@article { author = {Omoumi, Parisa and Mirlohi, Aghafakhr and Bahar, Masoud}, title = {Detection of lpsA Gene in Neotyphodium endophytic Fungi of Grasses in Iran}, journal = {Iranian Journal of Biotechnology}, volume = {6}, number = {1}, pages = {1-5}, year = {2008}, publisher = {National Institute of Genetic Engineering and Biotechnology of Iran}, issn = {1728-3043}, eissn = {2322-2921}, doi = {}, abstract = {The lpsA gene, a late acting gene in the biosynthetic pathway of ergovaline, a suspected causative agent for fescue toxicosis in cattle, has been cloned from Neotyphodium lolii, an endophytic fungus of Lolium perenne. In this study, a similar gene was detected in several strains of endophytic Neotyphodium spp. isolated from grass hosts endogenous to Iran using direct and nested-PCR assays. Except for Bromus tomentellus, most isolates from other hosts contained this gene. The 747-bp PCR products of the local strains had identical restriction patterns for all tested  restriction enzymes. Accordingly, sequence analysis of the nested PCR product amplified from the internal segment of 747-bp band, showed 99% similarity with the corresponding region of the lpsA gene of N. lolii. It therefore appears that prevalence of the lpsA gene with its conserved nature among Neotyphodium isolates is mainly host dependent.}, keywords = {Endophyte,lpsA gene,Ergovaline,Neotyphodium}, url = {https://www.ijbiotech.com/article_7054.html}, eprint = {https://www.ijbiotech.com/article_7054_2d4f7602a94f750d470fd2c6ba343b49.pdf} } @article { author = {Heydarnejad, Jahangir and Izadpanah, Keramatollah and Barclay, Wendy}, title = {In vitro Expression Studies of Three Proteins of Iranian Wheat Stripe Virus}, journal = {Iranian Journal of Biotechnology}, volume = {6}, number = {1}, pages = {6-10}, year = {2008}, publisher = {National Institute of Genetic Engineering and Biotechnology of Iran}, issn = {1728-3043}, eissn = {2322-2921}, doi = {}, abstract = {The genome of Iranian wheat stripe virus (IWSV), a tentative member of the genus Tenuivirus, is comprised of three ambisense and one negative sense RNA segments. The coat and non-structural proteins encoded by the vcRNA3 and vRNA4 genes, respectively, were efficiently translated in vitro. Translated proteins of vcRNA3 and vRNA4 transcripts were approximately 35000 and 22000 in Mr, respectively, which could be attributed to the corresponding open reading frames (ORFs). The pc4 protein encoded by the IWSV-vcRNA4 was also translated by the same method. Translation product of vcDNA3 transcript gave a band at the approximate position of 37 kDa. The direct translation product of the DNA clone from IWSV-RNA4 gave a band for pc4 similar to that obtained when transcript RNA was used as a messenger. Translation of NS4 and pc4 in viral and viral complementary strands of IWSV RNA4 confirm its ambisense coding strategy.}, keywords = {Iranian wheat stripe virus,Tenuivirus,Protein expression,ambisense genome segments}, url = {https://www.ijbiotech.com/article_7057.html}, eprint = {https://www.ijbiotech.com/article_7057_0df1ea9b25fad2005d110317dbfef596.pdf} } @article { author = {Lakzian, Amir}, title = {Gene Probe Designing for Evaluation of the Diversity of Bradyrhizobium japonicum Isolates}, journal = {Iranian Journal of Biotechnology}, volume = {6}, number = {1}, pages = {11-15}, year = {2008}, publisher = {National Institute of Genetic Engineering and Biotechnology of Iran}, issn = {1728-3043}, eissn = {2322-2921}, doi = {}, abstract = {Many researchers consider the use of different probes for hybridization assays as suitable for studying the genetic diversity of nitrogen fixing bacteria. In this study for asessing genetic diversity among Bradyrhizobium japonicum isolates, two different probes (sucA and topA) chosen from the chromosomal genome of Bradyrhizobium strain USDA 110 were designed, evaluated by DNAMAN software and implemented in the DNA/DNA hybridization of eighteen isolates. Hybridization patterns of the sucA and topA probes showed that all B. japonicum isolates were clustered into 4 and 5 groups, respectively. It was also found that the sequences of these genes among the isolates were different, thus making them suitable for studying the genetic diversity of rhizobial bacteria. The sequence diversity of topA gene was more variable than that of the sucA gene.