Search Results (1,285)

Background: Cytomegalovirus (CMV) viral load monitoring forms the basis of preemptive treatment strategies in patients undergoing solid organ and hematopoietic stem cell transplantation. This study aimed to evaluate the analytical performance and inter-method agreement of a laboratory-developed CMV real-time PCR (qPCR) test compared to a commercial reference method using plasma samples. Methods: A total of 100 EDTA plasma samples were analyzed in parallel using a laboratory-developed CMV qPCR test and the reference method (Roche Cobas^® CMV). Analytical sensitivity was determined us-ing synthetic DNA cloned into the pUC57 plasmid backbone containing the US17 region of the CMV genome, and the limit of detection (LoD₉₅) was calculated using probit regression analysis. The relationship between the quantitative results obtained from clinical samples was evaluated using the Spearman rank correlation coefficient, while inter-method clinical agreement was assessed using the Bland–Altman method. Results: The limit of detection (LoD₉₅) of the laboratory-developed CMV qPCR test, as determined by probit regression analysis, was 63.8 copies/µL. A weak and statistically non-significant correlation was ob-served between the laboratory-developed CMV qPCR test and the reference method in Spearman rank correlation analysis of samples for which numerical quantitative results were available from both methods (ρ = 0.32; p = 0.22; n = 16). Bland–Altman analysis showed a mean difference of −0.48 log₁₀ units, with the vast majority of measurements falling within the 95% limits of agreement. Conclusions: The assay demonstrated measurable analytical performance and inter-method agreement; however, its use for quantitative viral load monitoring, particularly at low CMV DNA levels, should be interpreted with caution. Full article

Minimal residual disease (MRD) is the most robust independent prognostic biomarker for pediatric acute lymphoblastic leukemia (ALL). Conventional MRD detection assays suffer from insufficient sensitivity and inherent technical limitations, failing to identify ultra-low-level leukemic blasts and thereby contributing to disease relapse. Next-generation sequencing (NGS)-based MRD detection (NGS-MRD) overcomes these drawbacks by targeting immunoglobulin (Ig)/T-cell receptor (TCR) gene rearrangements and enabling the precise quantification of residual leukemic clones. In recent years, NGS-MRD has undergone extensive technological optimization in target panel design, result interpretation and sample type expansion, and has been validated for its clinical utility in therapeutic threshold definition, prognostic stratification, post-therapy monitoring and treatment adjustments in pediatric ALL. This review synthesizes the latest technological refinements and clinical applications of NGS-MRD in pediatric ALL, critically discusses the current challenges that limit its routine clinical use, and proposes future research directions to address these issues. Full article

Macrophages play a crucial role in health and disease. Currently, reporter mice for tracking alternatively activated macrophages in vivo are lacking. We designed a transgenic mouse model in which luminescence and fluorescence proteins, click beetle red luciferase (CBRED2) and mKate2, report on the expression of the Mrc1/Cd206 promoter, active in the monocyte/macrophage population. The mouse line was named B6Mrc1-mKate2-CBRED2. Using this novel mouse model, we were able to develop in vitro assays to validate transgenic macrophage polarization and test them with compounds of repolarization potency. Furthermore, in the in vivo assays, we exploited the migratory and infiltrative potency of macrophages for detecting tumor locations via optical imaging. In fact, macrophages can act as universal cancer markers, as they infiltrate primary and secondary tumors, stimulating or suppressing tumor growth. We first characterized transgenic mice for reporter expression ex vivo, followed by the generation of luminescence-based assays to reflect the polarity of differentiated macrophages, and lastly, we visualized reporter macrophages accumulating and infiltrating the tumor microenvironment (TME) of murine pancreatic ductal adenocarcinoma (PDAC) at multiple time points. We found that the extent of macrophage recruitment and retention was dependent on the infiltrative T-cell and dendritic cell populations present in the TME, reflecting the immunologically hot or cold nature of the PDAC clones, respectively. In conclusion, the ability to optically detect light-emitting macrophages can be applied not only for cancer studies but also in the context of inflammatory diseases. Full article

