Association of IL-17A promoter region SNP-rs2275913 with urinary bladder cancer

Objective

Urinary bladder cancer (UBC) is the fourth most common cancer among men and tenth most common cancer in women. This study investigated an association of interleukins -17A promoter region single nucleotide polymorphism (SNP)-rs2275913 with UBC in Pakistani population.

Methods

Population-based study was designed with 127 UBC patients and 100 healthy individuals. Only UBC Patients were included and other diseases hepatitis or any other malignancy/cancer were excluded from the study. Polymerase chain reaction Restriction fragment length polymorphism technique was used to genotype the rs2275913 SNP in patients and control. Linear regression analysis was performed on the genotype data and allelic frequency data. Online statistical tool was used to calculate ratio of odds.

Results

Linear regression analysis showed that there was no association between rs2275913 SNP and UBC patients in the dominant model (OR = 0.815, CI = 0.415-1.6), recessive model (OR = 0.389, CI = 0.014-5.565), codominant model (OR = 0.376, CI=0.013-5.420) and (OR = 0.855, CI = 0.427-1.713). Moreover, among the UBC samples, low-grade non-muscle invasive UBC samples dominant model (OR = 0.722, CI = 0.316-1.637), recessive model (OR = 0.000, CI = 0.000-5.864), codominant model (OR = 0.864, CI = 0.030-12.668), and (OR = 0.788, CI = 0.341-1.806) did also not show any association. When same analysis was performed for high-grade muscle invasive UBC, dominant (OR = 0.936, CI = 0.403-2.155), recessive model (OR = 0.875, CI = 0.031-12.696), and codominant model (OR = 0.864, CI = 0.030-12.668,), and (OR = 0.942, CI = 0.394-2.232) did not show any association.

Conclusion

Results revealed that rs2275913 did not show any associated with the high risk of UBC in Pakistani population. Some limitations of the studies are firstly, the samples size and other are detailed information on UBC and role of inflammation.

Genotypic analysis of the FAS2-F1279Y (3836T>A) polymorphism conferring high ethyl caprylate productivity in industrial sake yeast strains

In Saccharomyces cerevisiae, ethyl caprylate is produced by the esterification of caprylic acid, which is synthesized through the action of fatty acid synthase. A recent study reported a yeast mutant with a single nucleotide substitution in the alpha subunit of fatty acid synthase (FAS2) gene (F1279Y; 3836T>A) that produced large amounts of ethyl caprylate. Here, we designed two primer sets (P1/P2 and P3/P4) with mismatches that incorporate restriction sites for the enzymes NdeI and SspI, respectively and developed an easy and rapid polymerase chain reaction-restriction fragment length polymorphism assay to identify yeasts harboring the FAS2-F1279Y mutation associated with high ethyl caprylate productivity.

Genetic polymorphism of prolactin and nitric oxide synthase in Holstein cattle

Background and Aim

Bacterial and viral infections affect the welfare of animals and lead to large economic losses in dairy cattle breeding due to decreased productive indicators and increased culling rates. In modern dairy farming, farmers are looking for effective solutions to prevent and minimize infectious disease risks. To this end, the most relevant study field is the search for gene sites that impact production and health. This study aimed to determine the nature of the distribution of the relative frequencies of alleles and genotypes of polymorphic prolactin (PRL) and nitric oxide synthase (NOS2) in Holstein cows and identify the relationship of these genes with resistance to mastitis and bovine leukemia.

Materials and Methods

For this study, we chose cows because infectious diseases affect the amount of lactation and milk quality. Holstein cattle with mastitis and bovine leukemia were selected. Animal genotypes were determined by restriction fragment length polymorphism (RFLP) of polymerase chain reaction (PCR) products. The results were analyzed using a nonparametric statistical method using Microsoft Excel 2010 and Statistica 6.0.

Results

In healthy animals, 94 genotypes were identified for both genes under study. For bPRL, bPRL-RsaI^AA (72) was the most common genotype and bPRL-RsaI^BB (4) the least; for NOS2, bNOS2 -HinfI^AB (47) was the most common genotype and bNOS2 -HinfI^AA the least (21). In animals with leukemia, 34 genotypes were identified. For PRL, bPRL-RsaI^AA (25) was the most common genotype and bPRL-RsaI^BB (2) the least; for NOS2, bNOS2 -HinfI^BB (17) was the most common genotype and bNOS2 -HinfI^AA (3) the least. In animals with mastitis, 67 genotypes were identified. For PRL, bPRL-RsaI^AA (43) was the most common genotype and bPRL-RsaI^BB (6) the least; for NOS2, bNOS2 -HinfI^BB (31) was the most common genotype and bNOS2-HinfI^AA (7) the least. The distribution of genotypes of polymorphic bPRL and bNOS2 generally coincides, and bPRL-RsaI^BB is the most common genotype. In groups of sick animals, the number of bNOS2 -HinfI^AA homozygotes was lower than that of the control group. In particular, the proportion of animals with the bNOS2 -HinfI^AA genotype with bovine leukemia was 8.7% and with mastitis was 10.3% compared with 22.4% in healthy animals. These data support the possible association of the bNOS2 -HinfI^AA genotype with resistance to infection. The frequency of the bPRL-RsaI^B allele was higher in groups of sick animals. This allele is associated with increased milk productivity, suggesting that highly productive animals are less resistant to the incidence of viral bovine leukemia and mastitis of bacterial etiology.

Conclusion

DNA amplification of Holstein cattle for the polymorphic regions of PRL and NOS2 using the PCR-RFLP method revealed a possible connection between the distribution of relative allele frequencies of bPRL and bNOS2 and resistance to viral and bacterial infections. Thus, in groups of sick animals, the frequency of bPRL-RsaI^BB, associated with increased milk production compared with the theoretically calculated equilibrium value was higher and the number of homozygotes bNOS2 -HinfI^AA was lower than in the control group. In conclusion, animals with increased milk production were more prone to diseases, such as mastitis and bovine leukemia.

Investigation of species distribution of nontuberculosis mycobacteria isolated from sputum samples in patients with suspected pulmonary tuberculosis

Aims

Rapid and accurate identification of mycobacteria is important for the species-specific treatment of the disease. The aim of this study was the identification at the species level of 34 nontuberculous mycobacteria strains isolated from respiratory tract samples and 14 reference strains as by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method.

Materials and Methods

Isolates derived from clinical specimens were subcultured in the Lowenstein-Jensen medium. Deoxyribonucleic acid isolation was carried out using the boiling method. PCR amplification was performed using primers specific to the hsp65 gene region. The PCR products were digested BstEII and HaEIII enzymes. All samples were studied comparatively by two different centers.

Results

In our study, the most common species were found to be Mycobacterium intracellulare in 23.52% (8/34). The performance of the PCR-RFLP method in detecting mycobacteria was found to be 82.35%.

Conclusions

The PCR-RFLP method is a rapid, cheap, and practical method for the identification of mycobacteria.

Undergraduate laboratory series that employs a complete polymerase chain reaction-restriction fragment length polymorphism experiment for determination of a single nucleotide polymorphism in CYP2R1 gene

Nowadays, novel Biochemistry lab techniques are being introduced at a very fast pace in scientific research. This requires development of new labs for undergraduate Biochemistry courses to equip the students with up-to-date techniques. However, the time limit of Biochemistry labs for undergraduate students represents a major obstacle. This article presents a clear set of laboratory exercises designed to introduce students to the use of polymerase chain reaction-restriction-fragment length polymorphism (PCR-RFLP) as a means of detection of genetic variants. Three consecutive lab experiments have been designed for the undergraduate students to serve this purpose. The first session was performed in a computer lab (dry lab) where students were taught how to obtain a specific gene sequence, identify an exact single nucleotide polymorphism location, choose the target sequence for amplification, design specific primers for this particular sequence and choose the most suitable restriction enzyme from web tools. The second and third lab sessions were performed as wet labs where in the second lab session, students optimized PCR conditions and performed a successful PCR. The PCR products were kept for use in the third lab session where they utilized the selected restriction enzyme and carried out gel electrophoresis to determine the exact genotype.

Bovine leukemia virus genotype surveillance in cattle at a slaughterhouse in Aichi Prefecture, Japan, in 2019 using polymerase chain reaction combined with restriction fragment length polymorphism

Polymerase chain reaction (PCR) combined with restriction fragment length polymorphism (RFLP) is commonly used for genotyping bovine leukemia virus (BLV) in slaughterhouses. However, unclassified BLV genotypes have been sporadically reported. To assess the current status of BLV genetic characterization in cattle, PCR-RFLP was performed on blood samples of 170 cattle (84 Japanese Black, 60 Japanese Black x Holstein, and 26 Holstein) from 17 farms (5 prefectures) at a slaughterhouse in Aichi Prefecture in 2019. A total of 65 samples (38.2%) were BLV positive, and genotype 1 was the most predominant (56/65 samples), followed by genotypes 3 (6 samples) and 5 (1 sample), and two unclassified samples. No relationship between the genotypes and breeds was observed. Sequence and phylogenetic analyses demonstrated that unclassified BLV genotypes clustered with genotype 1 sequences were, therefore, not new genotypes.

