Search Results (352)

The 2022 global mpox outbreak represented a turning point in the Monkeypox virus (MPXV) epidemiology, highlighting the incredible capability of this virus to adapt to different conditions, also in a non-endemic context. To investigate the genomic dynamics of MPXV 2022 strains, we performed whole-genome sequencing of 40 clinical samples from 16 Italian patients across multiple anatomical sites and timepoints between May and December 2022. Combining single-nucleotide analysis with detailed investigation of short tandem repeats (STRs), we explored inter- and intra-host viral dynamics. We identified 19 STR loci located near or within genes involved in immune modulation and virion morphogenesis. While most STRs remained stable across patients, a subset displayed locus- or matrix-specific variation. Among these, STR-VII—embedded within the coding sequence of OPG153, an envelope-associated protein implicated in viral attachment—showed a 12-nucleotide in-frame deletion, resulting in the loss of four aspartic acid residues (Δ4D variant). Structural modeling indicated that this deletion slightly alters a disordered acidic loop without affecting the global fold, potentially modulating surface charge and immune recognition. Integrating STR profiling into genomic surveillance may enhance resolution in outbreak reconstruction and reveal subtle adaptive processes underlying poxvirus–host interaction and immune escape. Full article

Triticale (×Triticosecale Wittmack), a synthetic hybrid of wheat (Triticum spp.) and rye (Secale cereale), is a valuable dual-purpose crop for its high yield and stress tolerance. Introducing beneficial alien chromatin is crucial for expanding genetic diversity and improving cultivars. This study aimed to introduce Thinopyrum intermedium St genome chromatin into hexaploid triticale via trigeneric hybridization to develop novel germplasm. Six stable lines were selected from crosses between an octoploid wheat-Th. intermedium partial amphiploid line Maicao 8 and a hexaploid triticale cultivar Hashi 209. Agronomic traits were evaluated over two cropping seasons, revealing that the translocation lines exhibited superior agronomic performance compared to the parental triticales. These lines showed longer spikes, higher tiller numbers, and increased grain protein content, without compromising thousand-kernel weight. Cytogenetic analysis using sequential multicolor genomic in situ hybridization (smGISH), fluorescence in situ hybridization (FISH), and oligonucleotide probes, alongside validation with species-specific molecular markers, identified all six lines as St-R terminal translocation lines containing 14 rye chromosomes. Three lines carried a small terminal St segment on chromosome 1R, while the other three carried St segments on both 1RL and 4RS chromosomes. This work demonstrates that trigeneric hybridization is an effective strategy for inducing intergeneric recombination between Thinopyrum intermedium and rye chromosomes, leading to stable, small-segment terminal translocations. The developed St-R translocation lines represent a novel and valuable germplasm resource for enriching genetic diversity and breeding improved triticale cultivars with enhanced yield and quality traits. Full article

Body fluid identification at crime scenes is the first step in the forensic biology workflow, leading to the identification of the perpetrator and/or, in some cases, the victim. Current methods that are regularly used in forensic criminal evidence analysis utilize well-studied properties of each fluid as the foundation of the protocol. Among these approaches, alternative light sources, chemical reactions, lateral flow immunochromatographic tests, and microscopic detection stand out to identify the main body fluids encountered at crime scenes: blood, semen, and saliva. However, these often come with limits for specificity and sensitivity. There is also difficulty with fluid mixtures, environmental degradation, and destruction of the sample by the method used. Other fluids, like vaginal fluid and fecal matter, lack standardized protocols and require innovative ideas for accurate analysis without compromising the sample. Emerging technologies based on molecular methods have been the focus of body fluid research, with emphasis on topics such as mRNA, microRNA, epigenetics, and microbial analysis. Additional information alongside the determination of fluid origin could be an advantage from new molecular techniques, such as the identification of donors from SNP analysis, if regular STR analysis is not possible. Validation studies and the integration of such research have the potential to expand and enhance the laboratory practices of forensic science. This article will provide an overview of the current methods applied in the crime lab for body fluid identification before exploring active research in this field, pointing out the potential of these techniques for application in forensic cases to overcome present issues and expand the variety of body fluids identified. Full article

