Polymerase Chain Reaction-restriction Fragment Length Polymorphism Research Articles

Molecular characterization of multidrug resistant (MDR) clinical isolates of Pseudomonas aeruginosa from Nsukka, South Eastern Nigeria.

P. aeruginosa is an important nosocomial pathogen with increasing resistance to antibiotics. Objective: This study was performed to evaluate the genetic relatedness of MDR clinical isolates of P. aeruginosa. A total of 1000 samples were analysed in the study. Antibiotic resistance profiles of the isolates were determined using Kirby Bauer disk diffusion method. Polymerase chain reaction (PCR) and sequencing were simultaneously used to detect the consensus region of 16S rRNA. Genetic relatedness of the isolates was determined using restriction patterns from ALU 1 digest and random amplified polymorphic DNA. Out of the 192 P. aeruginosa isolates recovered, 136 (78.83%) were multidrug resistant. Sequence analysis of the confirmed isolates (80.68%) revealed that all the isolates shared homology with each other and also showed sequence similarity to known strains of P. aeruginosa (ATCC 27853; KT 315654; KU 321274 and KT894767). The PCR-Restriction fragment length polymorphism (PCR-RFLP) analysis revealed that there was a lot of genetic relatedness among the isolates. The RFLP finger printing technique detected seven distinct RFLP types among the isolates. Thus, study shows that there is high prevalence of MDRPA and high degree of genetic relatedness among the MDRPA isolates circulating in Nsukka area.

Assessment of the relationship between miR-499C/T (rs3746444) polymorphism and lung carcinoma in Iranian population; a case-control study.

Lung carcinoma is characterized by uncontrollable division of respiratory system cells with detrimental and lethal consequences on human health. Critical roles of microRNAs (miR) are scientifically approved in biological and pathological pathways, such as the role of miR-499 (rs3746444) in lung carcinomas. Thus, in this case-control investigation, we aimed to assess the probable relationship between miR-499C/T variant and the occurrence of lung carcinoma in Iranian population for the first time. Genotype of miR-499 polymorphism was described by the Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) assay in patients and healthy individuals. Following definite diagnosis of lung carcinoma, the blood samples were collected, and the DNA extraction was performed by Salting-Out method. Finally, data were analysed by SPSS (v. 20) and the significant level was considered p-value<0.05. Statistically, the frequency of combined genotypes of CC+CT were 83.33% and 35% and TT+CT were 100% and 92% in case and control individuals, respectively. Also, individuals with genotypes of TC (OR: 3.08, CI95%: 3.03-3.17, p<0.0001), TC+CC (OR: 0.10, CI95%: 0.05-0.23, p<0.0001), CC (OR: 0, CI95%: 0.00-0.60, p=0.0214), and TC (OR: 0.07, CI95%: 0.030.15, p<0.0001) represented statistically significant (p<0.05) differences lung carcinoma than those with TT, TT, TT+TC, and TT+CC genotypes, respectively. The frequency of miR-499C (78.5%) and miR-499T (21.5%) alleles were also statistically significantly (p<0.05) difference associated with lung carcinoma in patients than controls. In this study, a possible relationship among miR-499C/T polymorphism and lung carcinoma was detected in Iranian population. Since this study was conducted for the first time, thus other supplementary assessments are needed for definite conclusion.

The Significant Impacts of Interleukin-8 Genotypes on the Risk of Colorectal Cancer in Taiwan.

Interleukin-8 (IL-8), a pro-inflammatory cytokine, is upregulated in CRC and plays an important role in its development and progression. Genetic variants in the IL-8 gene may impact the risk of CRC by modulating IL-8 levels. Our primary objective was to investigate the role of IL-8 genotypes in the development of CRC. To accomplish this, we employed the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method to analyze the genotypes of IL-8 rs4017, rs2227306, rs2227543, and rs1126647 in 362 CRC patients and 362 controls. Additionally, we evaluated the interactions between these genotypes and factors such as age, gender, smoking, alcohol consumption, and body mass index (BMI) status in relation to the risk of CRC. Furthermore, we utilized quantitative reverse transcription-PCR to measure the serum IL-8. The results demonstrated a significant difference in the distribution of rs4017 genotypes between the control and case groups (p for trend = 0.0059). Logistic regression analysis revealed that individuals with variant AA genotype had a 1.92-fold higher CRC risk (95% confidence interval [CI] = 1.28-2.89, p = 0.0023). Moreover, carriers of the IL-8 rs4017 AT + AA genotypes exhibited a significant association with CRC risk (odds ratio [OR] = 1.39, 95% CI = 1.02-1.91, p = 0.0460). Additionally, individuals with IL-8 rs4017 AA genotype displayed significantly elevated serum IL-8 compared to those with TT genotype at a 1.73-fold level (p < 0.0001), indicating a correlation between genotype and phenotype. In conclusion, the genotypes of IL-8 rs4017, along with their associated expression levels, can potentially serve as predictive markers for the risk of CRC.

