[Molecular characterization and phylogenetic study base on nucleocapsid gene of avian infectious bronchitis viruses isolated from broiler farms, 2014-2015]

Background: avian infectious bronchitis [IB] is an economically important poultry disease. The emergence of new infectious bronchitis virus genotypes has complicated IB control programs

Objectives: this is the first comprehensive molecular analysis of the Nucleocapsid [N] gene of Iranian IBVs

Methods: the nucleocapsid gene of ten IBV isolates [which belonges to four different genotypes] was amplified using specific primers. The phylogenetic trees were constructed based on nucleotide and amino acid sequences of "N" gene

Results: IBV genotyping based on "N" gene showed similar IBV classification which was obtained from spike gene analysis and ten isolates belonged to Massachusetts, QX, 793/B and Variant-2 genotypes. Different strains had 89.97- 99.75% homology in their amino acid sequences. The highest nucleotide sequence similarity was observed between IBKG-1 and IBKG-8 [793/B type IBVs], while the lowest was seen between IBKG-5 and IBKG-9 [QX- type and Variant-2 type] IBV isolates. This low similarity is of an interest because the N protein is highly conserved among different IBV strains. "N" Protein structural analysis revealed that the isolates has 8to 10 alpha helices and 6 to 8 beta sheets

Conclusions: the present study provided basic information to develop recombinant nucleocapsid proteins that are applicable in rapid diagnostic tests and ELISA and recombinant vaccines

Molecular characterization of recent Iranian infectious bronchitis virus isolates based on S2 protein gene

Background: avian infectious bronchitis [IB], with avian infectious bronchitis virus [IBV] as the causing agent, is a ubiquitous endemic disease of the chicken with devastating effects on its industry. A viral membrane surface protein called S not only induces neutralizing antibodies but also plays an important role in virus binding and entry to host cells. Technically, S1 protein gene sequencing also helps greatly in IBV genotyping

Objectives: the aim of this study was to characterize Iranian IBV based on S2 gene

Methods: after RT-PCR amplification, the S2 gene of nine Iranian IBV isolates were sequenced and then compared with reference strains

Results: the isolates were classified into genotype I as Massachusetts like IB Vs, genotype VII which clustered into two branches, VIIa [IS-1494 like IB viruses], and VIIb, and was related to QX- like viruses and Genotype VIII as 793/B like IBVs

Conclusions: as far as we know, this is the first S2-based classification study on Iranian IBV isolates providing a firm experimental basis to correlate with genotypic characterization

[Phylogenetic analysis comparing partial S1 gene of avian infectious bronchitis virus to commercial vaccine strains in Iran]

Background:Infectious bronchitis is a highly contagious disease which may cause poor weight gain and low feed efficiency in infected chickens. There are a large number of reported serotypes/genotypes, which makes the control of the disease more difficult through vaccination. However, there are only a few amino acid differences in the S1 protein of vaccine and wild type strains which are responsible for protection

Objectives: The purpose of this study is to compare IBV variants isolated from commercial chicken flocks in Iran with currently used vaccine strains

Methods: The partial S1 gene of the spike protein, covering a hypervariable and constant regions, was amplified and sequenced using conventional RTPCR

Results: Phylogenetic analysis of amino acid sequences revealed that eight of total nine isolates were divergence at least 21.8% from vaccinal Massachusetts serotypes, and six of nine isolates were divergence at least 22.7% from 4/91, and none of the nine isolates were similar to Dutch-type, D274,vaccine serotypes

Conclusions: These findings are essential for continuous surveillance disease control strategies and monitoring of variants, and thus emphasize on the importance of improving the vaccination program in Iran

Phylogenetic study based on the phosphoprotein gene of Iranian Newcastle disease viruses [NDV] isolates, 2010 -2012

Newcastle disease virus [NDV] is the causative agent of the Newcastle disease [ND], a highly contagious disease in birds that causes significant economic losses to the poultry industry worldwide. ND is endemic in Iran and outbreaks are reported regularly in commercial poultry flocks and different species of birds. The current study was carried out to characterize NDV based on phosphorprotein [P] gene from recent outbreaks in Iran, 2010-2012. The P gene fragment of NDV isolates of five chickens, 1 ostrich, and 1 Pigeon paramyxovirus-1 was obtained by RT-PCR and sequenced. Phylogenetic analysis of sequences revealed that chicken and ostrich NDV isolates were closely related and placed in the genotype VII and Pigeon Paramyxovirus-1 was located in the genotype V. This is the first report of Phosphoprotein gene sequences of NDV strains isolated in Iran. This study will help us to understand the epidemiology and molecular characteristics of Newcastle disease virus in Iran

