High-resolution Melting Analysis Research Articles

Multiplex digital profiling of DNA methylation heterogeneity for sensitive and cost-effective cancer detection in low-volume liquid biopsies.

Molecular alterations in cancerous tissues exhibit intercellular genetic and epigenetic heterogeneity, complicating the performance of diagnostic assays, particularly for early cancer detection. Conventional liquid biopsy methods have limited sensitivity and/or ability to assess epigenetic heterogeneity of rare epiallelic variants cost-effectively. We report an approach, named REM-DREAMing (Ratiometric-Encoded Multiplex Discrimination of Rare EpiAlleles by Melt), which leverages a digital microfluidic platform that incorporates a ratiometric fluorescence multiplex detection scheme and precise digital high-resolution melt analysis to enable low-cost, parallelized analysis of heterogeneous methylation patterns on a molecule-by-molecule basis for the detection of cancer in liquid biopsies. We applied the platform to simultaneously assess intermolecular epigenetic heterogeneity in five methylation biomarkers for improved, blood-based screening for early-stage non-small cell lung cancer. In a cohort of 48 low-volume liquid biopsy specimens from patients with indeterminant pulmonary nodules, we show that assessment of intermolecular methylation density distributions can notably improve the performance of multigene methylation biomarker panels for the early detection of cancer.

Association between the variations in metabolic pathways and oral cancer risk: results from a Pakistani case-control study.

Oral cancer (OC) is a significant global health concern, with Pakistan ranking 5th worldwide in OC incidence. Given the poor prognosis, early detection of at-risk individuals is crucial. Genetic factors, particularly single nucleotide polymorphisms (SNPs) in metabolic genes, may influence OC susceptibility. This study investigated the association between SNPs in CYP1A1, COX2, SOD2, and HIF1a genes and OC risk in the Pakistani population. A prospective study was conducted from October 2019 to March 2022, enrolling 215 newly diagnosed OC patients and 410 controls. Genetic variations were analyzed using High-Resolution Melting (HRM)analysis and Sanger sequencing, with protein expression evaluated by ELISA. No significant associations were found between the studied SNPs and OC risk. However, a non-significant trend was observed for the SOD2 variant (rs4880), where the G allele was associated with a higher OC risk than the A allele (p = 0.20). Elevated COX2 and HIF1α levels (p-values of 0.014 and <0.001, respectively) and reduced SOD2 levels (p < 0.0001) were observed in OC patients, while CYP1A1 levels remained similar in both controls and cases. Although SNPs in CYP1A1, COX2, SOD2, and HIF1α were not significantly associated with OC risk in the Pakistani population, altered protein expression levels of COX2, HIF1α and SOD2 suggest additional regulatory mechanisms. Further investigation into post-transcriptional modifications and epigenetic factors could lead to novel biomarkers and therapeutic targets for OC in Pakistan.

Rapid detection of the SARS-CoV-2 omicron variants based on high-resolution melting curve analysis

With the continuous spread of the SARS-CoV-2 globally, viral mutations have accumulated. As a result, SARS-CoV-2 became more contagious, and has a higher risk of immune escape and reinfection. To identify variants and have an awareness of the prevalence of these variants, this study selected four segments containing mutations on the S gene of the SARS-CoV-2. Then a rapid and convenient variants detection method was established using high-resolution melting(HRM) analysis combined with nested polymerase chain reaction(PCR). The total detection process takes about 5 h. Through comprehensive analysis of the results from the four reaction systems, the identification of seven important Omicron variants(BA.2, BA.2.75, BA.5.2, BF.7, BQ.1, XBB.1 and XBB.2) can be achieved, with significant differentiation in the melting curves of each variant group. The method established in this study was used to genotype positive specimens in COVID-19 nucleic acid testing, the overall concordance rate compared to whole genome sequencing results was 88.9%, and the positive concordance rate of each sublineage was greater than 80% and the negative concordance rate was greater than 94.4%. The detection of clinical specimens has demonstrated that the HRM analysis established in this study is an effective, rapid and convenient variant identification method, which can be used for monitoring SARS-CoV-2 variants and has important value in addressing public health issues caused by the ongoing mutations of the SARS-CoV-2.

A multiplex qPCR followed by high-resolution melting analysis for the detection of blood-feeding sources in Culex sp. mosquitoes.