Hemoglobin profile and molecular characteristics of the complex interaction of hemoglobin Doi-Saket [α9(A7) asn > lys, HBA2:c.30C > a], a novel α2α1 hybrid globin variant, with hemoglobin E [β26(B8) Glu > lys, HBB:c.79G > A] and deletional α+-thalassemia in a Thai family

Background An increasing number of α-hemoglobin (Hb) variants is causing various clinical symptoms; therefore, accurate identification of these Hb variants is important. Objective This study aimed to describe the molecular and hematological characteristics of novel Hb Doi-Saket that gives rise to a typical α+-thalassemia phenotype in carriers with and without other hemoglobinopathies. Materials and Methods Biological samples from a proband and his family members were analyzed. Hematological profiles were analyzed using a standard automated cell counter. Hb was analyzed by capillary electrophoresis and high-performance liquid chromatography. Mutations and globin haplotype were identified by DNA analysis. Novel diagnostic tools based on allele-specific polymerase chain reaction (PCR) and PCR–restriction fragment length polymorphism were developed. Results Hb analysis showed a major abnormal Hb fraction, moving slower than HbA, and a minor Hb fraction alongside HbA2 in the proband, his father, and son. DNA analysis of the α-globin gene identified the -α3.7 deletion and in cis the C > A mutation on codon 9 of the α2α1 gene, corresponding to Hb Doi-Saket [α9(A7) Asn > Lys]. This mutation could be identified using newly developed allele-specific PCR-based assays. The Hb Doi-Saket al.lele was significantly associated with haplotype [- + M + + 0 -]. Interaction of αDoi-Saket with βE globin chains led to a new Hb variant (HbE Doi-Saket). Phenotypic expression was clinically silent in heterozygotes and might present slight microcytosis. Conclusions Hb Doi-Saket emphasizes a great diversity present in α-globin gene. The mutation in this family from Thailand was linked to -α3.7 and caused mild microcytosis in the carriers. The combination of this variant with deletions in α genes might cause a severe clinical phenotype. Different methods of separation can provide useful information in diagnosis, and a complete molecular approach is needed for confirmation before considering patient management.

Endometrial receptivity defects MUC-1 and COX-2 polymorphisms in endometriosis.

The endometrium produces MUCIN-1 (MUC-1) and cyclooxygenase-2 (COX-2), which are essential for implantation. MUC-1 is required for adhesion, while COX-2 is necessary for decidualization. Variations or polymorphisms in MUC-1 and COX-2 can lead to changes in endometrial receptivity. This study investigated the relationship between MUC-1 and COX-2 polymorphisms and endometrial receptivity in endometriosis patients. Blood DNA samples were collected from 35 patients with endometriosis and 32 healthy patients between days 19 to 24 of their menstrual cycle (secretory phase). MUC-1 polymorphism was determined using the Amplification Refractory Mutation System (ARMS), and COX-2 gene polymorphism was assessed using Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP). The frequency distribution of gene polymorphisms between the two groups was compared using bivariate analysis. There were seven genotypic combinations of MUC-1 and COX-2: AAGC; AAGG; GACC; GAGC; GAGG; GGGC; GGGG. The AAGC genotype combination test was significant, with an OR=6.43 (95% CI:1.09-7.62) and p=0.01. In conclusion, combining MUC-1 and COX-2 (AAGC) genotypes results in endometrial receptivity defects in endometriosis.

An Association Between GAS5 rs145204276, NEAT1 rs512715, and MEG3 rs4081134 Gene Polymorphisms and Papillary Thyroid Carcinoma.

