Polymerase Chain Reaction-restriction Fragment Length Polymorphism Research Articles

Pediatric pharmacogenetics: profiling CYP2C8 polymorphisms at King Abdulaziz University Dental Clinic.

Ibuprofen, a widely used non-steroidal anti-inflammatory (NSAID) for managing pain and inflammation in pediatric patients, is metabolized by the CYP2C8 enzyme. Studies suggest that the CYP2C8*2, *3, and *4 variations of the CYP2C8 gene diminish ibuprofen metabolism, increasing the risk of adverse reactions. The aim of this study was to determine the frequency of the CYP2C8*2, *3, and *4 alleles and genotypes in a pediatric population attending the King Abdulaziz University dental clinic and compare our findings to those of other populations. A cross-sectional study was conducted with 140 healthy Saudi children ages 6-12. Saliva samples were collected using Oragene™ DNA Sample Collection Kits and analyzed for polymorphisms using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). The study identified that CYP2C8*2 AA, AT, and TT genotypes occurred at frequencies of 87.86 %, 9.29 %, and 2.86 %, respectively. For CYP2C8*3, AA, AG, and GG genotypes were found in 87.14 , 8.75, and 4.29 % of subjects, respectively. The CYP2C8*4 allele was less frequent, with CC and CG genotypes at 97.86 % and 2.14 %, respectively, and the GG genotype was absent. Allele frequencies for CYP2C8*2, *3, and *4 were 7.5 %, 8.57 %, and 1.07 %, respectively. Our findings reveal that the allelic frequencies for the CYP2C8 polymorphisms in the Saudi pediatric cohort are substantially elevated compared to those reported in other Asian populations. This suggests Saudis may experience more varied drug responses, especially for medications that undergo metabolism by the CYP2C8 enzyme, like ibuprofen.

Impacts of Matrix Metalloproteinase-11 Genotypes on Pterygium Risk.

The dysregulation of matrix metalloproteinase (MMP) proteins has been reported to be involved in the etiology of pterygium. However, studies about the role of matrix metalloproteinase-11 (MMP-11) are lacking. This study is the first to examine the genomic role of MMP-11 in pterygium. The genotypes of MMP-11 rs738791, rs2267029, rs738792, and rs28382575 were determined in 140 pterygium cases and 280 non-pterygium controls by utilizing polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and direct sequencing. The genotypic frequencies of MMP-11 rs738792 TT, CT and CC were 40.0%, 50.7%, and 9.3% in the pterygium group, significantly different from those in the non-pterygium group (55.0%, 37.1%, and 7.9%, respectively; p for trend=0.0139). Specifically, individuals carrying the variants CT and CC had a 1.88- and 1.63-fold odds ratio of pterygium risk [95% confidence interval (CI)=1.22-2.89 and 0.77-3.44, p=0.0054 and 0.2834, respectively]. In the dominant model, individuals carrying CT+CC had significantly higher pterygium risk (odds ratio=1.83, 95%CI=1.21-2.77, p=0.0052). No association was found for other MMP-11 polymorphisms. Allelic analysis showed that MMP-11 rs738792 C allele was significantly associated with pterygium risk (odds ratio=1.48, 95%CI=1.08-2.01, p=0.0169). for the variant alleles of other MMP-11 polymorphisms were not associated with pterygium risk. The MMP-11 rs738792 genotypes can serve as a predictive marker for pterygium risk in Taiwanese. Additionally, elucidating the role of MMP-11 in the pathogenesis of pterygium could inform targeted therapies based on MMP-11 modulation.

Associations of GST Gene Polymorphisms and GST Enzyme Activity with the Development of Noise-Induced Hearing Loss in Chinese Han Males

