Amplification Refractory Mutation System Research Articles

Association between TNFα-308 G/A and IFN-γ+874A/T Polymorphisms with Oral Lichen Planus

Background: Oral lichen planus (OLP) is a chronic disease that presents with inflammation and has a global prevalence of 0.1-4%. Lesions of the disease occur in the oral mucosa, gums, and rarely in the palate. This study aimed to investigate the relationship between this disease and TNFα-308G/A and IFN-γ+874A/T polymorphisms. Methods: In this case-control study, oral mucosal samples were collected from 50 healthy subjects, and 50 OLP patients presented to the Kerman Faculty of Dentistry were enrolled using a simple sampling method. Subsequently, we used the amplification refractory mutation system polymerase chain reaction (ARMS-PCR) technique followed by sequencing to determine the presence of TNFα-308G/A and IFN-γ+874A/T polymorphisms in cases and controls. Results: Compared to the control group, the prevalence of A and GA alleles of the TNF gene was higher than the prevalence of G and GG alleles in OLP patients, while the AA genotype of the gene was not found in OLP patients. Regarding IFN gene polymorphism, the relationship between the T allele and the risk of disease was discovered, but it was not statistically significant (P value: 0.068). Conclusion: Although there is a strong relation between the A allele of TNF-α (-308G/A) polymorphism and the risk of OLP, this association between IFN-γ+874A/T genotype and the disease was not strong enough to predict the possibility of developing OLP.

A novel tetra-primer ARMS-PCR approach for the molecular karyotyping of chromosomal inversion 2Ru in the main malaria vectors Anopheles gambiae and Anopheles coluzzii

BackgroundChromosomal inversion polymorphisms have been associated with adaptive behavioral, physiological, morphological and life history traits in the two main Afrotropical malaria vectors, Anopheles coluzzii and Anopheles gambiae. The understanding of the adaptive value of chromosomal inversion systems is constrained by the feasibility of cytological karyotyping. In recent years in silico and molecular approaches have been developed for the genotyping of most widespread inversions (2La, 2Rb and 2Rc). The 2Ru inversion, spanning roughly 8% of chromosome 2R, is commonly polymorphic in West African populations of An. coluzzii and An. gambiae and shows clear increases in frequency with increasing rainfall seasonally and geographically. The aim of this work was to overcome the constraints of currently available cytological and high-throughput molecular assays by developing a simple PCR assay for genotyping the 2Ru inversion in individual specimens of both mosquito species.MethodsWe designed tetra-primer amplification refractory mutation system (ARMS)-PCR assays based on five tag single-nucleotide polymorphisms (SNPs) previously shown to be strongly correlated with 2Ru inversion orientation. The most promising assay was validated against laboratory and field samples of An. coluzzii and An. gambiae karyotyped either cytogenetically or molecularly using a genotyping-in-thousands by sequencing (GT-seq) high-throughput approach that employs targeted sequencing of multiplexed PCR amplicons.ResultsA successful assay was designed based on the tag SNP at position 2R, 31710303, which is highly predictive of the 2Ru genotype. The assay, which requires only one PCR, and no additional post-PCR processing other than electrophoresis, produced a clear banding pattern for 98.5% of the 454 specimens tested, which is a 96.7% agreement with established karyotyping methods. Sequences were obtained for nine of the An. coluzzii specimens manifesting 2Ru genotype discrepancies with GT-seq. Possible sources of these discordances are discussed.ConclusionsThe tetra-primer ARMS-PCR assay represents an accurate, streamlined and cost-effective method for the molecular karyotyping of the 2Ru inversion in An. coluzzii and An. gambiae. Together with approaches already available for the other common polymorphic inversions, 2La, 2Rb and 2Rc, this assay will allow investigations of the adaptive value of the complex set of inversion systems observed in the two major malaria vectors in the Afrotropical region.Graphical

Clinical application value of hepatitis B virus basal core promoter 1762/1764 and GGTII and GGT in patients with HBV-DNA-positive primary liver cancer.