This study explores the association between growth arrest-specific 5 (GAS5) rs145204276, nuclear paraspeckle assembly transcript 1 (NEAT1) rs512715, and Maternally Expressed 3 (MEG3) rs4081134 polymorphisms and their impact on susceptibility to papillary thyroid carcinoma (PTC), considering differential expression of long noncoding RNAs (lncRNAs) in PTC. A case-control study involving 125 papillary thyroid carcinoma (PTC) patients and 125 controls was conducted. Genotyping of polymorphisms was performed using tetra-primer amplification refractory mutation system-polymerase chain reaction (ARMS-PCR) and PCR-restriction fragment length polymorphism (PCR-RFLP) methods. No significant association was found between the two groups regarding genotypes and allelic frequencies of GAS-5 145204276 and MEG3 rs4081134 polymorphisms. Genetic models also showed the same results. Regarding NEAT1 rs512715, The PTC group had more GC genotypes and over-dominant models of NEAT1 rs512715 than controls, while controls showed a higher frequency of recessive models. GAS5 rs145204276 and MEG3 rs4081134 polymorphisms showed no significant association with papillary thyroid carcinoma (PTC) risk. In contrast, NEAT1 rs512715 exhibited a significant impact on PTC development.

Prevalence of Factor V Leiden Mutation in Healthy Females of Sindh, Pakistan and Comparison of Three Detection Methods in Resource-Limited Settings

Factor V Leiden (FVL) mutation is related to venous thromboembolism and pregnancy complications. It is highly prevalent among Caucasians; however, few studies have been conducted on the Asian population. Objective: To find the prevalence, genotype, and allelic frequency of FVL mutation in females of Sindh, Pakistan, and to develop a valid and economical method for the detection of FVL mutation in resource-limited settings. Methods: Hundred (n=100), unrelated healthy females of Sindh, Pakistan, were recruited. FVL was detected using three methods, i.e., tetra primer amplification refractory mutation system (ARMS)-polymerase chain reaction (PCR), PCR-restriction fragment length polymorphism (PCR-RFLP), and PCR-sequencing. Prevalence, genotype, and allele frequencies were calculated. We compared the three mutation detection methods to find a suitable protocol for FVL detection in developing countries. Results: The prevalence of FVL mutation was 3% in healthy females of Sindh, Pakistan. No homozygous FVL mutation was found. The results from tetra primer ARMS-PCR, PCR-RFLP, and PCR-sequencing were 100% concordant. Tetra primer ARMS-PCR was a valid, reliable, faster, economical genotyping and screening method. Conclusions: In conclusion, FVL mutation was found in our population, and further studies should be conducted to find its role in thromboembolic and obstetrical complications. In addition, we have suggested tetra primer ARMS-PCR as an appropriate method for FVL detection in resource-limited settings.

B-262 Evaluation of the Genotypic Profile of the c.202 G&amp;gt;A Mutation in the G6PD Gene in Brazil