Introduction: In noise-induced hearing loss (NIHL), glutathione S-transferases (GSTs) play a pivotal role as antioxidants in cochlear protection. Nevertheless, the variability in population and environmental factors complicates the interpretation of research findings on the association among GST gene polymorphism, GST enzyme activity, and NIHL, leading to inconsistent results. To explore the potential correlation between them, we took a cross-sectional survey. Methods: For workers with NIHL, standard 1:1 propensity score matching was applied to create a highly comparable control group. Multiplex PCR was used to detect GSTT1 and GSTM1 gene deletions, PCR-restriction fragment length polymorphism was used to detect the GSTP1 rs1695 gene polymorphism, and a GST assay kit was used to measure total plasma GST activity. Furthermore, we analyzed the relationship among GST gene polymorphism, GST enzyme activity, and NIHL. Results: This study included 144 workers with NIHL and 144 workers with normal hearing. The GSTM1 null genotype was significantly higher among workers with NIHL than controls (64.6% vs. 49.3%), regression analysis revealed a significant correlation between GSTM1 null genotype and elevated susceptibility to NIHL (p = 0.013). Workers with NIHL had significantly lower GST activity than healthy controls (p < 0.05). GST enzymes were not affected by GSTT1, GSTM1, or GSTP1 polymorphisms. Conclusion: GSTM1 null genotype but not GSTM1 alone may confer susceptibility to NIHL, and serum GST enzyme activity is linked to NIHL.

The effect of VEGF and KDR gene variants on Crimean-Congo hemorrhagic fever

Background Crimean-Congo hemorrhagic fever (CCHF), an acute viral hemorrhagic fever disease, has a high mortality rate among humans. Hemorrhagic propensity is caused by coagulation malfunction and increased capillary permeability brought on by the resultant vascular injury. Vascular endothelial growth factor (VEGF) and VEGF receptor-2, or KDR (kinase insert domain containing receptor), are effective in vasculogenesis and angiogenesis. CCHF was stated to have endothelial dysfunction. This study aimed to evaluate whether the VEGF and KDR gene variants contribute to the development of CCHF in the Turkish population. Methods A total of 101 subjects, including 51 CCHF patients and 50 healthy controls, were included in the study. The polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) method was used to genotype VEGF 936 C > T (rs3025039) and KDR − 604 T > C (rs2071559) variants. The results were statistically analyzed. Results The VEGF 936 C > T genotype and allele distributions did differ significantly between the patients and the controls. The subjects carrying the C/C genotype and C allele had a higher risk of developing CCHF than the control group (p˂0.05). There was a statistically significant association between the controls and the patients in terms of VEGF 936 C > T C/C versus C/T + T/T (p˂0.05, OR:3.273, 95%Cl: 1.44–7.63). The KDR − 604 T > C variant’s allele and genotype distribution were not significantly different between the patients and controls. Conclusion This study suggests the VEGF 936 C > T variant is a genetic marker of sensitivity to CCHF among the Turkish population and may help protect against the disease.

The impact of LEP gene polymorphisms located at exon 2 (LEP-HinfI) and intron 2 (LEP-Sau3AI) on growth and reproductive traits in Saanen goats

Abstract. Leptin (LEP), alternatively recognized as the obesity gene, influences food consumption, energy balance, and lipid metabolism. Additionally, it plays a crucial role in energy metabolism, and variations in the LEP gene have been studied extensively among various livestock species. These investigations have unveiled correlations with traits such as meat quality, milk yield and composition, and growth characteristics. Nevertheless, the existing knowledge regarding its correlation with growth and reproductive traits in goats is comparatively limited, particularly when juxtaposed with studies of cattle. Hence, the objective of the current study was to investigate the relationship between polymorphisms in the intron 2 (Sau3AI) and exon 2 (HinfI) regions of the LEP gene and growth and reproductive traits in Saanen goats. The study comprised 185 Saanen goats in total. The PCR-RFLP (polymerase chain reaction restriction fragment length polymorphism) technique was employed to genotype these polymorphisms. Population genetic analysis included the number of effective alleles, heterozygosity, polymorphism information content, and compatibility with the Hardy–Weinberg equilibrium. The general linear model procedure's least-squares methods were used for the statistical analysis. The SNP (single-nucleotide polymorphism) located in exon 2 (LEP-HinfI) was monomorphic. Remarkably, the SNP located in intron 2 (LEP-Sau3AI) was associated with birth weight (p&lt;0.05) and average daily weight gain (p&lt;0.05). In this context, the AA genotype demonstrated higher birth weight and daily live weight gain means compared to other genotypes. No significant differences were observed in litter size, total weight gain, or morphometric measurements. The caprine LEP-Sau3AI polymorphism situated within intron 2 proved influential in traits critical for the profitability and sustainability of goat breeding. The findings of this study provide novel and valuable information for future research on the LEP gene in goats.

