@article { author = {Baesi, Kazem and Ravanshad, Mehrdad and Hosseini, Younes and Haji Abdolbaghi, Mahboubeh}, title = {Drug resistance profile and subtyping of HIV-1 RT gene among Iranian under-treatment patients}, journal = {Iranian Journal of Biotechnology}, volume = {10}, number = {1}, pages = {1-7}, year = {2012}, publisher = {National Institute of Genetic Engineering and Biotechnology of Iran}, issn = {1728-3043}, eissn = {2322-2921}, doi = {}, abstract = {Identification of drug resistant mutations is important in the management of HIV-1 infected patients. The aim of the current study was to evaluate drug resistance profile of RT gene and assess subtype among HIV-1 circulating strains and intensification of physician’s options for the best therapy. HIV-1 RNA of 25 sampleswas extracted from plasma and RT Nested- PCR was performed and the final products were sequenced andphylogenetically analyzed. Stanford HIV drug resistance sequence database was used for interpretationof the data. The results of phylogenetic analysis showed subtypes A1 and B in 14 (58%) and 10 (42%)patients respectively. Of the 24 patients, 23 (95%) had resistance to NRTIs, 8 individuals (32%) to NNRTIsand one patient was susceptible to NRTIs as well as NNRTIs. The drug resistance interpretation in thisstudy showed: 87.7% susceptible for AZT, 70.8% susceptible, and 25% high-level resistance for 3TC,87.7% susceptible for TDF, 29.1% high-level resistance for NVP and 70.8% susceptible and 25% highlevelresistance for EFV. Our data suggests that probably, the use of 2 NRTIs plus 1 protease inhibitor (PI)regimen is more effective than 2 NRTIs plus 1 NNRTI regimen in Iranian patients that use 2 NRTI plusNNRTI regimen and also continuous surveillance should be perform to evaluate resistance patterns formore effective therapeutic approaches.}, keywords = {HIV-1,Drug resistance,Phylogeny,Iran}, url = {https://www.ijbiotech.com/article_7188.html}, eprint = {https://www.ijbiotech.com/article_7188_90739cfb4845aa034b45c04eed94d490.pdf} } @article { author = {Rasti, Behnam and Shahangian, Seyedeh Shirin and Taghdir, Majid and Hassannia, Sadegh and Sajedi, Reza Hasan}, title = {Identification of RNA-binding sites in artemin based on docking energy landscapes and molecular dynamics simulation}, journal = {Iranian Journal of Biotechnology}, volume = {10}, number = {1}, pages = {8-15}, year = {2012}, publisher = {National Institute of Genetic Engineering and Biotechnology of Iran}, issn = {1728-3043}, eissn = {2322-2921}, doi = {}, abstract = {There are questions concerning the functions of artemin, an abundant stress protein found in Artemiaduring embryo development. It has been reported that artemin binds RNA at high temperatures in vitro, suggesting an RNA protective role. In this study, we investigated the possibility of the presence of RNA-bindingsites and their structural properties in artemin, using docking energy landscapes and molecular dynamicssimulation. Analysis of docking energy landscapes revealed sites in artemin with the potential of bindingRNAs. We found a good agreement between RNA binding sites of artemin and RNA-interacting sites of aspecific group of RNA-binding proteins called PUF, as regards to the type of their interactions with RNA molecules. Furthermore, the results from molecular dynamics simulation showed that firstly, the presenceof RNA molecule and its interaction with artemin cause significant decrease in the secondary structure contentof artemin; secondly, RNA-binding sites are mostly located in the low flexible regions. Finally, it seems thatthese binding sites are distributed in such a way that leads RNA molecule into the interior of the protein,strengthening the previous suggestion for RNA-protecting role of artemin.