Abstract Introduction Glucose 6 phosphate dehydrogenase (G6PD) is an enzyme found in the cytoplasm of all human cells and plays an important role in preventing cellular damage to reactive oxygen species (ROS). G6PD deficiency is inherited in an X-linked recessive genetic disorder that can destroy red blood cells (hemolysis) leading to acute hemolytic anemia during periods of increased ROS production. The disease prevalence is more frequent in male individuals. To date, more than 400 G6PD variants have been identified, and molecular studies have shown that G6PD deficiency can be associated with different mutations. The c.202 G &amp;gt; A mutation (rs1050828; NM_000402.4) was described as the most frequent. The rapid and accurate diagnosis of this condition is extremely important in neonatal screening and cases of diagnostic suspicion. Therefore, this study aims to describe the genotypic profile of the c.202 G &amp;gt; A mutation in the G6PD gene in Brazilian samples by two molecular assays. Methods Genomic DNA samples from 130 individuals previously genotyped by Restriction Fragment Length Polymorphism PCR were used for validation. DNA isolation was performed in MagNA Pure 24 Total NA Isolation Kit at the automated platform MagNA Pure 24 System (Roche Diagnostics, Basel, Switzerland), according to manufacturer instructions. Genotyping for rs1050828 was performed using TaqMan SNP Genotyping Assays (Thermo Fisher, Foster City, CA) at 7500 Fast Real-Time PCR System (Thermo Fisher, Foster City, CA), according to manufacturer instructions. The results were analyzed using TaqMan Genotyper Software version 1.0.1. Results This study evaluated 130 blood samples, of which 81 were men (62.3%) and 49 were women (37.7%). Male carriers of rs1050828 A genotype (hemizygotes) predominated (56/81, 69.1%) and the remaining carriers for allele G (wild type) were 25/81 (30.9%). While female carriers of rs1050828 GG (wild type) predominated (39/49, 79.6%), heterozygotes were 5/49 (10.2%), and homozygotes also were 5/49 (10.2%). The number of male individuals with the presence of the mutation in hemi/homozygotes was considerably higher when compared to female individuals. This is explained by the fact that the mutation is inherited in an X-linked recessive manner. The results showed agreement and reproducibility of 100% for both methodologies. However, the qPCR assay sensibility and efficiency (&amp;gt;99%) were higher than the RFLP PCR assay. Conclusions Here, we described an efficient molecular method to detect the mutation c.202 G&amp;gt;A in the G6PD gene. The frequency of c.202 G&amp;gt;A described in this study was similar to that observed in others population studies in Brazil. Detection of the mutation target requests an additional evaluation of the G6PD activity level. Obtained results should be evaluated in association with the clinical aspects. The absence of the c.202 G&amp;gt;A in the G6PD gene does not exclude the existence of other mutations in the same region.

B-217 The study of association of FokI Polymorphism of Vitamin D Receptor (VDR) Gene, Vitamin D and Parathyroid Hormone Levels in Stage 4–5 Chronic Kidney Disease Patients: A Cross-sectional Study

Abstract Background Chronic Kidney Disease (CKD) is an important public health problem globally and almost 35% patients of CKD have deficiency in vitamin D which progresses to 80% in stage 4–5 CKD patients. Active vitamin D binds to Vitamin D Receptor (VDR) to regulate target gene transcription. Various genetic variations (Single Nucleotide Polymorphism) such as FokI polymorphism, which is a T/C transition polymorphism (ACG to ATG) may affect the VDR gene expression and thus may play an important role in pathogenesis of CKD. The aim of the study is to study association between FokI Polymorphism of Vitamin D Receptor (VDR) Gene, serum Vitamin D and PTH levels in Stage 4–5 CKD patients. Methods A total of 150 patients, aged 25–60 years, attending the Department of Nephrology AIIMS New Delhi with chronic kidney disease (CKD) stage 4–5, were enrolled for the study. FokI polymorphism was analyzed by using polymerase chain reaction-restriction fragment length Polymorphism (PCR-RFLP) in study subjects. Following DNA isolation and PCR amplification, restriction digestion was done using FokI restriction endonuclease and visualised on 1.5 % agarose gel electrophoresis. The prevalence of different genotypes and allelic frequency distribution was compared between CKD patients and healthy controls (HC). Levels of PTH, Vitamin D were estimated by eCLIA. Results No significant differences in genotype and in allelic frequencies between CKD patients and HC were observed as shown in Table 1. No significant differences in biochemical parameters based on genotypic variations in CKD patients and in HC were observed. Conclusion The present study reveals no association of VDR FokI polymorphism with CKD. Furthermore, no significant differences in biochemical parameters were observed in FF, Ff and ff genotypic subgroups in CKD or HC groups. Further analysis revealed no significant differences in biochemical parameters based on genotypic variations in CKD patients and in HC. Table 1.Genotype frequency and allelic frequency of VDR FOK1 gene polymorphism in CKD patients and HC.Genotype(FOK1)Genotype frequency (%)P-valueX2 (chi2)Allelic frequencyCKD (n = 150)HC (n = 150)Total study group (n = 300)0.7700.5220CKD (n = 150)HC (n = 150)FF53.33 (n = 80)57.33 (n = 86)55.33 (n = 166)FfFfFf41.33 (n = 62)37.33 (n = 56)39.33 (n = 118)0.740.260.760.24ff5.33 (n = 8)5.33 (n = 8)5.33 (n = 16)

Molecular Characterization of Erythrocyte Glucose-6-Phosphate Dehydrogenase Deficiency in Different Ethnic Groups of Blood Donors in Mauritania.

