Search Results (123)

This study reports the valorization of oil palm empty fruit bunches into cellulose nanocrystals (CNCs) for the removal of the chemical oxygen demand (COD) from industrial wastewater generated by the same processing sector. Cellulose I_β was first isolated through sequential bleaching, delignification, and mercerization, and two hydrolysis routes were evaluated to obtain CNCs: a concentrated acid route (60% v/v H₂SO₄, 50 °C, 60 min) for CNCs-1 and a low-acid, long-duration route (1% v/v H₂SO₄, 80 °C, 12 h) for CNCs-2. Rietveld refinement of the X-ray diffractograms confirmed the polymorphic transition, assigning cellulose I_β to the intermediate materials and cellulose II to the CNC samples, with crystallite sizes of 4.99 nm for CNCs-1 and 5.43 nm for CNCs-2. attenuated total reflectance–Fourier transform infrared (ATR-FTIR) spectroscopy analysis showed the progressive removal of lignin and hemicellulose and supported the cellulose I_β to II transition through changes in hydroxyl bonding and crystallinity-related bands. Preliminary adsorption tests showed better COD removal with CNCs-2, which were therefore selected for optimization using a Box–Behnken design with the adsorbent mass, pH, and contact time as variables. The quadratic model was significant (R² = 0.9675; predicted R² = 0.8908), and the maximum COD removal reached 91.47%, decreasing the COD concentration from 2459.0 to 209.85 mg L⁻¹ under the optimum conditions of 0.09 g CNCs-2, pH 3, and 20 min. These results highlight cellulose II nanocrystals derived from oil palm waste as a promising and scalable adsorbent for industrial wastewater treatment. Full article

Background: Acinetobacter baumannii (A. baumannii) is a formidable nosocomial pathogen and is classified by the World Health Organization (WHO) as a critical-priority pathogen, owing to its rapid evolution into extensively drug-resistant (XDR) and pan-drug-resistant (PDR) strains. Colistin remains one of the last-resort therapeutic options, although resistance rates are increasing in endemic regions such as Greece. In this study, we investigated the molecular basis of colistin resistance and characterized the clonal backgrounds of clinical XDR/PDR A. baumannii isolates collected between January and June 2022 from two tertiary-care hospitals in Thessaloniki, Northern Greece. Methods: We analyzed forty non-duplicate XDR/PDR clinical isolates. Antimicrobial susceptibility was determined using the VITEK 2 system, broth microdilution, and gradient diffusion methods. The lipid A biosynthesis genes (lpxA, lpxC, lpxD) and the pmrCAB operon were amplified by PCR and sequenced for all isolates. A representative subset of strains (n = 10/40) underwent multilocus sequence typing (MLST) according to the Pasteur MLST scheme. Results: All isolates proved colistin-resistant (MIC ≥ 4 µg/mL), and 95% were classified as PDR. Sequence analysis revealed multiple nonsynonymous mutations in the pmrCAB operon, with the PmrB A226V substitution predominating and extensive amino-acid changes observed in PmrC. In contrast, lpx genes exhibited limited protein-level variation, limited to lineage-associated polymorphisms (LpxC N287D, LpxD E117K). A novel six-nucleotide insertion in pmrB was identified in one isolate. MLST demonstrated a predominance of ST2 (International Clone 2), with single representatives of ST115 (IC2) and ST1 (IC1). Conclusions: In this cohort from Northern Greece, chromosomal mutations in the pmrCAB operon, within a predominantly ST2/IC2 background, were strongly associated with colistin resistance. These findings underscore the urgent need for continued molecular surveillance and targeted infection-control measures to limit further spread of PDR A. baumannii. Full article

