• Journal of Animal Science and Technology
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• v.57 no.12
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• pp.47.1-47.10
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• 2015

Background: Knowledge of linkage disequilibrium (LD) levels among different populations can be used to detect genetic diversity and to investigate the historical changes in population sizes. Availability of large numbers of SNP through new sequencing technologies has provided opportunities for extensive researches in quantifying LD patterns in cattle breeds. The aim of this study was to compare the extent of linkage disequilibrium among Iranian cattle breeds using high density SNP genotyping data. Results: A total of 70 samples, representing seven Iranian indigenous cattle breeds, were genotyped for 777962 SNPs. The average values of LD based on the $r^2$ criterion were computed by grouping all syntenic SNP pairwises for intermarker distances from 0 Kb up to 1 Mb using three distance sets. Average $r^2$ above 0.3 was observed at distances less than 30 Kb for Sistani and Kermani, 20 Kb for Najdi, Taleshi, Kurdi and Sarabi, and 10 Kb for Mazandarani. The LD levels were considerably different among the Iranian cattle breeds and the difference in LD extent was more detectable between the studied breeds at longer distances. Lower level of LD was observed for Mazandarani breed as compared to other breeds indicating larger ancestral population size in this breed. Kermani breed continued to have more slowly LD decay than all of the other breeds after 3 Kb distances. More slowly LD decay was observed in Kurdi and Sarabi breeds at larger distances (>100 Kb) showing that population decline has been more intense in more recent generations for these populations. Conclusions: A wide genetic diversity and different historical background were well reflected in the LD levels among Iranian cattle breeds. More LD fluctuation was observed in the shorter distances (less than 10 Kb) in different cattle populations. Despite of the sample size effects, High LD levels found in this study were in accordance with the presence of inbreeding and population decline in Iranian cattle breeds.

• The Plant Pathology Journal
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• v.32 no.1
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• pp.33-46
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• 2016

In this study, the full-length nucleotide sequences of four Iranian PVY isolates belonging to $PVY^N$ strain were determined. The genome of Iranian PVY isolates were 9,703-9,707 nucleotides long encoding all potyviral cistrons including P1, HC-Pro, P3, 6K1, CI, 6K2, VPg, NIa-Pro, NIb and CP with coding regions of 825, 1,395, 1,095, 156, 1,902, 156, 564, 732, 1,557 and 801 nucleotides in length, respectively. The length of pipo, embedded in the P3 cistron, was 231 nucleotides. Phylogenetic analysis showed that the Iranian isolates clustered with European recombinant NTN isolates in the N lineage. Recombination analysis demonstrated that Iranian $PVY^N$ isolates had a typical European $PVY^{NTN}$ genome having three recombinant junctions while $PVY^N$ and $PVY^O$ were identified as the parents. We used dN/dS methods to detect candidate amino acid positions for positive selection in viral proteins. The mean ${\omega}$ ratio differed among different genes. Using model M0, ${\omega}$ values were 0.267 (P1), 0.085 (HC-Pro), 0.153 (P3), 0.050 (CI), 0.078 (VPg), 0.087 (NIa-pro), 0.079 (NIb) and 0.165 (CP). The analysis showed different sites within P1, P3 and CP were under positive selection pressure, however, the sites varied among PVY populations. To the best of our knowledge, our analysis provides the first demonstration of population structure of $PVY^N$ strain in mid-Eurasia Iran using complete genome sequences and highlights the importance of recombination and selection pressure in the evolution of PVY.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.10
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• pp.6049-6053
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• 2013

Background: Following research demonstrating an increased risk for meningiomas in the Jewish population of Shiraz (Iran) we conducted a cohort analysis of meningiomas among Jews originating in Iran and residing in Israel. Materials and Methods: We use the population-based registry data of the Israeli National Cancer Registry (INCR) for the main analysis. All benign meningioma cases diagnosed in Israel from January 2000 to the end of 2009 were included. Patients that were born in Iran, Iraq, Turkey, Bulgaria and Greece were used for the analysis, whereby we calculated adjusted incidence rates per 100,000 people and computed standardized incidence ratios (SIRs) comparing the Iranian-born to each of the three other groups. Results: Iranian-born Jews had statistically significant higher meningioma rates rates compared to other Jews originating in Balkan states: 1.46 fold compared to Turkish Jews and 1.86 fold compared to the Bulgaria-Greece group. There was a small increase in risk for the Iranian born group compared to those who were born in Iraq (1.06, not significant). Conclusions: Higher rates of meningiomas were seen in Jews originating in Iran that are living in Israel as compared to rates in neighboring countries of origin. These differences can be in part attributed to early life environmental exposures in Iran but probably in larger amount are due to genetic and hereditary factors in a closed community like the Iranian Jews. Some support for this conclusion was also found in other published research.