Effects of polymorphism of myostatin and fatty acid-binding protein 4 genes on the chemical composition of meat in cull female Aceh cattle

Aim:

This study aimed to investigate the association of single nucleotide polymorphism of the myostatin (MSTN) and fatty acid-binding protein 4 (FABP4) genes on the total water, ash, fat, protein, and cholesterol contents of sirloin (gluteus medius muscle) and silverside (biceps femoris muscle) meats of cull female Aceh cattle.

Materials and Methods:

This analysis covered a total of 27 cull female Aceh cattle slaughtered at the Animal Slaughterhouse of Banda Aceh that was purposively selected based on hair color referred to the criteria described in the Decree of Ministry of Agriculture of the Republic of Indonesia. Genomic DNA was extracted from 25 mg of fresh meat using the spin column method before subjected to a polymerase chain reaction amplification using primer sets specific for 1346-bp and 275-bp fragments of MSTN and FABP4, respectively. A 4-h digestion reaction was done separately for the MSTN/HaeIII and FABP4/NlaIII loci genotyping. The total protein, ash, and fat of the meat were measured using the Indonesian National Standard (SNI) methods whereas its cholesterol content was determined using the AOAC method. The association between each polymorphism and the variation in meat chemical parameters was analyzed using the Pearson correlation test.

Results:

The results showed that the MSTN/HaeIII locus was polymorphic in Aceh cattle, but the FABP4/NlaIII locus was monomorphic. Meat chemical parameters were not influenced by different commercial cuts and MSTNgenotypes, showing that there was no association between different commercial cuts, cattle hair colors, and MSTN/HaeIII and FABP4/NlaIII markers with the meat chemical parameters in Aceh cattle.

Conclusion:

These results suggest that focusing on the novel effects of MSTN and FABP4 gene polymorphisms on meat production traits might not be useful for marker-assisted selection in Aceh cattle.

Genomic Variant Analyses in Pyrethroid Resistant and Susceptible Malaria Vector, Anopheles sinensis

Anopheles sinensis is a major malaria vector in Southeast Asia. Resistance to pyrethroid insecticides in this species has impeded malaria control in the region. Previous studies found that An. sinensis populations from Yunnan Province, China were highly resistant to deltamethrin and did not carry mutations in the voltage-gated sodium channel gene that cause knockdown resistance. In this study, we tested the hypothesis that other genomic variants are associated with the resistance phenotype. Using paired-end whole genome sequencing (DNA-seq), we generated 108 Gb of DNA sequence from deltamethrin -resistant and -susceptible mosquito pools with an average coverage of 83.3× depth. Using a stringent filtering method, we identified a total of 916,926 single nucleotide variants (SNVs), including 32,240 non-synonymous mutations. A total of 958 SNVs differed significantly in allele frequency between deltamethrin -resistant and -susceptible mosquitoes. Of these, 43 SNVs were present within 37 genes that code for immunity, detoxification, cuticular, and odorant proteins. A subset of 12 SNVs were randomly selected for genotyping of individual mosquitoes by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and showed consistent allele frequencies with the pooled DNA-seq derived allele frequencies. In addition, copy number variations (CNVs) were detected in 56 genes, including 33 that contained amplification alleles and 23 that contained deletion alleles in resistant mosquitoes compared to susceptible mosquitoes. The genomic variants described here provide a useful resource for future studies on the genetic mechanism of insecticide resistance in this important malaria vector species.

Single nucleotide polymorphisms in the growth hormone receptor gene and Alu1 polymorphisms in the diacylglycerol acyltransferase 1 gene as related to meat production in sheep

Aim:

This study aimed to investigate the polymorphisms in genes related to meat production, including growth hormone receptor (GHR) and diacylglycerol acyltransferase 1 (DGAT1) genes, in different breeds of sheep, including Barki, Najdi, and Harri.

Materials and Methods:

Blood samples were collected from 75 randomly selected healthy Barki, Najdi, and Harri breeds of sheep, with 25 samples per breed. GHR and DGAT1 genes were identified using a single nucleotide polymorphism assay followed by digestion with the restriction enzyme Alu1.

Results:

The analysis of the GHR gene sequence showed nucleotide substitutions at nt 69 in exon 10 (c.69 G > A); this mutation is considered a transition mutation. The sequences of detected SNPs in the GHR gene in the different sheep breeds were submitted to the GenBank database with accession numbers MG906773 to MG906781. The substitutions at exon 10 (c.69 G > A) results in an alteration to the amino acid (p. Lysine > Arginine). At c.69, the A allele frequency was 0.61, 0.59, and 0.54, while the G allele frequency was 0.39, 0.41, and 0.46, for Barki, Najdi, and Harri breeds, respectively. The genotype AG at nt 69 locus had the highest frequency in the Najdi and Harri sheep. The frequency of AG was 0.62, 0.61, and 0.64, while the frequency of AA was 0.30, 0.28, and 0.22, for Barki, Najdi, and Harri sheep, respectively. After digestion with the restriction enzyme AluI, the DGAT1 locus had two genotypes, CC and CT. The highest frequency, 0.88, was found for allele C, which was detected in Barki breed. The lowest frequency, 0.75, for the same allele was found for Harri.

Conclusions:

The detected CT genotype may explain the moderate intramuscular fat content and muscle marbling in the Barki sheep breed.

Protein tyrosine phosphatase nonreceptor type 22 gene polymorphism in alopecia areata: Does it have an association with disease severity?

BACKGROUND

Alopecia areata is a condition involving hair loss from certain or all areas of the body. It has been considered as an immune-mediated disease, characterized by the infiltration of CD4+ and CD8+ lymphocytes in the hair follicles.

AIM OF THE STUDY

The study aimed to assess whether protein tyrosine phosphatase nonreceptor type 22 gene single nucleotide polymorphism 1858C/T has any relationship with alopecia areata in Egyptian patients and whether it is associated with disease severity or not.

SUBJECTS AND METHODS

Protein tyrosine phosphatase nonreceptor type 22 (PTPN22) C1858T gene polymorphism was identified using polymerase chain reaction-restriction fragment length polymorphism analysis technique in 60 patients suffering from alopecia areata and 30 age- and sex-matched healthy controls. Disease severity was assessed using SALT score.

RESULTS

CT and TT genotypes were significantly higher in the patients' group (P = .005), OR = 4.38 95% CI [1.48-12.96], with significant statistical predominance of T allele in patients, P = .003, OR = 3.86, 95% CI [1.52-9.77]. There was also a positive significant relationship between protein tyrosine phosphatase nonreceptor type 22 genotype CT and SALT score.

CONCLUSION

PTPN22 1858T allele is associated with the development and severity of alopecia areata in Egyptians.

Determination of antimicotic susceptibility pattern of Candida species isolated from patients with symptomatic candiduria

Background

The present study was conducted to determine antimicotic susceptibility of Candida species (sp.) from patients with symptomatic candiduria.

Materials and Methods

Identification of Candida sp. and determination of efficacy of most routine antifungals were done using polymerase chain reaction-restriction fragment length polymorphism method and E-test, respectively.

Results

The results from susceptibility test reveal that caspofungin and amphotericin B have high antifungal activity against both albicans (100% and 96%, respectively) and nonalbicans (95.11% and 72.72%, respectively) isolates.

Conclusion

The present study suggests that caspofungin and amphotericin B have the excellent ability to eradicate both Candida groups that showed decreased susceptibility to other compounds.

Species adulteration in raw milk samples using polymerase chain reaction-restriction fragment length polymorphism

Background and Aim:

Milk adulteration is pivotal because it leads to worse effects in public health as human adverse reactions with clinical signs ranged from gastrointestinal signs to anaphylactic shock. This study was carried out to estimate the prevalence of adulteration in buffalo’s milk sold in Assiut City, Egypt.

Materials and Methods:

A total of 50 raw buffalo’s milk samples were collected and examined for adulteration by addition of cow’s milk. The examination carried out by applying polymerase chain reaction-restriction fragment length polymorphism technique using cytochrome b (cyt b) gene primers and Hinf I enzymes. The size of target gene was 360 bp in both animal species and amplicon can be digested using Hinf I enzyme, this restriction enzyme divided the essential band to clear three bands at 360, 210, and 150 bp in cows’ milk, while, the enzyme could not be cleaved the amplicon in buffalo’s samples.

Results:

The obtained results cleared that the incidence of adulteration of buffalo’s milk very high percentage reaches 90%.

Conclusion:

It could be concluded that the raw buffalo’s milk sold in Assiut City subject to fraudulent practice and thus can lead to public health hazards.

