Vida Nadafi Sichani; Seyed Alireza Emami; Morteza Bitaraf Sani; Mohammadreza Nassiri; Vinod Gopalan
Abstract
Previous studies have found several distinct alleles at both levels of transcriptional activity and protein-DNA binding manners in breast cancer patients vs. healthy individuals through multi-step experimental approaches. This study presents a computational-based model to investigate ...
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Previous studies have found several distinct alleles at both levels of transcriptional activity and protein-DNA binding manners in breast cancer patients vs. healthy individuals through multi-step experimental approaches. This study presents a computational-based model to investigate the regulatory potential and functional properties of disease-related non-coding single nucleotide polymorphisms (SNPs) variants through several online in silico tools in the Iranian population. The association between the risk of breast cancer and its putative single nucleotide polymorphisms in the Iranian population was investigated through SNPedia database and genome-wide association studies (GWAS). Furthermore, a meta-analysis was performed by Comprehensive Meta-Analysis (CMA) software. Functional analyses were carried out through LDlink, HaploReg, and RegulomeDB. The impact of each single nucleotide polymorphism on gene expression profiles and transcription factor binding sites were predicted by the RegulomeDB. "5", "6", and "1d" scores were assigned to rs3746444, rs1062577, and rs1049174 by this scoring system, respectively. RegulomeDB scores of rs3746444-MYH7B/MIR499A and rs1062577-ESR1 suggested that they are not putative functional single nucleotide polymorphisms; and may not associate with significant eQTL signals. The “1d” score for rs1049174-RP11-277P12.20 confirmed an association with the expression of the target gene. Proxy variants rs6088678 and rs2617160 have been identified using LDlink in non-coding segments. They were in strong linkage disequilibrium (LD) with single nucleotide polymorphisms rs3746444 and rs1049174, respectively. Also, non-coding variants rs6088678-TRPC4AP and rs2617160- RP11-277P12.20 with high-ranked scores showed the strongest related-expression. This work provides a rapid and direct in silico-based approach for the identification of functional genetic variants in the breast cancer. These analyses were conducted to evaluate the association of intended SNPs with the regulatory elements of histones, DNases, motif changes, and selected eQTL signals. It can be extended to some other complex single nucleotide polymorphism-related diseases.
Yahya Mohammadi; Ali Asghar Aslaminejad; Mohammad Reza Nassiry; Ali Esmailizadeh Koshkoieh
Abstract
The purpose of this study was to investigate the polymorphism of K-casein (K-CN), β-Lactoglobulin (B-LG) and leptin (LP) genes in Iranian Holstein cattle by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique. DNA was extracted from blood samples of 139 cows using ...
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The purpose of this study was to investigate the polymorphism of K-casein (K-CN), β-Lactoglobulin (B-LG) and leptin (LP) genes in Iranian Holstein cattle by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique. DNA was extracted from blood samples of 139 cows using a modified phenol chloroform method. Association between K-CN, B-LG and LP genes’ polymorphism with milk production traits were investigated using mixed procedure of SAS software. The frequencies of AA, AB and BB genotypes for K-CN (0.72, 0.18 and 0.10), B-LG (0.43, 0.28 and 0.29) and LP (0.24, 0.63 and 0.13) were also calculated. Statistical results revealed a significant association between AA and BB genotypes of the K-CN gene with milk production and milk protein percentage, respectively. Also, BB genotype of the B-LG gene and AA genotype of the LP gene showed a significant association with protein percentage and milk production (P
Mahdi Soltani; Mohammadreza Nassiri; Alireza Sadrebazzaz; Mojtaba Tahmoorespoor
Abstract
Neospora caninum is an obligate intracellular parasitic protozoa and considered as causal agent of Neosporosis which infect wide variety of hosts. NcGRA7 is an immunodominant antigen recognized by sera from bovines, naturally infected by N. caninum, which is used as a powerful target for recombinant ...