ACE and ACE2 activities and polymorphisms assessment: A populational study from Ipaussu (SP, Brazil) during the COVID-19 pandemic

AimThe angiotensin-converting enzyme 2 (ACE2) and its homolog, the angiotensin converting enzyme 1 (ACE), are involved in COVID-19 physiopathology. Alterations in the enzymatic structure, expression, and/or activity may influence the risk of infection and severity of disease. For this reason, we aimed to identify different allelic forms of ACE2 G8790A and ACE I/D polymorphisms in a Brazilian cohort and evaluate their impact on ACE and ACE2 activities and their association with COVID-19 susceptibility and severity. Main methodsA total of 549 COVID-19-negative and 270 COVID-19-positive participants from Ipaussu, Sao Paulo, Brazil, were recruited. ACE2 and ACE activities were measured by fluorogenic assays using MCA-Ala-Pro-Lys(Dnp) as the substrate for ACE2 and Z-Phe-His-Leu-OH (Z-FHL) and Hippuryl-His-Leu-OH (h−HL) as substrates for ACE. Genomic DNA was extracted from EDTA-peripheral blood, and the regions of the genes containing ACE2 G8790A and ACE I/D polymorphisms were amplified by PCR-restriction fragment length polymorphism and real-time PCR, respectively. Key findingsThe G allele of ACE2 G8790A polymorphism and D allele of ACE I/D polymorphism are associated with increased ACE and ACE2 activities. ACE activity ratio (Z-FHL/h-HL), an inflammatory marker, is increased in women with GG genotype and COVID-19-positive diagnosis. SignificanceFor the first time, it was demonstrated that in females, the GG genotype is associated with increased ACE activity ratio (Z-FHL/h-HL) in the COVID-19-positive group. Elevated ACE activity ratio (Z-FHL/h-HL) is highly linked to inflammation and may justify the associations between the G genotype and COVID-19 severity of symptoms and outcomes.

The association between knockdown resistance and treatment outcome of 1% permethrin lotion in head lice infestations in Nonthaburi province, Thailand.

Head lice infestations significantly impact schoolchildren, with permethrin being the primary treatment. The escalation in the prevalence of the knockdown resistance (kdr) mutation, potentially affecting treatment efficacy, is highly concerning. This study examined head lice infestation prevalence, the efficacy of 1% permethrin lotion, kdr mutation frequency, and the association between kdr genotype and permethrin treatment outcomes in schoolchildren in Nonthaburi province, Thailand. Participants and lice samples were collected from six primary schools using cluster sampling. Clinical outcomes and adverse events were assessed on days 7 and 14 post-treatment. Kdr mutations (T917I) in head lice samples were analyzed using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique. Head lice infestation prevalence was 6.1%, with a kdr mutation frequency of 63.2% and a permethrin cure rate of approximately 50%. Multivariate regression analysis revealed the association between kdr genotype and clinical response to permethrin treatment (Odds Ratio (OR) = 13.15, p = 0.005). The presence of resistance genes hinders the cure rate (presence 35.9% versus absence 85.7%). These findings highlight the importance of the kdr genotype in predicting permethrin treatment responses in head lice infestations. Furthermore, in regions with documented reduced permethrin efficacy and a high prevalence of kdr mutations, alternative non-pyrethroid-based pediculicides should be considered. This research could help improve the control of head lice infestations, especially in problematic areas of Thailand.

Validation of gene polymorphisms (rs2682818 and rs2043556) in has-miR-618 and has-miR-605 with the breast cancer susceptibility