Background/Objectives: Cadherin-13 (CDH13), part of the cadherin family, is attached to the plasma membrane through glycosylphosphatidylinositol. CDH13 plays essential roles in the development of the neurological and vascular systems and is a risk factor for neural and cardiovascular diseases. CDH13 is expressed on the plasma membrane in both mature and uncleaved precursor forms with the prodomain. Although several anti-CDH13 monoclonal antibodies (mAbs) are available for basic research, there have been no reports of anti-CDH13 mAbs that can detect both the mature form and the uncleaved precursor in flow cytometry. Methods: We developed novel anti-human CDH13 mAbs (named Ca₁₃Mabs) using the mature form of CDH13-expressed cells as an antigen. Results: Among Ca₁₃Mabs, a clone, Ca₁₃Mab-17 (IgG_2b, κ) specifically recognized the mature and uncleaved precursor CDH13-overexpressed Chinese hamster ovary-K1 (CHO/CDH13) cells with no detectable cross-reactivity toward 21 other cadherins by flow cytometry. Ca₁₃Mab-17 also detected endogenous CDH13 in human glioblastoma (LN229 and U87MG) and lung mesothelioma (NCI-H2052) cell lines. The dissociation constant (K_D) value of Ca₁₃Mab-17 for LN229 was estimated at 4.1 × 10⁻⁸ M. Furthermore, Ca₁₃Mab-17 detected both the mature and uncleaved precursor CDH13 in Western blotting. It also identified new blood vessels and glioblastoma cells by immunohistochemistry. Conclusions: Ca₁₃Mab-17 is a versatile tool for detecting both mature and uncleaved precursor forms of CDH13 and has potential for tumor diagnosis and therapy. Full article

Recently, the existence of a new class of plant phosphotransfer proteins (HPts) with transmembrane (TM) domains was predicted by a large-scale bioinformatics method. These non-canonical proteins belong to the multistep phosphorelay (MSP) signal transduction system. The gene for one of these predicted TM-HPt was first cloned from tea (Camellia sinensis L.) plant cells. The membrane localization of the encoded protein (TM-CsHPt1) was confirmed using confocal microscopy and immunoblotting. These proteins were detected in the endoplasmic reticulum-enriched but not plasma membrane-enriched fractions. Using the BiFC method, the ability of TM-CsHPt1 to homodimerize was shown, similar to classical soluble HPt. However, heterodimerization between canonical and non-canonical CsHPts was not detected. Furthermore, TM-CsHPt1 was capable of specific interaction with the Arabidopsis cytokinin (CK) receptor AHK3, but not its paralogs AHK2 and AHK4. The obtained data are compatible with the involvement of TM-CsHPt1 in CK signaling (which utilizes the MSP system), possibly through a suggested non-canonical membrane branch. In addition, the key components of the CK signaling system in C. sinensis were uncovered and characterized by bioinformatics and phylogenetic analysis. The putative functions of the predicted MSP membrane branch in the tea plant are discussed. Full article

Today, access control systems are used in almost every institution and building. This is because they are an effective solution that provides a high level of security. There are many commercially available systems that provide security-related access features for buildings, including biometric options. Most use a centralized architecture, where each building can be remotely controlled via an Internet connection. This paper presents a completely different system from those on the market, a decentralized system with clone-detection and data-integrity verification mechanisms that allows access to buildings. The overall architecture includes hardware encoding of the access system’s location, and access is granted based on information written to the RFID card by the card-issuing center. This allows the system to be easily reconfigured at the hardware level prior to installation in the access area. The proposed system uses a confidential RFID card data integrity algorithm that uses the card data and immutable UID to determine a checksum in order to validate the RFID card data. As a result, any unwanted modification of at least one bit invalidates the card and blocks access to the building. The system was implemented, validated, and extensively tested over a one-year period with no reported operational issues. Full article

Background/Objectives: Acinetobacter baumannii is a critical opportunistic pathogen causing severe healthcare-associated infections, particularly in intensive care units. The global dissemination of carbapenem-resistant A. baumannii (CRAB) and its environmental persistence necessitate continuous genomic surveillance to monitor high-risk clones. Methods: We conducted whole-genome sequencing (WGS), core genome multi-locus sequence typing (cgMLST), and phylogenomic analyses on 26 CRAB isolates collected at the National Institute for Infectious Diseases (INMI) “Lazzaro Spallanzani” IRCCS (September 2023–September 2024). Antimicrobial resistance determinants, virulence-related genes, and capsular (KL) and lipooligosaccharide outer core (OCL) loci were characterized by interrogation of comprehensive bioinformatic pipelines. Results: All CRAB isolates displayed an extensively drug-resistant (XDR) phenotype, with a shared resistance pattern to carbapenems, aminoglycosides, fluoroquinolones, fosfomycin, and sulfonamides, while being susceptible only to colistin and cefiderocol. The carbapenemase gene bla_OXA-23 was detected in all CRAB isolates, together with clone-specific bla_OXA-51-like variants. For all isolates, the resistome profile fully matched the observed resistance phenotype. All isolates belonged to the International Clonal Lineage II (ICL II), Pasteur Sequence Type (ST) 2, and Oxford ST369, ST208, and ST455. Integration of cgMLST data with phylogenomic analyses and genome-based classification of KL and OCL loci revealed five distinct clusters, each one including nearly identical isolates, indicating both intra-hospital dissemination and possible inter-hospital transmission. Virulome profiling revealed heterogeneous repertoires of virulence-associated genes, resulting in cluster-specific patterns, while patristic analysis identified phylogenetic clusters linking the study isolates to other Italian and other European lineages. Conclusions: This study underscores the complex genomic landscape of CRAB in our setting, driven by the circulation of different ICL II clonal types, and reinforces the urgency of integrated genomic surveillance and robust antimicrobial stewardship to mitigate the spread of high-risk XDR A. baumannii clones. Full article