[Informativeness of D7S2456 marker for molecular diagnosis of autosomal recessive non syndromic hearing loss in five Iranian ethnic groups]

SLC26A4 gene mutations after GJB2 mutations are the second currently identifiable genetic cause of autosomal recessive non syndromic hearing loss [ARNSHL] which currently is used in molecular diagnosis of ARNSHL. Several potential STR markers related to this region have been reported .This study was carried out to identity the informativeness of D7S2456 CA repeat STR marker in SLC26A4 gene region in five ethnic groups of the Iranian population. In this descriptive study, The locus was genotyped in 165 unrelated healthy individuals of five different ethnics including Fars, Azari, Turkmen, Gilaki and Arabs ethnic groups using polymerase chain reaction [PCR] followed by polyacrylamide gel electrophoresis [PAGE] and fluorescent capillary electrophoresis. Data was analyzed by Gene Marker HID Human STR Identity software, Gene Pop program and Microsatellite Tools software. Analysis of the allelic frequency revealed the presence of 9 alleles for D7S2456 marker in the Iranian population, which allele 5 at the D7S2456 locus with 55% frequency was the most frequent. The most frequent heterozygosity with rate of 81.8% belongs to Azari ethnic group. Analysis of deviations from Hardy-Weinberg equilibrium demonstrated that all the ethnics except Fars were in equilibrium for D7S2456 locus. D7S2456 marker is a moderately informative marker in Iranian ethnic population [PIC value within 0.44 and 0.7]. D7S2456 is a moderately informative marker in diagnosis of SLC26A4 based autosomal recessive non syndromic hearing loss in Iranian population by linkage analysis

[Phylogenetic study of Iranian infectious bronchitis virus isolates during 2010-2011 using glycoprotein S1 gene]

Infectious bronchitis is an acute, highly contagious, viral disease of poultry with worldwide distribution, and is continuously evolving through point mutation and recombination of their genome; subsequently the emergence of IBV variants complicates disease control. To investigate genetic characterization of new IBV variants isolated from commercial chicken flocks in Iran collected between 2009 and 2010. The partial S1 gene of the spike protein, covering a hypervariable and constant regions, was amplified and sequenced using conventional RT-PCR. Phylogenetic analysis revealed four viruses designated as Razi-HKM891, Razi-HKM892, Razi-HKM893 and Razi-HKM894. Deduced amino acid sequence comparison with other IBV genotypes, published in the GenBank database, indicated that the isolates Razi-HKM891 and Razi-HKM894 were placed into the pathogenic 793/B serotype. However, the isolates Razi-HKM892 and Razi-HKM893 were different with previously described isolates in Iran. The Razi-HKM893 is closely related to recently published isolates from countries in Middle East and likely indigenous to Iran. These findings is essential for improving the disease control strategies and thus emphasize the importance of continuous surveillance of the disease and of sharing the information to the global scientific community, which would help to fill the epidemiological gaps in the regions and to validate the robustness of diagnostic screening

-514C/T polymorphism of hepatic lipase gene among Iranian patients with Coronary Heart disease

The T allele of the hepatic lipase [HL] C-514T polymorphism was previously found to be associated with lower plasma HL activity. Here, we examined the association between this polymorphism and plasma HDL-cholesterol concentrations in patients with coronary arteries stenosis. We studied 342 subjects undergoing coronary angiography in two groups of non CAD [n=146] and CAD [n=196]. -514C->T polymorphism was determined using polymerase chain reaction and restriction fragment length polymorphism [PCR-RFLP]. After adjustment for age, smoking and body mass index, HDL-cholesterol concentrations were significantly higher in men with the C/T and T/T genotype than those with the C/C genotype [mean 38.6 and 34.7 respectively P=0.01]. The frequency of T allele in non CAD was 0.136 and 0.226 in female and male respectively and 0.170 and 0.223 for female and male in CAD subjects. There was no difference in T allele frequency in CAD and none CAD groups in male and female [P=0.466 and 0.722 respectively]. -514C-"T of LIPC gene have a positive effect on HDL-C concentration especially in male gender. However, no difference was determined in frequency of T allele between CAD and normal arteries subjects