• The Plant Pathology Journal
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• v.33 no.3
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• pp.296-306
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• 2017

Sugarcane mosaic virus (SCMV) is one of the most damaging viruses infecting sugarcane, maize and some other graminaceous species around the world. To investigate the genetic diversity of SCMV in Iran, the coat protein (CP) gene sequences of 23 SCMV isolates from different hosts were determined. The nucleotide sequence identity among Iranian isolates was more than 96%. They shared nucleotide identities of 75.5-99.9% with those of other SCMV isolates available in GenBank, the highest with the Egyptian isolate EGY7-1 (97.5-99.9%). The results of phylogenetic analysis suggested five divergent evolutionary lineages that did not completely reflect the geographical origin or host plant of the isolates. Population genetic analysis revealed greater between-group than within-group evolutionary divergence values, further supporting the results of the phylogenetic analysis. Our results indicated that natural selection might have contributed to the evolution of isolates belonging to the five identified SCMV groups, with infrequent genetic exchanges occurring between them. Phylogenetic analyses and the estimation of genetic distance indicated that Iranian isolates have low genetic diversity. No recombination was found in the CP cistron of Iranian isolates and the CP gene was under negative selection. These findings provide a comprehensive analysis of the population structure and driving forces for the evolution of SCMV with implications for global exchange of sugarcane germplasm. Gene flow, selection and somehow homologous recombination were found to be the important evolutionary factors shaping the genetic structure of SCMV populations.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.20
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• pp.8789-8791
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• 2014

Estrogen receptor alpha ($ER{\alpha}$) is one of the major sub-types of estrogen receptors. $ER{\alpha}$ plays an important role in cellular proliferation and differentiation, chiefly in mammary tissues. In the present study we aimed to quantify of $ER{\alpha}$ mRNA and protein expression in breast tissues from the Iranian population using a real-time PCR assay. Twenty nine breast tissues including 19 adenocarcinomas and 10 normal controls were recruited from the Iranian population. mRNA extraction and cDNA synthesis were performed from these tissues using commercial kits. $ER{\alpha}$ mRNA and protein expression was quantified using real-time PCR and immunohistochemistry respectively. The results showed high expression of $ER{\alpha}$ mRNA (68%) and protein (53%) in the majority of breast cancer tissues compared to normal breast tissues (p= 0.035). Also, high $ER{\alpha}$ mRNA was associated with tumour size of breast carcinomas. In this study, we first reported the expression of $ER{\alpha}$ in Iranian patients with breast cancers and demonstrated prevalence of the expression to be similar to breast cancers noted in other populations.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.3
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• pp.853-857
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• 2015

Background: Gastric cancer is the most common cancer in the Iranian population. The aim of this study was to determine the effect of clinicopathological factors on prognosis by meta-analysis. Materials and Methods: A literature search was conducted using MEDLINE, EMBASE and Cochrane library and extensive literature search using the Persian databases until February 2011. Prospective follow up studies with multivariate analysis of overall survival of the patients with gastric cancer were included in this review. The data were analyzed by CMA.2. Publication bias are checked by funnel plot and data are shown as Forest plots. Results: From a total of 63 articles, 14 retrospective studies which examined 5 prognostic factors and involving 10,500 patients were included. Tumor size (>35mm) was the main significant factor predicting an unfavorable prognosis for the patients with gastric cancer (RR=1.829, p<0.001) followed by presence of distant metastases (RR=1.607, p<0.001), poor differentiation (RR=1.408, p<0.001) and male sex (RR=1.194, p<0.001). Lymph node metastases (RR=1.058, p=0.698) and moderate differentiation (RR=0.836, p=0.043) were not statistically significant as prognostic factors. Conclusions: This meta-analysis suggests that tumor size>35mm, poor differentiation, presence of distant metastasis and male gender are strongly associated with a poor prognosis in Iranian patients with gastric cancer.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.11
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• pp.5525-5528
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• 2012

