Determination of High-Resolution HLA-DQB1 Suballeles and IL-17 Polymorphisms in Turkish Pediatric Patients

Celiac disease (CD) is an autoimmune enteropathy in the small intestine caused by gluten intolerance of the patients. The most important genetic disease-related factor is human leukocyte antigen (HLA)-DQ polymorphism. Association between interleukin (IL)-17A expression of CD4+ T cells and various autoimmune diseases has been reported. The aim of this study was to investigate the relationship between single nucleotide polymorphism (rs2275913) IL-17A and HLA-DQ polymorphisms in Turkish pediatric celiac patients. Study group included 125 pediatric celiac patients with CD and 100 healthy pediatric controls. Deoxyribonucleic acid was isolated from peripheral blood samples. IL-17A polymorphism (rs2275913) was analyzed by polymerase chain reaction-restriction fragment polymorphism method. IL-17A polymorphism and low-/high-resolution HLA-DQ results of patients were evaluated. GG and GA genotype frequencies of IL-17A (rs2275913) polymorphism were significantly higher (p < 0.05) in the CD patients than the control group. HLA-DQB1*02 and HLA-DQA1*05 alleles were detected in patients, while HLA-DQB1*03 and HLA-DQA1*01 alleles in the control group. Also, when we compared the patient and control groups in terms of HLA-DQ-DR haplotypes, HLA-DQB1*02-DQA1*05-DRB1*03 was found with the relative risk of 42.5 (p < 0.05). As a result of high-resolution HLA-DQB1 typing, DQB1*02:01 and DQB1*03:02 were at high frequency (p < 0.05; in 25 patient group). IL-17A (rs2275913) polymorphism genotype frequency was found to be significant in the patient group compared with the control group. The most common HLA-DQB1 suballele was observed as DQB1*02:01.

Molecular Characterization of Fasciola spp. from Some Parts of Iran

Background: Identification of liver flukes, Fasciola hepatica, and Fasciola gigantica by morphometric parameters is not always reliable due to the overlapping measurements. This study aimed to characterize the liver flukes of animals from different parts of Iran by the genetic markers, ITS1, and COXI. Methods: We collected flukes from infected livestock in six provinces of Iran from Sep to Nov 2016. The flukes were identified by amplification of a 680 bp sequence of ITS1 locus followed by a restriction fragment polymorphism (RFLP) assay. The genetic diversity among isolates was evaluated by amplification and sequencing of a 493 bp fragment of the COXI gene. Results: We obtained 38 specimens from Khuzestan, 22 from Tehran, 10 from Isfahan, 10 from Mazandaran, 4 from Kurdistan, and 3 from Ardabil provinces. PCR-RFLP analysis revealed two patterns, representing F. hepatica, and F. gigantica. Fifty specimens from cattle and sheep exhibited F. hepatica pattern and 37 from the cattle, sheep, buffalo, and goat that of F. gigantica. The phylogeny based on COXI revealed two distinct clades separating F. hepatica from F. gigantica. In our phylogeny, the Iranian F. gigantica isolates showed a distinct separation from the African flukes, while grouped with the East Asia specimens demonstrating a common ancestor. The F. hepatica isolates clustered with the flukes from different parts of the world, including East Asia, Europe, and South America. Conclusion: The present study revealed a substantial genetic difference between F. gigantica populations of Asia and Africa, while F. hepatica isolates from different parts of the world shared high similarities.

Genetic Variation of Calpastation Gene of Indigenous Bali Cattle (Bos javanicus) in Indonesia

Calpastatin is one of gene markers affecting meat tenderness. The study aimed to evaluate genetic variation of calpastatin (CAST) gene of Bali cattle (Bos javanicus) in lndonesia. A total of 61 samples consisting of 21 Bali cattle, 22 Ongole cattle (Bos indicus), and 18 Friesian Holstein (FH) cattle (Bos taurus) were applied. The Ongole and FH cattle were involved for breed comparison. DNA was extracted from fresh blood using a High Salt method and measured their quality by a Spectrophotometer. A 523 bp of Calpastatin gene fragment was amplified by Polymerase Chain Reaction and Restriction Fragment Polymorphism (PCR-RFLP) technique with RsaI restriction enzyme for genotyping. Result showed that two variants alleles (C and G) and three genotypes (CC, GC, GG) were found in those Bali, Ongole and FH samples. Allele G was dominant allele with the highest G allele was in Bali cattle population (0.88). The higher percentage of allele C was found in Ongole and Friesian Holstein compared to that in Bali cattle. The Ongole breed tends to have a potential source of lean meat quality. This finding identified that genetic variation of CAST gene was exist in Bali cattle and adapted cattle of Ongole and FH in Indonesian.

HER1R497K andHER2I655V Polymorphisms Are Linked to Development of Breast Cancer

BACKGROUND: Polymorphism of the genes of Human Epidermal growth factor receptor1 (HER1) and receptor2 (HER2) have been reported to be linked to pathogenesis of several malignant tumors but still there is contradiction regarding their association with breast cancer.OBJECTIVE: In this case control study we aimed to analyze the frequency ofHER1R497K (rs 11543848) andHER2I655V (rs 1136201) Polymorphisms in breast cancer.SUBJECT AND METHOD: The frequency ofHER1Arg(R) 497Lys (K) andHER2Ile (I) 655Val (V) polymorphisms were tested in 64 breast cancer patients and 86 normal control by polymerase chain reaction followed by restriction fragment polymorphism detection. Immunohistochemical analysis was done for HER2 protein on the available 18 malignant tissue samples.RESULTS:HER1497K andHER2655V variant had significantly increased breast cancer risk (OR=2.6, 95% CI 1.6–4.2, OR=2.2, 95% CI 1.2–4.1, p< 0.05) respectively. Moreover, combinedHER1K497 andHER2V655 variant was detected in 26.6% malignant in comparison to 8.14% of control group (OR=4.1, 95% CI 1.58–10.57), but, no significant association was noticed between both Polymorphisms and clinicopathological features of the disease. As regard HER2 immunohistochemical expression no significant correlation was revealed with HER2 655V polymorphism.CONCLUSIONS: Our findings suggest thatHER1497K andHER2655V polymorphisms are potential risk factor for development of breast cancer.