BackgroundBreast cancer (BC) is one of the most frequent types of cancer and the second leading cause of cancer-affiliate death among ladies. BC is a heterogeneous sickness that is impacted by environment and genetic elements. Diagnosis in the early stages impacts treatment and patient survival rate. miRNA can play a vital role in BC's early stages of tumorigenesis. Single nucleotide polymorphism (SNP) can cause changes in miRNA expression and function, which are related to the risk of several cancers. AimThe goal of this examination is to assess the affiliation among two has-miR-605 (rs2043556A > G) and has-miR-618 (rs2682818 C > A) gene polymorphisms with the risk of BC in the Iranian ladies. MethodsOur case-control examination assessed two hundred whole blood samples of one hundred ladies with BC and one hundred healthy ladies. Hence, to assess the connection between the presence of SNP miRNA genes and the risk of BC, genotyping was done by the usage of the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method, then the usage of the Chi-square test of SPSS software statistically analyzed the acquired result. ResultsOur findings confirmed a statistically substantial distinction within the genotype frequency of the has-miR-618 gene polymorphism among the groups (P = 0.043), whereas no statistically substantial distinction inside the genotype frequency of the has-miR-605 gene polymorphism among the control and case (P = 0.183). In addition, the allelic frequency of two polymorphisms, (rs2043556 A > G) G allele (OR = 2.163, CI 95 % = 1.56–2.988, P = 0.022) and (rs2682818 C > A) A allele (OR = 3.997, CI 95 % = 1.584–10.081, P = 0.002) substantially enhance the risk of BC. ConclusionThe results show that the G allele of rs2043556 and the A allele of rs2682818 increase the risk of BC in the women population of East Azerbaijan province.

Infection Frequency and Allelic Variants of Toxoplasma gondii in Wildlife from the Panama Canal Zone

Panama has a large number of wild animal species, which could host a highly diverse amount of genetic variants of Toxoplasma gondii (T. gondii). In this context, we highlight the importance of understanding the population structure of T. gondii in Panamanian wildlife and the genetic variants that can be rapidly transferred to domestic environments. This study analyzed the infection frequency and allelic composition of T. gondii in different tissue samples from wild animals. The infection frequency was measured by the PCR technique using the B1 gene as a molecular marker. The results showed a high frequency (65.6%) of infection in tissue samples collected from 221 wild animals. Stratified analyses for bird and mammal samples showed positivity rates of 67.2% and 70.12%, respectively, with no statistically significant differences. Infection frequency was also measured in five types of organs (brain, liver, heart, lung, and skeletal muscle), which showed homogeneous frequencies. The genetic diversity of the T. gondii population contained in the tissues of wild animals was analyzed by the Multilocus Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) technique, using five genes called SAG1, SAG2, SAG3, GRA6, and Apico. This analysis revealed the presence of alleles of these genes corresponding to T. gondii lineages I, II, and III. Allele III was only identified with the Apico gene in a single reptile individual analyzed. Our findings indicated diverse allelic distribution at the analyzed loci, suggesting that the tissues were probably infected by non-archetypal individuals of T. gondii.

A comprehensive analysis of the effects of DGAT1 K232A polymorphism on milk production and fertility traits in Holstein Friesian and Jersey cows reared in Türkiye

Abstract. Research on the diacylglycerol acyltransferase 1 (DGAT1) K232A marker in cattle shows inconsistent results across regions, largely due to small sample sizes, limited genetic variation, and data restricted to few lactations, which complicates establishing a reliable genotype–phenotype correlation. This research aimed to determine the effect of the K232A polymorphism of the bovine DGAT1 gene on milk production and quality traits in dairy cattle. We used 1104 cattle, including 828 Holstein Friesian and 276 Jersey cows. The analysis utilized extensive data from six lactations of cows raised on four commercial dairy farms. We genotyped the population using the polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP) technique and Sanger sequencing for verification. We then evaluated the 305 d and test-day milk yields as well as fat and protein yields and percentages. The number of inseminations per conception and calving ease were also assessed as reproduction indices. Genotype–phenotype associations were quantified using linear mixed models. The AA genotype was absent in Jersey cows, and the heterozygous genotype was predominant in both breeds. The K232A marker was significantly associated with test-day milk yield, fat, and protein content in Jersey cows. Further, it substantially affected the fat percentage of milk in Holstein Friesian cows (p&lt;0.001). We found that the KK genotype is highly desirable for milk quality and especially fat content. This comprehensive assessment demonstrated that the KK genotype of the DGAT1 K232A polymorphism significantly influenced fat and protein contents in dairy cattle.