Hepatitis B virus (HBV) is closely related to the occurrence and development of primary liver cancer (PLC). The early diagnosis of PLC is difficult. The study explored the clinical application value of the HBV gene basal core promoter (BCP) region 1762/1764 combined with gamma-glutamyl transpeptidase (GGT) and its isozyme II (GGTII) in PLC. From June 2017 to June 2021, 145 hepatitis B surface antigen-positive and HBV DNA-positive patients were enrolled in the Third People Hospital of Zigong. Of them, 67 were chronic hepatitis B (CHB) patients, 30 were liver cirrhosis patients, and 48 were patients with hepatitis B-associated PLC. The HBV BCP 1762/1764 mutation was detected through the amplification refractory mutation system fluorescence PCR method, and GGTII was detected using the double-antibody sandwich method. The results showed that the serum GGT activity, GGTII level, aspartate aminotransferase (AST) activity, AST/alanine aminotransferase (ALT) ratio, GGT/ALT ratio, and GGT/AST ratio were significantly different between the PLC and CHB groups. Statistically significant differences in serum GGT activity, AST activity, and GGT/ALT ratio were observed between the PLC and LC groups. The BCP 1762/1764 mutation rate between the PLC and CHB groups was statistically significant. The GGTII level in the early PLC (stage I + II) group and the advanced PLC (stage III + IV) group was higher than that in the N-PLC group. Serum GGT activity in the early PLC and advanced PLC groups was higher than that in the N-PLC group. The area under the curve of the receiver operator characteristic curve of GGT and GGTII for diagnosing PLC was 0.775 (95% confidence interval [CI] [0.697, 0.854]) and 0.608 (95% CI [0.512, 0.704]), respectively. The area under curve of GGT and GGTII for diagnosing early PLC was 0.732 (95% CI [0.620, 0.845]) and 0.579 (95% CI [0.452, 0.706]), respectively. HBV gene BCP 1762/1764 mutation, GGT, and GGTII may be related to PLC occurrence. The HBV gene BCP region 1762/1764 combined with GGT has certain clinical diagnostic values for PLC and early PLC. However, GGTII is not a good indicator of early PLC and is more relevant to advanced PLC.

Impact of Survivin rs9904341 and rs17878467 Polymorphisms On Risk of Preeclampsia in Iran.

Preeclampsia (PE) is a hypertensive disorder that affects pregnancy, mother, and fetus. Early diagnosis of PE remains a challenge. This study aimed to investigate the association between survivin two (rs9904341 and rs17878467) SNPs and PE risk in healthy pregnant women compared to women with preeclampsia. A sample of 166 healthy pregnant women and 160 cases with preeclampsia was included and genotyped for rs9904341 with polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and rs17878467 with amplification-refractory mutation system (ARMS) PCR. The genotypic and allelic assessments were performed using various statistical approaches. The frequency of rs9904341 and rs17878467 polymorphisms was not significantly different between PE and healthy pregnant women. rs9904341: codominant (p = 0.5), dominant (p = 0.24), recessive (p = 0.61), over-dominant model (p = 0.38), and log additive (p = 0.25). rs17878467: codominant (p = 0.41), dominant (p = 0.23), recessive (p = 0.4), over-dominant model (p = 0.42), and log additive (p = 0.24). The frequency of survivin rs9904341 CG and CC genotypes was higher in severe PE women compared to controls and this polymorphism was associated with PE severity only in the dominant model (OR = 1.84, CI 1.04-3.26, P = 0.034). There was a significantassociation between survivin rs9904341 polymorphism and PE severity. No relationship was found between survivin rs9904341 and rs17878467 polymorphisms and PE onset. The allelic and genotypic frequencies of survivin rs9904341 and rs17878467 polymorphisms are not significantly different between the preeclampsia and control groups in all genetic models.Haplotype analysis showed lower frequency G rs9904341 Trs17878467 haplotype in PE womanand this haplotype was associated with lower risk of PE (OR = 0.54, CI 0.33-0.91, P = 0.02).