Culex species, such as Culex quinquefasciatus and Culex nigripalpus display a range of feeding habits and act as vectors for pathogens that can cause diseases in both humans and animals. Understanding their feeding habits is pivotal for enhancing disease prevention strategies. The present study introduces the application of two multiplex real-time PCR (qPCR) followed by high-resolution melting (HRM) as a cost-effective and time-efficient alternative. This investigation involved the development of two multiplex qPCR-HRM: assay 1 detects human, dog and chicken, while assay 2 detects cat, cattle and horse in Culex sp. engorged female mosquitoes. The qPCR-HRM reactions showed a detection limit of one copy of genomic DNA when performed as single and multiplex qPCR-HRM. The reaction efficiencies were 97.96% for human, 100.60% for dog, 99.03% for chicken, 99.92% for feline, 99.18% for cattle and 97.68% for horse. The qPCR-HRM method, employing multiplex 1 and 2, was applied to field-collected mosquitoes and demonstrated the ability to detect DNA from multiple blood sources within a single sample. By analysing both multiplexes, it was possible to identify up to five distinct blood sources in Cx. quinquefasciatus and Cx. nigripalpus, and up to two sources in Culex coronatus. Sequencing corroborated the qPCR-HRM results, confirming the presence of DNA from one to four different blood sources with 100% accuracy. The development of these molecular methods may contribute for identification of blood-feeding patterns in mosquitoes. It contributes to studies on the dissemination and transmission of pathogens among various animals and humans, thereby bridging the gap between epidemiology and vector monitoring.

Upregulation of interferon gamma gene expression among asymptomatic malaria adults in Bayelsa State, Nigeria

Despite concerted efforts, malaria remains a global public health problem. Treatment for asymptomatic malaria will reduce the health care burden of malaria. However evidence-based data for the presence of systemic pathology in asymptomatic malaria, which might inform treatment remains limited. The present study investigated the current prevalence of asymptomatic malaria in Bayelsa State, Nigeria and differences in interferon gamma (IFNγ) mRNA expression between asymptomatic malaria individuals (AMIs) and uninfected individuals (UIs), in relation to ABO blood groups and hemoglobin genotype (Hb) variants. A cross-sectional design was employed to randomly select 146 non-febrile participants from Sagbama LGA, Bayelsa State. Plasmodium falciparum infection was determined using high-resolution melting analysis and participants were grouped into UIs and AMIs. Hb, blood groups, and IFNγ mRNA expression were determined using electrophoresis, agglutination, and real-time PCR method respectively. Logistic regression and t-test were used to determine significant differences between groups at p < 0.05. The current prevalence of asymptomatic malaria in Bayelsa State was found to be 89.73 %. Age and sex were associated with asymptomatic malaria (p < 0.05). Plasmodium falciparum DNA melt curves for AMIs aligned at 83.89 ± 0.34 °C, while the amplification cycle thresholds were below 30 cycles. Compared with UIs, the gene expression of IFNγ mRNA was significantly (p < 0.001) higher among AMIs. Also, among AMIs those with A, B, and AB blood groups expressed significantly higher levels of IFNγ mRNA compared with blood groups O AMIs. Furthermore, AMIs with HbAA expressed significantly higher levels of IFNγ mRNA compared with HbAS AMIs. The novelty of the present study is the demonstration of the existence of systemic pathology in asymptomatic malaria and the demonstration that the intensity of systemic pathology is dependent on blood types and haemoglobin genotype variants. Findings of the present study have implications for policy creation towards asymptomatic malaria treatment.

Integrating Clinical and Microbiological Expertise to Improve Vaginal Candidiasis Management.