Detection of species and molecular typing of Leishmania in suspected patients by targeting cytochrome b gene in Zahedan, southeast of Iran

Aim:

Cutaneous leishmaniasis (CL) is one of the most important health problems that are capable of involving both tropical and subtropical areas, especially in Iran. This cross-sectional study aimed to differentiate the species that are able to cause CL in Zahedan city by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method.

Materials and Methods:

It was conducted on 145 suspected CL patients in Zahedan city between 2014 and 2016. The smears were initially prepared, air-dried, fixed with absolute methanol, and stained with 10% Giemsa. Then, we examined the stained samples by a light microscope under 1000× magnifications. PCR assay targeted cytochrome b(cyt b) gene using LCBF1 and LCBR2 primers and the products digested by Ssp1 enzymes.

Results:

From 145 suspected CL patients, 76 (52.4%) were positive in microscopic examination. In addition, we detected gene of interest (cyt b) in 98 (67.5%). The results of PCR-RFLP indicated that 53/98 (54%) cases were Leishmania major and 45/98 (46%) were Leishmania tropica, and the main species in these areas was L. major.

Conclusion:

We concluded that the microscopic examination is not sensitive enough and is not able to distinguish between different Leishmania species. Instead, molecular methods like PCR-RFLP can be appropriately used with promising results.

Screening of Polymorphisms of Transcription Factor 7-like 2 Gene in Polycystic Ovary Syndrome using Polymerase Chain Reaction-restriction Fragment Length Polymorphism Analysis

Background:

Polycystic ovary syndrome (PCOS) is a common endocrine disorder occurring in premenopausal women, with a prevalence rate of 5%–7%. It has been observed in multiple number of studies the coexistence between diabetes mellitus 2 and obesity with this endocrinopathic disorder. Transcription factor 7-like 2 (TCF7L2) gene is shown to be associated with insulin secretion.

Aim:

To screen whether the gene variant of TCF7L2 (formerly TCF4) gene is significantly associated and has susceptibilities with type 2 diabetes in PCOS. This study is essential to uncover diabetogenic association of the TCF7L2 gene variants with PCOS.

Design:

This was a hospital-based study.

Methods:

In this work, blood samples from 43 PCOS patients with age and sex similar to 43 control samples were collected, followed by isolation of DNA. Further genotyping of the TCF7L2 gene was carried out by performing polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP).

Statistical Analysis:

Genotype frequencies of the TCF7L2 rs7903146 gene were checked by Hardy–Weinberg equilibrium of genotype in both PCOS and the control group, and also, the frequencies of the genotype were performed accordingly.

Results:

There was no significant allelic variation observed among the patient and the control samples. From the patient details, it was observed that women between the age group of 21 and 25 years are susceptible to PCOS.

Conclusion:

From the PCR-RFLP analysis, it can be stated that there are no expected gene polymorphisms seen in this study, unlike the study carried out on the Chinese population where they observed genotype variations CC, CT, and TT. From this study, we can conclude that TCF7L2 rs7903146 gene cannot be considered as the candidate gene for the occurrence of PCOS.

Influence of interferon-gamma Receptor 1 gene polymorphisms on the susceptibility to pulmonary tuberculosis among sudanese population

Background

A variety of genetic mutations are thought to be responsible for acquisition of different infections such as tuberculosis (TB). An obvious example for these variations is the link between pulmonary TB and polymorphisms within interferon-gamma receptor 1 (IFN-γ R1) gene. This project is designed to identify the role of IFN-γR1 gene polymorphism in the development of pulmonary TB among Sudanese patients attending several hospitals in Khartoum State.

Methods

One hundred (n = 100) patients with active TB and fifty (n = 50) matched healthy controls were investigated for the association of two genetic polymorphisms within IFN-γR1 gene and their risk of developing pulmonary tuberculosis. Polymerase chain reaction (PCR) assay and PCR-restriction fragment length polymorphism were performed.

Results

Migrated IFN-γR1 DNA bands representing genotypes and polymorphic alleles were identified. Molecular findings revealed that two genetic variants, namely, -56C and +295C deletion 12 within IFN-γR1 gene, were nonsignificantly linked with increased risk of development of pulmonary TB, P = 0.771 and 0.343, respectively. Two genetic variants within IFN-γR1 gene were examined for suggested role in inducing development of TB.

Conclusion

The two genetic variants were found to have potential risk in association with active disease development among Sudanese patients. Further intensive research work involving use of large collection of samples should be conducted to verify these findings.

Molecular identification and antifungal susceptibility profile of Candida species isolated from patients with vulvovaginitis in Tehran, Iran

Background

Rapid and accurate identification and evaluation of antifungal susceptibility pattern of Candida isolates are crucial to determine suitable antifungal drugs for the treatment of patients with vulvovaginitis candidiasis.

Materials and Methods

Vaginal samples were collected from 150 women with suspicious vaginal candidiasis, and then cultured on Sabouraoud's Dextrose Agar with chloramphenicol to isolate Candida species. After identification of Candida isolates using polymerase chain reaction-restriction fragment length polymorphism technique, antifungal susceptibility testing of four azolic antifungal drugs was carried out using broth microdilution method according to the CLSI M27-A3.

Results

Candida species were isolated from eighty suspected patients (61.79%). The most common pathogen was Candida albicans (63.75%). Resistance to fluconazole and ketoconazole was observed in 27.5% and 23.75% of Candida isolates, respectively, and only 2% of Candida isolates were resistant to miconazole. Interestingly, resistance to fluconazole in C. albicans was more than other Candida species.

Conclusion

The results indicated that therapy should be selected according to the antifungal susceptibility tests for the prevention of treatment failure and miconazole therapy can be considered as the best therapeutic choice in the management of vulvovaginitis.

Assessment of the role of plasma nitric oxide levels, T-786C genetic polymorphism, and gene expression levels of endothelial nitric oxide synthase in the development of coronary artery disease

Background:

Reduced bioavailability of nitric oxide (NO) and the T-786C polymorphism of endothelial nitric oxide synthase (eNOS) gene have been reported as risk factors for the development of coronary artery disease (CAD) with conflicting results. We investigated the association of plasma NO levels, T-786C genetic polymorphism, and gene expression levels of eNOS with CAD risk in an Iranian subpopulation.

Materials and Methods:

Studied population included 100 patients with angiographically verified CAD and 100 ethnically matched controls. Analysis of T-786C genetic polymorphism and gene expression levels of eNOS was conducted by polymerase chain reaction (PCR) restriction fragment length polymorphism and real-time reverse transcription-PCR methods, respectively. Plasma levels of NO were measured using Griess method.

Results:

The CC genotype distribution (15% vs. 6%, P = 0.011) and minor C allele frequency (36.5% vs. 21.5%, P = 0.001) of eNOS T-786C polymorphism differed significantly between CAD patients and control. Furthermore, eNOS T-786C polymorphism was more common among smoker than nonsmoker CAD patients (27.7% vs. 7.8%, P = 0.044). The association of the eNOS T-786C polymorphism with the severity of CAD (number of diseased vessel) was significant (P < 0.05). The gene expression levels of eNOS were significantly lower in the heterozygote (0.49 ± 0.1, P = 0.023) and mutant homozygote (0.36 ± 0.09, P = 0.011) genotypes than that of wild-type genotype (P < 0.05). In addition, NO levels were significantly lower in CAD patients compared with control subjects (42.62 ± 12.26 vs. 55.48 ± 16.57, P = 0.002) and showed intergenotypic variation in the CAD patients.

Conclusion:

Our study indicated that reduced NO levels and eNOS T-786C genetic polymorphism are significant risk factors for the development and severity of CAD in the Iranian population.

Toxoplasma gondii Type I, predominant genotype isolated from sheep in South of Iran

Aim:

This study was performed to determine the genetic diversity of Toxoplasma gondii in sheep using nested-polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) in Southern Iran.

Materials and Methods:

The tissue samples of diaphragm and heart from 125 sheep were collected from the main slaughterhouses of Jahrom district in South of Fars province, Iran, between Aprils and June 2013. The DNA were extracted and analyzed by nested-PCR using specific primers for SAG2 and GRA6 loci. RFLP was used to classify strains into one of the three major lineages of T. gondii.

Results:

T. gondii Type I was predominant in this area. The data obtained from both loci demonstrated that the frequency of each genotype was 72% Type I, 2.4% Type III, 7.2% mixed Type I and II, 16.8% mixed Type I and III, 0.8% mixed Type II and III, and 0.8% mixed Type I, II and III.

Conclusions:

Although the previously published data indicated that Type II is the predominant T. gondii genotype in sheep in the other parts of the world, this study showed that genotype I is the dominant genotype of T. gondii in the southern Iran; however, other genotypes were detected. High diversity of T. gondii genotypes including mix genotypes in lambs is of importance for the public health. These studies depict a new mapping of T. gondii genotypes pattern which could be very helpful in toxoplasmosis control and prevention.