[Study of three common mitochondrial mutations in Arab patients with nonsyndromic hearing loss in Khuzestan province, I.R.Iran]

Hearing Impairment [HI] is the most prevalent neurosensory disorder occurs in 1/1000 newborn. The majority of hearing deficiencies are of genetic origin. About%0-2 of the genetic HI cases are due to mutations in mitochondrial genes. In the present study we investigated the frequency of 3 mtDNA A1555G, A3243G and A7445G mutation of 62 patients with nonsyndromic hearing loss in Khuzestan province. In this descriptive study, we investigated the presence of three mitochondrial mutations; A1555G, A3243G and A7445G in 62 Arab subjects with autosomal recessive non syndromic hearing loss in Khuzestan province. DNA was extracted using standard phenol -chloroform method. The screening of the mitochondrial gene mutations was performed by PCR-RFLP procedure.The possible mutations were confirmed by direct sequencing. None of the investigated mutations; A1555G, A3243G and A7445G were detected in this study. However PCR-RFLP revealed two mutations; G3316A, A7445C in 2 deaf subjects studied. This study is shown that mtDNA mutations consist of G3316A and A7445C are responsible for few of ARNSHL in sample studied and none of the A1555G, A3243G and A7445G mutations are responsible for ARNSHL in this population. The data presented here will improve the genetic counseling of hearing impaired patients in Khuzestan province

[Frequency of the common mitochondrial DNA [mtDNA] mutations in non-syndromic hearing impairment in southwest subpopulations of Iran]

Although, most hereditary non-syndromic hearing impairment [NSHI] is due to mutation in nuclear genes, role of mtDNA mutations in causing deafness becoming much more clear in recent years. The aim of the present study was to screen the A1555G, C1494T, A3243G and A7445G mutations in non-syndromic hearing impairment patients in two provinces of southwest of Iran. In this descriptive laboratory study, 150 subjects with acquired and prelingual autosomal recessive NSHI from Chaharmahal va Bakhtiari province and 46 unrelated probands with postlingual NSHI from Bushehr province [negative for GJB2 mutations] were screened for the presence of the common mtDNA mutations using PCR-RFLP method that followed by direct sequencing for confirming the observed mtDNA mutations. None of these mutations was found in subjects with acquired and prelingual autosomal recessive NSHI from Chaharmahal va Bakhtiari province, but mutation A1555G with frequency of 4.35% was found in postlingual NSHI patients in Bushehr province. This investigation shows that apparently, mtDNA mutations play a more significant role role in the etiology of postlingual NSHI in comparison with prelingual NSHI

[Study of I405V polymorphism of cholesterol ester transfer protein gene in efficacy of statins on plasma level of high density lipoprotein cholesterol]

Cholesterol ester transfer protein [CETP] plays a pivotal role in high density lipoprotein [HDL] metabolism and reverse cholesterol transport [RCT] pathway. CETP gene variants such as I405V that affect HDL cholesterol directly modulate CETP gene transcriptional activity. This study aims to determine influence of I405V polymorphism of CETP in statin effects with regard to plasma HDL cholesterol levels. In this descriptive analytical study, 196 adult patients with LDL-C more than 120 mg/dL were divided into two groups based on the lovastatin and atorvastatin using. There was no significant difference in demographic characteristics between two groups. Lipid profile was measured in all subjects before and after treatment and I405V polymorphism of CETP promoter was studied using polymerase chain reaction/restriction fragment length polymorphism method [PCR-RFLP]. Data were compared using paired t-test and ANOVA. Cholesterol was decreased and HDL was increased in VV genotype more than other genotypes by lovastatin and atorvastatin [P<0.05] but ApoA1 was increased in II genotype. ApoA1 also was increased in IV by atorvastatin despite of lower HDL. Lovastatin and specially atorvastatin increased ApoA1 in HDL particles in II genotype more than other genotypes. Therefore, treatment with lovastatin and atorvastatin is more effective in patients with II genotype for preventing of CAD