Aspergillus fumigatus is the primary pathogen causing aspergillosis. Recent molecular population genetic studies have demonstrated that A. fumigatus exhibits high local genetic diversity, with evidence for limited differentiation among geographic populations. However, research on the impacts of geomorphological factors on shaping the population genetic diversity patterns of this species remains scarce. In this study, large-scale sampling and in-depth population genetic analysis were performed on soil-derived A. fumigatus from Guizhou Province, a representative karst landscape in southern China. This area is dominated by plateaus and mountains (accounting for 92.5% of the total area) and represents a classic example of conical karst landscapes. A total of 206 A. fumigatus strains were isolated from 9 sampling sites across Guizhou. Genetic diversity, genetic differentiation, and population structure of these strains were analyzed based on short tandem repeats (STRs) at 9 loci. The results revealed that A. fumigatus in the karst region of Guizhou harbors abundant novel alleles and genotypes, with high genetic diversity. Gene flow among geographical populations was infrequent, and significant genetic differentiation was detected between 30 of the 36 pairs of geographical populations where mountain ranges played a very important role, with the overall regional genetic differentiation reaching PhiPT = 0.061 (p = 0.001). Furthermore, the Guizhou populations showed significant differences from those reported in other regions worldwide. Surprisingly, only one of the 206 (0.49%) A. fumigatus isolates from this region exhibited resistance to the two medical triazoles commonly used for treating aspergillosis, and this resistance frequency was far lower than those reported in previous studies from other regions. We discuss the implications of our results for evolution and environmental antifungal resistance management in this important human fungal pathogen. Full article

Background: Short tandem repeats (STRs) are highly variable sequences present along the human genome, including the Y-chromosome. Y-STRs are exclusive to males, and the haplotypes they define are informative. Objectives: Twenty-six Y-STR loci were genotyped in 252 males from Northern Portugal to characterise Y-chromosome genetic variation using the Investigator Argus Y28 QS Kit. Methods: The kit mentioned was used to amplify male DNA samples, and capillary electrophoresis was used to analyze the fragments. Forensic parameters and haplotype diversity were computed, and samples’ haplogroups were predicted. A multidimensional scaling (MDS) plot was used to graphically represent the R_ST genetic distances, including reference populations. Results: A total of 250 different haplotypes were observed, including 248 unique ones, yielding a very high haplotype diversity (HD = 0.999) and discriminatory power (DP = 0.992). Haplogroup analysis indicated a predominance of R1b (58.7%), followed by E1b1b, I and J, pointing to a population history shaped by Mediterranean and North African gene flow. Comparative analysis between Portugal and 5 other populations showed greater genetic affinity with Spain and Italy, while revealing marked differentiation from Greece, Morocco, and former Portuguese colonies. Conclusions: The results confirm that the Northern Portuguese Population exhibits high Y-STR variability and robust forensic resolution. The dataset was submitted to the YHRD database, enhancing the representation of the Portuguese population and underscoring the value of the 26 locus panel for applications in forensic science, genealogy, and population genetics. Full article