Background/Objectives: Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a major nosocomial pathogen. Although newer agents have reduced colistin use in high-income countries, this polymyxin remains important in many low- and middle-income settings. Colistin resistance in K. pneumoniae is most commonly associated with chromosomal alterations affecting the MgrB–PhoPQ pathway, or with plasmid-mediated mcr genes. This study aimed to investigate chromosomally mediated colistin resistance in CRKP clinical isolates from a Tunisian tertiary hospital. Methods: Between 2010 and 2015, 317 non-duplicate CRKP isolates were collected at Charles Nicolle Hospital, Tunis. Colistin MICs were determined by broth microdilution. Phenotypic tests and PCR characterized carbapenemases, extended-spectrum β-lactamases, AmpC, plasmid-mediated quinolone resistance, mcr and virulence genes. Porins (OmpK35/OmpK36) and the mgrB, phoP and phoQ loci were analyzed by SDS-PAGE and sequencing. Clonal relatedness was assessed by ERIC-PCR and multilocus sequence typing. We additionally compared colistin-resistant isolates with a panel of colistin-susceptible CRKP controls and assessed phenotypic stability after serial passages without colistin. Results: Five isolates (1.6%) were colistin-resistant. All were multidrug-resistant, produced OXA-48, and two also carried NDM-1. The isolates belonged to five distinct sequence types, including high-risk clones (ST11, ST101, ST147). No mcr genes were detected. Four isolates carried disruptive mutations in mgrB, and the remaining strain harbored inactivating mutations in both phoP and phoQ with an intact mgrB. Truncating alterations in PhoP/PhoQ and frequent loss or truncation of OmpK35/OmpK36 were observed. No mgrB/phoP/phoQ alterations were detected among colistin-susceptible controls, and colistin MICs remained stable after 7 days of drug-free passaging. Conclusions: In Tunisian CRKP, colistin resistance was associated with chromosomal alterations, predominantly involving disruption of the MgrB–PhoPQ pathway, in the absence of mcr genes. These mechanisms in both high-risk and emerging sequence types underscore the adaptability of CRKP and the need for surveillance where colistin remains an important therapeutic option. Full article

Ooencyrtus kuvanae is an egg parasitoid species that attacks the egg masses of Dendrolimus spp. and Lymantria spp. in China, which gives it a temporal niche advantage against pest infestations by Dendrolimus spp. and Lymantria spp. Moreover, it has a short life cycle, high offspring outcome, and female-biased population, showing distinctive ovarian development and oviposition behaviors and thus providing an ideal model for reproductivity and regulatory mechanisms. Previous studies have found that the Vitellogenin (Vg) and Vitellogenin Receptor (VgR) genes play important regulatory roles in the ovarian development of a few wasp species, but little is known about how these two genes work within O. kuvanae. Therefore, we observed their oviposition traits, characterized their gene structure, and clarified the function of Vg and VgR. The results showed that continuous daily oviposition significantly reduced the daily mature eggs and offspring per female by providing a single host egg for oviposition in each experimental trial, while the proportion of female offspring reached 100%, indicating that thelytokous parthenogenesis occurred. The full-length sequences of OkVg and OkVgR were cloned and submitted to GenBank. qPCR detection revealed that the transcription levels were the highest in adults. Feeding 20-hydroxyecdysone can increase OkVg gene expression (by 2.4-fold), while feeding juvenile hormone can promote their OkVgR expression (by 2.3-fold). RNA interference significantly downregulated OkVg and OkVgR expression in adult ovaries. And dsVg significantly reduced the ovarian egg load by 45% (p < 0.05), while dsVgR caused oviduct contraction and offspring decrease. Simultaneous silencing of OkVg and OkVgR significantly reduced offspring outcomes, indicating both genes may jointly dominate oocyte development. This study provides functional evidence of molecular regulation and interaction between OkVg and its receptor genes. Full article

