular Biology)
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16 pages, 1328 KB  
Article
Anaerococcoides asporogena gen. nov., sp. nov., a Strictly Anaerobic Bacterium, Isolated from the Dehydrated Sludge of a Steel Factory’s Wastewater Treatment Plant
by Wanling Qiu, Yen-Chi Wu, Fuying Li, Yin Li, Jingjing Zhao, Shu-Jung Lai, Wangchuan Xiao, Chih-Hung Wu, Guowen Dong, Wei-Ling Zhang, Chao-Jen Shih, Sheng-Chung Chen, Hangying Zhang, Song Wang and Lintao Wu
Microorganisms 2026, 14(5), 1066; https://doi.org/10.3390/microorganisms14051066 - 9 May 2026
Viewed by 444
Abstract
A microbial community study using a culture-dependent method was conducted on dehydrated sludge collected from a steel factory’s wastewater treatment plant. One isolate, designated QWL-01T, was a strictly anaerobic, Gram-stain-negative, non-motile, non-spore-forming bacterium with coccoid cells measuring 0.6–0.9 μm in diameter. [...] Read more.
A microbial community study using a culture-dependent method was conducted on dehydrated sludge collected from a steel factory’s wastewater treatment plant. One isolate, designated QWL-01T, was a strictly anaerobic, Gram-stain-negative, non-motile, non-spore-forming bacterium with coccoid cells measuring 0.6–0.9 μm in diameter. The growth of strain QWL-01T was observed at 4–40 °C (optimum at 28–35 °C), pH 5.5–8.0 (optimum at pH 7.1), and a range of 0–3% NaCl (optimum at 0.5%). An analysis of the Biolog AN plate revealed positive carbon source utilization only for palatinose, α-ketovaleric acid, and pyruvic acid. The predominant fatty acids were iso-C13:0 (17.0%), C16:0 dimethyl acetal (12.0%), and anteiso-C13:0 (9.2%). A 16S rRNA gene sequence analysis through BLASTN demonstrated that the nearest phylogenetic neighbors of the novel strain were Youngiibacter multivorans DSM 6139T (93.82%) and Proteiniclasticum ruminis JCM 14817T (93.75%). The genome size of strain QWL-01T was 3.69 Mbp, with a G+C content of 50.8 mol%. Comparing strain QWL-01T with closely related species of genera Proteiniclasticum and Youngiibacter, the digital DNA-DNA hybridization (dDDH), average nucleotide identity (ANI), and average amino acid identity (AAI) values ranged from 26.60% to 36.80%, 65.89% to 68.30%, and 49.27% to 51.58%, respectively. Based on phenotypic, physiological, phylogenetic, and genomic relatedness evidence, strain QWL-01T represents a novel genus in the family Clostridiaceae, for which the name Anaerococcoides asporogena gen. nov. sp. nov. is proposed. Strain QWL-01T (=BCRC 81396T = CICC 25258T = NBRC 117088T) is the type strain of the proposed novel species. Full article
(This article belongs to the Section Environmental Microbiology)
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