Profile of molecular markers of Sulfadoxine-Pyrimethamine-resistant Plasmodium falciparum in individuals living in southern area of Brazzaville, Republic of Congo

BackgroundAlthough the seasonal and perennial malaria chemopreventions are not implemented in the Republic of Congo, resistance to Sulfadoxine-pyrimethamine (SP) threatens the intermittent preventive treatment during pregnancy (IPTp-SP) and others treatments using the drug. The objective of this study was to determine the prevalence of molecular markers of P.falciparum resistance to SP in individuals with microscopic malaria infection in the south of Brazzaville. MethodsTwo parallel surveys (health facilities and community-based cross sectional studies) were carried out in urban and rural areas in southern Brazzaville. Between March and October 2021, blood samples were collected from 328 P. falciparum microscopic positive individuals (1- 83 years old, and sex ratio female/male of 1.1) to characterize dhfr and dhps genes involved in the P.falciparum resistance to SP. Restriction Fragment Length Polymorphism PCR was used for the detection of mutations within these parasite genes. ResultsHigh prevalence of mutations was reported within Pfdhfr gene: N51I; 328/328 (100%) ratio (prevalence) [95 CI uncertainty], C59R; 317/328 (96.6 %) [94.1-98.1%], S108N; 326/326 (100%), N164L; 3/326 (0.9%) [0.3-2.7%], and Pfdhps gene: A437G; 292/327 (89.3%) [85.5-92.2%], K540E; 140/327(42.8 %) [37.6-48.2%], A581G; 136/325 (41.8%) [36.6-42.3%]. The quintuple mutant (N51I+ C59R + S108N + A437G + K540E) and sextuple mutant haplotypes (N51I+ C59R + S108N + A437G + K540E + A581G) were reported for 11/144 (7.6%) [4.3-13.2%] and 5/144 (3.4% ) [1.5-7.9%]) of the participants respectively. The K540E and A437G mutants were more prevalent in the rural community; 81/139 (58.3%) [50.0-66.1%] and 135/139 (97.1%) [92.8-98.9%] respectively) than in the urban community; 21/50 (46.3%) [33.7-59.4%] and 47/54(87.0%) [75.6-93.6%] (p= 0.004 and p˂0.0001 respectively) ConclusionThese results indicate high prevalence of SP resistance mutations within the dhfr and dhps genes of P. falciparum isolates circulating in study sites, which may limit the efficacy of treatments using SP in these settings.

Effects of solute carrier family 27 member 1 (SLC27A1) genotypes on fat content and major fatty acids in colostrum and milk from Murrah and “Murrah × Carabao” crossbred buffaloes

This study analyzed the effect of Solute carrier family 27 member 1 (SLC27A1) genotypes on fat content and major fatty acids (lauric acid C12:0, myristic acid C14:0, palmitic acid C16:0, stearic acid C18:0, and oleic acid C18:1n-9) in milk and colostrum of 46 Murrah and “Murrah × Carabao” crossbred buffaloes at the Philippine Carabao Center - University of the Philippines Los Baños dairy herd. The SLC27A1 genotypes (CC and CT) were determined by the polymerase chain reaction-restricted fragment length polymorphism (PCR-RFLP) method using DNA extracted from hair follicles. This study found polymorphism in the SLC27A1 gene that were consistent with Hardy Weinberg’s law of equilibrium (HWE), with a polymorphic information content (PIC) and heterozygosity (H) estimate of 0.2915 and 0.3542, respectively, for Murrah; and 0.3219 and 0.4032, respectively for “Murrah × Carabao” crossbreeds. In Murrah buffaloes, the CT genotype was significantly associated (P&lt;0.05) with higher colostrum yield and milk fat content, compared to CC. In “Murrah × Carabao” crossbreds, CT was associated with higher C12:0, C14:0, and C16:0, but lower C18:1n-9 in colostrum; and lower C16:0 in milk compared to CC. This study showed polymorphisms in SLC27A1 genotypes and their significant effects on colostrum yield and milk fat content in Murrah buffaloes and some major fatty acids in colostrum and milk from “Murrah × Carabao” crosses.

Association of ERCC1 Gene Polymorphisms (rs3212986 and rs11615) With the Risk of Lung Cancer in a Population From Southeast Iran.