In this study, the phenotypic consequences of naturally occurring single nucleotide polymorphisms (SNPs) in the Middle East respiratory syndrome coronavirus (MERS-CoV) Spike protein were investigated. The impact of Spike mutations on the syncytia formation and neutralisation of contemporary MERS-CoV strains is not currently well understood. Mutations were identified by aligning 584 MERS-CoV Spike sequences from either human clinical isolates collected between 2012 and 2024 or from a clinical isolate that had been passaged in human cells. Fifteen SNPs of interest occurring in the N-terminal domain (NTD), receptor binding domain (RBD) and adjacent to the S1/S2 cleavage site were selected for further characterisation based on their location in the Spike protein, frequency and identification in previous studies. A contemporary clade B, lineage 5 wildtype Spike sequence, obtained from a human MERS-CoV clinical isolate, was used as the backbone in this study. The mutations of interest were introduced to the wildtype backbone to generate Spike variants. Spike variants were characterised via cell–cell fusion assays, and a lentiviral pseudotyping system was used to investigate the impact of these Spike mutations on neutralisation. The I529T, E536K and L745F mutations were shown to increase fusion and syncytia formation. The L411F, T424I, L506F, L745F and T746K mutations were found to increase resistance to neutralisation by pooled patient sera. This study has identified novel naturally occurring Spike mutations that resulted in phenotypic differences in the syncytia formation and neutralisation of contemporary MERS-CoV strains. Continued investigation of the phenotypic consequences of MERS-CoV Spike mutations is essential for assessing the risk to public health, especially given the pandemic potential of this virus. Full article

Background: Early diagnosis of familial hypercholesterolemia (FH) is crucial to improve long-term outcomes. FH diagnosis relies on elevated low-density lipoprotein cholesterol (LDL-C) levels, familial clinical characteristics, and identification of pathogenic variants in FH-related genes. Secondary factors, such as overweight and obesity, are known to influence lipid profiles in the general population. More recently, polygenic risk scores based on single-nucleotide polymorphisms (SNPs) have been proposed as additional determinants of LDL-C levels. Methods: We enrolled 214 pediatric subjects with LDL-C levels ≥95th percentile (after 6 months of dietary intervention) and with at least one parent with LDL-C levels ≥ 95th percentile. All participants underwent biochemical and auxological assessment and genetic testing for FH. In a subgroup of 60 subjects, LDL-C polygenic scores based on 6- and 12-SNPs were calculated. Results: Pathogenic variants confirming heterozygous FH were identified in 190 subjects (variant-positive, V+); 17 were variant-negative (V−), yielding a mutation detection rate of 91.8%. An additional seven patients carrying variants of uncertain significance were excluded from the primary analysis. LDL-C was modestly higher in V+ than V− subjects using both Friedewald (212 vs. 188 mg/dL; p = 0.035) and Martin–Hopkins formulas (208 vs. 187 mg/dL; p = 0.041), while the other main clinical and laboratory parameters were similar. In V+, LDL-C was higher in subjects with null variants, compared to those with defective variants. Body mass index (BMI SDS) was inversely correlated with HDL-C (p < 0.001), and obesity (BMI z-score > 2 SDS) was associated with lower HDL-C and higher LDL-C, non-HDL-C, and ApoB. With regard to the polygenic scores, 12- and 6-SNP scores showed overlap between V+ and V−, and published cut-offs did not discriminate lipid severity in our population; however, in V+ subjects, the 12-SNP score acted as a phenotype modifier, being independently associated with higher LDL-C and non-HDL-C levels after adjustment for age, sex, and BMI SDS. Conclusions: In children selected by LDL-C ≥ 95th percentile, together with autosomal dominant familial hypercholesterolemia, genetic confirmation of FH is achieved in the vast majority of cases. Variant type (null vs. defective), BMI, and polygenic background contribute to phenotypic heterogeneity, supporting the need to address other factors alongside genetic diagnosis. Further validation is needed before polygenic scores can be implemented in routine clinical practice. Full article