[Association of [Ile462Val in genetic polymorphisms CYP1A1] and uterine leiomyoma risk in women in Charmahal va Bakhtiari, I.R. Iran]

Uterine leiomyoma is a benign solid tumor of smooth muscle and the most common type of gynecological tumor. It occurs in approximately 25-30% of women over 30 years old. Studies have shown that the growth of uterine leiomyma was related to estrogen, cousidering the effect of CYP1A1 gene in estrogen metabolism, this study was done to evaluate the association of CYP1A1 [Ile462Val] polymorphisms with uterine leiomyoma in Charmahal va Bakhtiari women. In this case - control study, 156 non menopause women with the age ranges of 17-57, with clinically diagnosed uterine leiomyoma and 151 healthy normal subjects were investigated. The Ile462Val [AG] Polymorphism between the two groups [P=0.306]. The results of this study demonstrated that the CYP1A1Ile462Val polymorphism was not correlated with an increased risk of uterine leiomyoma in the study population

[Screening of mitochondrial mutations of A1555G, A 3243G, and A7445G in MTRNR1, MTTL1 and MTTS1 genes in subjects with nonsyndromic sensorineural hearing loss]

Various frequencies of the mtDNA mutations have been reported from different population world wild. Three mitochondrial DNA [mtDNA] mutations including A1555G, A 3243G, and A7445G which occurred in MTRNR1, MTTL1 and MTTS1 genes were considered as the main causes of mitochondrial hearing loss in some populations. To determine the frequency of the A1555G, A3243G, and A7445G mutations in nonsyndromic sensorineural hearing loss subjects in Gilan. Forty six subjects with nonsyndromic sensorineural hearing loss were screened by provided questionnaire and audiogram from Gillan Welfare Organization. PCR-RFLP procedure was used in order to presence the MtDNA of A1555GA 3243G and A7445G mutations and was confirmed by subsequent direct sequencing. There was no MtDNA of A1555G, A3243G and A7445G mutation in the cohort study of 46 deaf individuals. Investigation of PCR-RFLP of the MTTL1 gene for existence A3243G mutation lead to identification a G3316A variant that destroyed other restriction site, in the other site of PCR fragment. Our finding indicated that possibility the association of mitochondrial mutations with deafness is very low in deaf subjects in north of Iran. According to existence the G3316A that its pathogenesis in relation to hearing loss phenotype has not stabilized, the frequency of G3316A is 1.46% that can be had highlights role of mitochondrial mutation in deafness

[Study of deafness associated with DFNB59 gene [Pejvakin] mutation in Fars province]

Hearing loss is the most frequent sensory disorder affecting 1 in 500 neonates with more than 50% of inherited cases. This trait is a very heterogeneous disorder and happens due to genetic or environmental causes or both. More than 46 genes may be involved in non-syndromic hearing loss. Recently, DFNB 59 gene has been shown to cause deafness in some Iranian populations. The aim of this study was to determine the role of DFNB 59 gene mutations causing deafness in a group of 130 deaf pupils in Fars province. This descriptive-laboratory based study investigated the frequency of DFNB59 gene mutations using PCR-SSCP/HA strategy. Two different DFNB59 polymorphism including 874G>A and 793C>G were found in 1 and 9 of 130 patients studied respectively. However, no DFNB59 mutation was identified. The results of this study shows that the association of DFNB59 mutations with deafness in Fars province is very low

Genetic linkage analysis of 15 DFNB loci in a group of Iranian families with autosomal recessive hearing loss

Hearing loss [HL] is the most frequent sensory birth defect in humans. Autosomal recessive non-syndromic HL [ARNSHL] is the most common type of hereditary HL. It is extremely heterogeneous and over 70 loci [known as DFNB] have been identified. This study was launched to determine the relative contribution of more frequent loci in a cohort of ARNSHL families. Thirty-seven Iranian families including 36 ARNSHL families and 1 family with Pendred syndrome each with >/= 4 affected individuals, from seven provinces of Iran, were ascertained. DFNB1 contribution was initially studied by DNA sequencing of GJB2 and linkage analysis using the relative STR markers. The excluded families were then subjected to homozygosity mapping for fifteen ARNSHL loci. Sixteen families were found to be linked to seven different known loci, including DFNB1 [6 families], DFNB4 [3 families +1 family with Pendred syndrome], DFNB63 [2 families], DFNB2 [1 family], DFNB7/11 [1 family], DFNB9 [1 family] and DFNB21 [1 family]. DNA sequencing of the corresponding genes is in progress to identify the pathogenic mutations. The genetic causes were clarified in 43.2% of the studied families, giving an overview of the causes of ARNSHL in Iran. DFNB4 is ranked second after DFNB1 in the studied cohort. More genetic and epigenetic investigations will have to be done to reveal the causes in the remaining families