This study investigated the epidemiology, antimicrobial resistance, and transmission risks of β-lactamase, cefotaxime-hydrolyzing, Munich (bla_CTX-M)-positive Escherichia coli (CTX-M-EC) in large-scale pig farms in Jiangxi Province (China). In total, 278 samples (manure, wastewater, drinking water, and flies) were collected. CTX-M-EC strains were isolated and analyzed using antimicrobial susceptibility testing, resistance gene profiling, multilocus sequence typing, and genetic environment analysis with gene transfer assessed by transduction experiments. Twenty-seven CTX-M-EC strains (9.71%) were isolated, all exhibiting multi-drug resistance with 100% resistance to cefotaxime, ciprofloxacin, and tetracycline, and >90% resistance to ceftazidime, florfenicol, and trimethoprim-sulfamethoxazole. Four bla_CTX-M subtypes were identified. bla_CTX-M-55 was the predominant subtype (70.37%) and was distributed across diverse sequence types and serotypes. Each strain harbored multiple antibiotic resistance genes, plasmids, and virulence genes. Mobile elements such as ISEcp1 and IS26 were detected surrounding the bla_CTX-M gene, and 96.29% of strains successfully transferred the bla_CTX-M gene via transduction. Clones highly homologous to pig manure strains were detected in flies and sewage, suggesting that this resistance gene can spread between animals, the environment, and vectors. These findings highlight the high transmission risk of bla_CTX-M and underscore the need for rational antibiotic use, waste management, and vector control within a One Health framework. Full article

Clonal hematopoiesis of indeterminate potential (CHIP) is an age-related condition affecting over 10–20% of individuals older than 70 years, characterized by the expansion of hematopoietic stem cell clones carrying somatic mutations in leukemia-associated driver genes in the absence of overt hematologic disease. Initially recognized as a precursor to hematologic malignancies, CHIP has since been implicated in diverse non-malignant disorders, notably increasing the risk of cardiovascular events by 40%. Recent epidemiological and experimental evidence suggests a potential disease-modifying influence of CHIP in neurodegenerative diseases, particularly Alzheimer’s disease (AD), although findings remain heterogeneous and sometimes contradictory. This review synthesizes recent evidence linking CHIP to AD risk, neuropathology, and disease progression. In this study, we summarize population-based cohort studies reporting a 36 to 54% reduction in the odds of clinical AD among CHIP carriers, alongside emerging data indicating that DNMT3A and TET2 mutations may exert divergent effects on neurodegeneration. Mechanistic insights from experimental models are examined, highlighting the ability of mutated myeloid cells to infiltrate the central nervous system and modulate neuroinflammation and amyloid clearance. We discuss conflicting findings and analyze how CHIP-driven vascular disease and stroke confound neuroprotective signals. We propose that CHIP may differentially influence AD and vascular contributions to cognitive impairment and dementia, shaping mixed dementia phenotypes. Methodological challenges, including survivor bias, competing risks, variable mutation detection thresholds, and incomplete Apolipoprotein E stratification, are discussed. Ultimately, our review clarifies that CHIP is not a simple protective factor, but a complex systemic modulator that reshapes the neurodegenerative and vascular drivers of cognitive decline, necessitating cross-disciplinary neuro-hematology collaboration to establish its role as a novel risk stratificator for improving diagnostic precision and personalizing clinical outcomes in Alzheimer’s disease. Full article

Background/Objectives: Staphylococcus aureus, particularly methicillin-resistant strains, is a leading cause of severe pneumonia. Understanding local molecular epidemiology, including virulence gene profiles and antimicrobial resistance (AMR) mechanisms, is crucial for effective infection control. This pilot study aimed to characterize S. aureus isolates from pneumonia patients in Karaganda, Kazakhstan. Methods: We collected 48 respiratory samples from patients with pneumonia across three medical institutions. Bacterial identification was performed using MALDI-TOF MS. Antimicrobial susceptibility testing (AST) was carried out using European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines. Whole-genome sequencing of S. aureus isolates was conducted on an Ion Torrent S5 platform. Genomic analysis included multilocus sequence typing (MLST), identification of virulence and AMR genes, and phylogenetic reconstruction. Results: S. aureus was identified in 14.6% (n = 7) of pneumonia cases included in this study. All isolates (100%, n = 7) were phenotypically resistant to benzylpenicillin. The mecA gene was detected in 57.1% of isolates (n = 4), while phenotypic resistance to methicillin was observed in 28.6% (n = 2) of the isolates. Resistance to azithromycin (57.1%, n = 4) and levofloxacin (42.9%, n = 3) was observed among the isolates. Two isolates (28.6%) were multidrug-resistant (MDR). Genomic analysis revealed the prevalence of the ST22 clone (57.1%, n = 4) in the studied cohort. Other sequence types were ST97, ST8, and ST45 (14.3% each). Phylogenetic analysis showed clustering consistent with MLST profiles. All isolates carried a conserved core virulence arsenal, including hemolysin (hla, hlg), biofilm-forming genes (icaADBC), immune evasion genes (sak, scn), and iron acquisition genes (isd). The Panton–Valentine leukocidin (PVL) genes were detected in three isolates. AMR gene analysis revealed the ubiquitous presence of mepA and tetracycline efflux pump genes, along with regulatory genes (arlRS, mepR, mgrA). The blaZ and ermA genes were not detected despite high phenotypic resistance to penicillin and macrolides. Conclusions: This study reports the identification of the virulent and resistant ST22 S. aureus clone in pneumonia cases in Karaganda, Kazakhstan. The discordance between phenotypic and genotypic AMR profiles underscores the necessity for integrated diagnostic approaches. Full article