Glucose-6-phosphate-dehydrogenase (G6PD) deficiency is the most frequent enzymopathy worldwide; it is a genetic disorder that affects red blood cells and causes hemolysis. Here, we conducted a study on G6PD-deficient subjects in Mauritania to evaluate the molecular characteristics associated with a deficiency in this enzyme and the frequency of nucleotide polymorphisms in the glucose-6-phosphate dehydrogenase gene. A total of 943 blood samples were collected from blood donors (803 males and 140 females; 364 white Moors; 439 black Moors; 112 Pulaar; 18 Wolof; 10 Soninke). All blood samples were analyzed using a rapid screening test. G6PD status was analyzed quantitatively by the Randox G6PD test. Samples deficient in G6PD were extracted from the whole blood samples and subjected to DNA genotyping. The most frequent G6PD variants were determined by two molecular techniques: restriction fragment length polymorphism (RFLP) and multiplex PCR using the GENESPARK G6PD African kit. A total of six single nucleotide polymorphisms (SNPs) (G202A, A376G, A542T, G680T, C563T, and T968C) were identified. The prevalence of G6PD deficiency in this population sample was 8.1%. The most common mutation was A376G/202A and was characterized by the G6PD A-phenotype, which is more common in the G6PD-deficient black Moors population. The wilaya in Nouakchott was the most affected among the 13 wilayas studied. This study shows, for the first time, the presence of the G680T mutation.

Evaluating interleukin-6 levels and the rs1800795 variant in Turkish patients with COVID-19: a prospective cohort study

Background Coronavirus disease 2019 (COVID-19) is a multisystem disease of global significance. Interleukin (IL)-6 is a soluble cytokine with a pleiotropic effect on inflammation and the immune response. Objectives Investigate the relationship between the interleukin 6 (IL6) rs1800795 variant and IL6 level in Turkish patients with COVID-19 disease. Design Prospective cohort study. Settıng Tertiary care hospital. Patients and Methods Real-time polymerase chain reaction (RT-PCR)-positive and/or chest computerized tomography (CT) scan - compatible COVID-19 patients were enrolled in the study. The clinical data and whole blood samples were collected from April 1, 2020, to August 1, 2020. IL6 rs1800795 genotyping was performed by the PCR-restriction fragment-length polymorphism (RFLP) method in 148 patients. Serum IL-6 concentrations were measured using the ELISA method in 89 patients. We evaluated the patients in three groups: asymptomatic, symptomatic, and intensive care unit patients. Main Outcome Measures IL6 rs1800795 genotype frequencies and serum IL-6 levels in COVID-19 patients with different clinical presentations. Sample size 148 cases. Results IL6 rs1800795 GG genotype and G allele frequency increased in PCR positive patients compared to PCR-negative patients (p ˂ 0.000). IL6 rs1800795 GC genotype and C allele frequency were lower in PCR-positive patients than in PCR-negative patients. IL6 rs1800795 GG genotype and G allele frequency were higher in asymptomatic patients than in the symptomatic and intensive care unit groups. The IL6 rs1800795 C allele frequency was lower in asymptomatic patients than in the symptomatic and intensive care unit groups. IL6 rs1800795 GG genotype and G allele frequency were higher in CT negative patients than CT positive patients, while IL6 GC genotype and C allele frequency were higher in CT positive patients than negative patients. IL6 level elevation was seen in the asymptomatic patients compared to the symptomatic and intensive care unit groups. Conclusions These findings suggest that IL6 rs1800795 may contribute to the susceptibility of COVID-19 in people to Turkish origin. Limitations Further large-scale studies in different genetic populations are needed as this is a single-center, prospective study.

Associations of leptin receptors and miRNA polymorphisms with susceptibility to hypertension.

