Genotyping of Mycobacterium avium subspecies paratuberculosis (MAP) remains a challenge in epidemiology of paratuberculosis even with availability of the traidional molecular techinques such as PFGE, RFLP, SSR and MIRUVNTR assays as MAPs are genetically monomorphic bacteria. In the Iranian environment MAP seems to have extensively scatterd across the country as reports indicating frequent occurrence of the disease in bovine, caprine and ovine populations are now on rise. However, only little is known on population structure of MAP in this country. The few conducted observations are in support of existence of cattle (C) type of MAP with no trace of sheep (S) type isolates ever found. In this work, a recently-developed PCR-based Single nucleotide polymorphism (SNP) assay concentrating on 13 individual loci across the MAP genome was conducted on a Single endogenous Iranian MAP isolate of caprine origin. PCRs were conducted using universal protocol with all amplicons Sanger sequenced in search for target SNPs. An identical pattern of SNPs with that of the MAP K10 laboratory strain was revealed to confirm the identity of this local strain as a cattle type. The Leao’ s SNP analysis is a simple, straightforward assay that if used extensively, we might expect a better understanding of evolutionary scenario behind todays’ epidemiology of paratuberculosis in Iran.

Single nucleotide polymorphisms (SNPs) are the most usual form of polymorphism in human genome.Analyses of genetic variations have revealed that individual genomes share common SNP-haplotypes. The particular pattern of these common variations forms a block-like structure on human genome. In this work, we develop a new method based on the Perfect Phylogeny Model to identify haplotype blocks using samples of individual genomes. We introduce a rigorous definition of the quality of the partitioning of haplotypes into blocks and devise a greedy algorithm for finding the proper partitioning in case of perfect and semi-perfect phylogeny. It is shown that the minimum number of tag SNPs in a haplotype block of Perfect Phylogeny can be obtained by a polynomial time algorithm.We compare the performance of our algorithm on haplotype data of human chromosome 21 with other previously developed methods through simulations.The results demonstrate that our algorithm outperforms the conventional implementation of the Four Gamete Test approach which is the only available method for haplotype block partitioning based on Perfect Phylogeny.

Background: The association between HER2 Ile655Val Single nucleotide polymorphism and cancer is controversial.Objectives: The aim of our study was to investigate this polymorphism in patients with ovarian cancer.Patients and Methods: Genomic DNA was extracted from peripheral blood leukocytes of 107 patients and 130 healthy women. HER2 gene polymorphism was assessed by PCR-RFLP.Results: No significant difference was observed in genotype and allele frequency between patient and control groups according to HER2 Ile655Val polymorphism. The disease stage, age, and histological type were also not associated with the polymorphism.Conclusions: our data showed that HER2 Ile655Val Single nucleotide polymorphism was not significantly associated with onset, histological type, age, and stage of ovarian cancer in Iranian patients.

Background: Single nucleotide polymorphism (SNPs) are considered as one of the underlying causes of male infertility. Proper sperm chromatin packaging which involves replacement of his tones with protamines has profound effect on male fertility. Over 20 SNPs have been reported for the protamine 1 and 2. Materials and Methods: The aim of this study was to evaluate the frequency of two previously reported SNPs using polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP) approach in 35, 96 and 177 normal, oligozoospermic and azoospermic individuals. These SNPs are: 1. A base pair substitution (G) at position 197 instead of T in protamine type 1 Open reading frame (ORF) including untranslated region, which causes an Arg residue change to Ser residue in a highly conserved region. 2. cytidine nucleotide change to thymidine in position of 248 of protamine type 2 ORF which caused a nonsense point mutation.Results: The two mentioned SNPs were not present in the studied population, thus concluding that these SNPs can not serves as molecular markers for male infertility diagnosis.Conclusion: The results of our study reveal that in a selected Iranian population, the SNP G197T and C248T are completely absent and are not associated with male infertility and therefore these SNPs may not represent a molecular marker for genetic diagnosis of male infertility.

Fibroblast growth factor 2 (FGF2) serves in the uterine endometrium during estrous presenting in the bovine mammary gland which is responsible to express interferon-T (IFNT), and is an important agent to encourage the continuation of pregnancy in the ruminants. Significant associations have been found between genes affected by IFNT and genes that are responsible for milk production traits. Semen samples from 101 Iranian Holstein proven bulls were collected to extract the genomic DNA. Forward and reverse primers were designed and a 710-base-pair fragment in intron 1 was amplified using PCR technique. To detect Single nucleotide polymorphism (SNP), all samples were sequenced. Three positions including 11474 (C/G), 11513 (C/G) and 11646 (A/G) were considered. The 11474C, 11513C and 11646A alleles are known as wild type alleles. In this study all animals were distinguished as the11474C, 11513C and 11646A alleles. Furthermore, amplified fragments were under consideration to detect new SNPs. Only one new SNP in one sample was observed at position 11863 resulting substitution of thymine to cytosine. This new mutation has been registered on the NCBI database with accession number HM597774.

Rheumatoid arthritis (RA) is a progressive and common autoimmune disease with multifactorial etiology. Several pieces of research show that genetic factors play a major role in the incidence of RA. Several genome-wide association studies (GWAS) have identified the autoimmune regulator (AIRE) gene as one of the candidate loci. This gene encodes a transcription factor, which is involved in the presentation of self-antigens and the negative selection of self-reactive T-cells in the thymus. Studies have indicated that Single nucleotide polymorphisms (SNPs) in the AIRE gene can change the gene expression and/or function. In the present study, we assessed the possible association between SNP rs2075876 (intronic variant) in the AIRE gene with RA risk in the Iranian population. A case-control study using 56 RA patients and 58 control subjects was undertaken to evaluate rs2075876 genotypes using the real-time PCR high resolution melting method (HRM). Logistic regression analysis demonstrates that homozygous AA and heterozygous AG genotypes compared with GG genotype increase the risk of RA (AA vs. GG; OR=16. 43; 95% CI [5. 33-50. 71] and AG vs. GG; OR=3. 21; 95% CI [1. 22-8. 45]). Also, individuals with allele A were more frequently affected with RA than subjects with G allele (OR=5. 81; 95% CI [3. 28-10. 30]). Furthermore, in the patient group, we found a significant correlation between erythrocyte sedimentation rate and C-reactive protein concentration with rs2075876 polymorphism (P<0. 05). Our findings propose a substantial correlation between rs2075876 polymorphism and RA risk.