}, keywords = {Artemin,docking energy landscapes,Molecular Dynamics Simulation,RNA-protecting role}, url = {https://www.ijbiotech.com/article_51454.html}, eprint = {https://www.ijbiotech.com/article_51454_d14bfe096ac5bd236a02dbe58ac13bf5.pdf} } @article { author = {Sohrabvandi, Sarah and Mortazavian, Amir-Mohammad and Dolatkhahnejad, Mohammad-Reza and Monfared, Ayad Bahadori}, title = {Suitability of MRS-bile agar for the selective enumeration of mixed probiotic bacteria in presence of mesophilic lactic acid cultures and yoghurt bacteria}, journal = {Iranian Journal of Biotechnology}, volume = {10}, number = {1}, pages = {16-21}, year = {2012}, publisher = {National Institute of Genetic Engineering and Biotechnology of Iran}, issn = {1728-3043}, eissn = {2322-2921}, doi = {}, abstract = {Measuring the viability of probiotic microorganisms in food products using plate count methodology is a common practice due to the simplicity (ease of performance), inexpensive and routine testing characters ofthis method. In present study, the suitability of de man rogosa and sharpe agar (MRS) bile agar medium forthe selective enumeration of mixed probiotic bacteria (Lactobacillus acidophilus LA-5, L. casei 431 andBifidobacterium lactis BB-12) in presence of mesophilic lactic cultures (Lactococcus lactis ssp. lactisand Lactococcus lactis ssp. cremoris) and yoghurt bacteria (Streptococcus thermophilus and Lactobacillus delbrueckii ssp. bulgaricus) was investigated. Yoghurt bacteria did not grow neither in presence of 0.15% nor 0.30% of bile salts, as was expected. Mesophilic lactic starters could grow at both concentrations of bile salts at all incubation temperatures except 37°C. According to these results, MRS-bile agar (0.15 bile salts) could be successfully used for selective enumeration of mixed probiotic cultures in presence of mesophilic culture and/or yoghurt bacteria when plates were incubated at 37°C for 72 h.}, keywords = {Enumeration,mesophilic,MRS-bile agar,Probiotic}, url = {https://www.ijbiotech.com/article_7189.html}, eprint = {https://www.ijbiotech.com/article_7189_486fe98d751d8447cb131f7345290822.pdf} } @article { author = {Aghdasi, Mahnaz and Schluepmann, Henriette}, title = {Functional analysis of Glycin Rich- RNA Binding protein, a suppressor of Trehalose-6-Phosphate mediating growth arrest in Arabidopsis thaliana}, journal = {Iranian Journal of Biotechnology}, volume = {10}, number = {1}, pages = {22-31}, year = {2012}, publisher = {National Institute of Genetic Engineering and Biotechnology of Iran}, issn = {1728-3043}, eissn = {2322-2921}, doi = {}, abstract = {Metabolism of the alpha-1,1 glucose disaccharide, trehalose, is indispensable in plants. In the Murashigeand Skoog (MS) medium, trehalose inhibits plant growth and allocation of carbon to roots. A suppressorof trehalose-6-phosphate (T6P) mediated growth arrest, GR-RBP2, is characterized in more detail.Phylogenetic analysis revealed that GR-RBP2 is a protein of likely prokaryotic origin. A knockout mutantof GR-RBP2 was identified in the T-DNA insertion line SALK-059714, yet plants of this line were not alteredwith regard to growth on different carbon sources and on trehalose compared to WT. GUS expression analysisshowed that GR-RBP2 was detected in adult leaves, flowers and siliques. Expression was particularlyhigh in root tips. GR-RBP2 expression also is insensitive to 100 mM trehalose. TAP-tagged versionsof this protein showed that GR-RBP2 is part of a protein complex in planta.}, keywords = {Arabidopsis,GR-RBP2,Gus fusion,Taptaged,Trehalose}, url = {https://www.ijbiotech.com/article_7191.html}, eprint = {https://www.ijbiotech.com/article_7191_53439d85ae2b3d255d42a23b5030adda.pdf} } @article { author = {Ziaei, Mahboobeh and Sharifi, Mozafar and Behmanesh, Mehrdad and Razavi, Khadijeh}, title = {Gene expression and activity of phenyl alanine amonialyase and essential oil composition of Ocimum basilicum L. at different growth stages}, journal = {Iranian Journal of Biotechnology}, volume = {10}, number = {1}, pages = {32-39}, year = {2012}, publisher = {National Institute of Genetic Engineering and Biotechnology