Leptin receptors (LEPR) are located in the central nervous system and other tissues including adipocytes and endothelial cells, where they play a key role in mediating the effects of leptin. MicroRNA (miR/miRNA)-27a and miR-155 have been shown to play an important role in the regulation of LEPR expression and are differentially expressed in various diseases. Therefore, the present study analyzed potential associations of LEPR deletion/insertion (Del/Ins), miR-27aA>G (rs895819) and miR-155T>A (rs767649) polymorphisms with a predisposition to hypertension (HTN). Genotyping was performed by a PCR-restriction fragment length polymorphism assay. Frequencies of LEPR Del/Ins and miRNA gene polymorphisms in patients diagnosed with HTN (n=232) and randomly selected healthy controls (n=247) were assessed. The present study found that Del/Ins and Ins/Ins genotypes and the Ins allele of the LEPR Del/Ins polymorphism were associated with a decreased risk of HTN compared with controls, whereas the miR-27aA>G rs895819 polymorphism was associated with an increased risk of HTN. Combined genotype and allele analyses for LEPR Del/Ins and two miRNA polymorphisms revealed an association with an increased risk or a decreased risk of HTN. Furthermore, stratification analysis revealed that HTN risk factors were associated with waist circumference (WC) and high-density lipoprotein cholesterol (HDL-C) values in LEPR Del/Ins polymorphism. They were also associated with body mass index, WC, triglyceride and HDL-C values in miR-27aA>G polymorphism. The present study revealed a combined effect of LEPR Del/Ins and miR-27aA>G polymorphisms on the risk of HTN in Koreans, suggesting that these gene polymorphisms could be potential markers for predicting HTN risk.

Multiplex PCR-based RFLP assay for early identification of prevalent Mycobacterium leprae genotypes

Mycobacterium leprae is classified into four SNP genotypes and 16 subtypes (from 1A to 4P) that exhibit phylogeographical association reported from around the world. Among them, genotypes 1D and 3I represent more than 60% of M. leprae strains. Here, we report a new method for M. leprae genotyping which identifies the genotypes 1D and 3I by combining multiplex PCR amplification and restriction fragment length polymorphism (RFLP) of a M. leprae DNA amplicons using AgeI restriction enzyme. Agarose gel electrophoresis showed a deletion of 11 bp only among 3I genotypes by electrophoresis. When this multiplex PCR reaction is subjected to AgeI digestion, successful restriction digestion shows three bands for all the genotypes except 1D where only two bands were observed due to loss of restriction site. This method gives us the advantage of 1-step identification of the two most prevalent strains of M. leprae without using specialized equipments such as the Sanger sequencing system or quantitative PCR.

Investigation of the relationship between monocyte chemoattractant protein 1 rs1024611 variant and severity of COVID-19

BackgroundHigher expression of Monocyte Chemoattractant Protein 1 (MCP-1) was reported in several studies. The clinical severity of Coronavirus disease 2019 (COVID-19) could be affected by genetic polymorphisms in MCP-1. This study aimed to examine the impact of MCP-1 2518A/G polymorphism and clinical parameters with COVID-19 severity. MethodsThe polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method was used for MCP-1 rs1024611 (A/G) genotyping in 116 outpatients, hospitalized, and ICU patients. The biochemical and hematological profiles were collected from the patient’s medical records. ResultsBased on the statistical analysis, there was no significant relationship between the −2518A/G (rs1024611) genetic polymorphism in the regulatory region of the MCP-1 gene and the severity of the COVID-19. Multivariate logistic regression analysis has shown that the severity of COVID-19 infection was associated with decreased levels of eosinophils, neutrophils, lymphocytes, and, monocyte and higher levels of SGPT, SGOT, NLR, CRP, ferritin, urea, and D-Dimer (P < 0.05). ConclusionThe MCP-1 gene polymorphism had no impact on COVID-19 severity. However, to confirm these results, a large-scale study needs to be conducted.

Association of Interleukin-6 and Tumor Necrosis Factor-alpha Gene Polymorphisms with Gnetic Susceptibility of Psoriatic Arthritis in Kuwaiti Arab Patients