Background: Postmortem DNA identification of highly decomposed human remains is often limited by the availability and quality of conventional biological samples. Keratinized tissues, such as fingernails, represent a potentially valuable alternative due to their anatomical resistance to environmental degradation, however, their use as primary biological material for DNA profiling remains underreported in forensic practice. Case presentation: We report a case involving the recovery of a highly decomposed body of a missing woman, in which DNA samples were collected from a fingernail and a tooth. DNA extraction was performed using the PrepFiler Forensic DNA Extraction Kit for the fingernail sample and PrepFiler BTA Forensic DNA Extraction Kit for the tooth sample. No usable DNA profile was obtained from the tooth sample; however, the fingernail sample yielded a complete and high-quality STR profile with successful amplification across all 24 loci (GlobalFiler PCR Amplification Kit). Reference buccal swabs from the presumed biological parents were collected for subsequent kinship analysis. Discussion: Kinship analysis based on allele frequencies in the Croatian population resulted in a combined paternity index (CPI) corresponding to a probability of paternity of 99.99999812%, providing strong genetic support for the proposed identity of the deceased. Notably, this is the first documented forensic case in Croatia in which nail material served as the primary—and ultimately successful—biological sample for postmortem identification. Conclusions: This case highlights the evidentiary value of fingernails as a robust, accessible, and forensically valid DNA source in postmortem identification, particularly in cases of advanced decomposition where conventional biological materials are unavailable or degraded. Further studies involving larger sample sets and diverse postmortem conditions are needed to support the broader implementation of nail material in routine forensic identification workflows, particularly within the Croatian medico-legal context. Full article

Germline genetic testing plays a critical role in diagnosing inherited predispositions and increasingly guides therapeutic and surveillance choices—but becomes technically challenging after allogeneic hematopoietic stem cell transplantation (HSCT), when donor-derived DNA contaminates host tissues. To address this, we compared donor-derived DNA across three accessible tissues—buccal swab, nail, and eyebrow follicles—in recipients after hematopoietic stem cell transplantation using two orthogonal assays (34-SNP next-generation sequencing and a 27-marker short tandem repeat panel) and modeled clinical covariates that influence chimerism. Eyebrow follicles showed consistently low donor DNA (median 1% by NGS; 3% by STR) whereas buccal swabs and nails carried substantially higher donor fractions (+25 and +22 percentage points versus eyebrow, respectively; both p < 0.01). Across methods, STR yielded on average ≈6 percentage points higher donor fractions than NGS at low-level chimerism. Several transplant covariates correlated with chimerism: matched-related donors and a perfect HLA match (10/10) were each associated with lower donor DNA (≈12–14 and 15–20 percentage points, respectively); longer times since hematopoietic stem cell transplantation correlated with lower levels for nail samples, and donor–recipient sex match correlated with higher donor DNA (~7–8 percentage points). Even low-level chimerism can distort germline variant interpretation. We propose a pragmatic protocol for post-hematopoietic stem cell transplantation germline testing that prioritizes eyebrow follicles as the default tissue. An SNP-based quality control assay is used to flag unsafe donor fractions (≥ 5–10%) before comprehensive germline analysis, reducing the risk that chimeric donor DNA distorts germline variant interpretation. Full article

Background: Glioblastoma (GB) carries a dismal prognosis, with survival outcomes particularly poor in older patients. With the fastest-growing global demographic being those aged over 65, the incidence of GB is expected to rise. Objective: To evaluate predictors of survival in patients aged ≥70 years with histologically confirmed GB, focusing on surgical resection, adjuvant therapy, and comorbidities. Methods: A retrospective review was performed of all patients aged ≥70 undergoing index surgery for GB between January 2021 and March 2025 at a single tertiary neurosurgical centre. Demographics, pre-operative fitness scores (Karnofsky Performance Status [KPS]., Charlson Comorbidity Index [CCI].), tumour characteristics, extent of resection, adjuvant treatment, and survival were analysed. Tumour volume was estimated using the ABC/2 method. Survival outcomes were assessed using Kaplan–Meier curves and multivariable Cox proportional hazards regression. Results: A total of 124 patients aged ≥70 years (median 74 years, range 70–86) were included. Median overall survival was 8 months (IQR 4–15). On multivariable analysis, adjuvant chemoradiotherapy (HR = 0.30, 95% CI 0.17–0.52; p < 0.001) and gross total resection (GTR) (HR = 0.41, 95% CI 0.20–0.86; p = 0.019) were independently associated with improved survival. Smoking history was associated with increased hazard of death (HR = 2.02, 95% CI 1.07–3.81; p = 0.029), an effect robust to multiple sensitivity analyses. No significant associations were found for age, pre-operative KPS, comorbidity index, tumour volume, or methylation status (all p > 0.10). Tests for non-proportional hazards indicated that the survival benefit of adjuvant therapy diminished over time (interaction p = 0.0002), with early post-operative benefit (HR ≈ 0.35 at 1 month) that attenuated towards unity by 6–12 months. The effects of GTR and smoking were time-invariant. RMST analysis suggested a modest, non-significant absolute survival advantage of GTR over STR (mean difference = 2.0 months at 18 months; p = 0.11). After exclusion of early post-operative deaths (<6 weeks), adjuvant therapy (HR = 0.34; p < 0.001) and GTR (HR = 0.33; p = 0.005) remained independent predictors of improved survival. Conclusions: Among patients aged ≥70 years with glioblastoma, adjuvant therapy and extent of resection remain key independent predictors of survival, while smoking is associated with poorer outcomes. The survival benefit of adjuvant chemoradiotherapy is strongest in the early post-operative period and diminishes over time, underscoring the importance of early multidisciplinary intervention. These findings highlight that aggressive multimodal treatment may confer survival advantage even in older patients. Full article