Plasma concentration, genetic variation, and gene expression levels of matrix metalloproteinase 9 in Iranian patients with coronary artery disease

Background:

Matrix metalloproteinase 9 (MMP9) -1562C>T (rs3918242) polymorphism has been proposed as a risk factor for coronary artery disease (CAD) with conflicting results. The aim of the present study was to investigate the association of -1562C>T genetic polymorphism, gene expression and circulating levels of MMP9 with CAD risk in an Iranian subpopulation in in Zanjan City.

Materials and Methods:

This was a retrospective case–control study we investigated retrospectively 100 patients with angiographically verified CAD and 100 matched controls. Genotyping of -1562C>T polymorphism was done by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Gene expression levels and circulating levels of MMP9 was determined by real-time reverse transcription-PCR and enzyme immunoassay method, respectively. Statistical analysis was done using Student's t-test or Chi-square test by SPSS 16 software.

Results:

The mean circulating levels of MMP9 were significantly higher in CAD Group than control group (P = 0.002). Mean plasma levels of MMP9 were also significantly higher in triple vessel stenosis patients than double vessel or single vessel stenosis patients (P < 0.001). Moreover, mean plasma levels and gene expression levels of MMP9 were significantly higher in T allele carrier than C allele carrier of MMP9 -1562C>T polymorphism (P = 0.002, P = 0.01, respectively). However, genotype and allele frequencies of MMP9 -1562C>T polymorphism were similar between CAD patients and controls (P > 0.05). Additionally, the -1562C>T polymorphism of MMP9 gene didn't increase the risk of CAD in dominant (P = 0.537) or recessive (P = 0.249) genetic models.

Conclusion:

Our study demonstrated that circulating levels of MMP9 but not -1562C>T polymorphism of MMP9 gene may be a risk factor for development and severity of CAD in an Iranian subpopulation in Zanjan.

Expression of Human Papillomavirus DNA and p53 Polymorphisms through Polymerase Chain Reaction in Normal Mucosa and Oral Leukoplakia Individuals with Deleterious Oral Habits

Context:

Oral leukoplakia (OL) is a well-recognized precancerous lesion with various etiological factors. Most commonly deleterious oral habits such as tobacco smoking and viral etiologies mainly human papillomavirus (HPV) play an important role. p53 polymorphisms mostly homozygous Arginine (Arg) allele has a greater risk of degradation by HPV. Hence, HPV infection and p53 polymorphisms may act as synergistic factors for increased the risk of malignant transformation in oral precancerous lesions.

Aims:

The aim of this study is to evaluate the risk of OL and its malignant transformation due to infection by HPV and p53 polymorphisms in the oral biopsy samples through polymerase chain reaction (PCR).

Subjects and Methods:

A total of 40 individuals were involved– 10 individuals were controls without deleterious habits, 15 were controls with deleterious habits, and 15 were with histologically confirmed OL individuals with deleterious habits. PCR and restriction fragment length polymorphism using sma1 enzyme were carried out to evaluate the expression of HPV and p53 polymorphisms.

Statistical Analysis Used:

Chi-square test, Fischer's exact t-test, and odds ratio.

Results:

(1) HPV DNA expression was higher in Leukoplakia individuals than controls. (2) p53 genotype with homozygous Arg was more in HPV-infected individuals.

Conclusions:

To conclude HPV infected OL cases were mostly with Arg/Arg type of p53 polymorphism.

Molecular variation analysis of Aspergillus flavus using polymerase chain reaction-restriction fragment length polymorphism of the internal transcribed spacer rDNA region

Aspergillus flavus is the second most common disease-causing species of Aspergillus in humans. The fungus is frequently associated with life-threatening infections in immunocompromised hosts. The primary aim of the present study was to analyze the genetic variability among different isolates of A. flavus using polymerase chain reaction (PCR)-based restriction fragment length polymorphism (RFLP). A total of 62 A. flavus isolates were tested in the study. Molecular variability was searched for by analysis of the PCR amplification of the internal transcribed spacer (ITS) regions of ribosomal DNA using restriction enzymes. PCR using primers for ITS1 and ITS4 resulted in a product of ~600 bp. Amplicons were subjected to digestion with restriction endonucleases EcoRI, HaeIII and TaqI. Digestion of the PCR products using these restriction enzymes produced different patterns of fragments among the isolates, with different sizes and numbers of fragments, revealing genetic variability. In conclusion, ITS-RFLP is a useful molecular tool in screening for nucleotide polymorphisms among A. flavus isolates.

OPG rs2073617 polymorphism is associated with upregulated OPG protein expression and an increased risk of intervertebral disc degeneration

The present study aimed to investigate the associations between three distinct osteoprotegerin (OPG) gene polymorphisms and the risk of intervertebral disc degeneration (IDD). A total of 200 IDD patients and 200 healthy controls were recruited from the Department of Spine Surgery at the First Affiliated Hospital of the University of South China (Hengyang, China) between January 2013 and May 2014. The allele, genotype and haplotype frequency distributions of three OPG polymorphisms in the study and control populations were analyzed by polymerase chain reaction prior to restriction fragment length polymorphism or high resolution melting assays. In addition, serum OPG levels were measured via an ELISA. The genotype and allele frequencies of the OPG rs2073617 polymorphisms were significantly higher in the IDD patients, as compared with the control group (P<0.05). Furthermore, carriers of the C allele exhibited a higher risk of IDD, as compared with carriers of the T allele (P<0.001). Conversely, the genotype and allele frequencies of the two other gene polymorphisms, rs2073618 and rs3102735, showed no significant differences between the patients and controls (P>0.05). The serum OPG levels were significantly higher in IDD patients with TT, TC and CC genotypes at the OPG rs2073617 polymorphism, as compared with the control group (P<0.05). Logistic-regression analysis suggested that high serum levels of OPG were positively correlated with IDD risk, whereas the T-C-A, T-G-A and T-G-G haplotypes were negatively correlated with IDD risk (P<0.05). Furthermore, the G-T-G haplotype was associated with protection against IDD (P=0.008), whereas the G-C-G haplotype was associated with an elevated susceptibility to IDD (P=0.007). The results of the present study suggested that OPG rs2073617 polymorphisms and upregulated serum levels of OPG were associated with an increased risk of IDD, whereas the T-C-A, T-G-A and T-G-G haplotypes were protective factors for IDD. The results of the present study suggested that the OPG gene polymorphism may have an important role in the progression of IDD, and its serum level may function as a valuable predictive indicator of the severity of degenerative disc diseases.

An improved polymerase chain reaction-restriction fragment length polymorphism assay for the detection of a PON2 gene polymorphism

In recent research, it has been shown that there have been variants of rs12026 within the paraoxonase 2 (PON2) gene, which have been associated with cardiovascular disease, cerebrovascular disease, diabetes and other diseases. The isochizomers, such as the BsoFI enzyme, required for the detection of this polymorphism are expensive. Therefore, an improved and less expensive polymerase chain reaction (PCR)-restriction fragment length polymorphism method was established for the detection of the single-nucleotide polymorphism rs12026 in the exon 5 of chromosome 7 of the human PON2 gene using the method of amplification-created restriction site. Subsequent to assessing 302 individuals, the genotype frequencies were 68.9% for CC, 29.8% for CG and 1.3% for GG, and the allelic frequencies were 83.8% for C and 16.2% for G. The PCR results were confirmed by DNA sequencing. The χ² test showed that the genotype and allele frequencies of PON2-148 do not deviate from Hardy-Weinberg equilibrium, and the sequences of amplified products were consistent with the sequence published in GenBank with the exception of a mismatched base.

Analysis of the rDNA internal transcribed spacer region of the Fusarium species by polymerase chain reaction-restriction fragment length polymorphism

The Fusarium species are a widely spread phytopathogen identified in an extensive variety of hosts. The Fusarium genus is one of the most heterogeneous fungi and is difficult to classify. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis is a useful method in detection of DNA polymorphism in objective sequences. The aim of the present study was to identify the phylogenetic associations and usefulness of the internal transcribed spacer (ITS) region as a genetic marker within the most clinically important strain of the Fusarium species. A total of 50 strains of Fusarium spp. were used in the study, including environmental, clinical and reference isolates. The primers ITS1 and ITS4 were used in the study. Two restriction enzymes, HaeIII and SmaI, were assessed for the digestion of PCR products. A PCR product of ~550-base pairs was generated for each Fusarium species. The digested products with HaeIII and SmaI demonstrated that the bands generated for the medically significant Fusarium species, including F. solani, F. oxysporum, F. verticillidea, F. proliferatum and F. fujikuri, have different restriction enzyme patterns. In conclusion, it appears that the PCR-RFLP method used in the present study produces a sufficient restriction profile for differentiation of the most medically significant Fusarium species.