Vaginal candidiasis (VC) is a prevalent condition among women of reproductive age and poses a significant global public health challenge. However, the disease is often diagnosed and treated without mycological information. We investigated the epidemiology, laboratory diagnostics, and antifungal susceptibility of VC. We included 300 women from Çukurova University Obstetrics and Gynecology outpatient clinic in Adana, Türkiye. Participants underwent a health survey and provided vaginal swab samples for microscopic examination and fungal culture. The microscopic analysis involved wet-mount and gram-stained slides, whereas fungal identification involved CHROMAgar Candida, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), and real-time polymerase chain reaction high-resolution melting analysis (RT-PCR HRMA). Antifungal susceptibility tests were conducted at pH 7 and 4 using the CLSI document M44-A2. Of the 106 women with positive fungal cultures, 86.8% were diagnosed with VC, whereas 13.2% showed Candida colonization. Among those with VC, 55.4% had acute and 44.6% had recurrent VC; a family history of allergies increased the risk for both types. We recovered 115 yeast isolates, predominantly C. albicans, C. glabrata, and C. krusei. Diagnostic accuracy of CHROMAgar Candida was 91.3% for the most common isolates, and HRMA was consistent in differential diagnosis. Antifungal resistance varied with pH; susceptibility to fluconazole, itraconazole, and ketoconazole decreased at pH 4, whereas susceptibility to miconazole increased. Our findings underscore the need for a diagnostic algorithm and enhanced collaboration between clinicians and microbiologists to improve VC management. Recommendations include using Gram staining, CHROMAgar Candida, MALDI-TOF MS, and antifungal susceptibility tests at both pH levels.

High-Resolution Melting Assay to Detect the Mutations That Cause the Y132F and G458S Substitutions at the ERG11 Gene Involved in Azole Resistance in Candida parapsilosis.

Candida parapsilosis is a pathogenic yeast that has reduced susceptibility to echinocandins and ranks as the second or third leading cause of candidaemia, depending on the geographical region. This yeast often causes nosocomial infections, which are frequently detected as outbreaks. In recent years, resistance to azoles in C. parapsilosis has increased globally, primarily due to the accumulation of mutations in the ERG11 gene. In this study, we have developed an assay based on real-time PCR and high-resolution melting (HRM) curve analysis to detect two of the most prevalent mutations at ERG11 that confer resistance to fluconazole (Y132F and G458S). We designed allele-specific oligonucleotides that selectively bind to either the wild type or mutated sequences and optimised the conditions to ensure amplification of the specific allele, followed by detection via high-resolution melting (HRM) analysis. The designed oligonucleotides to detect the Erg11Y132F and Erg11G458S mutations produced specific amplification of either WT or mutated alleles. We conducted a duplex real-time PCR combining oligonucleotides for the wild-type sequences in one mix, and oligonucleotides for the mutated alleles in another. Following this, we performed an analysis of the HRM curve to identify the amplified allele in each case. This technique was blindly evaluated on a set of 114 C. parapsilosis isolates, all of which were unequivocally identified using our approach. This technique offers a new method for the early detection of azole resistance mechanism in C. parapsilosis.

Bringing Hope to Improve Treatment in Pancreatic Ductal Adenocarcinoma—A New Tool for Molecular Profiling of KRAS Mutations in Tumor and Plasma Samples

Background/Objectives: Pancreatic ductal adenocarcinoma (PDAC) incidence is rising, and prognosis remains poor due to late diagnosis and limited effective therapies. Currently, patients are treated based on TNM staging, without molecular tumor characterization. This study aimed to validate a technique that combines the amplification refractory mutation system (ARMS) with high-resolution melting analysis (HRMA) for detecting mutations in codon 12 of KRAS in tumor and plasma, and to assess its prognostic value. Methods: Prospective study including patients with newly diagnosed PDAC with tumor and plasma samples collected before treatment. Mutations in codon 12 of KRAS (G12D, G12V, G12C, and G12R) were detected using ARMS–HRMA and compared to Sanger sequencing (SS). Univariate and multivariate analyses were used to evaluate the prognostic significance of these mutations. Results: A total of 88 patients, 93% with ECOG-PS 0–1, 57% with resectable disease. ARMS–HRMA technique showed a higher sensitivity than SS, both in tumor and plasma (77% vs. 51%; 25 vs. 0%, respectively). The most frequent mutation was G12D (n = 32, 36%), followed by G12V (n = 22, 25%). On multivariate analysis, patients with G12D and/or G12C mutations, either in tumor or plasma, had lower PFS (HR 1.792, 95% CI 1.061–3.028, p = 0.029; HR 2.081, 95% CI 1.014–4.272, p = 0.046, respectively) and lower OS (HR 1.757, 95% CI 1.013–3.049, p = 0.045; HR 2.229, 95% CI 1.082–4.594, p = 0.030, respectively). Conclusions: ARMS–HRMA is a rapid and cost-effective method for detecting KRAS mutations in PDAC patients, offering the potential for stratifying prognosis and guiding treatment decisions. The presence of G12D and G12C mutations in both tumor and plasma is associated with a poorer prognosis.