An optimized method for PCR-based genotyping to detect human APOE polymorphisms

BackgroundApolipoprotein E (APOE) is one of the most polymorphic genes at two single nucleotides (rs429358 and rs7412). The various isoforms of APOE have been associated with a variety of diseases, including neurodegenerative, type 2 diabetes, etc. Hence, predicting the APOE genotyping is critical for disease risk evaluation. The purpose of this study was to optimize the tetra amplification refractory mutation system (Tetra-ARMS) PCR method for the detection of APOE mutations. Material and methodsHere, in our optimized Tetra-ARMS PCR method, different factors like cycle conditions, using HiFidelity enzyme instead of Taq polymerase and setting its best concentration, and the lack of using dimethylsulfoxide (DMSO) for amplifying the GC-regions were set up for all primer pairs. The sensitivity and accuracy were tested. For validation of the assay, the results were compared with known genotypes for the APOE gene that were previously obtained by two independent methods, RFLP and Chip-typing. ResultsSuccessful Tetra-ARMS PCR and genotyping are influenced by multiple factors. Our developed method enabled us to amplify the DNA fragment by 25 cycles without adding any hazardous reagent, like DMSO. Our findings showed 100 % accuracy and sensitivity of the optimized Tetra-ARMS PCR while both criteria were 95 % for RFLP and 100 % for the chip-typing method. In addition, our results showed 91 % and 100 % consistency with RFLP and chip typing methods, respectively. ConclusionsOur current method is a simple and accurate approach for detecting APOE polymorphisms within a large sample size in a short time and can be performed even in low-tech laboratories.

Development of a novel panel for blood identification based on blood-specific CpG-linked SNP markers.

Blood-containing mixtures often appear in murder and robbery cases, and their identification plays a significant role in solving crimes. In recent years, the co-detection of DNA methylation markers (CpG) and single nucleotide polymorphism (SNP) markers has been shown to be a promising tool for the identification of semen and its donor. However, similar research on blood stains that are frequently found at crime scenes has not yet been reported. In this study, we employed blood-specific CpG-linked SNP markers (CpG-SNP) for blood-specific genotyping and the linking of blood and its donor. The tissue-specific CpG markers were screened from the literature and further verified by combining bisulfite conversion with amplification-refractory mutation system (ARMS) technology. Meanwhile, adjacent SNP markers with a minor allele frequency (MAF) greater than 0.1 were selected within 400 bp upstream and downstream of the CpG markers. SNP genotyping was performed using SNaPshot technology on a capillary electrophoresis (CE) platform. Finally, a multiplex panel, including 19 blood-specific CpG linked to 23 SNP markers, as well as 1 semen-specific CpG, 1 vaginal secretion-specific CpG, and 1 saliva-specific CpG marker, was constructed successfully. The panel showed good tissue specificity and blood stains stored at room temperature for up to nine months and moderately degraded (4 < DI < 10) could be effectively identified. Moreover, it could also be detected when blood content in the mixed stains was as low as 1%. In addition, 15 ng of DNA used for bisulfite conversion was required for obtaining a complete profile. The cumulative discrimination power of the panel among the Han population of northern China could reach 0.999983. This is the first investigation conducted for the simultaneous identification of blood and its donor regardless of other body fluids included in mixed stains. The successful construction of the panel will play a vital role in the comprehensive analysis of blood-containing mixtures in forensic practice.

FRI031 A Novel Strategy To Detect Leptin Receptor (Lepr, fa) Mutation In Obesity And Diabetic Animal Model (Zucker Rats)

Abstract Disclosure: X. Xu: None. X. Hu: None. G. Ma: None. T. Wang: None. J. Wang: None. G. Chen: None. L. Zhao: None. J. Chen: None. Globally, diabetes is among the leading causes of premature morbidity and mortality. Early intervention is crucial to achieve optimal outcomes and minimize the burden of diabetes. Animal models are indispensable tools to investigate etiology and explore novel strategies for diabetes treatment and prevention. Zucker strain and its derivatives, Zucker Fatty (ZF) and Zucker Diabetic Fatty (ZDF) rats, are one of the most used rodent models to study diabetes and diabetes-associated metabolic disorders. Homozygous Zucker rats with leptin receptor gene mutation (Lepr, fa-/-) spontaneously develop obesity, hypercholesterolemia, and hyperlipidemia. The wildtype (fa+/+) and heterozygous (fa+/-) littermates phenotypically are indistinguishable. Furthermore, early stages of diabetes are asymptomatic, and the obese phenotype is not appreciable in homogenous (fa-/-) Zucker rats until week 4 of age. Therefore, a rapid, cost-effective, and reliable genotyping method is essential to differentiate homozygous (fa-/-) rats from either wildtype (fa+/+) or heterozygotes (fa+/-) in early interventional studies. We reported a tetra-primer Amplification-Refractory Mutation System (ARMS)—PCR approach to detect leptin receptor fa mutation using genome DNA collected from ear and tail tissues of Zucker rats. Three different types of amplicon patterns are easily identified by agarose gel electrophoresis. Wildtype (fa+/+) genotype displays a 401 bp and a 201 bp amplicon band; heterozygous (fa+/-) consists of a 401 bp, a 263 bp, and a 201 bp amplicon band on the gel; homozygous (fa-/-) comes up with two bands of 401 bp and 263 bp. The genotypes identified by our tetra-primer ARMS—PCR method are further confirmed by sequence analysis. This method requires neither DNA purification nor restriction enzyme digestion, which is suitable for research exploring gene-environment interaction, as well as implementing appropriate intervention approaches in the research areas of diabetes and metabolic diseases. Presentation: Friday, June 16, 2023