Genetic Polymorphism of Manganese Superoxide Dismutase in Behçet's Disease

Objectives

This study aims to investigate the genetic association between single nucleotide mutation in mitochondrial manganese superoxide dismutase and a Behçet's disease (BD) population by using molecular techniques.

Patients and methods

Ninety-three BD patients (45 males, 48 females; mean age 33.15±8.99 years; range 17 to 65 years) and 125 controls (58 males, 67 females; mean age 28.33±7.31 years; range 18 to 62 years) were genotyped by polymerase chain reaction-restriction fragment length polymorphism method. The genotypic distributions in BD patients and controls were consistent with the Hardy-Weinberg equilibrium.

Results

Significant differences were observed between BD patients and controls in terms of genotypic distribution. Frequencies of alanine (Ala)/Ala, Ala/valine (Val), and Val/Val were 14.0% (n=13), 45.2% (n=42), and 40.9% (n=38) in BD patients and 21.6% (n=27), 53.6% (n=67), and 24.8% (n=31) in controls, respectively (p=0.033).

Conclusion

The Val/Val genotype of the manganese superoxide dismutase gene is associated with the physiopathology of BD in a group of Turkish patients.

Association study of methylenetetrahydrofolate reductase A1298C mutation with cerebral venous thrombosis risk in an Iranian population

BACKGROUND

Cerebral venous thrombosis (CVT) is an uncommon condition characterized by severe clinical manifestations and high mortality rate. There is limited data on the role of methylenetetrahydrofolate reductase (MTHFR) A1298C mutation as a risk factor for CVT development in Iranians.

AIM

The aim was to investigate a possible association between fasting plasma homocysteine (Hcy) levels, MTHFR A1298C mutation, and CVT in Iranian population.

MATERIALS AND METHODS

The study population consisted of 50 patients with a diagnosis of CVT (20-63 years old) and 75 healthy subjects (18-65 years old) as control. Genotyping of the MTHFR A1298C mutation and Hcy measurement was carried out by polymerase chain reaction-restriction fragment length polymorphism technique and enzyme immunoassay method, respectively.

RESULTS

Fasting plasma total Hcy levels were significantly higher in CVT patients than controls (P = 0.015). No significant differences were observed in the MTHFR A1298C genotypes frequency between CVT patients and controls (P > 0.05). The frequency of the 1298C allele was 36% and 37.5% in CVT patients and controls, respectively and did not differ significantly between the two groups (P = 0.16).

CONCLUSIONS

Our study demonstrated that MTHFR A1298Cmutation is not a significant risk factor for CVT.

Genotyping of major histocompatibility complex Class II DRB gene in Rohilkhandi goats by polymerase chain reaction-restriction fragment length polymorphism and DNA sequencing

Aim:

To study the major histocompatibility complex (MHC) Class II DRB1 gene polymorphism in Rohilkhandi goat using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and nucleotide sequencing techniques.

Materials and Methods:

DNA was isolated from 127 Rohilkhandi goats maintained at sheep and goat farm, Indian Veterinary Research Institute, Izatnagar, Bareilly. A 284 bp fragment of exon 2 of DRB1 gene was amplified and digested using BsaI and TaqI restriction enzymes. Population genetic parameters were calculated using Popgene v 1.32 and SAS 9.0. The genotypes were then sequenced using Sanger dideoxy chain termination method and were compared with related breeds/species using MEGA 6.0 and Megalign (DNASTAR) software.

Results:

TaqI locus showed three and BsaI locus showed two genotypes. Both the loci were found to be in Hardy–Weinberg equilibrium (HWE), however, population genetic parameters suggest that heterozygosity is still maintained in the population at both loci. Percent diversity and divergence matrix, as well as phylogenetic analysis revealed that the MHC Class II DRB1 gene of Rohilkhandi goats was found to be in close cluster with Garole and Scottish blackface sheep breeds as compared to other goat breeds included in the sequence comparison.

Conclusion:

The PCR-RFLP patterns showed population to be in HWE and absence of one genotype at one locus (BsaI), both the loci showed excess of one or the other homozygote genotype, however, effective number of alleles showed that allelic diversity is present in the population. Sequence comparison of DRB1 gene of Rohilkhandi goat with other sheep and goat breed assigned Rohilkhandi goat in divergence with Jamanupari and Angora goats.

Association between PTPN22 C1858T polymorphism and alopecia areata risk

Alopecia areata (AA) is a skin condition in which hair is lost from certain or all areas of the body. This condition has been described as an immune-mediated complex genetic disease, characterized by the presence of lymphocytes that are directed to the hair follicles in the anagen phase. The gene encoding the protein tyrosine phosphatase, non-receptor type 22 (PTPN22), which is exclusively expressed in immune cells, has been considered as a risk factor associated with a number of autoimmune diseases. In AA, the single nucleotide polymorphism, rs2476601, has been identified as a risk factor in several populations. The aim of the present study was to investigate the effect of PTPN22 C1858T inherited genetic polymorphism on the predisposition to severe forms of AA, in a case-control study on individuals. The study included 64 unrelated patients diagnosed with several types of AA, as well as 225 healthy unrelated subjects. The DNA samples were genotyped for PTPN22 C1858T polymorphism using the polymerase chain reaction-restriction fragment length polymorphism technique. Causal associations were determined by χ² test and their respective odds ratio (OR) was assessed in a 2×2 contingency table. The results demonstrated a significant association of the T allele [P=0.040; OR=3.196; 95% confidence interval (CI), 0.094-10.279] and the CT genotype (P=0.038; OR=3.313; 95% CI, 1.008-10.892) with patchy AA. In conclusion, the results of the present study suggested the possible involvement of the T allele of the PTPN22 C1858T SNP as a genetic risk factor for this type of AA in the population studied.

Polymorphism and association of growth hormone gene with growth traits in Sirohi and Barbari breeds of goat

AIM

The aim was to study the polymorphism of exon 2 and exon 3 of growth hormone (GH) gene, to test the polymorphic variants for Hardy-Weinberg equilibrium and to investigate association of these polymorphisms with chest girth and paunch girth in Sirohi and Barbari breeds of goat.

MATERIALS AND METHODS

A total of 80 kids involving forty each of Sirohi and Barbari breeds of goat were included in the study. A good quality genomic DNA isolated from the whole blood using standard protocol were used for polymerase chain reaction (PCR) amplification and products obtained on restriction digestion of amplicon with enzyme HaeIII were separated on 2% agarose gel, and documented in a gel doc system. The chest girth and paunch girth of kids at birth and weekly intervals up to 4 weeks of age and subsequently at 2 months, 3 months and 6 months of age were recorded. Allele frequency and genotype distribution of polymorphism were tested for Hardy-Weinberg equilibrium by program me Genepop package. Association between different genetic variants on chest girth and paunch girth were analyzed by least squares analysis employing suitable statistical model.

RESULTS

The PCR product of genomic DNA isolated from kids of Sirohi and Barbari breeds of goat on digestion with the restriction enzyme HaeIII revealed two genotypic variants viz., AB and BB. None of the two breeds was in Hardy-Weinberg equilibrium for these variants. The least squares analysis of variance revealed non-significant effect of GH genotype and breed × genotype interaction on chest girth and paunch girth from birth to 180 days of age. The effect of breed was highly significant (p<0.01) at all ages.

CONCLUSION

The present study showed that both the breeds were polymorphic at the exon 2 and exon 3 loci of GH gene under study with respect to HaeIII restriction endonuclease. None of the breeds was in Hardy-Weinberg equilibrium for this region of GH gene. In the present study, no significant association between GH genotype and chest girth and paunch girth could be established but comparatively higher chest girth and paunch girth were observed for AB genotype across the breeds.

Protein tyrosine phosphatase PTPN22 +1858C/T polymorphism is associated with active vitiligo

Vitiligo is characterized by a skin depigmentation disorder resulting from an autoimmune response targeting melanocytes. Within the genetic factors involved in the development of the vitiligo immune response, various genes in the major histocompatibility complex (MHC) and non-MHC loci have been considered to be risk factors. The PTPN22 gene encodes for a lymphoid protein tyrosine phosphatase, a regulator of the activation and development of T-cells. The +1858C/T polymorphism has been associated to autoimmune disease susceptibility in different populations and could be implicated in the onset of vitiligo. To assess the possible association between the presence of PTPN22 +1858C/T and vitiligo, 187 patients with vitiligo and 223 control subjects were analyzed in the study. Genomic DNA was isolated using the salting-out method and samples were subjected to polymerase chain reaction-restriction fragment length polymorphism in order to detect the PTPN22 +1858C/T polymorphism. Causal associations were determined by χ² test and their respective odds ratio (OR) was assessed in a 2×2 contingency table. The results showed an association between active vitiligo and the allele T load [P=0.0418; OR, 2.5706; 95% confidence interval (CI), 1.0040-6.5816], and active vitiligo-CT genotype (P=0.0389, OR, 2.6548; 95% CI, 1.0191-6.9156). In conclusion, the present data indicates a possible association between the PTPN22 +1858C/T genotype and a significant susceptibility of developing an active form of vitiligo.