Background/Objectives: Pregnancy is characterized by complex immunological adaptations that may increase susceptibility to infections, including SARS-CoV-2. Interleukin-6 (IL-6), a key pro-inflammatory cytokine, plays a crucial role in the immune response and has been strongly implicated in the pathogenesis of COVID-19. Genetic variations in the IL6 gene, particularly single-nucleotide polymorphisms (SNPs) in the promoter region, can modulate IL-6 expression and potentially influence individual susceptibility to viral infections. This study aimed to evaluate the relationship between promoter region IL6 gene polymorphisms and COVID-19 susceptibility, as well as the inflammatory response, in pregnant women. Methods: We enrolled in this study 204 pregnant women with evidence of SARS-CoV-2 infection in pregnancy and 134 pregnant women with no evidence of SARS-CoV-2 infection in the past. Genotyping was conducted for the two functional SNPs in the IL6 promoter region, rs1800796 and rs1800797, via Sanger sequencing, and for associations with COVID-19 susceptibility and IL-6 levels were analyzed. Results: No significant association was found between IL6 polymorphisms and COVID-19, IL-6 levels, age, or immunization status. IL-6 levels > 5 pg/mL were more frequent in SARS-CoV-2-negative pregnant women than in SARS-CoV-2-positive pregnant women (p = 0.032). Among vaccinated participants, IL-6 levels were significantly higher in SARS-CoV-2-negative pregnant women (p = 0.044), while no difference was observed in the unvaccinated group. Conclusions:IL6 polymorphisms rs1800797 and rs1800796 were not associated with infection susceptibility or IL-6 levels. These results highlight the complex immunological interplay between pregnancy, infection, and genetic background and support the need for further research in larger cohorts. Full article

Chronic thromboembolic pulmonary disease (CTEPD) is a severe long-term complication of acute pulmonary thromboembolism (PTE). Its pathogenesis is multifactorial, involving incomplete thrombus resolution, hemodynamic burden, comorbidities, and genetic factors. However, the contribution of inherited thrombophilic mutations to CTEPD development remains controversial. This retrospective cohort study included 204 patients diagnosed with acute PTE at a tertiary referral center between December 2023 and December 2024. Baseline demographic, clinical, laboratory, and echocardiographic data were collected. Genetic analysis assessed Factor II, Factor V Leiden, MTHFR C677T, MTHFR A1298C, Factor XIII V34L, and PAI-1 4G/5G polymorphisms. Patients were followed for at least 12 months for the development of CTEPD, defined according to guideline-based hemodynamic and imaging criteria. During follow-up, 17 patients (8.3%) developed CTEPD. Patients with CTEPD were significantly older and had higher baseline and follow-up systolic pulmonary artery pressure (sPAP) (p < 0.001), elevated NT-proBNP and troponin levels (both p < 0.001), and more frequent comorbidities, including cardiac and renal disease. Multivariate logistic regression identified comorbid diseases (HR: 0.17, 95% CI: 0.039–0.80, p = 0.025) and genetic thrombophilic factors (HR: 0.30, 95% CI: 0.10–0.91, p = 0.034) as independent predictors. Among genetic variants, only the PAI-1 4G/5G polymorphism was significantly associated with CTEPD (p = 0.001). Our study demonstrates that advanced age, comorbid diseases, elevated cardiac biomarkers, and genetic predisposition are associated with the development of CTEPD after acute PTE, while the PAI-1 4G/5G polymorphism may contribute to CTEPD susceptibility within a multifactorial context. Full article

The extended application of pesticides has intensified the resistance problem in Liriomyza trifolii within Hainan Province. This study aimed to elucidate the underlying mechanisms contributing to the elevated resistance observed in this pest by employing Whole-Genome Re-sequencing (WGR) technology. Through the analysis and comparison of WGR data focusing on voltage-gated sodium channel (VGSC) from diverse regions and LT-S of L. trifolii in Hainan Province, we identified a total of six nonsynonymous single nucleotide polymorphisms (nsSNPs) and thirty-one synonymous single nucleotide polymorphisms (sSNPs) in five wild populations MY, TS, DA, TY, and JY. Among the six nsSNPs, three (PyR1: M918T, L1014F, and PyR2: T933I) have been confirmed as linked to pyrethroid resistance, while one (D IVS6: V1845I) was associated with resistance to indoxacarb. Moreover, the frequency of these four mutations generally increases with decreasing latitude. Additionally, under sustained pesticide selection pressure, L. trifolii exhibits an evolutionary pattern characterized by a dN/dS ratio (nsSNP/sSNP = 6/31 ≈ 0.19) of less than 1. Among the 31 sSNPs that held an absolute quantitative advantage, the highest occurrence frequency reached 94.44% (G2033: JY), and this sSNP occurred in all populations. In contrast, among a limited number of 6 nsSNPs, the highest occurrence frequency attained 100% (L1014F: all populations). This study substantiates that the elevated resistance observed in L. trifolii within Hainan Province can be ascribed to the presence of four nsSNPs-M922T, T933I, L1018F, and V1845I in their VGSC. Furthermore, the emergence of cross-resistance between pyrethroids and indoxacarb has been identified. This research offers a novel theoretical foundation for future investigations into the resistance mechanisms of L. trifolii. Full article