To systematically investigate how the olfactory system of Bombus terrestris adapts to its social division of labor and reproductive strategies, this study integrated the micromorphology of antennal sensilla and the expression profiles of olfactory receptor (OR) genes from the heads of its three castes (workers, drones, and queens) for a multi-level analysis. Scanning electron microscopy (SEM) revealed that drones possess significantly longer chaetic sensilla (Sch), sensilla trichodea (Str A/B), and sensilla basiconica (Sba A), as well as larger-diameter sensilla coeloconica (Sco) compared to workers and queens, indicating structural and functional specialization for sensitive detection of single key signals (e.g., queen pheromones). In contrast, workers and queens exhibited a more complete composition of sensilla types and a higher sensilla distribution density, suggesting the construction of a perceptual system capable of processing multiple chemical signals simultaneously. RNA-seq combined with qRT-PCR confirmed the significant upregulation of seven OR genes (e.g., BterOR3, BterOR4) in drones, while workers showed upregulation of BterOR3/5/7 accompanied by enrichment of P450 detoxification pathways. Phylogenetic analysis suggested that BterOR5 serves as a conserved co-receptor, and some OR genes may originate from recent duplication events. In summary, distinct differences were observed in the morphological structure and molecular expression of the olfactory system among B. terrestris castes. Drones exhibited structural and gene expression features consistent with specialization in queen pheromone detection, while workers and queens demonstrated sensilla diversity and olfactory receptor expression patterns indicative of a broader response capacity to diverse chemical signals. These findings support the view that the olfactory system has undergone multi-level adaptive evolution driven by social division of labor and reproductive roles. Full article

N₂-fixing bacteria have great potential to be used as biofertilizer in agriculture to promote plant growth via nitrogen fixation. In this study, a novel species Fontibacillus forbon sp. nov., with strain BL-9^T as the type strain, was isolated from the rhizosphere of Fraxinus chinensis. Strain BL-9^T was able to fix nitrogen and grow on nitrogen-free medium. Phylogenetic analysis of 16S rRNA gene revealed that strain BL-9^T was most closely related to Fontibacillus phaseoli BAPVE7B (98.03%), followed by Fontibacillus solani A4STR04 (96.72%), Fontibacillus panacisegetis (96.6%), Paenibacillus vini (96.6%), and Paenibacillus segetis DB13260 (96.57%). The phylogenomic tree supported that strain BL-9^T was most closely related to F. phaseoli BAPVE7B. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) between strain BL-9^T and its closely related type strain, F. phaseoli BAPVE7B, were 42.5% and 90.94%, respectively, which were below the values (70% for dDDH and 95% for ANI) for species discrimination. The DNA G+C content of strain BL-9^T was 49.7%. The genome of strain BL-9^T had a nif (nitrogen fixation) gene cluster containing 10 genes (nifB nifH nifD nifK nifE nifN nifX orf1 hesA nifV). The predominant fatty acid was anteiso-C15:0, the major menaquinone was MK-7, and the major polar lipid was diphosphatidylglycerol. Strain BL-9^T and its closely related species of Fontibacillus had some common and distinguished physiological characteristics. Based on genomic, phylogenetic, chemotaxonomic, and phenotypic features, strain BL-9^T represents a novel species of the genus Fontibacillus. The name proposed for this species is Fontibacillus forbon sp. nov., with the type strain BL-9^T. Full article