Polymorphisms within the excision repair cross-complementation group 1 (ERCC1), an essential component of DNA repair mechanisms, have been associated with various malignancies. This study aimed to evaluate the association of the single-nucleotide polymorphisms (SNPs) rs3212986 and rs11615 within the ERCC1 gene in non-small cell lung cancer (NSCLC) patients. Study Design: A case-control study. Genomic DNA was extracted from the peripheral blood samples of 83 NSCLC patients and 119 healthy individuals. The genetic diversity of SNPs rs3212986 and rs11615 was determined using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. The RFLP results were confirmed through sequencing. The TT genotype of the rs11615 SNP was associated with a higher risk of NSCLC development (odds ratio: 3.900, 95% confidence interval: 0.603, 22.866, P=0.050). Furthermore, the AA genotype of rs3212986 was related to a higher risk of NSCLC development (OR: 2.531, 95% CI: 1.017, 6.300, P=0.046). A significant association was observed between smoking and lung cancer (OR: 3.072, 95% CI: 1.715, 5.503, P<0.001). Moreover, among non-smokers, there was an association between lung cancer risk and the AA (OR: 6.825, 95% CI: 1.722, 27.044, P=0.006) and AC (OR: 2.503, 95% CI: 0.977, 6.412, P=0.056) genotypes of rs3212986. However, no correlation was found between the genotypes of these SNPs and patients' sensitivity to cisplatin and carboplatin (P ˃ 0.05). The rs11615-related TT genotype and the rs3212986-related AA genotype may be associated with a higher risk of lung cancer development.

Polymorphisms in the genes encoding RLR and TLR3 and CMV DNAemia in subjects coinfected with human immunodeficiency virus and cytomegalovirus

Cytomegalovirus (CMV) is a pathogen that is common worldwide and is often present in individuals infected with human immunodeficiency virus (HIV). Pattern recognition receptors (PRRs) are host sensors that activate the immune response against infectious agents. However, it is unclear whether PRR single-nucleotide polymorphisms (SNPs) are associated with the occurrence of CMV DNAemia in subjects coinfected with HIV and CMV. HIV/CMV-coinfected patients with and without CMV DNAemia were recruited for this study. The DDX58 rs10813831 and IFIH1 (rs3747517 and rs1990760) polymorphisms were genotyped using the TaqMan Allelic Discrimination Assay, whereas the DDX58 rs12006123 and TLR3 (rs3775291 and rs3775296) SNPs were analyzed using a polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) assay. A mutation present in at least one allele of the DDX58 rs12006123 SNP occurred at least two times more frequently in HIV/CMV-coinfected patients with CMV DNAemia than in coinfected subjects without CMV DNAemia (OR, 2.50; 95% CI, 1.33–4.68; p = 0.004, in the dominant model). A higher level of CMV DNAemia was observed in subjects who had the heterozygous (GA) or homozygous recessive (AA) genotype for the DDX58 rs12006123 SNP compared with those who had the wild-type (GG) genotype (p = 0.0003). Moreover, in subjects with a mutation detected in at least one allele of the DDX58 rs12006123 SNP, a lower serum IFN-β concentration was found compared with those who had a wild-type (GG) genotype for this polymorphism (p = 0.024). The DDX58 rs12006123 SNP is associated with CMV DNAemia in HIV/CMV-coinfected patients.

Single nucleotide polymorphisms of CFAP43 and TEX14 associated with idiopathic male infertility in a Vietnamese population.

Male infertility is a multifactorial disease due to spermatogenesis impairment, with etiology remaining unknown for roughly one-third of infertile cases. Several studies have demonstrated that genetic variants are male infertility risk factors. CFAP43 and TEX14 are involved in the spermatogenesis process. The present study aimed to assess the association between single-nucleotide polymorphisms (SNPs) in CFAP43 (rs17116635 and rs10883979) and TEX14 (rs79813370 and rs34818467) and idiopathic male infertility in a Vietnamese population. A cohort of 206 infertile men and 195 controls were recruited for the study. CFAP43 and TEX14 SNPs were genotyped using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Genotypes of randomly selected samples, accounting for 10% of the total, were confirmed using Sanger sequencing. The obtained data were analyzed using statistical methods. The results showed that 4 SNPs (rs17116635, rs10883979, rs79813370, and rs34818467) were in accordance with Hardy-Weinberg Equilibrium (HWE; P > .05). CFAP43 rs10883979 and TEX14 rs79813370 were associated with male infertility. For CFAP43 rs10883979, in the recessive model, the combination AA + AG was associated with male infertility when compared to the GG genotype (OR = 0.26; 95% CI: 0.06-0.85; P = .02). For TEX14 rs79813370, a protective effect against infertility risk was identified in the presence of the T allele of rs79813370 when compared to the G allele (OR = 0.48; 95% CI: 0.32-0.72; P < .001). Our results suggest that CFAP43 rs10883979 and TEX14 rs79813370 are likely associated with male infertility in the Vietnamese population, in which the G allele of rs79813370 may be a risk factor for male infertility.