Evaluation the -174G>C Genetic Polymorphism of Interleukin-6 in Iranian Patients with Chronic Lymphocytic Leukemia.

Interleukin-6 (IL-6) is involved in inflammation and has a significant role in chronic lymphocytic leukemia (CLL) progression. Accordingly, IL-6 level may increase in CLL-affected patients compared to healthy individuals. The -174G>C single nucleotide polymorphism (SNP) in IL-6 promoter region has been related to differences in IL-6 transcription. Therefore, we investigated the possible association of IL-6 polymorphism with CLL. We examined the -174G>C SNP in IL-6 gene and studied its possible relationship with CLL in affected patients and in healthy controls using Amplification Refractory Mutation System- polymerase chain reaction genotyping method. IL-6 plasma level was measured in both studied groups. According to the results, IL-6 mean plasma concentration was increased significantly in the CLL patients compared to the controls. However, 174G>C genotype of the IL-6 gene was not associated with CLL. Furthermore, there were no significant differences in the distribution of allele and genotype frequencies between the CLL-affected patients and the controls (P>0.05). Our study showed that -174G>C SNP in promotor of IL-6 gene could not be considered a risk factor for CLL. Larger prospective studies should be performed to confirm our results.

Non-Small Cell Lung Cancer: Targetable Variants in Concurrent Tissue and Liquid Biopsy Testing in a North Indian Cohort.

Testing for EGFR, ALK, ROS1 and MET alterations in paired tissue and plasma samples of treatment-naïve patients of NSCLC and correlating their status with overall survival. One hundred treatment-naïve patients were recruited after obtaining informed consent. Ten ml of blood was collected within a period of two weeks from histological diagnosis, prior to the start of any treatment. DNA & RNA extraction was done from formalin-fixed paraffin embedded (FFPE) tissue and total cell-free nucleic acid extraction was done from plasma samples. EGFR mutation, ALK, ROS1 and MET rearrangements were tested by ARMS (Amplification Refractory Mutation System) PCR. All statistical analyses were conducted in R version 4.1.1. A total of 61 cases showed molecular alterations in tissue samples which included EGFR mutations (47), ALK rearrangements (12), ROS1 fusion (2). MET alteration was not detected. Forty-three cases showed EGFR mutations in plasma, 26 of which were concurrently positive in tissue. Concordance observed was 62%. ALK-EML4 rearrangement, ROS1 fusion and MET were not detected in plasma samples. Sensitivity and specificity for detection of EGFR mutation in plasma were 55.3% and 67.9% respectively. Univariate Cox regression analysis showed a positive association between EGFR mutation in tissue and overall survival (HR = 0.4; 95% CI: 0.2-0.7; p = 0.003) and improved overall survival in those who received targeted therapy (HR = 0.29; 95% CI: 0.1-0.8; p = 0.02). Concurrent testing in tissue and liquid biopsy in NSCLC increased the detection of EGFR mutations (47% to 64%). This has substantial implications in deciding treatment and administration targeted therapy and the consequent overall survival.

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.

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.