Background: This study investigated the phenotypic and genotypic antibiotic resistance profiles of 50 Lactic Acid Bacteria (LAB) strains—25 Lactiplantibacillus plantarum and 25 Lacticaseibacillus paracasei—isolated from traditional Sardinian fermented foods of animal origin. Methods: The sensitivity of the isolates to antibiotics such as β-lactams, tetracyclines, aminoglycosides, macrolides, phenicols, and glycopeptides was initially assessed using disc diffusion and minimum inhibitory concentration (MIC) tests. Subsequently, PCR analyses were performed on both genomic DNA and plasmid DNA to detect blaZ, tet(W), strA, aac(6′)-Ie–aph(2″)-Ia, and vanX genes associated with resistance to ampicillin, tetracycline, streptomycin, gentamicin, and vancomycin. Results: The analysis revealed that L. plantarum strains frequently carried the tet(W) gene on the chromosome and strA on plasmids, while vanX was detected in most strains as a chromosomal determinant. By contrast, L. paracasei strains exhibited a predominantly plasmid-mediated distribution of resistance genes. For example, strA, aac(6′)-Ie–aph(2″)-Ia and blaZ were often found on plasmids, whereas vanX remained chromosomally encoded. Phenotypic assays confirmed high intrinsic resistance to vancomycin in both species, with L. plantarum showing a higher overall frequency and diversity of resistant phenotypes compared to L. paracasei. Conclusions: The co-occurrence of multiple resistance determinants, including plasmid-encoded ones, in most strains suggests that even autochthonous isolates from artisanal products may represent potential reservoirs for transmissible resistance genes. Full article

Dog bite incidents represent a significant public health concern, and DNA analysis, in addition to morphological comparison, has been recognized as a useful tool for identifying the offending dog. STR typing has been established as a reliable method for individual identification in dogs, with many successful applications reported. However, most previous studies have analyzed samples showing visible traces such as blood or saliva, and there have been no documented cases in which the offending dog was identified from clothing without apparent evidence. In the present study, STR analysis was performed on trace DNA extracted from the clothing of a victim who sustained a minor dog bite injury. The STR profile obtained from the sample completely matched that of one of the three suspected dogs, a Weimaraner, at all 19 loci examined. No visible saliva or blood contamination was observed on the clothing. This case demonstrates that even trace DNA from clothing without visible markings can yield a complete STR profile when appropriate sampling and analytical methods are applied. The findings highlight the potential of canine DNA forensics to contribute to animal-related investigations and underscore the importance of accumulating allele frequency data and standardizing analytical procedures for future applications. Full article