Voice cloning enables realistic fake speech in which a speaker’s identity is preserved while the spoken message is semantically altered. This paper asks whether such meaning-level manipulation leaves detectable traces in transcripts alone. To study this problem, we introduce FakeSpeech+, a paired real–fake dataset built from authentic speech clips and their matched semantically altered counterparts, re-embedded into cloned voices while preserving speaker identity. Using this dataset, we conduct a transcript-first analysis based on interpretable text-only features from two groups: (i) linguistic content organization and discourse dynamics, and (ii) compact production-related proxy cues, including hesitation and disfluency markers. We evaluate these cues under transcript-length control through residualization and compare authentic and manipulated transcripts using statistical and experimental analyses. The results show that only a limited subset of features retains strong separation after length control, with coordination-related structure and emotion anchoring emerging as the clearest cues, while several production-related and discourse-variability features show weaker but still informative differences. In contrast, a number of syntactic, lexical-diversity, and other discourse-level features show substantial overlap after residualization. These findings indicate that transcript-level structure and selected production-related cues remain informative under realistic content-manipulation threats, supporting the value of transcript-based analysis for identity-preserving fake speech. Full article

Achromobacter spp. are opportunistic pathogens in people with cystic fibrosis (PwCF), yet the role of the upper airways in their persistence and adaptation remains poorly understood. We investigated whether the sinonasal compartment may act as reservoir and evolutionary niche for Achromobacter spp. during airway infection. Twenty-two isolates obtained from paired nasal lavage and sputum samples of seven PwCF were analysed by whole-genome sequencing. Within each PwCF, identical clone types were detected in both airway compartments, supporting bacterial exchange between upper and lower airways. Despite clonal relatedness, substantial genomic diversification was observed between paired isolates. Genomic signatures indicative of elevated mutation rates were detected in a high number of isolates (73%) and in both airway compartments, highlighting widespread genomic diversification across the respiratory tract. Mobilome analysis revealed compartment-specific variations in insertion sequences, prophages, and integrative elements, suggesting genome plasticity. Additionally, mutation in an aspartate kinase gene was consistently associated with loss of biofilm formation in vitro, highlighting a potential link between this pathway and biofilm phenotype. Overall, our findings indicate that upper and lower airways represent interconnected but partially independent ecological niches where Achromobacter populations can diverge during colonization, supporting the view that both compartments contribute to their persistence and evolution in CF airways. Full article

Rice blast, caused by the fungus Magnaporthe oryzae, is one of the most devastating threatening to global rice production. The narrow genetic background of modern rice cultivars exacerbates the shortage of durable resistance resources. In contrast, the wild rice species Oryza officinalis harbors abundant stress-resistance alleles and represents a valuable gene pool for identifying novel broad blast-resistance genes. The cloned resistance gene Pid2 is encoded in a receptor-like protein kinase conferring race-specific resistance against the M. oryzae isolate ZB15. In this study, three Pid2 homologs were isolated from O. officinalis. The special allele Pid2of-MD33 was transformed into “Yunjing 37(YG37), a blast-susceptible japonica rice cultivar” via Agrobacterium-mediated transformation. Quantitative real-time PCR analysis showed that Pid2of-MD33 was consistently expressed in various tissues of O. officinalis, with the highest transcript abundance detected in leaf mesophyll cells and plasma membranes. Inoculation with the M. oryzae isolate ZB15 revealed that transgenic YG37 lines expressing Pid2of-MD33 displayed significantly reduced lesion size and pathogen proliferation, suggesting recovered race-specific resistance. These results enrich the resistance gene resources for rice blast research and provide a promising candidate gene for rice blast resistance breeding. Full article