}, keywords = {Probe designing,DNA Hybridization,Bradyrhizobium japonicum,Diversity}, url = {https://www.ijbiotech.com/article_7058.html}, eprint = {https://www.ijbiotech.com/article_7058_beaddabfdd695055b485bfd258ea5011.pdf} } @article { author = {Mirdamadi, Saeed and Atashgahi, Siavash and Rajabi, Afsaneh and Aziz-Mohseni, Farzaneh and Roayaei, Mohamad and Hamedi, Javad}, title = {Cell Entrapment of Lactobacillus casei subsp. casei ATCC 39392 for Lactic Acid Production}, journal = {Iranian Journal of Biotechnology}, volume = {6}, number = {1}, pages = {16-21}, year = {2008}, publisher = {National Institute of Genetic Engineering and Biotechnology of Iran}, issn = {1728-3043}, eissn = {2322-2921}, doi = {}, abstract = {In this study, lactic acid production by repeated batch fermentation using cell entrapped methods was compared. Barium alginate beads, agar gel and polyurethane foam cubes were employed as carriers to immobilize Lactobacillus casei subsp. casei for the purpose of L (+)-lactic acid production. Increasing concentrations of lactic acid during fermentation were better tolerated by barium alginate entrapped cells. Alginate beads had a considerable effect on lactic acid production and reduced the fermentation time by half. The volumetric productivity with barium alginate and agar immobilized cells were 0.625 and 0.425 (g/lh)  respectively, whereas it was 0.375 (g/lh) for conventional free-cell fermentation. Beside biocompatibility, barium alginate immobilized cells exhibited good mechanical strength during repetitive fermentations and could be used in repetitive batch cultures for more than 40 days. The novelty of this study is lactic acid production by repeated batch fermentation with immobilized L. casei using polyurethane foam (PUF) in an economical culture medium composed of whey and corn steep liquor supplemented by glucose.}, keywords = {Cell immobilization,Entrapment,Lactic acid production,Lactobacillus casei subsp. casei}, url = {https://www.ijbiotech.com/article_7059.html}, eprint = {https://www.ijbiotech.com/article_7059_abf02d8e76452253e4b2eec2f21ccb51.pdf} } @article { author = {Farzami, Jalal and Hajizadeh, Ebrahim and Babaei-Rochee, Gholamreza and Kazemnejad, Anoshirvan}, title = {Evaluation of First and Second Markov Chains Sensitivity and Specificity as Statistical Approach for Prediction of Sequences of Genes in Virus Double Strand DNA Genomes}, journal = {Iranian Journal of Biotechnology}, volume = {6}, number = {1}, pages = {22-28}, year = {2008}, publisher = {National Institute of Genetic Engineering and Biotechnology of Iran}, issn = {1728-3043}, eissn = {2322-2921}, doi = {}, abstract = {Growing amount of information on biological sequences has made application of statistical approaches necessary for modeling and estimation of their functions. In this paper, sensitivity and specificity of the first and second Markov chains for prediction of genes was evaluated using the complete double stranded  DNA virus. There were two approaches for prediction of each Markov Model parameter, initial probability and transition matrix, which together with the first and second Markov chains resulted in development of eight algorithms for gene prediction. In order to compare the algorithms, a sensitivity and specificity repeated measure with 3 factors (Markov model, type of selection and estimation of transition probabilities) were utilized. Results significantly revealed that the second order Markov chain had more sensitivity and specificity than the first order Markov chain, with “p-Value” < 0.001. By adding the covariates, the number of annotated genes per length of genome as well as the A & T and C & G contents of genomes in the repeated measure showed an insignificant difference between the sensitivities of the two Markov models (0.407, 0.071 and 0.120, respectively). It was also proved that gene base-pairs per genome length and A & T contents of the genome, as model covariates, resulted in significant differences between the specificities of the Markov models.}, keywords = {Gene prediction,Markov chain,Virus genome}, url = {https://www.ijbiotech.com/article_7060.html}, eprint = {https://www.ijbiotech.com/article_7060_d62a34372985dfd7df16c2ffcc8060cf.pdf} } @article { author = {Jazayeri, Maryam and Allameh, Abdolamir and Soleimani, Masoud and Jazayeri, Seyed Hamid and Kaviani, Saeid and Kazemnejad, Somaieh}, title = {Capillary Network Formation by Endothelial Cells Differentiated from Human Bone Marrow Mesenchymal Stem Cells}, journal = {Iranian Journal of Biotechnology}, volume = {6}, number = {1}, pages = {29-35}, year = {2008}, publisher = {National Institute of Genetic Engineering and Biotechnology of Iran}, issn = {1728-3043}, eissn = {2322-2921}, doi = {}, abstract = {Human bone marrow derived mesenchymal stem cells (HBMSCs) have the potential to differentiate into cells such as adipocyte, osteocyte, hepatocyte and endothelial cells. In this study, the differentiation of hBMSCs into endothelial like-cells was induced in presence of vascular endothelial growth factor (VEGF) and insulin-like growth factor (IGF-1). The differentiated endothelial cells were examined for their ability to express VEGF receptor-2 (VEGFR2) and von willebrand factor (vWF). Then the cells were adopted to grow and develop capillary network in a semisolid gel matrix in vitro. The capillary network formation in a well of 24-well plate was found to be 85% in presence of VEGF (50ng/ml) and IGF-1 (20ng/ml) of the culture media. These data may suggest that the expression of endothelial markers in endothelial like-cells derived from hBMSCs is associated with their ability to form capillaries.