Association of HHV‑6 reactivation and SLC6A3 (C>T, rs40184), BDNF (C>T, rs6265), and JARID2 (G>A, rs9383046) single nucleotide polymorphisms in depression.

Major depressive disorder (MDD) is a global health concern with a complex etiology involving genetic, environmental and infectious factors. The exact cause of MDD remains unknown. The present study explored the association between genetic factors, human herpesvirus 6 (HHV-6) and MDD. The present study analyzed single nucleotide polymorphisms (SNPs) and HHV-6 viral load in oral buccal samples from patients with MDD (with and without blood relatives with MDD) and healthy controls. The study used high-resolution melt analysis to examine rs40184 (C>T) in the solute carrier family 6 member 3 (SLC6A31) gene, rs6265 (C>T) in the brain-derived neurotrophic factor (BDNF) gene and rs9383046 (G>A) in the jumonji and AT-rich interaction domain-containing 2 (JARID2) gene. HHV-6 infection and viral load was assessed using the quantitative PCR. Whole-exome sequencing was used to examine SNPs. The variant alleles of SNPs rs40184 [18/40 (45.00) vs. 29/238 (12.55%)] and rs6265 [30/54 (55.46) vs. 117/292 (40.06%)] were significantly more common in patients with MDD than in healthy controls, indicating they may be probable hereditary risk factors for MDD. HHV-6 positivity was significantly more common in carriers of the G/A genotype (12/15, 80%) than carriers of the G/G genotype (75/363, 20.7%) for rs9383046, implying that genetic variations may affect HHV-6 risk and MDD onset. Similarly, HHV-6 viral loads were significantly higher in carriers of the G/A genotype (99,990.85±118,392.64 copies/ng DNA) than carriers of the G/G genotype (48,249.30±101,216.28 copies/ng DNA) for rs9383046. Whole-exome sequencing identified two SNPs in JARID2 (rs11757092 and rs9383050) associated with MDD, highlighting its genetic complexity. The present study helps explain the complex interactions between HHV-6 infection, genetics and MDD onset, improving understanding of how SNPs in JARID2 contribute to HHV-6 infection and MDD onset; these findings may impact future approaches to diagnosing and treating MDD.

Genotyping methods to distinguish Plasmodium falciparum recrudescence from new infection for the assessment of antimalarial drug efficacy: an observational, single-centre, comparison study

Distinguishing Plasmodium falciparum recrudescence from new infections is crucial for the assessment of antimalarial drug efficacy against Pfalciparum. We aimed to compare the efficacy of different genotyping methods to assess their effect on drug efficacy estimates, particularly in patients from high-transmission settings with polyclonal infections. In this head-to-head comparison study, we compared five different genotyping methods currently used: fast capillary electrophoresis (F-CE) using msp1, msp2, and glurp; high-resolution capillary electrophoresis (H-CE) using msp1, msp2, and glurp; H-CE using microsatellites; targeted amplicon deep sequencing (TADS) using single nucleotide polymorphism (SNP)-rich markers; and high-resolution melting (HRM) analysis using msp1 and msp2. We assessed their sensitivity in detecting minority clones in polyclonal infections, their reproducibility, and the genetic diversity of the markers used. Our study used four well characterised Pfalciparum laboratory strains mixed in varying ratios, and 20paired samples collected from an in-vivo clinical trial. The experiments were performed at the Swiss Tropical and Public Health Institute in Basel, Switzerland between May 5, 2020, and Aug 23,2021. H-CE using msp1 and msp2 and TADS revealed the highest sensitivity in detecting minority clones (up to ratios of 1:100 for H-CE and 50:1:1:1 for TADS in the FCB1:HB3 and 3D7:K1:HB3:FCB1 laboratory strain mixtures, respectively), highest reproducibility (intra-assay: 99% and 91% for H-CE and TADS, respectively; inter-assay: 98% and 92% for H-CE and TADS, respectively), and highest genetic diversity in the used markers (up to 36and32unique genotypes in 20paired samples for H-CE using msp2 and TADS using cpmp, respectively). Microsatellites assessed by H-CE had a lower genetic diversity compared with msp1, msp2, and glurp assessed by H-CE and the SNP-rich markers assessed by TADS, with a maximum of 13unique genotypes, and some genotypes having allelic frequencies larger than 30%.Markers used by TADS gave the most consistent results in distinguishing recrudescence from new infection across all methods (in 18of 20pairs of samples vs 15of 20pairs for H-CE). WHO currently recommends replacing glurp with microsatellites. However, in this study, the replacement of glurp with microsatellites did not change the genotyping outcome, probably due to the lower genetic diversity of microsatellites. More studies with large sample sizes are required to identify the most suitablemicrosatellites that could replace glurp. Our study indicates that TADS should be considered the gold standardfor genotyping to distinguish recrudescence from new infection, and that it should be used to validate other methods. Swiss Tropical and Public Health Institute.