[Detection of A1430G mutation in SCN1A gene in a patient affected by GEFS-like epilepsy in Chaharmahal va Bakhtiari province]

Background and aim: SCN1A gene encodes for neuronal voltage-gated sodium-channel ?-subunit. Mutations in this gene are the major cause of severe myoclonic epilepsy of infancy [Dravet syndrome] and generalized epilepsy with febrile seizures plus [GEFS[+]]. GEFS[+] is a heritable benign type of epilepsy associated with febrile seizures which belongs to Idiopathic Generalized Epilepsies with a marked clinical and genetic heterogeneity. The main objective of this research is screening of mutations in scn1a gene in patients affected by GEFS[+] and Idiopathic Generalized Epilepsy [IGE]

Methods: Genetic counseling was carried out with 30 patients and their family. Peripheral blood samples were collected from patients and DNA was extracted using salting out method. Standard PCR on 16[th]-26[th] exons of scn1a gene was optimized by employment of specific primers. PCR products were analyzed by SSCP in denaturant condition and sequenced in the next step

Results: Results showed a 4289c>g missense mutation in one patient affected by idiopathic generalized epilepsy. This mutation changes the alanine residue in 1430 position to glycine [A1430G]

Conclusion: More studies are needed to identify the direct role of this mutation in pathogenesis, however, heterozygotic genotype of this mutation is consistent with dominant feature of inheritance of Epilepsy

[Molecular investigation of mtDNA A1555G, A3243G and A7445G mutations among the non syndromic hearing loss cases in Fars, Iran]

Hearing loss is a sensorineural disorder occuring in 1 out of 500 births. It happens due to some genetic/environmental causes or both. More than 60% of cases are noninherited and 80% non syndromic with autosomal recessive inheritance. In the present study we investigated the frequency of mtDNA A1555G, A3243 and A7445G mutations among the patients in Fars province. Seventy two non syndromic hearing loss subjects were studied. DNA was extracted using standard phenol-chloroform method. The screening of the mitochondrial gene mutations were performed using PCR-RFLP procedure. Finally, the possible mutations were confirmed by direct sequencing. None of the A1555G, A3243G and A7445G mutations was detected in this study. However, destroying a MTTL1 restriction site for the investigation of A3243G mutation, revealed a G3316A with allelic variant of 1.4% in the deaf subjects. Our data indicated that the mitochondrial A1555G, A3243 and A7445G mutations have no role in auditory deficits in patients studied

[Study of-629C/A polymorphism of cholesteryl ester transfer protein gene in statin effects on plasma high density lipoprotein cholesterol level]

Cholesteryl ester transfer protein [CETP] plays pivotal role in HDL metabolism and in reverse cholesterol transport [RCT] pathway. CETP gene variants such as-629C/A that affect HDL cholesterol directly, modulates CETP gene transcriptional activity. This study was aimed to determine influence of-629C/A polymorphism of CETP in statin effects with regard to plasma HDL cholesterol levels. In this descriptive-analytical study, 196 adult patients with LDL-C more than 120mg/dL were divided into two groups base on lovastatin and atorvastatin using. Lipid profile was measured in all subjects before and after treatment and-629C/A polymorphism of CETP promoter was studied using polymerase chain reaction/restriction fragment length polymorphism method. Data were compared with paired t-test and ANOVA in SPSS software. Cholesterol was decreased and HDL was increased in AA genotype more than other genotypes by lovastatin, but ApoA1 was increased in CC genotype. ApoA1 also was increased in CC genotype more than AA or AC genotypes by atorvastatin. In CC genotype, lovastatin and specially atorvastatin increased ApoA1 in HDL particles more than other genotypes. Therefore, treatment with lovastatin and atorvastatin is more effective in patients with CC genotype for raising HDL particles activity