Introduction: Breast cancer is the most common cancer in women. Improvements of early diagnosis modalities have led to longer survival rates. This study aimed to determine the 5, 10 and 15 year mortality rates of breast cancer patients compared to the normal female population. Materials and Methods: The follow up data of a cohort of 615 breast cancer patients referred to Iranian Breast Cancer Research Center (BCRC) from 1986 to 1996 was considered as reference breast cancer dataset. The dataset was divided into 5 year age groups and the 5, 10 and 15 year probability of death for each group was estimated. The annual mortality rate of Iranian women was obtained from the Death Registry system. Standardized mortality ratios (SMRs) of breast cancer patients were calculated using the ratio of the mortality rate in breast cancer patients over the general female population. Results: The mean age of breast cancer patients at diagnosis time was 45.9 (${\pm}10.5$) years ranging from 24-74. A total of 73, 32 and 2 deaths were recorded at 5, 10 and 15 years, respectively, after diagnosis. The SMRs for breast cancer patients at 5, 10 and 15 year intervals after diagnosis were 6.74 (95% CI, 5.5-8.2), 6.55 (95%CI, 5-8.1) and 1.26 (95%CI, 0.65-2.9), respectively. Conclusion: Results showed that the observed mortality rate of breast cancer patients after 15 years from diagnosis was very similar to expected rates in general female population. This finding would be useful for clinicians and health policy makers to adopt a beneficial strategy to improve breast cancer survival. Further follow-up time with larger sample size and a pooled analysis of survival rates of different centres may shed more light on mortality patterns of breast cancer.

• Asian-Australasian Journal of Animal Sciences
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• v.21 no.4
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• pp.465-470
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• 2008

This study describes genetic variability in the BoLA-DRB3 gene in Iranian native cattle (Bos Indicus and Taurus) and relationships between these breeds. This is the first study of genetic polymorphism of the BoLA-DRB3 gene in Iranian native cattle. We examined exon 2 of the major histocompatibility complex (MHC) class II DRB3 gene from 203 individuals in four populations of Iranian native cattle (52 Sarabi, 52 Najdi, 49 Sistani, 50 Golpayegani cattle) using the hemi-nested PCR-RFLP method. We identified the 36 previously reported alleles and one novel pattern (*eac). Analysis of the frequencies of the various BoLA-DRB3.2 alleles in each breed indicated that DRB3.2*52 in Sarabi cattle (23%), DRB3.2 *14 and *24 alleles in Najdi cattle (13%), DRB3.2 *8 allele in Sistani cattle (22%) and DRB3.2*16 allele in Golpayegani cattle (14%), were the most frequent alleles. Allelic frequencies ranged from 1 to 23% among the 36 alleles and there were some alleles that were found only in Iranian cattle. Effective number of alleles in the four breeds was estimated to be 7.86, 11.68, 7.08 and 3.37 in Sarabi, Najdi, Sistani and Golpayegani, respectively. Observed heterozygosities were the highest in Sarabi (94%) and Najdi (94%). A population tree based on the frequency of BoLA-DRB3.2 alleles in each breed suggested that Najdi, Sarabi and Golpayegani cattle clustered together and Najdi and Sarabi were the closest breeds. Sistani cattle differed more from these three breeds. These new data suggest that allele frequencies differ between Iranian cattle breeds.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.15
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• pp.6205-6210
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• 2014

Background: The aim of this study was to investigate Iranian cancer patient perceptions of their prognosis, factors that influence perceptions of prognosis and the effect this has on patient level of hope. Materials and Methods: Iranian cancer patients (n=200) completed self-report measures of their perceptions of their prognosis and level of hope, in order to assess the relationship between the two and identify factors predictive of perceptions by multiple linear regression analysis. Results: Cancer patients perceived of their prognosis positively (mean 11.4 out of 15), believed their disease to be curable, and reported high levels of hope (mean 40.4 out of 48.0). Multiple linear regression analyses demonstrated that participants who were younger, perceived they had greater family support, and had higher levels of hope reported more positive perceptions of their cancer prognosis. Conclusions: Positive perceptions of prognosis and its positive correlation with hope in Iranian cancer patients highlights the importance of cultural issues in the disclosure of cancer related information.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.2
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• pp.841-844
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• 2015

Background: Gastric cancer as one of the most important diseases affecting health in all worldwide. Current studies have confirmed associations of cytokine gene polymorphisms with the risk of gastric cancer development. The current research aimed to assess the association of IL-1B+3954 genotypes with the risk of gastric cancer in the Iranian population. Materials and Methods: This case-control study covered 49 gastric cancer patients compared to 53 cancer free individuals as a control group. Genomic-DNA extraction was carried out from bioptic samples of patients and peripheral blood of healthy volunteers. Polymorphism of IL-1B +3954 genotypes were analysed with a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Results: The frequencies of IL-1B +3954 A1A1, A1A2 and A2A2 genotypes in healthy individuals were 26.4, 66 and 7.6 %, respectively. However, in gastric cancer patients, A1A1, A1A2 and A2A2 with 4.1, 51 and 44.9% were observed (p<0.05). Conclusions: The findings of our results show a positive association between the IL-1B+3954 genotype distribution and the risk of gastric cancer disease in the Iranian population.