The Effects of PON1 (Q192R, rs662) Gene Polymorphism, Heavy metals and Oxidative Stress on Risk of Recurrent Spontaneous Abortion in Samples of Iraqi Women

Recurrent spontaneous abortion (RSA) is defined as the occurrence of two or more spontaneous pregnancy losses before reaching the midpoint of gestation. Oxidative stress plays a pivotal role in the pathogenesis of RSA, serving as a key factor in its underlying causes. This research aims to investigate the connection between the Q192R polymorphisms identified in the PON1 gene, responsible for encoding an antioxidant enzyme and the vulnerability to RSA. Paraoxonase 1 (PON1) is a critical enzyme in the body's antioxidant defence system, safeguarding cells against damage caused by reactive oxygen species and heavy metal concentrations that affect pregnancy. The most prevalent PON1 polymorphism is Q192R (rs662), known to influence the antioxidant activity and power of the PON1 enzyme. In this research, blood samples were collected from two groups: 50 women with RSA and 50 women who were apparently in good health. Following DNA extraction, high-resolution melting (HRM) analysis was used to identify the studied SNP; Elisa was used to determine DNA damage and MDA concentrations in serum and heavy metals were determined by a Graphite Furnace-Atomic Absorption Spectrophotometer (GFAAS). The results of this study showed significantly higher levels of 8-OHdG, MDA, arsenic and lead in serum in RSA patients than in apparently healthy women. The genotype findings indicated that the prevalence of the QR (AG) genotype in women experiencing recurrent spontaneous abortion was notably greater than that in seemingly healthy women (74% compared to 16%, respectively, with an odds ratio of 27.2). The values of allele frequency for the A allele were 0.76 and 0.51 for apparently healthy women and women with recurrent spontaneous abortion respectively. The G allele frequency was 0.24 and 0.49 for apparently healthy women and women with recurrent spontaneous abortion respectively. The heterozygous QR genotype is related to the risk of RSA and the minor allele (G allele) is increased in women with RSA.

Decoding the genetic influence of CT60 non-coding polymorphism in CTLA-4 gene and sCTLA-4 biomarker with rheumatoid arthritis in the Indian population.

Cytoplasmic T Lymphocyte Antigen - 4 (CTLA-4) gene encodes an immunoregulatory receptor expressed on surface of activated T-cells to mediate peripheral tolerance against self-antigen. It suppresses auto-reactive T-cell proliferation either by inactivation or apoptosis of T-cells. The CTLA-4 mRNA undergoes alternative splicing to synthesize a native soluble form of CTLA-4 (sCTLA-4) protein, which lacks exon 3 that encodes for transmembrane region. As a result, sCTLA-4 circulates as a soluble serum protein and acts as an immunoregulator molecule to maintain homeostasis in the blood. Techniques coupled with quantitative Polymerase Chain Reaction (qPCR) and High-Resolution Melting Analysis (HRMA) were used to screen CTLA-4 3'Untranslated Region (UTR) CT60 (A/G) rs3087243 Single Nucleotide Polymorphism (SNP) and their association with Rheumatoid Arthritis (RA) in the Indian population. In addition, we also evaluated the concentration of sCTLA-4 serum protein in RA patients carrying rs3087243 SNP with different genotypes (A/A, G/A, and G/G). Statistical analysis of Odds Ratio (OR), Confidence Interval (C.I), and Relative Risk (RR) have shown that frequency of CTLA-4 rs3087243 SNP G/G genotype was significantly associated with RA in the Indian population (OR 1.7140; CI = 1.0765 to 2.7290; RR = 1.5434; p = 0.0232). The sCTLA-4 concentration was also significantly lower in RA patients carrying rs3087243 SNP G/G genotype than control group (p < 0.001). Co-inheritance of CTLA-4 signal peptide and 3'UTR SNPs may activate RAPP pathway. Downregulation of CTLA-4 and sCTLA-4 serum protein by rs3087243 SNP can increase the hyperactivation of T-cells, which causes RA.