}, keywords = {Mesenchymal stem cell,Endothelial cell,Angiogenesis,differentiation,In vitro}, url = {https://www.ijbiotech.com/article_7061.html}, eprint = {https://www.ijbiotech.com/article_7061_52509e5d74faca863ce46886af9c9ebe.pdf} } @article { author = {Honardoost, Maryam and Sabahi, Farzaneh and Amini-Bavil-Olyaee, Samad and Behzadian, Farida and Merat, Shahin and Malekzadeh, Reza}, title = {Interferon Resistance of Hepatitis C Virus Genotypes 1a/1b: Relationship to Structural E2 Gene Quasispecies Mutations}, journal = {Iranian Journal of Biotechnology}, volume = {6}, number = {1}, pages = {36-44}, year = {2008}, publisher = {National Institute of Genetic Engineering and Biotechnology of Iran}, issn = {1728-3043}, eissn = {2322-2921}, doi = {}, abstract = {Hepatitis C virus (HCV) envelope glycoprotein-2 (E2) inhibits the interferon (IFN)–induced, double –stranded RNA activated protein kinase (PKR) via PKR eukaryotic initiation factor-2α phosphorylation homology domain (PePHD). Present study examined the genetic variability of the PePHD in patients receiving interferon therapy. The PePHD region from HCV genotype 1a/1b infected patients receiving IFN was amplified by reverse transcriptase polymerase chain reaction (RT-PCR) and analyzed using bidirectionaly sequencing. The PePHD sequence was different in pretreatment isolates from three months treated patients. It was shown that the major PePHD quasispecies could change after three months IFN therapy and in one patient; the major PePHD quasispecies could change after six months IFN therapy. These mutations were occurred at codons 665, 666 and 667 of followed-up samples and at codons 660, 661, 666 and 670 of randomly treated patients. Some of these mutations were similar to those reported in previous studies. Other mutations were also detected in upstream and downstream regions of PePHD which may have influenced the structure, conformation and configuration of this region and thereby suppressing PePHD inhibitory properties. In conclusion our data suggested that HCV E2 PePHD may play an important role in determining the interferon response among Iranian HCV infected patients.}, keywords = {Hepatitis C Virus,E2 glycoprotein,PePHD region,IFN therapy,Treatment resistance}, url = {https://www.ijbiotech.com/article_7062.html}, eprint = {https://www.ijbiotech.com/article_7062_4cef073e0ce79458e1871bf7e2be3a10.pdf} } @article { author = {Motovali-Bashi, Majid and Hojati, Zohreh and Hajihoseiny, Samaneh}, title = {The Role of Matrix Metalloproteinase-3 Functional 5A/6A Promoter Polymorphism in Tumor Cell Progression and Metastasis of Breast Cancer}, journal = {Iranian Journal of Biotechnology}, volume = {6}, number = {1}, pages = {45-49}, year = {2008}, publisher = {National Institute of Genetic Engineering and Biotechnology of Iran}, issn = {1728-3043}, eissn = {2322-2921}, doi = {}, abstract = {In the human genome, chromosome 11 contains a cluster of matrix metalloproteinase (MMP) genes. Single nucleotide polymorphisms in the promoter region of MMP genes are important for MMP expression. A common adenine deletion polymorphism (5A) at position -1171 of the MMP-3 gene promoter (5´-AAAAAACCAT-3´ change to 5´-AAAAACCAT-3´) facilitates transcriptional factor binding and MMP-3 promoter activity. A case-control study was performed including 120 breast cancer patients (60 patients with metastatic activity and 60 patients without metastatic activity); and 60 healthy controls. Whole blood samples were obtained from patients and healthy controls. Genomic DNA was extracted from samples and the MMP-3 5A/6A genotypes were determined using PCR-RFLP. MMP-3 genotype distributions between patients and controls were similar (OR= 0.89, 95%CI, 0.43-1.84, P= 0.047). It was observed that the 5A allele was more frequent among patients with metastatic activity than controls (OR= 2.9, 95%CI, 0.94-8.9, P= 0.074). Therefore, the 5A polymorphism in the MMP-3 promoter showed correlation with the metastasis group than patients without metastasis; both at the time of diagnosis. However our results do not show evidence for correlation between 5A/6A polymorphism and breast cancer susceptibility.}, keywords = {Matrix metalloproteinase-3,Single nucleotide polymorphism,breast cancer,Metastasis}, url = {https://www.ijbiotech.com/article_7063.html}, eprint = {https://www.ijbiotech.com/article_7063_2cbf2f3103774e257d6dd9b6bf2efd87.pdf} }