Molecular technique for detection of Leishmania infantum isolates in Iran

Introduction:

Leishmania infantum is the causative agent of autochthonous cutaneous and visceral cases of leishmaniasis and transmitted by female sandflies. The dogs are considered the main reservoir hosts; however, there are the reports on Leishmania infection in other animals. In this study, occurrence types of L. infantum isolates have been analyzed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique.

Materials and Methods:

In this experimental study, 77 samples were cultured and prepared for microscopic study and examined through PCR-RFLP. The samples were used for both deoxyribonucleic acid (DNA) and smear-slide preparations. The DNAs were amplified by PCR for the detection of Leishmania subgenus and PCR products were restricted with HaeIII for the species differentiation.

Results:

The visceral Leishmania parasites were genotyped as L. infantum. It was also determined sensitivity in PCR (100%) was higher than microscopic examination.

Conclusion:

PCR-RFLP technique appears to be most sensitive for the detection and differentiation of L. infantum. There exists a relationship between genetic heterogeneousness and clinical manifestation and geographical regions of this disease in human.

Role of interstitial collagenase gene promoter polymorphism in the etiology of gastric cancer

BACKGROUND/AIMS

Gastric cancer (GC) is a multifactorial disorder mediated by genetic, epigenetic, and environmental risk factors. GC is the most common cancer in India and it is the third prominent cause of cancer death worldwide. A single nucleotide polymorphism (SNP) in the promoter region of interstitial collagenase (MMP-1) gene appears to have an impact on the transcriptional activity and regulation of its expression. Hence, the present study is aimed to evaluate the role of interstitial collagenase gene-1607 1G/2G (rs1799750) promoter polymorphism in the etiology of GC.

PATIENTS AND METHODS

The study included 166 GC patients and 202 control subjects. Genomic DNA was isolated from whole blood samples of the subjects, and the genotyping of interstitial collagenase promoter polymorphism was carried out by polymerase chain reaction-restriction fragment length polymorphism method followed by agarose gel electrophoresis. Appropriate statistical methods were applied to test the significance of the results.

RESULTS

The risk factor profile of the patients revealed that male gender, age above 50 years, addiction to alcohol and smoking were the most common risk factors (P < 0.05). There was a significant difference in the distribution of 2G/2G genotype (2G/2G vs. 1G/1G, P = 0.016) and 1G/2G genotype (2G/2G + 1G/2G vs. 1G/1G, P = 0.010) in patient group compared with that of the control subjects.

CONCLUSION

The present study provides indirect evidence for the role of interstitial collagenase gene 1G/2G promoter polymorphism in the etiology of GC in South Indian population.

Effect of CYP1A2 polymorphism on the pharmacokinetics of agomelatine in Chinese healthy male volunteers

WHAT IS KNOWN AND OBJECTIVE

Agomelatine is a melatonin (MT) analogue with agonistic properties and has been proven to be effective for various types of depressive symptoms. Following oral administration, agomelatine is primarily metabolized by the hepatic cytochrome P450 isoenzyme CYP1A2. The purpose of this study was to assess the influence of CYP1A2 single nucleotide polymorphisms (SNPs, rs762551, rs2069514, rs2472304, rs2470890) on agomelatine pharmacokinetics in the Chinese population.

METHODS

Seventy-two healthy Chinese male volunteers enrolled in the study received an oral dose of 25 mg of agomelatine after providing written informed consent. CYP1A2 SNPs were genotyped by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Agomelatine plasma concentrations were determined by high performance liquid chromatography-tandem mass spectrometry, and the pharmacokinetics analyses were evaluated by nonparametric methods.

RESULTS AND DISCUSSION

After a single oral dose of 25 mg agomelatine, no significant differences existed in agomelatine pharmacokinetics between the rs2069514 GG homozygotes (n = 35) and the rs2069514 AG allele (n = 35) in all subjects. The mean agomelatine AUC0-7 , AUC0-∞ and Cmax for the rs762551 CC homozygotes (n = 9), rs2470890 CC homozygotes (n = 54) and rs2472304 GG homozygotes (n = 51) were much higher than the rs762551 AA allele (n = 31), rs2470890 CT allele (n = 17) and rs2472304 AG allele (n = 20) respectively (P < 0.05).

WHAT IS NEW AND CONCLUSION

The rs762551 A, rs2470890 T and rs2472304 A genotype presented a significantly lower level of agomelatine exposure (AUC, Cmax ) compared with the rs762551 C, rs2470890 C and rs2472304 G genotype in Chinese healthy subjects. It suggested that the rs762551, rs2470890 and rs2472304 genetic polymorphism might be associated with the marked interindividual variability of agomelatine, and the pharmacokinetic profile of agomelatine may be different in different races.

Polymorphisms of the TLR4 gene and risk of gastric cancer

OBJECTIVE

Toll-like receptor 4 (TLR4) is an important lipo-polysaccharide (LPS) receptor in gastric epithelial cell signaling transduction and plays critical roles in the development and progression of gastric cancer (GC). We investigated the effects of TLR4 gene polymorphisms and gene-environmental interactions on the risk of GC in Northeastern China.

METHODS

We genotyped two single-nucleotide polymorphisms (SNPs) in TLR4 (rs10116253 and rs1927911) in 217 GC patients and 294 cancer-free controls using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Odds ratio (OR) and 95% confidence intervals (CIs) were estimated by unconditional logistic-regression models.

RESULTS

Individuals carrying CC genotype of rs10116253 and TT genotype of rs1927911 had a significantly decreased risk of GC (adjusted OR=0.33, 95% CI 0.18-0.60, P<0.001 and adjusted OR=0.37, 95% CI 0.21-0.67, P=0.001 respectively), compared with TT genotype of rs10116253 and CC genotype of rs1927911. In addition, the SNP effects were additive to the effects of some known environmental factors without any interaction between them in the susceptibility to GC.

CONCLUSION

Our data suggested that TLR4 gene polymorphisms may be associated with a decreased risk of GC in Chinese population. And these SNPs and their combined effects with environmental factors may be associated with the risk of GC.

Association of nicotinamide-N-methyltransferase (NNMT) gene rs694539 variant with bipolar disorder

Here we report the association of the rs694539 variant of nicotinamide-N-methyltransferase gene with bipolar disorder in a case-control study of 95 bipolar disorder patients and 201 healthy controls (χ(2)=13.382, P=0.001). With the polymerase chain reaction restriction fragment length polymorphism method we developed we were able to show the association for the first time. This new finding may provide evidence to understand the mechanism of the disease.

Expression, SNV identification, linkage disequilibrium, and combined genotype association analysis of the muscle-specific gene CSRP3 in Chinese cattle

The cysteine and glycine-rich protein 3 (CSRP3) plays an important role in the myofiber differentiation. Here, we identified five SNVs in all exon and intron regions of the CSRP3 gene using DNA sequencing, PCR-RFLP and forced-PCR-RFLP methods in 554 cattle. Four of the five SNVs were significantly associated with growth performance and carcass traits of the cattle. In addition, we evaluated haplotype frequency and linkage disequilibrium coefficient of five sequence variants. The result of haplotype analysis demonstrated 28 haplotypes present in Qinchuan and two haplotypes in Chinese Holstein. Only haplotypes 1 and 8 were being shared by two populations, haplotype 14 had the highest haplotype frequency in Qinchuan (17.4%) and haplotype 8 had the highest haplotype frequency in Chinese Holstein (94.4%). Statistical analyses of combined genotypes indicated that some combined genotypes were significantly or highly significantly associated with growth and carcass traits in the Qinchuan cattle population. qPCR analyses also showed that bovine CSRP3 gene was exclusively expressed in longissimus dorsi muscle and heart tissues. The data support the high potential of the CSRP3 as a marker gene for the improvement of growth performance and carcass traits in selection programs.