Persistent infection with high-risk human papillomavirus (HPV), particularly genotype 16, is the main driver of anogenital and oropharyngeal cancers. However, data on HPV16 genetic variability in anal and oral samples from people living with HIV are limited. In this study, we investigated the diversity of HPV16 E6 and E7 genes in anal and oral samples collected from HIV-positive men who have sex with men (MSM) according to different cytological outcomes and anatomical site. Among 53 MSM patients, we obtained 51 E6 and 52 E7 sequences. Lineage A predominated (96.1%), mainly represented by sublineages A1 (84.3%) and A2 (9.8%). The E6 region showed higher variability than E7: 31.4% were identical to the reference (K02718), 51.0% carried the L83V (T350G) mutation, while Q14H, D25N, and D25E were also observed. In E7, only one non-synonymous substitution was detected (N29S). No site-specific variants were detected between anal and oral samples. Overall, these findings confirm the predominance of European A1/A2 variants in Italian MSM and suggest that E6/E7 polymorphisms are not directly linked to lesion grade or anatomical localization. Full article

Background and Objectives: Thrombophilia is a prothrombotic disorder that increases the risk of blood clotting and can pose serious health problems. It is considered a condition of gene–gene or gene–environment interactions. Variation in the prevalence of thrombophilia mutations and their interaction among populations necessitates localized genetic assessments. However, population-based genetic data remains limited for developing effective preventive strategies. Materials and Methods: This cross-sectional observational study was conducted over five years (2020–2024) at a tertiary university hospital in Northern Greece. A total of 2961 individuals aged 18–85 years (mean: 50.5) were registered based on family or medical history of venous thromboembolism (VTE) or clinical symptoms of VTE. The final analysis included 2078 participants comprising 1143 males (55%) and 935 females (45%), who met all the inclusion criteria. Inclusion criteria were absence of acute illness or malignancy, informed consent, and an adequate DNA quantity for genotyping, whereas excluded criteria included incomplete laboratory data, active inflammatory or malignant disease, and cognitive or psychiatric conditions. Peripheral blood samples were collected in 2 mL K₃-EDTA tubes, and genomic DNA was analyzed using real-time polymerase chain reaction (PCR) with melting curve analysis and hybridization probes (LightMix^® in vitro diagnostics, TIB MolBiol, Berlin, Germany). Five thrombophilia-related polymorphisms, Factor V Leiden (F5 G1691A), prothrombin (F2 G20210A), methylenetetrahydrofolate reductase (MTHFR C677T and MTHFR A1298C), and Plasminogen Activator Inhibitor-1 (PAI-1) 4G/5G, were examined for allele and genotype frequencies, Hardy–Weinberg equilibrium testing, pairwise linkage disequilibrium (D′ and r²), and power analysis. For subjects tested for Factor V Leiden (n = 1476), the activated protein C resistance (APC) ratio was additionally evaluated using the ACL TOP 750 analyzer. Results: Allele frequencies were 7.3% for FV Leiden and 3.7% for FII. The PAI-1 allele was distributed at 44%, while the MTHFR (C677T and A1298C) alleles were each present at 33%. Significant linkage disequilibrium was identified between MTHFR (C677T and A1298C) and between MTHFR A1298C and PAI-1. No evolutionary pressure or demographic bias was found in the Hardy–Weinberg equilibrium. The APC ratio demonstrated a high sensitivity (99.2%) and specificity (96.6%), indicating that it may serve as a reliable screening method. Conclusions: Our findings highlight informative patterns in the genetic predisposition to thrombophilia, which may help develop rule-based strategies for implementing thromboprophylaxis guidelines and personalized medical interventions. Full article