Background: Psoriatic arthritis (PsA) is an inflammatory arthritic disease in which joint inflammation occurs with psoriasis. It results from a complex interplay between genetic, immunological and environmental factors. In PsA, the activation of T cells is considered as a crucial step in the disease process. The T-lymphocytes affect the proliferation of epidermal skin cells and result in abnormal differentiation. Altered cytokine networks have been shown to play a central role in the pathogenesis of PsA. Psoriasis is characterized by Th-1 type cytokine pattern in which there is a marked variation in the secretion of interleukin-6 (IL6), interleukin-13 (IL13) and Tumor necrosis factor-alpha (TNF-alpha). This study investigated the association of IL6, IL13 and TNF-alpha gene polymorphisms with genetic susceptibility of PsA in Kuwaiti patients. Methods: The genotypes of IL6 gene (-174G/C; rs1800795), IL13 gene (R130Q; rs20541) and TNF-alpha gene (-308A/G’ rs1800629) polymorphisms were detected in 113 Kuwaiti PsA patients and were compared to that in 104 healthy controls. The PsA patients were diagnosed on the basis of the presence of inflammatory arthritis with psoriasis with no rheumatoid factor in the serum. The genotypes for IL6, IL13 and TNF-alpha gene polymorphisms were determined by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) methods and were confirmed by DNA sequencing. Results: The frequency of IL6 gene (-174G/C; rs1800795) and TNF-alpha gene (-308A/G’ rs1800629) polymorphisms manifested a statistically significant difference between Kuwaiti PsA patients and controls. However, the frequency of IL13 gene (R130Q; rs20541) polymorphism did not show a significant difference between Kuwaiti PsA patients and the controls. Conclusion: Our data show an association of two cytokine gene polymorphisms in IL6 gene (-174G/C; rs1800795) and TNF-alpha gene (-308A/G’ rs1800629) with PsA in Kuwaiti patients highlighting their significant contribution to genetic susceptibility of this chronic disease possibly along with other factors.

Polymorphism of the growth hormone (GH) gene and its association with growth traits in the Kilakarsal breed of sheep

The goal of this study was to investigate the single nucleotide polymorphism of the growth hormone gene and its association with growth traits in the Kilakarsal breed of sheep. Polymerase Chain Reaction – Restriction Fragment Length Polymorphism (PCR-RFLP) of the growth hormone gene (422 bp) with HaeIII restriction enzyme revealed an A781G transition mutation at the exon 2 and the existence of two genotypes, viz., AA (366 bp and 56 bp) and AB (422 bp, 366 bp and 56 bp). The occurrence of the B allele is due to the A781G transition in the exon 2 of the growth hormone gene, which causes an amino acid change from Serine to Glycine. The genotype BB was absent in the Kilakarsal sheep population. The absence of the BB genotype at the A781G locus of the growth hormone gene in the Kilakarsal sheep population indicates that the natural selection process might be acting against this particular genotype through reduced viability or early embryonic death. Further, the statistical analysis revealed the significantly higher yearling weight of the AB than the AA genotype (P=0.038), and an appreciable difference of 1.40 kg in 9-month weight. The highly significant (P&lt;0.001) Chi-square value (29.94) showed that the population is not the under Hardy-Weinberg equilibrium. This indicates that molecular markers associated with body weight should be explored for their use in marker assisted selection in Kilakarsal population.

Genetic Polymorphisms and Their Impact on Body Composition and Performance of Brazilians in a 105 Km Mountain Ultramarathon.

Although the studied polymorphisms affect muscular proteins, aerobic adaptations, and recovery, their influence on the anthropometric variables and performance in ultramarathon runners is still poorly understood. This study aimed to determine the influence of ACTN3 R577X, ACE I/D, and CK MM A/G NcoI polymorphisms on the changes in the anthropometric variables and running time of 105 km mountain runners, in which 22 male Brazilian elite athletes (35.9 ± 6.5 years) were evaluated. Genotyping of the R577X (RR, RX, and XX), ACE I/D (DD, ID, and II), and CK MM A/G Ncol (AA, AG, and GG) polymorphisms was performed using the Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) technique with DNA extracted from saliva. Body composition was determined via bioimpedance. Pre- and post-race weight differences were observed on athletes with the AA genotype (77.1 ± 5.9 kg; 74.6 ± 5.6 kg) compared with those with the AG genotype (74.5 ± 8.0 kg; 68 ± 5.1 kg) (p = 0.02; p = 0.02). The RR genotype showed a correlation between BMI and running time (R = 0.97; p = 0.004). The genotype II showed a correlation with % fat and fat mass concerning running time (R = 0.91; p = 0.003; R = 0.99; p < 0.0001). The AA genotype was associated with post-race weight and lean mass loss, while the RR genotype correlated with BMI, and the genotype II correlated with % body fat and fat mass in relation to times in the 105 km mountain ultramarathon.