Chloroplast mini-barcodes combined with high resolution melting analysis to identify herbal medicine Difengpi (Illicium difengpi)

Difengpi, derived from the air-dried stem bark of Illicium difengpi and enlisted in the Chinese Pharmacopoeia for its therapeutic effect against common ailments, confronts challenges due to dwindling wild resources and intentional substitution with potentially harmful botanical relatives. The imperative need to authenticate this herbal remedy has led to the development of robust methods. Here, we integrated chloroplast mini-barcoding and high resolution melting (HRM) analysis to distinguish Difengpi from the reported adulterants. We assembled the complete chloroplast (cp) genomes of I. difengpi and substituted close relatives I. jiadifengpi and I. majus, and conducted an in-depth comparative analysis to screen divergent regions for exploiting as DNA mini-barcodes. Despite the conservativeness characterizing the whole cp genomes among these Illicium species, we identified some highly variable regions with promising potential as molecular markers for species identification. Subsequently, we designed DNA mini-barcodes and subjected them to HRM analysis to assess their efficacy in species discrimination. Melting profiles unveiled that mini-barcodes designed from four divergence regions trnL–trnF, trnF–ndhJ, ycf1–ndhF and rpl32–trnL exhibited substantial discriminatory power, distinctly differentiated I. difengpi from I. jiadifengpi, I. majus and I. verum. We tested ten commercially available Difengpi products from online stores and local traditional markets using these four mini-barcodes. All ten samples clustered closely with the reference I. difengpi with genotype confidence higher than 93 %, indicating the presence of the claimed species in these samples, sans any reported toxic adulterants. Consequently, we simulated Difengpi mimic samples utilizing I. jiadifengpi, I. majus and I. verum and subjected them to evaluate the practicability of these mini-barcodes. The outcomes confirmed the precision of the four mini-barcodes in accurately discerning the mimic samples. In conclusion, integrating taxon-specific DNA mini-barcodes with HRM analysis is an efficient strategy for the authentication of species identity within commercial herbal products.

Possible effects of ancestry-related oxysterol-binding protein-like 10 genetic polymorphisms on dengue virus replication and anti-dengue immune response

PurposeOxysterol-binding protein-like 10 (OSBPL10) gene has been associated with reduced susceptibility to severe dengue in individuals of African descent. The aim of this study was to determine the possible effect of OSBPL10 on dengue virus (DENV) replication as well as the impact of African and European haplotypes of six OSBPL10 small nuclear polymorphisms (SNPs) on dengue multiplication and innate immune response. MethodsWe conducted gene knockdown experiments targeting OSBPL10 in THP-1 and Huh-7D12 cell lines, followed by a DENV-2 replication assay. Extracellular viral load was determined using qRT-PCR. To investigate the impact of SNPs haplotypes on viral replication and gene expression we cultured peripheral blood mononuclear cells (PBMC) from individuals with homozygous African and European haplotypes of OSBPL10 with DENV-2. Individual genotyping was performed using High Resolution Melt (HRM) analysis. The level of viral replication was assessed through plaque assay, while RT-PCR was employed to determine the expression levels of RXR-α, IFN-γ, IL-10 and IL-8 genes. ResultsIn vitro OSBPL10 knockdown significantly reduced DENV-2 replication. Individuals carrying European haplotypes showed higher DENV titers along with elevated levels of RXR-α and IL-8 mRNA compared to those carrying African haplotypes, who exhibited lower viral loads alongside increased IFN-γ and IL-10 expression. ConclusionsOur findings further explore the role of OSBPL10 in DENV multiplication, immune response to infection. The European haplotypes of OSBPL10 appear to increase DENV replication and promote RXR-α and IL-8 mRNA expression which correlates with the suppressive effect of these mediators on type I IFN, promoting viral replication and a deficient antiviral response. In contrast, the African haplotype showed a reduction in DENV replication and enhanced IFN-γ and IL-10 mRNA expression, which could be related to the better management of dengue infection and the low frequency of severe disease in this ethnic groupe.