A Novel PCR-Based Functional Marker of Rice Blast Resistance Gene Pi25

Rice blast is arguably the most devastating fungal disease of rice. Utilization of resistance genes to breed resistant cultivars is one of the most economical and environmentally friendly approaches to combat the disease. Pi25, a major resistance gene conferring broad-spectrum resistance to both leaf and neck blast, is an ideal gene resource to improve the resistance of rice varieties to blast. Recently, several allele-specific markers were developed. However, they were deficiently efficient due to either an additional process of restriction enzyme digestion for cleaved amplified polymorphic sequence (CAPS) markers or the risk of false-positive error in identifying susceptible Tetep allele (Pi25TTP) for PCR-based markers. In this study, based on a conserved single nucleotide polymorphism (SNP) between resistant and susceptible alleles, a tetra-primer amplification refractory mutation system (ARMS)-PCR marker was developed. The new marker, namely Pi25-2687R3, could effectively distinguish the resistant Gumei 2 (GM2) allele (Pi25GM2) and the susceptible allele Pi25TTP. Moreover, a perfect consistency of genotyping was exhibited between Pi25-2687R3 and published CAPS marker CAP3/Hpy 99I. A more accurate genotyping was also displayed compared to the previous PCR-based SNP marker Pi25-2566. Our finding proved that Pi25-2687R3 could achieve the same result as CAP3/Hpy 99I with less workload and cost and could promote the accuracy in the identification of genotypes superior to Pi25-2566. This study provided a quick and reliable functional marker for discriminating Pi25 alleles, which would be a valuable tool for genotypic assay and rice molecular breeding of blast resistance.

Rs1800890 Polymorphism of IL-10 and Susceptibility to Idiopathic Thrombocytopenic Purpura

AbstractImmune thrombocytopenic purpura (ITP) is an immune bleeding disorder that is reported in approximately 2 out of every 100,000 adults with a mean age of 50 years. Several factors such as various genetic backgrounds are associated with the pathogenesis of ITP. Interleukin (IL)-10 is a complicated cytokine that has a role in tumor progression, antitumor immunity, and immune system regulation. rs1800890 is an IL-10 single nucleotide polymorphism linked to lower levels of IL-10. A total of 67 patients with ITP and 70 healthy individuals (controls) were considered in this study. The IL-10 polymorphism was detected by the amplification refractory mutation system–polymerase chain reaction technique. According to our analysis, individual carriers of the AA genotype were less likely to develop ITP. The AT genotype was more common in patients with ITP in comparison to the control group. However, there was no significant association between rs1800890 genotypes (p = 0.775, odds ratio =1.517, 95%) in the acute and chronic groups. We observed that women had a higher mean frequency of this polymorphism (p = 0.0012). The rs1800890 AA genotype was associated with the highest platelet counts. However, the mean platelet volume and platelet distribution width values among alleles of the polymorphisms did not vary significantly. The IL-10 rs1800890 polymorphism may have a role in idiopathic thrombocytopenic purpura etiology. As a result, more research with a larger number of sample sizes is suggested.

Investigating mutations in the genes GDF9 and BMP15 in Pelibuey sheep through the amplification-refractory mutation system with tetra-primers

Single Nucleotide Polymorphisms (SNP) or mutations are variations with a broad distribution in the genome and, as part of genetic studies, SNP allow the identification of allelic variants related to characteristics of economic importance in sheep production. However, the identification of SNP and their genotypes through sequencing is expensive, as it requires specialized materials and equipment. The objective of this study was to identify polymorphisms and their genotypes in the growth differentiation factor 9 (GDF9) and bone morphogenetic protein 15 (BMP15) genes in Pelibuey sheep using the tetra-primer amplification-refractory mutation system through polymerase chain reaction (T-ARMS-PCR). DNA extraction and amplification of BMP15 and GDF9 were conducted from blood samples contained in WhatmanTM FTATM cards from 60 multiparous Pelibuey ewes with reproductive records. The T-ARMS-PCR methodology allowed the identification of wild-type genotypes and mutated homozygous genotypes in polymorphisms G4 and G6 of GDF9, whereas mutations in the BMP15 gene were not found. These results were confirmed by sequencing. In conclusion, the T-ARMS-PCR methodology allowed the identification of mutated and wild-type genotypes in SNP G4 and G6 of GDF9, although no mutations were found in BMP15 in Pelibuey sheep. This technique was found to be reliable, rapid, and easily applied to identify polymorphic genotypes.