Ambrosia artemisiifolia is one of the invasive plants found in Europe. Research into this species is important not only in terms of environmental consequences but also in terms of human health, as it is an allergenic weed. Here, the genetic variability in the accessions of common ragweed from three localities of the Slovak Republic was analysed. A Bet v 1-based amplified polymorphism was applied for degenerated and non-degenerated primers. Three of the five primer variants were able to distinguish all analysed accessions, and two primer combinations were able to distinguish two accessions in the same amplified fingerprint profile from Kicsina. Using the BBAP technique, between of 1 to 16 amplicons were obtained per 1 genotype of common ragweed within a range of 68 to 3266 base pairs. Using two of the BBAP primer variants, unique fragments were obtained. The results indicate that the outcrossing among Slovak genotypes of Ambrosia artemisiifolia L. as non-specific BBAP profiles of individual analysed localities was observed. Full article

Potato (Solanum tuberosum L.) crop yields may be reduced by nitrogen deficiency stress tolerance. An evaluation of 144 tetraploid potato genotypes was carried out during two consecutive seasons (2019 and 2020), with the objective of characterizing their variability in key physiological and agronomic parameters. Physiological parameters included chlorophyll content and fluorescence, stomatal conductance, NDVI, leaf area, and perimeter, while agronomic characteristics such as yield, tuber fresh weight, tuber number, starch content, dry matter, and reducing sugars were evaluated. To genotype the population, the GGP V3 Potato array was used, generating 18,259 high-quality SNP markers. Marker–trait association analysis was conducted using the GWASpoly package in R, applying Q + K linear mixed models to enhance precision. This methodology enabled the identification of 18 SNP markers that exhibited statistically significant associations with the traits analyzed in both trials and periods, relating them to genes whose functional implication has already been described. Genetic loci associated with chlorophyll content and tuber number were detected across non-stress and stress treatments, while markers linked to leaf area and leaf perimeter were identified specifically under nitrogen deficiency stress. The genomic distribution of these markers revealed that genetic markers or single-nucleotide polymorphisms (SNPs) correlated with phenotypic traits under non-stress conditions were predominantly located on chromosome 11, whereas SNPs linked to stress responses were mainly identified on chromosomes 2 and 3. These findings contribute to understanding the genetic mechanisms underlying potato tolerance to nitrogen deficiency stress, offering valuable insights for the development of future marker-assisted selection programs aimed at improving nitrogen use efficiency and stress resilience in potato breeding. Full article

Complete chloroplast genome sequences are widely used in the analyses of phylogenetic relationships among angiosperms. As a species-rich genus, species diversity centers of Saxifraga L. include mountainous regions of Eurasia, such as the Alps and the Qinghai–Tibetan Plateau (QTP) sensu lato. However, to date, datasets of chloroplast genomes of Saxifraga have been concentrated on the QTP species; those from European Alps are largely unavailable, which hinders comprehensively comparative and evolutionary analyses of chloroplast genomes in this genus. Here, complete chloroplast genomes of 19 Saxifraga species were de novo sequenced, assembled and annotated, and of these 15 species from Alps were reported for the first time. Subsequent comparative analysis and phylogenetic reconstruction were also conducted. Chloroplast genome length of the 19 Saxifraga species range from 149,217 bp to 152,282 bp with a typical quadripartite structure. All individual chloroplast genome included in this study contains 113 unique genes, including 79 protein-coding genes, four rRNAs and 30 tRNAs. The IR boundaries keep relatively conserved with minor expansion in S. consanguinea. mVISTA analysis and identification of polymorphic loci for molecular markers shows that six intergenic regions (ndhC-trnV, psbE-petL, rpl32-trnL, rps16-trnQ, trnF-ndhJ, trnS-trnG) can be selected as the potential DNA barcodes. A total of 1204 SSRs, 433 tandem repeats and 534 Large sequence repeats were identified in the 19 Saxifraga chloroplast genomes. The codon usage analysis revealed that Saxifraga chloroplast genome codon prefers to end in A/T. Phylogenetic reconstruction of 33 species (31 Saxifraga species included) based on 75 common protein coding genes received high bootstrap support values for nearly all identified nodes, and revealed a tree topology similar to previous studies. Full article