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Neospora caninum is an obligate intracellular parasitic protozoa and considered as causal agent of Neosporosis which infect wide variety of hosts. NcGRA7 is an immunodominant antigen recognized by sera from bovines, naturally infected by N. caninum, which is used as a powerful target for recombinant or DNA vaccine preparation against neosporosis. There is no study about identifying the molecular structure of Neospora caninum in Iran, so as first step, current study tried to identify NcGRA7 gene in this parasite in Iran. After extraction of total RNA from N. caninum tachyzoites, cDNA was synthesized and NcGRA7 gene was amplified using cDNA as template. Then the PCR product was cloned into pTZ57R/T vector and transformed into Escherichia coli (DH5α strain), and the resulted recombinant plasmid was submitted for sequencing, followed by bioinformatics analysis. The data obtained from sequencing of native NcGRA7 was recorded in GenBank. The deduced amino acid sequence of NcGRA7 in current study was compared with other N. caninum NcGRA7 sequences and showed some identities and differences. NcGRA7 gene of N. caninum was successfully cloned into the pTZ57R/T vector and recombination was confirmed by sequencing, colony PCR, and enzymatic digestion, making it ready expression of recombinant protein for further studies.
Balal Sadeghi; Mohammadreza Nassiri; Ali Masoudi-Nejad; Mojtaba Tahmoorespour; Hesam Dehghani; Hamed Ahmadi
Abstract
MicroRNAs (miRNA) are a class of noncoding and regulatory RNA molecules about 22 nucleotides in
length. MicroRNAs regulate gene expression by an RNA interfering pathway through cleavage or inhibition of
the translation of target mRNA. Many miRNAs have been reported for their important roles in developmental
processes ...
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MicroRNAs (miRNA) are a class of noncoding and regulatory RNA molecules about 22 nucleotides in
length. MicroRNAs regulate gene expression by an RNA interfering pathway through cleavage or inhibition of
the translation of target mRNA. Many miRNAs have been reported for their important roles in developmental
processes in various animals, but there is limited information about cattle and sheep miRNAs. The comparative
genomics approach due to their conserved nature is a good source for the miRNAs discovery. Cattle and sheep
are ideal model organisms for biological and comparative genomics studies. In our study, a computational
method based on expressed sequence tag (EST) analysis was used for detection of cattle and sheep miRNAs. In
cattle, 25 miRNA candidates found by homology searching frequently clustered at certain chromosomes and
28 miRNAs in sheep had been detected. Our results show that the cattle and sheep miRNA database can be
providing useful information for investigating biological functions of miRNAs in cattle and sheep.
Furthermore, the bioinformatics approach is a good manner for studying these functions.
Abdul-raoof Al-shawkany; Mohammadreza Nassiri; Saied Zibaei; Mojtaba Tahmoorespour; Sayed Mahdi Ziaratnia; Mohsen Fathi Najafi; Alireza Haghparast; Shahrokh Ghovvati; Seyed Hassan Pourseyed; Mohammad Rashtibaf
Abstract
Foot-and-mouth disease (FMD) is a major cause of endemic outbreaks in livestock in Iran. In this study, clinical field samples of foot-and-mouth disease virus were collected from an outbreak in Khorasan Razavi Province during April and August of 2010, and subjected to indirect sandwich ELISA and RT-PCR. ...
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Foot-and-mouth disease (FMD) is a major cause of endemic outbreaks in livestock in Iran. In this study, clinical field samples of foot-and-mouth disease virus were collected from an outbreak in Khorasan Razavi Province during April and August of 2010, and subjected to indirect sandwich ELISA and RT-PCR. The viral serotype circulating during the period was confirmed to be type O. The virus was then genetically characterized for its complete P1 genomic sequences to compare with nine corresponding nucleotide sequences of representative foot-and-mouth disease viruses (FMDVs) registered in the GenBank. The P1-coding region was 2208 nucleotides in length with 736 encoded amino acid residues. Phylogenetic analysis revealed two major lineages of A (with three additional clusters) and B. Iranian field isolate was grouped within cluster I, most closely related to Pakistani strains PAK/39/2008 and PAK/29/2008 sharing 98.37 and 98.1% amino acid identity, respectively, demonstrating the close epidemiological links between countries in the region. In contrast, our isolate showed low amino acid identity with Italian isolate O-2-Brescia (93.48%) and Argentinean isolate O1 Caseros (93.75%). Based on multiple sequence alignments, comparison of sequences showed that the characteristic amino acid mutations were found in the VP1, VP2 and VP3 proteins of isolated virus. This article is the first to report on the complete P1 genomic characterization of type O FMDV circulating in Iran