The Relationship between T1DM and the Polymorphisms of IL2RA (Rs2104286) and PTPN22 (Rs2476601) Genes among Children

Background: Type 1 diabetes mellitus (T1DM) is an autoimmune condition caused by T lymphocytes that results in the death of pancreatic cells. Protein tyrosine phosphate non-receptor type 22 (PTPN22) and interleukin 2 receptor alpha (IL2RA) polymorphisms have been discovered to have a connection to a number of autoimmune illnesses, including T1D. Objective: The purpose of this study is to clarify the significance of the polymorphisms PTPN22 (rs2476601) and IL2RA (rs2104286) in the susceptibility to T1DM in young Iraqi children. Methods: The study included 60 Iraqi children diagnosed with T1DM within the past three years and a control group of 30 healthy individuals without diabetes or autoimmune diseases. In order to conduct a molecular investigation. Five ml of venous blood from 90 participants (60 patients and 30 controls) was collected for nucleic acid extraction. Results: The PTPN22 (rs2476601) and IL2RA (rs2104286) polymorphisms were genotyped using the amplification refractory mutation system (ARMS) technique and specific primers. According to the results, PTPN22 (rs2476601) has a wild-type homozygous C/C genotype and C allele frequency of 90%, a mutant C/T genotype frequency of 10%, and no T allele. Following were the genotype frequencies for IL2RA (rs2104286): AA, AG, and GG in T1DM patients were 79%, 16%, and 4%, respectively, compared to 83%, 13%, and 3% in controls. Conclusion: The polymorphisms of PTPN22 rs2476601 and IL2RA rs2104286 did not significantly differ in their connection with type 1 diabetes. It does not appear to affect the susceptibility of Asian Iraqis to T1D.

Anemia in female adolescents at Karanganyar regency: A cross-sectional study associated with polymorphism of duodenal cytochrome B gene and daily consumptions of fruits and vegetables.

The prevalence of anemia in female adolescents increases every year. A duodenal Cytochrome B (CYBRD1) enzyme is involved in the regulation of iron metabolism. G797A gene polymorphism of the CYBRD1 reduces nonheme iron transport into the enterocytes, which was mediated by the divalent metal transporter 1 protein. Daily consumption of fruits and vegetables has been recommended for the prevention of non- communicable diseases, including anemia. This study aimed to analyze the association of CYBRD1 polymorphism and daily consumption of fruits and vegetables with anemia in female adolescents in the Karanganyar regency. This cross-sectional study recruited 233 female students in 6 senior and vocational high schools in Karanganyar regency, which were selected using purposive sampling. Data on fruit and vegetable consumption were collected using Semi-Quantitative Food Frequency Questionnaire (SQ-FFQ). Polymorphism of the G797A CYBRD1 gene was determined using the amplification refractory mutation system polymerase chain reaction. All collected data were analyzed using chi-square and multiple logistic regression tests with p < 0.05. Anemia was found in 13.73% of female students. Inadequate intakes of fruits and vegetables were found in 63.09 and 51.07% of female students, respectively. The AA genotype (OR = 5.779; 95%CI: 0.974-34.289; p = 0.053), inadequate fruit consumption (OR = 1.497; 95%CI: 0.603-3.718; p = 0.133), and inadequate vegetable consumption (OR = 11.99; 95%CI: 3.457-41.586; p < 0.001) increased higher risk of anemia, compared with their counterparts. G797A CYBRD1 gene polymorphism and daily consumption of vegetables increase the risk of anemia but not for daily consumption of fruits in female adolescents in the Karanganyar regency.

Detecting fa leptin receptor mutation in Zucker rats with tetra-primer amplification-refractory mutation system (ARMS)-PCR

Due to the genetic mutation (fa) in the gene encoding for leptin receptor, homozygous Zucker rats (fa−/−) develop excessive adiposity and become an experimental animal model in obesity and metabolic-related diseases research. Based on tetra-primer amplification refractory mutation system-polymerase chain reaction (ARMS-PCR), we developed a method to quickly genotype Zucker rats with a mutated fa allele from their wildtype littermates. The three genotypes are clearly discriminated on 2.0% agarose gel. Our method can be used as a reliable tool to set up and maintain the breeding colony in animal facilities as well as assign animals to control and treatment groups based on their genotypes for animal studies.