Comparing the joint effect of arsenic exposure, cigarette smoking and risk genotypes of vascular endothelial growth factor on upper urinary tract urothelial carcinoma and bladder cancer

Arsenic exposure and cigarette smoking are environmental risk factors for urothelial carcinoma (UC). Vascular endothelial growth factor (VEGF) is the key regulator of angiogenesis in various malignancies. This study investigates the joint effect of arsenic exposure, cigarette smoking, and VEGF polymorphisms on UC risk. This was a hospital-based case-control study consisting of 730 histopathologically confirmed UC cases, including 470 bladder cancers, 260 upper urinary tract UCs (UUTUCs), and 850 age-matched controls, recruited from September 1998 to December 2009. UC risk was estimated by odds ratios and 95% confidence intervals using unconditional logistic regression. Ever smokers with high arsenic exposure had significantly increased risks of 5.7 and 6.4 for bladder cancer and UUTUC, respectively. Moreover, ever smokers with high arsenic exposure carrying 1 or 2 risk genotypes of the VEGF gene had a significantly increased risk of 6.6 for bladder cancer and a strikingly higher risk of 9.9 for UUTUC. Additionally, UUTUC cases with high arsenic exposure carrying 1 or 2 risk genotypes of the VEGF gene had a non-significant increased risk of advanced tumor stage. Our findings suggest that arsenic exposure, cigarette smoking, and risk genotypes of VEGF contribute to a higher risk of UUTUC than of bladder cancer.

Association between MDR1 C3435T polymorphism and risk of breast cancer

The C3435T (rs1045642) polymorphism, located in multi-drug resistance gene 1 (MDR1), has demonstrated its role in decreasing the P-gp activity level which is related to the carcinogenesis. Many published studies have evaluated the association between the MDR1 C3435T polymorphism and breast cancer risk. However, the results remain conflicting rather than conclusive. To derive a more precise estimation of the association between MDR1 C3435T polymorphism and risk of breast cancer, we performed a meta-analysis comprised of 10 case-control studies, including 5282 breast cancer cases and 7703 controls. Odds ratios (ORs) and 95% confidence intervals (CIs) were used to evaluate the strength of the association. The overall results indicated that the variant genotypes were associated with a significantly increased risk of breast cancer (TT versus CC: OR=1.45, 95% CI=1.14-1.30, TT versus CT/CC: OR=1.13, 95% CI=1.04-1.23, TT/CT versus CC: OR=1.22, 95% CI=1.02-1.46). Our results suggest that the MDR1 C3435T polymorphism may contribute to individual susceptibility to breast cancer.

The genetic polymorphisms of cathepsin S were associated with metabolic disorders in a Chinese Han population

Cathepsin S (CTSS) played an important role in the etiology of cardiovascular disease and metabolic syndrome. Few studies had been reported on the association between the polymorphisms of CTSS and metabolic disorders in Asian population. Therefore we explored the association between the polymorphisms of CTSS and metabolic disorders in a Chinese Han population. The subjects were a Chinese Han cohort with 1160 participants, and the genotyping was performed with PCR-RFLP. Polymorphism rs16827671 was associated with BMI and serum total cholesterol (P=0.001; P=0.02, respectively). Subjects with CT genotype of rs16827671 had a higher risk of hypercholesterolemia (OR=1.64, 95% CI: 1.15-2.33, P=0.006) compared with TT genotype. Subjects with AG genotype of rs11576175 had lower risks of hypertriglyceridemia and borderline hypercholesterolemia (OR=0.52, 95% CI: 0.36-0.73, P=0.0001; OR=0.52, 95% CI: 0.35-0.77, P=0.001, respectively) compared with GG genotype. Compared with the haplotype TG, haplotype TA had a lower risk of hypertriglyceridemia and a higher risk of borderline hypercholesterolemia (OR=0.62, 95% CI: 0.44-0.88, P=0.002; OR=1.59, 95% CI: 1.10-2.31, P=0.008, respectively), and haplotype CA had a lower risk of hypercholesterolemia (OR=0.35, 95% CI: 0.18-0.68, P=0.002). In conclusion, we found that the genetic polymorphisms of CTSS were associated with metabolic disorders in a Chinese Han population, which would enrich the knowledge on genetic mechanisms of the pathogenesis of metabolic disorders.

Identification of mutation in NPC2 by exome sequencing results in diagnosis of Niemann-Pick disease type C

We report identification of a homozygous mutation in NPC2 in two Iranian siblings with a neurologic dysfunction whose disease had not been diagnosed prior to our genetic analysis. The mutation was identified by exome sequencing. The finding resulted in diagnosis of Niemann-Pick disease type C (NPC) in the siblings, and initiation of treatment with Miglustat. The clinical features of the patients are presented. It has been suggested that NPC is under diagnosed, particularly when presentations are not very severe, as was the situation in the cases studied here. NPC is a fatal autosomal recessive disorder clinically characterized by hepatosplenomegaly and progressive neurological deterioration. At the cellular level, it causes aberrant cholesterol trafficking and accumulation of unesterified cholesterol in lysosomes. Mutations in NPC1 and NPC2 are cause of disease in respectively, 95% and 5% of NPC patients. The p.Pro120Ser causing mutation in NPC2 observed in the Iranian patients was earlier observed in the only other NPC2 patient reported from the Middle East. The study demonstrates that in addition to greatly facilitating gene discovery, exome sequencing has notable potentials for diagnosis, particularly for diagnosis of atypical cases.

Use of polymerase chain reaction: Restriction fragment length polymorphism to detect acaricidal resistance to synthetic pyrethroids in Boophilus microplus ticks of South India

Background:

Boophilus microplus is an important ectoparasite of livestock. Apart from transmitting diseases, heavy tick burden can decrease production and damage hides. The synthetic pyrethroids which are advantageous over other acaricides for treatment of this infestation are now losing their efficacy due to development of resistant strains of ticks.

Materials and Methods:

Boophilus microplus ticks with a previous history of acaricidal treatment especially synthetic pyrethroids (SP) such as cypermethrin, deltamethrin and flumethrin were randomly collected from different pockets of four Southern States of India namely Tamil Nadu, Kerala, Karnataka, Andhra Pradesh, and Puducherry from cattle. Deoxyribonucleic acid extracted from pooled adult B. microplus tick from each State was subjected to polymerase chain reaction-restriction fragment length polymorphism to detect point mutation in carboxyl esterase gene.

Results:

A product size of 372 bp was obtained for cattle tick samples collected from all over Southern States of India.

Conclusions:

B. microplus ticks found in Southern part of India are not resistant to commonly used SP.

Single nucleotide polymorphism of CD40 in the 5'-untranslated region is associated with ischemic stroke

OBJECTIVES

Ischemic stroke is influenced by both environmental and genetic factors. The CD40/CD40L system is related to proinflammatory and prothrombogenic responses, which are involved in the pathophysiology of ischemic stroke. The aim of this study was to evaluate association between the CD40 -1C/T single nucleotide polymorphism (SNP) and ischemic stroke in a Chinese population.

METHODS

We conducted a case-control study including 286 ischemic stroke patients and 336 controls. CD40 -1C/T SNP was genotyped using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and DNA sequencing methods, and evaluated its relevance to ischemic stroke susceptibility.

RESULTS

Significantly increased ischemic stroke risk was found to be associated with the T allele of CD40 -1C/T (OR=1.273, 95% CI=1.016-1.594). The frequencies of CT and TT/CT genotypes of CD40 -1C/T in ischemic stroke patients were significantly higher than those of controls, respectively (for CT: OR=2.350, 95% CI=1.601-3.449; for TT/CT: OR=2.148, 95% CI=1.479-3.119). And, similar results were obtained after adjusting non-matched variables. We found that the frequency of carried T genotypes (TT and TT/CT) was significantly increased in patients with history of stroke compared with patients without (for TT: OR=6.538, 95%CI=1.655-25.833; for TT/CT: OR=3.469, 95%CI=1.031-11.670), respectively.

CONCLUSIONS

The findings suggested that the CD40 -1C/T polymorphism might contribute to the susceptibility to ischemic stroke in the Chinese population, and might be associated with history of previous stroke.

Effect of genetic variations within the SH2B2 gene on the growth of Chinese cattle

As an adaptor protein, apart from potentiating Janus kinase 2 (JAK2) activation and promoting the insulin signaling pathway, Src homology 2 B 2 (SH2B2) indirectly takes part in the regulation of glucose uptake through the c-Cb1/CAP/TC10 pathway, which can in turn affect growth. In this study, we identified a 4bp indel mutation and three single nucleotide polymorphisms (SNPs) within the SH2B2 gene in 959 individuals from five Chinese cattle breeds by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and sequencing. Based on the four variations, 12 haplotypes were identified. Additionally, there was a tendency that in every population pair-wise linkages increased progressively from V1-V2 to V3-V4. By association analysis, positive effects of genotypes CC and CT (snp1220 locus), DI (4bp indel locus), and CC (snp21049 locus) on growth traits were obtained. Furthermore, when combined, individuals with the combination CCDITTCC showed the best performance at an early age. These results were suggestive of an association of snp1220, 4bp indel and snp12049 with growth performance in Nanyang cattle, indicating possibly the candidate role of the SH2B2 gene in marker assisted selection in a beef cattle breeding program.