Genetic Polymorphism of NQO1 Influences Susceptibility to Coronary Heart Disease in a Chinese Population: A Cross-Sectional Study and Meta-Anaylsis.

The present study is to explore the association between NQO1 gene polymorphism and coronary heart disease (CHD) risk. This research were selected 80 CHD patients as the observation group and 130 healthy people who participated in normal physical examination during the same period as the control group. NQO1 gene polymorphism was detected by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. In addition, we conducted a meta-analysis to summarize the results of three relevant previously published adult population studies on the association between NQO1 gene polymorphism and coronary heart disease (CHD) risk. There were three genotypes (CC, CT, and TT) for NQO1 C609T polymorphism. The significant associations were found in TT genotype and T allele (all p<0.05). Specifically, People with the TT genotype have 2.06 times CHD risk as those with the CC genotype. And People with the T allele have 1.62 times CHD risk as those with the C allele. No significant association was found by any genetic models in the meta-analysis (all p >0.05). NQO1 gene polymorphism increased the CHD risk in a Chinese population. Combined with individual gene polymorphism, the accuracy of risk assessment for CHD can be improved and individualized health education can be provided for CHD patients by nurses.

Genotyping of toxoplasma gondii isolates from México reveals non-archetypal and potentially virulent strains for mice.

Genotyping and virulence studies of Toxoplasma gondii are essential to investigate the pathogenesis of strains circulating worldwide. In this study, eight T. gondii isolates obtained from a congenitally infected newborn, a calf, two cats, three dogs, and a wallaby from five states of México were genotyped by Mn-PCR-RFLP with 11 typing markers (SAG1, SAG2 5'3', altSAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1 and Apico), five virulence markers (CS3, ROP16, ROP17, ROP18 and ROP5), 15 microsatellite markers (TUB-2, W35, TgM-A, B18, B17, M33, IV.1, XI.1, M48, M102, N60, N82, AA, N61, N83), and sequencing. A phylogenetic network was built to determine the relationship between Mexican isolates and those reported worldwide. Six different genotypes were identified by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), ToxoDB #8, #10, #28 (n = 3), #48, #116, and #282. Genotyping by microsatellite analysis differentiated the three PCR-RFLP genotype #28 isolates into two strains, revealing a total of seven microsatellite genotypes. Three different allele combinations of ROP18/ROP5 virulence markers were also found, 3/3, 1/1, and 4/1. The last two combinations are predicted to be highly virulent in the murine model. According to the phylogenetic network, the T. gondii strains studied here are related to archetypal strains I and III, but none are related to the strains previously reported in México. The genotypes identified in this study in different species of animals demonstrate the great genetic diversity of T. gondii in México. The ToxoDB-PCR-RFLP #28 genotype was found in three isolates from different hosts and states. Additionally, four of the isolates are predicted to be highly virulent in mice. The next step will be to perform in vitro and in vivo assays to determine the phenotype of these T. gondii isolates in murine models.

Molecular diagnosis of 5 silkworm strains endemic to South Korea using single-nucleotide polymorphisms selected from whole-genome sequences.

The domesticated silkworm, Bombyx mori Linnaeus (Lepidoptera: Bombycidae), often poses a challenge in strain identification due to similarities in morphology and genetic background. In South Korea, around 40 silkworm strains are classified as premium, including 5 endemic tri-molting strains: Goryeosammyeon, Sammyeonhonghoeback, Hansammyeon, Sun7ho, and Sandongsammyeon. These strains have potential for breeding programs in response to emerging industry demands, necessitating a reliable strain identification method. In this study, we established a molecular diagnosis approach for these 5 strains. We selected 2-4 single-nucleotide polymorphisms (SNPs) for each strain from whole-genome sequences of 39 strains, encompassing 37 previously studied and 2 newly added. These SNPs were utilized to construct decision trees for each endemic strain identification. The SNPs can be used to distinguish each target strain from the 38 nontarget strains by the tetra-primer amplification refractory mutation system-polymerase chain reaction, with the exception of HMS which needs the addition of PCR-restriction fragment length polymorphism method at the final step. This decision tree-based method using genomic SNPs, coupled with the 2 typing methods, produced consistent and accurate results, providing 100% accuracy. Additionally, the significant number of remaining SNPs identified in this study could be valuable for future diagnosis of the other strains.