Hemophilia A (HA) is an X-linked recessive bleeding disorder that predominantly affects males but rarely manifests clinically in females. We report an unusual case of a woman with HA carrying a de novo heterozygous F8 variant, skewed X chromosome inactivation (XCI), and mosaic monosomy X without the Turner syndrome phenotype. DNA was extracted from whole blood. After excluding F8 inversions and large rearrangements, Sanger sequencing of coding regions was performed. XCI was assessed by STR analysis of the AR gene. Haplotypes were identified by fragment analysis of three polymorphic sites. Karyotyping was performed using G-banding. A heterozygous missense variant in the F8 gene, c.6545G>A (p.Arg2182His), was detected with allelic imbalance. STR analysis confirmed ~93% skewed XCI. Karyotyping revealed mosaicism: 45,X [7]/46,XX [14]. Neither parent carried the c.6545G>A variant or karyotype aberrations. We suggest that 46,XX cells carried c.6545G/A with preferential inactivation of the normal X chromosome, whereas 45,X0 cells carried the mutant allele only. The limited proportion of active normal X chromosomes led to a mild rather than severe phenotype. This case highlights complex genetic mechanisms underlying HA in females and underscores the importance of comprehensive molecular and cytogenetic testing for accurate diagnosis, clinical management, and genetic counseling. Full article

This study presents a robust methodology for analyzing 3D roughness parameters to characterize sandblasted surfaces, identifying the most relevant descriptors for process optimization. Sandblasting with irregularly shaped corundum particles is performed using five grit sizes (25, 50, 90, 125, and 250 µm) and three pressure levels (2, 3, and 4 bar). The resulting surfaces are characterized through eight 3D roughness parameters: Sa, Spc, Sal, Sfd, Sdq, Sdr, Spd, and Str. A linear model of the form Q = a + b.D + d.D.P, where Q represents the roughness parameter, D is the average grit size, and P is the sandblasting pressure, is employed. For Spd, a nonlinear model, Spd = (a + b.D + d.D.P)², yields a significantly improved determination coefficient, demonstrating the model’s enhanced ability to capture the complexity of the Spd parameter. The double-bootstrap analysis validates the statistical significance of all models, providing confidence intervals for each parameter. This approach emphasizes the importance of advanced 3D roughness descriptors for accurately analyzing surface textures in sandblasting processes, offering a reliable framework for surface characterization and industrial optimization. Full article

Objectives: To investigate the phenotypic and genotypic changes of Acinetobacter baumannii collected from the tertiary oncology setting in Lithuania. Methods:A. baumannii isolates (n = 61) were collected in the years 2013–2014 (n = 28) and 2017–2019 (n = 33) from a tertiary care cancer center in Lithuania. Antimicrobial susceptibility was determined according to EUCAST and for piperacillin/tazobactam and cefepime, according to CLSI guidelines. PCR, pulsed-field gel-electrophoresis, and multi-locus sequence typing were used for resistance gene detection and genotyping. The biofilm formation ability was determined by a microtiter plate assay. Results: Of 61 A. baumannii isolates obtained, 84% (51/61) and 71% (43/61) were multi-(MDR) and extensively (XDR) drug-resistant, respectively. Carbapenem-resistant isolates comprised 77% (47/61); of these, 92% (43/47) harbored genes encoding the OXA-23-like, and 4% (2/47) OXA-24-like carbapenemases. All isolates were susceptible to colistin. Genotyping analysis revealed six groups with the highest prevalence of international clones 1 (IC1) and 2 (IC2), which dominated during 2013–2014 and 2017–2019, respectively. Notably, the A. baumannii diversity increased in 2017–2019 with the emergence of 3-LST groups G4, G8, G12, and G14, which included isolates of ST276, ST78, ST1463, and ST1336 sequence types, respectively. The IC1 and IC2 isolates displayed characteristic gene profiles aacC1, aacC2, aphA6, sul1, and armA, strA-strB, bla_TEM, respectively, whereas isolates from other groups had lesser resistance gene content. Isolates from IC2, G12, and G14 groups were strong biofilm producers; IC1, G4, and G8 isolates displayed no/weak biofilm formation capacity. Conclusions: A. baumannii from the cancer center showed a high prevalence of MDR and XDR phenotypes. Clonal dominance and diversity changed during the surveillance periods with the replacement of IC1 by IC2 clone isolates and the emergence of higher clonal diversity of isolates with stronger biofilm-forming capacity. The observed changes indicate a concerning trend of the establishment of a more virulent A. baumannii in the cancer setting. Full article