Culture-Based Assessment of Microbial Communities in Soil Suppressive to Potato Common Scab

A field in East Lansing, MI, showed a decline of potato common scab compared with an adjacent potato field. To confirm that the decline was due to biological factors, the soil was assayed. In the greenhouse, putative common-scab-suppressive soil (SS) was either treated with various temperatures or mixed with autoclaved SS at various ratios. Pathogenic Streptomyces scabies was incorporated into the treated soil at 106 CFU/cm3 of soil, followed by planting of either potato or radish. Disease severity was negatively correlated with the percentage of SS in the mixture and positively correlated with temperature above 60°C. The soil was screened for four groups of potential antagonists (general bacteria, streptomycetes, fluorescent pseudomonads, and bacilli) pairing in culture with S. scabies. The frequency of antagonistic bacteria in SS was higher than common-scab-conducive soil (CS) in all four groups but only pseudomonads and streptomycetes were significantly higher. The population of pathogenic Streptomyces spp. in the rhizosphere of CS was significantly higher than SS. Dilution plating of CS and SS samples showed no clear trends or differences in populations of total fungi, total bacteria, streptomycetes, fluorescent pseudomonads, and bacilli but terminal restriction fragment polymorphism analysis revealed two distinct microbial communities were present in SS and CS.

Analysis of Kinetoplast DNA from Mexican Isolates ofLeishmania (L.) mexicana

This study analyzed DNA minicircles of Mexican isolates ofL. (Leishmania) mexicanato look for genetic differences between strains isolated from patients with diffuse cutaneous (DCL) and localized (LCL) leishmaniasis. The kDNA was analyzed using polymerase chain reaction (PCR), restriction fragment polymorphism analysis of the PCR products (PCR-RFLP) and the PCR products were sequenced. In the PCR with primers specific for the subgenusLeishmania, the Mexican isolates gave higher amplification products than the otherL. mexicanacomplex strains and with specific primers for theL. mexicanacomplex they were poorly amplified. In the PCR-RFLP analysis with theEco RV,Hae III, andMbo Iendonucleases, the Mexican isolates displayed similar restriction patterns, but different from the patterns of the other members of theL. mexicanacomplex. In the phylogenetic tree constructed, the kDNA sequences of the Mexican clones formed two groups including sequences of LCD or LCL clones, apart from the otherL. mexicanacomplex members. These results suggest that the kDNA minicircles of the Mexican isolates are more polymorphic than the kDNA of other members of theL. mexicanacomplex and have different recognition sites for the restriction enzymes used in this study.

Patterns of amplified restriction fragment polymorphism in the germination of Festuca hallii seeds

Timing of seed germination influences plant lifetime fitness and can affect the ability of plant populations to colonize and persist in changing environments. However, the genetic variation of the seed germination response remains poorly understood. The amplified restriction fragment polymorphism (AFLP) technique was applied to characterize the genetic variation of germinated seeds collected from three Festuca hallii populations in the Canadian prairie. Three subpopulations with early, intermediate and late germination were identified from each population, based on germination tests at 10, 15 and 20°C in controlled growth chambers. Three AFLP primer pairs were employed to screen a total of 540 assayed seedling samples and 188 polymorphic AFLP bands were scored for each sample. None of the assayed AFLP bands were significantly associated with seed germination, but marked differences in estimates of mean band frequency were observed for various groups of germinating seeds under different test temperatures. Partitioning of the total AFLP variation showed that 5.9% AFLP variation was present among seeds of the three populations, 0.3% among seeds of three germination subpopulations, and 0.5% among seeds grouped for germination temperature. Genetic differentiation was significant among 27 groups of seeds representing population, germination timing and test temperature. Subpopulations with early and intermediate germination shared similar genetic backgrounds and were genetically differentiated from the late germination subpopulation. These results indicate that seed genotypes respond slightly differently to environmental variation, resulting in significant but weak genetic differentiation in the germination of F. hallii seeds. Implications for plant establishment and fescue restoration are discussed.

GSTT1, GSTM1, GSTM3 and NAT2 polymorphisms in laryngeal squamous cell carcinoma in a Greek population

Objective:It is well known that laryngeal squamous cell carcinoma is strongly related to tobacco and alcohol consumption. Accumulating evidence suggests that alterations of detoxification enzymes, such as glutathione S-transferases and N-acetyltransferases, influence the risk of cancers associated with tobacco smoke and alcohol.Methods:This was a retrospective case–control study. The study group consisted of 88 Greek patients with laryngeal squamous cell carcinoma; there were also 102 control subjects. Frequencies of the genotypes GSTT1, GSTM1, GSTM3 and NAT2 were evaluated by polymerase chain reaction restriction fragment polymorphism.Results:The distribution of overall genotypes was 55.68 per cent rapid acetylator and 44.32 per cent slow acetylator in patients, and 36.27 per cent rapid acetylator and 63.72 per cent slow acetylator in controls. The odds ratio for rapid acetylator status in cases versus controls was 2.207 (95 per cent confidence interval 1.23–3.95, p = 0.0087).Conclusion:This study demonstrated a significant relationship between rapid acetylator genotypes and laryngeal squamous cell carcinoma in a Greek population.