Methionine synthase A2756G polymorphism and breast cancer risk: an up-to-date meta-analysis

The methionine synthase (MTR) gene polymorphism A2756G has been linked to the risk of developing breast cancer, but the available results were inconsistent and underpowered. To derive a more precise estimation of the association between A2756G and breast cancer risk, an updated meta-analysis of 16 available studies with 9866 cases and 11,702 controls estimating the association between MTR A2756G and breast cancer risk was conducted. The quality of these studies was generally good except 2 studies with a lowest score 4 according to the Newcastle-Ottawa Scale (NOS). The results suggested that there is no significant association between A2756G and breast cancer risk in overall results. In the stratified analysis by ethnicity, source of controls (population or hospital-based), Hardy-Weinberg equilibrium (HWE) in controls, sample size (≥1000 and <1000 subjects), and menopausal status, the 2756G allele was associated with a decreased risk in Caucasians, PB (population-based) subgroup, and large studies. But the associations disappeared after removing the studies not in HWE. On the contrary, an increased risk was found in small studies. In conclusion, the findings suggest that MTR A2756G polymorphism is not associated with altered susceptibility to breast cancer, while the observed decreased risk in Caucasians, PB subgroup, and large studies and increased risk in small studies may be due to selection bias or other unknown factors.

Association study of CD36 single nucleotide polymorphisms with essential hypertension in the Northeastern Han Chinese

We found that cluster determinant 36 (CD36) gene is up-regulated in essential hypertension (EH) patients in our former research, but the association between CD36 gene variations and EH has not yet been clearly demonstrated. The relationship between CD36 gene single nucleotide polymorphisms (SNPs) and EH in the northeastern Han Chinese was examined in the present study through direct sequencing and genotype-detection. A total of 589 unrelated northeastern Han Chinese including 276 with EH and 313 controls were studied. SNPs in exon 7, exon 13 and intron 4 were detected using PCR-sequencing. The genotypes were determined by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) or polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP). +216T/C, +273A/G, +132C/T, +217T/C, +212T/G and +233T/C polymorphisms were identified. Distributions of genotypes AA, GA and GG of +273A/G polymorphism were significantly different between EH group and the control group (χ2: 9.056, p=0.011) and G allelic frequency was higher in EH (p=0.006, OR=1.629, 95% CI [1.224-2.168]). Logistic regression analysis showed that +273A/G polymorphism was closely associated with blood pressure (BP) after adjusting for ages. When subclassified by sex, the genotype distribution of +273A/G (p=0.011) and allelic frequency of G allele (p=0.006) were significantly different between EH participants and controls in males, but not in females. Subgroup analysis performed by body mass index (BMI) suggested that the genotype distribution of +273A/G and allelic frequency were significantly different in non-obese group and non-obese men, but the associations were not significant (non-obese group: p=0.016, OR=1.664, 95% CI [1.459-2.409]; non-obese men: p=0.073, OR=1.898, 95% CI [1.033-3.487]). +273A/G polymorphism in CD36 gene was associated with EH, and +273G could be an independent predictor.

Three common functional polymorphisms in microRNA encoding genes in the susceptibility to hepatocellular carcinoma: a systematic review and meta-analysis

Emerging evidences have shown that common genetic polymorphisms in microRNAs may be associated with the development of hepatocellular carcinoma (HCC); but individually published studies and previous meta-analyses revealed inconclusive results. The aims of this review and meta-analysis are to assess whether common single-nucleotide polymorphisms (SNPs) in the genes encoding the microRNAs are associated with susceptibility to HCC development and clinicopathologic characteristics of hepatitis B virus (HBV) related HCC. A computerized search was performed in PubMed, Embase, Web of Science and China BioMedicine (CBM) databases to identify relevant articles published before January 1st 2013. Ten case-control studies were assessed with a total of 3437 cases and 3437 healthy controls. Three common functional SNPs in miRNA-encoding genes were found, including miR-146a G>C (rs2910164), miR-196a-2 C>T (rs11614913) and miR-499 T>C (rs3746444). This meta-analysis revealed that the miR-146a C variant was associated with a decrease in HCC risk, especially among Asian and male populations; while the miR-196a-2 T variant was associated with susceptibility to HCC among Caucasian populations. However, we failed to find any significant correlations between the miR-499 C polymorphism and HCC risks. When further stratification on HBV status was conducted, a similar trend of association between the three SNPs and the HBV-related HCC risks was observed, but these results were not statistically significant due to small sample sizes. The current meta-analysis demonstrates that SNPs contained in the genes encoding miR-146a and miR-196a-2 may play a major role in genetic susceptibility to HCC.

Three common functional polymorphisms in microRNA encoding genes in the susceptibility to hepatocellular carcinoma: a systematic review and meta-analysis

Emerging evidences have shown that common genetic polymorphisms in microRNAs may be associated with the development of hepatocellular carcinoma (HCC); but individually published studies and previous meta-analyses revealed inconclusive results. The aims of this review and meta-analysis are to assess whether common single-nucleotide polymorphisms (SNPs) in the genes encoding the microRNAs are associated with susceptibility to HCC development and clinicopathologic characteristics of hepatitis B virus (HBV) related HCC. A computerized search was performed in PubMed, Embase, Web of Science and China BioMedicine (CBM) databases to identify relevant articles published before January 1st 2013. Ten case-control studies were assessed with a total of 3437 cases and 3437 healthy controls. Three common functional SNPs in miRNA-encoding genes were found, including miR-146a G>C (rs2910164), miR-196a-2 C>T (rs11614913) and miR-499 T>C (rs3746444). This meta-analysis revealed that the miR-146a C variant was associated with a decrease in HCC risk, especially among Asian and male populations; while the miR-196a-2 T variant was associated with susceptibility to HCC among Caucasian populations. However, we failed to find any significant correlations between the miR-499 C polymorphism and HCC risks. When further stratification on HBV status was conducted, a similar trend of association between the three SNPs and the HBV-related HCC risks was observed, but these results were not statistically significant due to small sample sizes. The current meta-analysis demonstrates that SNPs contained in the genes encoding miR-146a and miR-196a-2 may play a major role in genetic susceptibility to HCC.

Methylenetetrahydrofolate reductase C677T mutation and risk of retinal vein thrombosis

BACKGROUND

Elevated plasma homocysteine (Hcy) level has been established as a significant risk factor for venous thrombosis and cardiovascular disease. Homozygosity for the methylenetetrahydrofolate reductase (MTHFR) C677T mutation has been associated with elevated plasma Hcy concentration and may contribute to retinal vein thrombosis (RVT) development. The aim of the present study was to investigate whether the hyperhomocysteinemia and/or homozygosity for the MTHFR C677T mutation are associated with an increased risk for RVT.

MATERIALS AND METHODS

Our study population consisted of 73 consecutive patients (50-78 years old) with RVT and 73 control subjects (51-80 years old), matched for age and sex. Genotyping for the MTHFR C677T mutation was performed by polymerase chain reaction-restriction fragment length polymorphism technique and Hcy level was determined by an enzyme immunoassay kit.

RESULTS

The prevalence of 677TT genotype was higher in patients than control subjects, but the difference in frequency didn't reach a significant value (P = 0.07). The frequency of the 677T allele was 26% and 21.2% in patients and controls, respectively and did not differ significantly between the two groups (odds ratio = 1.3, 95% confidence interval (0.75-2.24), P = 0.33). Fasting plasma total Hcy level was significantly higher in patients than controls (P = 0.001).

CONCLUSION

Our study demonstrated that hyperhomocysteinemia, but not the MTHFR C677T mutation, is associated with RVT.

Single nucleotide polymorphism in hMLH1 promoter and risk of tobacco-related oral carcinoma in high-risk Asian Indians

hMLH1 is a member of mismatch repair genes (MMR) that plays a crucial role in correcting replication errors, cell cycle arrest, apoptosis and oxidative stress. We explored the risk associated with hMLH1 -93 A>G (rs 1800734) single nucleotide polymorphism (SNP) with the oral squamous cell carcinoma (OSCC) in Asian Indians. We genotyped 242 patients with tobacco-related OSCC and 205 healthy controls by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique. The frequency of AA genotype was found to be significantly (Pc<0.0006) lower in patients as compared to the controls (21.49% vs. 47.8%) while GG genotype showed significantly higher (Pc<0.0006) prevalence in patients as compared to the healthy controls (41.32% vs. 13.66%). In logistic regression analysis AG (adjusted OR=1.95, 95% CI=0.72-5.26) and GG genotype (adjusted OR=4.5, 95% CI=1.54-13.16, P=0.006) appeared susceptible when compared with the wild-type AA genotype. The allelic distribution showed that variant G allele is significantly higher (Pc<0.0004) in patients and associated with increased risk (adjusted OR=2.36, 95% CI=1.33-4.19, P=0.003) as compared to the wild-type A allele. Altogether, our results suggest that the hMLH1 -93 A>G polymorphism is associated with the higher risk of tobacco-related OSCC in Asian Indians and could be useful in screening population at a higher risk.