[Mutation screening of GJB2 and GJB6 and genetic linkage study of three prevalent DFNB loci in Iranian families with autosomal recessive non-syndromic hearing loss]

The incidence of prelingual hearing loss [HL] is about 1 in 1000 neonates of which, more than 60% of cases are inherited. Non-syndromic HL [NSHL] is extremely heterogeneous: more than 100 loci have been identified. The most common form of NSHL is the autosomal recessive form [ARNSHL]. Here, we have investigated CX26 [GJB2] and CX30 [GJB6] gene mutation and linkage analysis of 3 known loci in Iranian families. A cohort of 36 big ARNSHL pedigrees from 7 provinces of Iran was investigated. All of the families were examined for the presence of GJB2 and GJB6 [del D13S1830 and del D13S1854] mutations using direct sequencing and multiplex PCR, respectively. The negative mutations pedigrees for the above-mentioned mutations, were then tested for the linkage to the 3 known loci, including DFNB3[MYO7A], DFNB4[SLC26A4] and DFNB7/11[TMC1], using STR markers and conventional PCR and PAGE. Six families had GJB2 mutations. No GJB6 mutation was found. Totally, 3 families showed linkage to DFNB4 and 1 family was linked to DFNB7/11. DFNB1 [GJB2] and DFNB4 are the main causes of ARNSHL in our study samples and GJB6 mutations are apparently absent in the Iranian population

[DFNB59 gene mutations and its association with deafness in schoolchildren in kohgilooyeh and Boyerahmad province]

Hearing loss is a common disease affecting millions of people worldwide. Hearing loss can be caused due to genetic or environmental factors or even both. The genetic of hearing defect is highly heterogeneous and more than 100 genes are predicted to cause this disorder in humans. A newly identified gene [DFNB59] has been shown to cause deafness in some populations. Here we report mutation analysis for DFNB59 gene in 88 genetic non-syndromic hearing loss subjects. In this descriptive-lab based study which was conducted at the Cellular and Molecular Research Center of Shahrekord University of Medical Sciences, DNA was extracted from the peripheral blood samples using standard phenol chloroform procedure. Mutation analysis for DFNB59 gene was performed using PCR-SSCP/HA protocol. The suspected DFNB59 which was detected as shifted bands on PAGE were then confirmed by direct sequencing strategy. Two DFNB59 polymorphisms including c.793C>G and c.793C>T were detected in 8 and 1 deaf subjects respectively. We conclude that there is no association between DFNB59 mutations and deafness in the studied patients in the region

[Frequency of 35delG mutation in GJB2 gene in non-syndromic prelingual hearing loss in 3 provinces of Iran]

Hearing loss is the most common inherited sensory disorder. At least 50% of hearing loss is inherited and about half of the genetic hearing loss is autosomal recessive non-syndromic. Mutations in GJB2 gene is the most frequent cause of autosomal recessive non-syndromic hearing loss. A single 35delG mutation is the most common allelic variant of GJB2 in most parts of the world. The aim of this study was to determine the rate of 35delG mutation in non-syndromic prelingual hearing loss in 3 provinces of Iran. In this descriptive experimental study, 240 cases with autosomal recessive non-syndromic hearing loss in 3 provinces of Iran, including Azarbaijan Sharghi [97 cases], Chaharmahal va Bakhtiari [98 cases] and Gilan [45 cases] were screened for 35delG mutation in the GJB2 gene. Blood samples [5 ml] were taken for genomic DNA extraction. The mutation was screened using Nested-PCR method and the positive results were confirmed by subsequent direct sequencing. Results of this study showed that from 240 studied patients [480 chromosomes], 35delG mutation was found in 58 chromosomes [24 patients were homozygote and 10 patients were heterozygote]. The frequency of 35delG mutation was 12.08%, including 18.04% in Azarbaijan Sharghi, 3.06% in Chaharmahal va Bakhtiari and 18.88% in Gilan province. Prevalence of 35delG mutation in Chaharmahal va Bakhtiari population was lower than other provinces studied. These results indicate that the other genes or mutations could result in autosomal recessive non-syndromic hearing loss in Chaharmahal va Bakhtiari population. However, as we found a low rate of 35delG in the populations studied, the cause of deafness remains to be detected in other loci or genes