A Novel Approach Based on Real-Time PCR with High-Resolution Melting Analysis for the Simultaneous Identification of Staphylococcus aureus and Staphylococcus argenteus.

Staphylococcus (S.) aureus is a pathogenic bacterium able to cause several diseases in humans and animals as well as foodborne intoxications. S. argenteus, being phenotypically and genotypically related to S. aureus, is part of the so-called S. aureus complex and recently recognized as an emerging pathogen able to cause, like S. aureus, several diseases both in humans and animals, and foodborne poisoning outbreaks. However, it has been reported that the widely used conventional PCR of Brakstad et al. [Journal of Clinical Microbiology, 30(7), 1654-1660, (1992)] targeting the thermostable nuclease gene may provide false-positive S. aureus, as it is able to amplify also S. argenteus. Here, we developed a novel two-step approach that, following the PCR of Brakstad et al. (1992), discriminates S. aureus from S. argenteus by a real-time PCR with high-resolution melting analysis (rt-PCR-HRM). In particular, targeting a polymorphic 137 bp region of the sodA gene, our developed rt-PCR-HRM method clearly discriminated S. aureus from S. argenteus, showing a remarkable difference in their amplification product melting temperatures (approximately 1.3 °C) as well as distinct melting curve shapes. The good sensitivity, reproducibility, user friendliness, and cost effectiveness of the developed method are advantageous attributes that will allow not only its easy employment to correctly identify misidentified isolates present in various collections of S. aureus, but also expand the still lacking knowledge on the prevalence and distribution of S. argenteus.

Characteristics of Candida albicans Derived From HIV-Positive Individuals With Oral Candidiasis: Genotyping, Phenotypic Variation, Antifungal Susceptibility, and Biofilm Formation.

Oral candidiasis (OC) is one of the most common mucosal infections in those afflicted with HIV/AIDS. This study aimed to provide detailed information on the phenotype, genotype, antifungal susceptibility, and biofilm formation ability of oral Candida albicans isolated from HIV-infected patients with OC. A total of 25 C. albicans isolates were collected from oral lesions of HIV-infected patients referred to Behavioral Diseases Counseling Center affiliated with Ahvaz Jundishapur University of Medical Sciences, Iran. The antifungal susceptibility testing was done according to CLSI M27 guideline (fourth edition). The crystal violet method was used to evaluate the biofilm formation ability of isolates. Different phenotypes were identified on yeast extract-peptone-dextrose agar medium supplemented with phloxine B. Genotyping analysis of the isolates was performed using high-resolution melting (HRM) assays and ABC genotyping. The highest and lowest susceptibility of the C. albicans isolates was found for fluconazole 24 (96%) and ITC 18 (72%), respectively. Forty-eight percent of the isolates had high biofilm formation ability and exhibited gray cell type. The most common genotype was genotype B (52%). HRM analysis of HIS3, EF3, and CDC3 markers showed three, four, and five different groups, respectively. Investigating the phenotype, antifungal susceptibility and biofilm formation ability of the C. albicans isolates obtained from oral lesions of HIV-infected patients revealed that the dominant genotypes in the current research could cause more serious infections from the oral source. We recommend further research with a larger sample size to determine the molecular epidemiology of C. albicans among HIV patients in Iran.

Identification of Capsicum species from Colombia by DNA barcoding and high resolution melting (HRM) analysis

AbstractDNA barcoding allows the use of molecular markers to differentiate the species of an interest group. This is especially useful when morphological characters are insufficient due to high similarity between species. The genus Capsicum contains some species that are difficult to determine by taxonomic means, in particular the annuum complex. Thus, the objective of this study was to investigate the discriminatory ability of two molecular markers in Colombian Capsicum accessions, including three wild species belonging to the Andean clade of the genus. A total of 95 Capsicum accessions, representing eight species, were genotyped by high resolution melting analysis (HRM) using the Waxy and C2_At5g04590 markers. Waxy could discriminate the Andean clade species (C. rhomboideum, C. dimorphum and C. lycianthoides), C. baccatum, C. pubescens and C. chinense, while C2_At5g04590 could discriminate C. frutescens, C. annuum var. annuum and C. annuum var. glabriusculum. Hence, a combination of the two markers could be used for discrimination of the eight species including the wild variety of C. annuum: C. annuum var. glabriusculum. Most nucleotide substitutions and indels were found in the sequences of the three Andean species, indicating that the Andean clade has a high genetic diversity compared to the other species. The incorporation of more wild species and varieties in this study allowed to correct the power of both markers to discriminate Capsicum species, besides the registration of new haplotypes.