CSMD1 rs10503253 increases schizophrenia risk in a Tunisian population-group

ObjectivesSchizophrenia is a complex and chronic neuropsychiatric disorder. Recent genome-wide association studies have identified several at risk genetic variants, including two single nucleotide polymorphisms, namely the rs10503253 and the rs1270942 respectively located in the CSMD1 and the CFB loci. The present case-control study was designed to assess potential associations between the two variants and the risk of developing schizophrenia and disease severity. Further we demonstrate the relationship between these variants and clinical characteristics in a population-group from Tunisia. Patients and methodsIn total, 216 patients diagnosed with schizophrenia along with176 healthy controls were included in this case–control study. The molecular analysis of the two polymorphisms was performed using tetra the Primer Amplification Refractory Mutation System–Polymerase Chain method. The statistical analysis was done using Compare V2.1 software, and correlations between genetic results and clinical characteristics were examined by Kruskal-Wallis testing. ResultsThe frequency of the rs10503253A allele was found significantly higher among patients with schizophrenia as compared to healthy controls and associated with high negative PANSS scores. While no association was found concerning the implication of the rs1270942 variant in schizophrenia risk, a positive correlation with high positive PANSS scores was further observed. ConclusionThe present finding confirms the previously reported association between the Cub and Sushi multiple Domain 1 rs10503253A allele and the risk to develop schizophrenia and identified the rs1270942 variant as a potential disease risk modifier. Such observations may be important for the definition of the susceptible immunogenetic background in North African individuals at risk to develop mental disorders.

Development of a T-ARMS-PCR Assay for Detecting Genetic Polymorphism in the Catalase (rs7943316) Gene in the Iraqi Population with Breast Cancer.

Numerous investigations have demonstrated that oxidative stress is markedly increased in breast cancer patients compared to their healthy counterparts. Catalase (CAT), a crucial antioxidant enzyme, plays a pivotal role in safeguarding cells against oxidative damage initiated by reactive oxygen species (ROS). The CAT (rs7943316) gene encodes catalase, and certain genetic variations in this gene have been observed to modify catalase activity and levels. Such changes can lead to an altered response to oxidative stress, potentially increasing the risk of breast cancer. In light of this, a novel tetra-primer amplification-refractory mutation system (T-ARMS)-PCR assay was developed to investigate the possible correlation between the CAT (rs7943316) gene polymorphism and the development of breast cancer in patients. This method employs a one-step PCR, which is faster, more cost-effective, and more precise than existing techniques. Sanger sequencing was performed to validate the accuracy of our findings. The T-ARMS-PCR assay revealed a significant association between the A/T allele of the CAT (rs7943316) gene and breast cancer. Specifically, individuals with the TT genotype had a higher risk of developing breast cancer than those with the AA genotype. The T allele frequency was greater among breast cancer patients than in the control group, and genotype frequencies were consistent with the principles of the Hardy-Weinberg Equilibrium. This study is the first to showcase a rapid, cost-effective, and high-throughput method for detecting the SNP in the CAT (rs7943316) gene. This method has the potential to be employed in large-scale clinical trials.

Species-Level Monitoring of Key Bacteria in Fermentation Processes Using Single-Nucleotide Resolved Nucleic Acid Assays Based on CRISPR/Cas12.

Microorganisms can determine the flavor and quality of fermented food, such as Baijiu, which is produced via Daqu fermentation. Therefore, monitoring key microorganisms during fermentation is important for ensuring high-quality fermented food. Here, we report a single-nucleotide resolved nucleic acid assay based on the CRISPR/Cas12 system, enabling the quantification of Bacillus amyloliquefaciens, a key microorganism in Daqu fermentation at the species level. The assay employs an amplification-refractory mutation system derived from PCR to analyze minor genetic differences between different Bacillus species. The utilization of CRISPR/Cas12 further guaranties the specificity of identifying the PCR amplicon and enables the quantification of Bacillus amyloliquefaciens via end-measurement fluorescence. Compared to conventional qPCR, the assay allows for species-level detection of bacteria, thus enabling the precise detection of the Bacillus strain that yields high-level 2,3,5,6-tetramethylpyrazine. The assay promises the precise monitoring of bacterial growth and contribution to flavor during Daqu fermentation, thus facilitating fermented food quality control.