Investigation of the association between polymorphisms in DNA repair enzymes and STEMI

STEMI (ST-elevation myocardial infarction), a condition in which DNA damage likely contributes to its pathogenesis, is among the most severe manifestations of coronary artery disease. There are very few publications in this field in the literature. In our study, we examined the association between four polymorphisms in repair enzymes (LIG4 Thr9Ile, XRCC6 promoter C-57G, XPA -4A/G, OGG1 Ser326Cys) involved in three distinct DNA repair mechanisms [NHEJ (non-homologous end joining)], NER (nucleotide excision repair), and BER (base excision repair), and their impact on the risk of STEMI. This study involved 185 patients diagnosed with STEMI and included 155 healthy controls. The genotyping of SNPs was conducted through the PCR-RFLP (Polymerase chain reaction-restriction fragment length polymorphism) method for the following variants: XRCC6 (rs2267437), XPA (rs1800975), LIG4 (rs1805388), and OGG1 (rs1052133). No significant differences were observed in the genotype distributions of the XRCC6 and OGG1 variations between the control and patient groups. On the other hand, our findings indicate that individuals carrying the mutant G allele for XPA polymorphism and the mutant T allele for LIG4 polymorphism are susceptible to STEMI. Our findings demonstrate the significance of NHEJ and NER DNA repair processes in the pathogenesis of STEMI, as evidenced by the observed relationship between LIG4 and XPA polymorphisms.

Investigation of the relationship between adiponectin gene polymorphism (ADIPOQ SNP rs-266729) and obesity Patients / Basra-Iraqi

Adiponectin is one of the most important hormones secreted by adipose tissue and plays a major role in the development of obesity. A variant-specific ADIPOQ single nucleotide polymorphism (SNP rs-266729) with a C to G missense mutation can be strongly associated with obesity. Therefore, this study aims to evaluate the association of single nucleotide polymorphisms (SNP rs-266729) of the ADIPOQ gene with obesity and some biochemical markers in these patients. The case-control study included 186 participants (106 patients and 80 healthy control). DNA was extracted from whole blood and then the Restriction Fragment Length Polymorphism Polymerase Chain Reaction (RFLP-PCR) technique was used to limit the genotype of the ADIPOQ gene (rs266729) polymorphism. Also, the lipid profile, glycated hemoglobin (HbA1C), fasting blood glucose (FBG), insulin, and adiponectin were measured by standard methods. Results: The allele G in the ADIPOQ-gene polymorphism (rs266729) was a significantly higher frequency of 23 (21.6%) in the obese patients (P_Value = 0.039) compared with the control subject of 10 (12.5%). It significantly increased the risk in the additive model and allele frequency (P = 0.0139 and 0.0133), respectively. The rs266729 SNP showed a significant association with increased BMI, insulin, HOMO-IR, TG, VLDL, and lower adiponectin at a p-value of 0.001 for all, after adjustments for age and sex. Lower levels of high-density lipoprotein (HDL) were observed in the CG and GG genotypes compared to the ADIPOQ rs266729 SNP C.C genotype (p = 0.032). In obese individuals, there was no significant relationship between rs266729 SNP and HbA1C, FBS, TC, and LDL. In conclusion, the single nucleotide polymorphism (rs266729) of the ADIPOQ gene has a significant difference with BMI, insulin, TG, VLDL, and HOMO-IR in obese patients, which might be the cause of obesity.