Exploring somatic mutations in POLE and POLD1: Their role in colorectal cancer pathogenesis and potential therapeutic strategies

Colorectal cancer (CRC) is one of the major causes of morbidity and mortality worldwide, resulting from the accumulation of genetic and epigenetic alterations in several oncogenes and tumor suppressor genes. Recent studies have identified germline and somatic mutations in the exonuclease domain regions of both epsilon polymerase (POLE) and delta polymerase (POLD1) genes in CRCs. We sought to examine the mutation of these genes in a series of sporadic CRCs. To do this, we extracted DNA from 100 primary CRC samples and 40 corresponding normal tissue samples, which had been previously characterized for clinicopathological and molecular features. We employed a combination of quick-multiplex consensus (QMC)-polymerase chain reaction (PCR) and co-amplification at lower denaturation temperature (COLD)-PCR, followed by high-resolution melting (HRM) analysis and Sanger sequencing, to investigate the exonuclease domain regions of POLE and POLD1 genes for somatic mutations that may potentially alter the proofreading activities of these genes. In silico predictions of the functional significance of the identified genetic alterations were performed using the protein variation effect analyzer, sorting intolerant from tolerant, and PON-P2 algorithms. We identified a total of eight new and non-recurrent somatic variants in the endonuclease domains of POLE and two in POLD1. Nine out of ten variants caused amino acid substitutions, whereas one resulted in a stop codon. Although no significant associations or correlations were found between the POLE/POLD1 mutations and the clinicopathological or molecular features of the CRC cases, most of the POLE/POLD1-mutated cases were microsatellite stable (90%) and aneuploid (80%). Furthermore, in silico analyses showed that nine of the ten variants would likely cause some adverse effect on protein function. Ten somatic variants with predicted proofreading activity-altering effects have been identified in the endonuclease domains of POLE and POLD1 in CRC using a combination of QMC-PCR, COLD-PCR, HRM analyses, and Sanger sequencing.

Response of Some Pepper Genotypes to Cucumber Mosaic Virus (CMV) and Discrimination of Kilis Isolates Using High-Resolution Melting (HRM) Method

The escalating global population, diminishing agricultural lands, and the overarching global climate crisis are significantly impacting pepper cultivation. These challenges exacerbate the vulnerability of pepper plants to various biotic and abiotic factors, particularly viral diseases, resulting in diminished yield and quality. Cucumber mosaic virus (CMV), a notable concern for peppers in the Solanaceae family, is causing substantial quality and yield losses, with no effective chemical control methods currently available. This study focuses on exploring the genetic structure of CMV isolates obtained from pepper production areas in Kilis province and comparing these regions through the High-Resolution Melting (HRM) method. CMV isolates, cultivated in tobacco plants, have their partial coat protein sequences compared with those of other CMV isolates registered in the gene bank. The nucleotide sequences of identified CMV isolates are phylogenetically grouped and compared using an HRM graph. The HRM graph effectively distinguishes Kilis 3 and Kilis 4 isolates, clustered similarly to sequence patterns, from other isolates. The study highlights the utility of HRM analyses in identifying differences between isolates before determining sequence patterns. In the gene bank comparison, Kilis CMV isolates distinguished from others. Similarities were observed with isolates from Iran's Balsam (Impatiens balsamina - LC066478), Türkiye's Radish (Raphanus sativus - LC0665051), and Wild Turnip (Rapistrum rugosum - LC066514, LC066511, LC066517). The study found that Kilis 7 CMV isolate, transferred mechanically to 24 different pepper genotypes (C. annuum) from the local population, revealed susceptibility to CMV in the 24 lines developed from the Elbeyli population in Kilis province.

High-resolution melting assay for rapid, simultaneous detection of JAK2, MPL and CALR variants

AimsIdentification of recurrent genetic alterations in JAK2, MPL and CALR remains crucial in the diagnosis of Philadelphia-negative myeloproliferative neoplasms (MPNs). Current laboratory testing algorithms may entail batching and/or sequential testing,...