During the last 20 years, there has been increasing concern about inefficient vector control efforts due to insecticide resistance. A common mechanism causing insecticide resistance is mutational changes in the voltage-gated sodium channel, deemed knockdown resistance (kdr), resulting from continued pyrethroid application. Although closely related, there have been documented kdr differences and frequencies between Aedes aegypti and Aedes albopictus. Individual Ae. aegypti and Ae. albopictus from five counties in Texas, USA were tested using four single nucleotide polymorphisms genotyping assays to assess the kdr (F1534C, V1016I, V410L, and S989P) differences between the two species. Each mutation was analyzed independently by calculating frequencies and analyzing the difference using a Wilcox Rank Sum test. Significant differences were observed between Ae. aegypti and Ae. albopictus when comparing F1534C and V410L (p-value < 0.0001). Knockdown resistant mutation V1016I was not different between the two species. Individuals from both species had di-locus mutations, and individuals from Ae. aegypti had tri-locus mutations detected in combinations that have been reported to influence insecticide resistance. Given our findings, one can speculate that populations of both species are resistant to pyrethroids, thus likely limiting the success of control methods. Full article

In nature, orchid seed germination is extremely low, making in vitro asymbiotic seed germination essential for the propagation and conservation of endangered Vanda coerulea. This study optimized a micropropagation protocol and evaluated the genetic homogeneity of regenerated orchids. The synergistic effect of kinetin (KN) with auxins in the Mitra (M) medium best supported protocorm formation and seedling development. The highest shoot multiplication (5.62 ± 0.09) was achieved with 1.2 mg L⁻¹ KN and 0.6 mg L⁻¹ IBA (indole-3-butyric acid) in the medium. Enhanced leaf production (4.81 ± 0.37) was observed when 3.2 mg L⁻¹ KN was combined with 1.8 mg L⁻¹ IAA (indole-3-acetic acid), while root development was superior when 3.2 mg L⁻¹ KN together with 2.4 mg L⁻¹ IAA was incorporated in the medium. Anatomical sections confirmed well-developed leaf and root structures. Genetic fidelity assessment using random amplified polymorphic DNA (RAPD), inter-simple sequence repeat (ISSR), inter-primer binding site (iPBS), and start codon targeted (SCoT) markers revealed 97.17% monomorphism (240/247 bands) and low Nei’s genetic distances (0.000–0.039), indicating high similarity among the regenerants. Dendrogram clustering was supported by a high cophenetic correlation coefficient (CCC = 0.806) and strong resolution in Principal Coordinate Analysis (PCoA) (44.03% and 67.36% variation on the first two axes). The Mantel test revealed a significant correlation between both ISSR and SCoT markers with the pooled marker data. Flow cytometry confirmed the genome stability among the in vitro-propagated orchids, with consistently low CV (FL2-A) values (4.37–4.94%). This study demonstrated the establishment of a reliable in vitro protocol for rapidly propagating genetically identical V. coerulea via asymbiotic seed germination. Full article

The pandemic of coronavirus disease 2019 (COVID-19), brought about by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has significantly impacted public health and the economy. A fundamental aspect of addressing this virus lies in elucidating the mechanisms through which it induces disease. Our study reveals that Non-structural protein 6 (NSP6) of SARS-CoV-2 promotes the initiation of autophagy by activating Beclin1. In the later stage of autophagy, however, NSP6 causes a blockage in the autophagy–lysosome degradation via the inhibition of Mucolipin 1 (MLN1). The single nucleotide polymorphism (SNP) L37F in NSP6, which is associated with asymptomatic infection, similarly enhances the initiation of autophagy but displays a reduced ability to impede lysosome-dependent degradation. In summary, we demonstrated the dual-regulation mechanism of NSP6 in autophagy, which may be one of the reasons for targeting cellular autophagy to induce viral pathogenesis. This finding may provide promising new directions for future research and clinical interventions. Full article