Polymorphisms of CD247 gene is associated with dilated cardiomyopathy in Chinese Han population

BackgroundDilated cardiomyopathy (DCM) is a major cause of heart failure and heart transplantation. Recently, some studies have reported that the autoimmune response in myocardial cells might be related to the pathogenesis of DCM. The CD247 gene has been previously found to be involved in autoimmune disease. Therefore, our study aimed to clarify the hypothesis that there is a certain linkage between polymorphisms of the CD247 gene and the triggering of DCM risk.MethodsIn the present study, two single nucleotide polymorphisms (SNPs) of the CD247 gene, rs12141731 and rs858543, were genotyped by polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP) in 355 DCM patients and 404 age- and sex-matched controls.ResultsPearson’s chi-squared test for the CD247 gene revealed that SNP rs858543 (p = 0.001, OR = 0.72, 95% CI = (0.588–0.882), but not SNP rs12141731, was associated with DCM in the Chinese Han population. Haplotype analysis revealed that the CC haplotype was associated with increased DCM susceptibility, while CT was a protective haplotype. Cox multivariate survival analysis indicated that the rs858543 TT genotype (HR: 0.608, 95% CI = 0.402–0.921, p = 0.019) was an independent multivariate predictor for longer overall survival in DCM patients. CD247 mRNA expression levels were significantly decreased in DCM patients (p = 0.02).ConclusionsOur study suggested that a polymorphism in the CD247 gene may be a risk factor for DCM in the Chinese Han population.Trial registrationChiCTR2000029701.

Surviving the extinction vortex? Discovering remnant stands of Senecio hercynicus (Compositae, Senecioneae) evading genetic swamping by its congener S. ovatus in the Bavarian and Bohemian Forest region

Genetic swamping by introgressive hybridisation threatens diversity, caused by climate warming particularly in mountainous regions worldwide. Recent studies resulted in a threatening perspective for Senecio hercynicus in the Bavarian Forest due to genetic swamping by introgressive hybridisation with its cogener S. ovatus. To examine the situation more closely, the distribution and hybridization of S. hercynicus and S. ovatus in high elevation regions of the Bavarian and Bohemian Forest was analyzed by restriction enzyme digestion of nrDNA ITS1 (PCR-RFLP; PCR restriction fragment length polymorphism). For a total of 706 samples from 94 different sample localities a hybrid index was inferred from the fragment band intensities after PCR-RFLP digestion. Boxplot diagrams of the hybrid indices show a tendency of western populations towards S. ovatus genotypes and for populations to the east towards S. hercynicus genotypes. When the hybrid index data was subjected to a regression analysis with nine factors (five habitat patterns inferred during sampling and four bioclimatic variables), only geographical longitude and latitude seemed to describe the observed distribution of S. hercynicus and S. ovatus significantly, arguing for the distribution and hybridisation patterns being shaped rather due to historical than to eco-climatological determinants. While a broad zone of hybridisation between the two species in the Bavarian and Bohemian Forest region was inferred, our study demonstrates that purebred S. hercynicus still exists and remnant stands of this species should be the target of species conservation measures.

A comprehensive study of CYP2E1 and its role in carcass characteristics and chemical lamb meat quality in different Indonesian sheep breeds.

The role of CYP2E1 in oxidation is essential for its effects on meat quality. This study used 200 Indonesian sheep (Ovis aries) to determine the SNP g allele frequencies. g. 50658168 T>C of CYP2E1 gene located in 3´-UTR region and their genetic association with lamb quality traits, including carcass characteristics, retail cut carcass, physicochemical lamb, fatty acid, cholesterol, flavor and odor, and mineral content. Further, the level of CYP2E1 mRNA and CYP2E1 protein expression in muscle were determined and correlated with lamb quality traits. CYP2E1 gene polymorphisms were identified using Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) analysis. The CYP2E1 mRNA expression levels in phenotypically divergent sheep populations were analyzed using Quantitative Real Time-PCR (qRT-PCR). Immunohistochemistry (IHC) and hematoxylin-eosin (HE) staining analysis used three samples each in the high and low lamb quality groups based on pH value and tenderness. An association study of CYP2E1 gene polymorphisms was performed using General Linear Model (GLM) analysis. The genetic association between the CC, CT, and TT genotypes at the SNP g. 50658168 T>C CYP2E1 gene and lamb quality traits were significant (P<0.05), including carcass characteristics, retail cut carcass, fatty acid, cholesterol, flavor, and odor. Lambs with the CT genotype had a higher mRNA and protein expression in high lamb quality traits. The highest CYP2E1 protein expression was localized in the longissimus dorsi. The group sample with high lamb quality had a higher area and perimeter of muscle cells. CYP2E1 can be used as a genetic marker for selecting sheep with high meat quality.