of Iran}, issn = {1728-3043}, eissn = {2322-2921}, doi = {}, abstract = {Phenylalanine amonia-lyase (PAL) is one of the most important enzymes that plays a key role in regulationof phenylpropanoid production in plants. It catalyzes the first step of the phenylpropanoid pathway in whichL-phenylalanine is deaminated to trans-cinnamic acid. This step is significant for metabolic engineering andhyper-expression of the major phenylpropanoid, methyl chavicol. We followed gene expression andactivity of PAL in Ocimum basilicum L. at different stages of growth including seedling, beginning andmiddle of growth phase, budding stage and flowering, and their correlation with final concentration of phenylpropanoid compounds. The level of gene expression was monitored by semi quantitative RT-PCR andphenylpropanoid compounds were identified by gas chromatography/mass spectrometry (GC/MS). PALactivity was assayed using spectrophotometer. The results indicated that the level of gene expression andactivity of PAL enzyme are altered during the plant development, where the highest expression and activity(0.851 μmol cinnamic acid/mg/min) was achieved at budding stage. In this experiment, changes ofmethylchvicol content were correlated to the transcription and activity of PAL enzyme.}, keywords = {Essential oil,Methyl chavicol,Ocimum basilicum L,phenylalanine amonia-lyase,phenylpropanoid}, url = {https://www.ijbiotech.com/article_51455.html}, eprint = {https://www.ijbiotech.com/article_51455_d66d8df400d836aac30d0ea782b40637.pdf} } @article { author = {Soltani Najafabadi, Masood}, title = {Improving rice (Oryza sativa L.) drought tolerance by suppressing a NF-YA transcription factor}, journal = {Iranian Journal of Biotechnology}, volume = {10}, number = {1}, pages = {40-48}, year = {2012}, publisher = {National Institute of Genetic Engineering and Biotechnology of Iran}, issn = {1728-3043}, eissn = {2322-2921}, doi = {}, abstract = {The response to drought stress is a complicated process involving stress sensing, intracellular signaltransduction, and the execution of a cellular response. Transcription factors play important roles in the signaling pathways including abiotic stress. In the present study a rice NF-YA transcription factor gene was partially characterized following dehydration. Disrupting the gene via a T-DNA insertion resulted in drought tolerant plants and a high rate of recovery after water resupply. It was demonstrated that the improved drought tolerance of the mutant is primarily due to non-stomatal mechanisms such as free radical scavenging,which might be related to changes in metabolism of carbohydrates.}, keywords = {Drought stress,Nuclear Factor Y,Rice (Oryza sativa L.)}, url = {https://www.ijbiotech.com/article_7166.html}, eprint = {https://www.ijbiotech.com/article_7166_4ee280e9cfe398707bc47d9b3ee19872.pdf} } @article { author = {Zahraei Salehi, Taghi and Gharagozlou, Mohammad Javad and Shams, Nemat and Madadgar, Omid Madadgar and Nayeri Fasaei, Bahar and Yahyaraeyat, Ramak}, title = {Molecular characterization a Salmonella Typhimurium isolate from Caspian pony}, journal = {Iranian Journal of Biotechnology}, volume = {10}, number = {1}, pages = {49-54}, year = {2012}, publisher = {National Institute of Genetic Engineering and Biotechnology of Iran}, issn = {1728-3043}, eissn = {2322-2921}, doi = {}, abstract = {Typhoid disease or salmonellosis is a common sickness in horses. In several epidemiological studies inhospitalized horses, several serotypes of Salmonella often are predominant in nosocomial infections.Transportation, overcrowding, dehydration, oral antimicrobial therapy and infections are the risk factorswhich may activate latent or subclinical salmonellosis. In this study, the occurrence of typhoid due toSalmonella serogroup B was considered in a Caspian ponies flock kept in a husbandry center of poniesaround Tehran. During transportation of 19 ponies, two pregnant ponies aborted and four cases died becauseof acute septicemia. Pathological and bacteriological follow up showed salmonellosis. A multiplex polymerasechain reaction (m-PCR) assay was used for detection and identification of Salmonella to confirmpathological and bacteriological studies. Salmonella Typhimurium was isolated from bone marrow, mesentericlymph nodes, liver and intestinal contents of died pony. Salmonella was not isolated from stools of otherponies. Pulsed Field Gel Electrophoresis (PFGE) and antibiotic susceptibility test were also performed.PFGE pattern was similar to the other collected isolates which have existed since more than 30 years agoin Iran. Because of importance of salmonellosis in ponies, Using of rapid methods are recommended toconfirm the presence of Salmonella. Results showed that m-PCR permit to evaluate samples more rapidlythan other methods and also can detect multiple genes simultaneously like virulence factors which declare virulence of the isolates and have surveillance significance.}, keywords = {Caspian pony,Salmonella Typhimurium,Transportation,Multiplex PCR,PFGE}, url = {https://www.ijbiotech.com/article_7169.html}, eprint = {https://www.ijbiotech.com/article_7169_28d26622d01c383462cb96741e9b719a.pdf} } @article { author = {Pilehchian Langroudi, Reza and Aghaei pour, Khosrow and Shamsara, Mahdi and Ghorashi, Saied Ali}, title = {In silico fusion of epsilon and beta toxin genes of Clostridium perfringens types D and B}, journal = {Iranian Journal of Biotechnology}, volume = {10}, number = {1}, pages = {55-61}, year = {2012}, publisher = {National Institute of Genetic Engineering and Biotechnology of Iran}, issn = {1728-3043}, eissn = {2322-2921}, doi = {}, abstract = {Fusion protein technology represents the strategy to achieve rapid, efficient, and cost-effective proteinexpression. Epsilon and Beta toxins are the most potent Clostridial toxins and cause disease in animals.This study describes in silico fusion of Clostridium perfringens types D and B epsilon and beta toxin genesthat was used for cloning in E.coli. The etx and cpb genes were retrieved from the GenBank and a fusiongene was designed to produce a chimeric fusion protein. Secondary and tertiary structures and specificitiesof fusion protein were determined by online software. Results showed that the designed fusion gene construction is suitable for chimeric fusion protein expression.}, keywords = {Clostridium perfringens,epsilon toxin,Beta toxin,Fusion,In Silico}, url = {https://www.ijbiotech.com/article_51471.html}, eprint = {https://www.ijbiotech.com/article_51471_db3f75654d8fa3ab5ae1b718b3cde540.pdf} } @article { author = {Farazmand, Abbas and Yakhchali, Bagher and Shariati, Parvin and Minuchehr, Zarrin and Ofoghi, Hamideh}, title = {In silico genome-wide screening for TnrA-regulated genes of Bacillus clausii}, journal = {Iranian Journal of Biotechnology}, volume = {10}, number = {1}, pages = {62-66}, year = {2012}, publisher = {National Institute of Genetic Engineering and Biotechnology of Iran}, issn = {1728-3043}, eissn = {2322-2921}, doi = {}, abstract = {Bacillus clausii TnrA transcription factor is required for global nitrogen regulation. In order to obtain anoverview of gene regulation by TnrA in B. clausii KSMK16, the entire genome of B. clausii was screened forthe consensus sequence, 5’-TGTNAN7TNACA-3’ known as the TnrA box, and 13 transcription units werefound containing a putative TnrA box. The TnrA targets identified in this study were tnrA, glnA, nrgA,nasFDEB, puc genes, licT, the two operons of the oligopeptide ABC transporter, lytR, transcriptional regulatorof the Lrp/AsnC family, sodium-dependent transporter of SNF family, hyu genes and a biochemicallyuncharacterized protein.}, keywords = {Gene regulation,TnrA,Bacillus clausii,nitrogen metabolism}, url = {https://www.ijbiotech.com/article_7163.html}, eprint = {https://www.ijbiotech.com/article_7163_3485c683bb2838f13a5a904a344e7617.pdf} }