Baqiyatallah University of Medical SciencesJournal of Applied Biotechnology Reports2322-11861120140301A Review on Engineering of Organophosphorus Hydrolase (OPH) Enzyme11068935ENGholamrezaFarnooshApplied Biotechnology Research Center,
Baqiyatallah University of Medical Sciences, Tehran, IranAli MohammadLatifiApplied Biotechnology Research Center,
Baqiyatallah University of Medical Sciences, Tehran, IranJournal Article20180113Organophosphorus chemicals are compounds which have been used as pesticides and insecticides in agriculture. They’re also used as nervous agents and have raised many problems for human and environment. Among the most important methods of decontamination from these compounds are biodegradation methods. Using OPH enzyme in degradation the mentioned compounds is seen as one of the desirable ways, but low activity and specification and low thermostability are among factors significantly decreasing the optimal application of this enzyme. Using methods of protein engineering based on the alteration of specific protein positions in order to improve the activity, specification and thermostability are some common ways used currently. Numerous studies have been done to increase activity and thermostability of OPH enzyme with alteration of some special amino acids the result of which was an increase against different substrates. OPH enzyme active site connected to substrates that consisted of three large, small and releasing packets were one of the goal areas of changing amino acids used by researchers to improve engineered activities. Among other ways of making enzymes more rigid and stable were bending loops by replacing Proline, creating disulfide bonds, ionic bonds by replacing charged amino acids.https://www.biotechrep.ir/article_68935_384d7f2cc5c8a093fed8035c59c06ede.pdfBaqiyatallah University of Medical SciencesJournal of Applied Biotechnology Reports2322-11861120140301Effects of missense R84Q mutation on human Pyrroline-5-carboxylate synthase enzyme properties, an in-silico analysis111668937ENMaryamZareDepartment of Biology, Payame Noor University, Avaj, IranFaranakHadiDepartment of Biology, Faculty of Science, Lorestan University, Khoramabad, IranZarrinMinuchehrIndustrial and Environmental Biotechnology Department, National Institute of Genetic Engineering & Biotechnology (NIGEB), Tehran, IranJafarAmaniApplied Microbiology Research Center, Baqiyatallah University of Medical Sciences, Tehran, IranAliHatef SalmanianDepartment of Plant Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran0000-0002-9984-7441Journal Article20140215Mammalian ∆-(1)-Pyrroline-5-carboxylate synthase (P5CS) enzyme catalyzes the coupled phosphorylation and reduction-conversion of glutamate to ∆-(1)-pyrroline-5-carboxylate (P5C), a critical step in the proline, ornithine, citrulline and arginine biosynthesis. In plants and mammals, P5CS consists of two separate enzymatic domains: N-terminal γ-glutamyl kinase (γ-GK) and C-terminal γ-glutamyl phosphate reductase (γ–GPR). Hyperammonemia has been reported as a new inborn disorder, with a range of clinical symptoms which is associated with a reduced synthesis of proline, ornithine, citruline and arginine. A missense mutation, R84Q, which alters the conserved residue in γ-GK domain, is responsible for this disorder. In this study using <em>in-silico</em> approaches as a new bioinformatics method, sequence analysis was performed and the tertiary structure of γ-GK domain of human P5CS, which includes the R84Q missense mutation, was predicted and the mutation effects on structural and functional features of P5CS enzyme were analyzed. Our analysis showed that this substitution has an affect on the molecular surface accessibility and total energy of the modeled structure. We conclude that this mutation results in a reduced activity of P5CS enzyme and an impaired synthesis of these amino acids.https://www.biotechrep.ir/article_68937_fb9d83e7ff505a7c71d64894ccf2305a.pdfBaqiyatallah University of Medical SciencesJournal of Applied Biotechnology Reports2322-11861120140301Improvement of maize (Zea mays L.) anther culture embryogenesis and direct regeneration by differentplant growth regulators and gelling agent172168938ENSeyedeh ZahraHosseiniDepartment of Plant Biology, Faculty of Basic Sciences, Behbahan Khatam Alanbia University of Technology, Behbahan, IranAhmadIsmailiDepartment of Agronomy and Plant Breeding, Faculty of Agriculture, Lorestan University, Khoram Abad, IranPayamPour MohammadiDepartment ofBiotechnology and Plant Breeding, Faculty of Agriculture, Ramin University of Agriculture and Natural Resources, Khouzestan, IranJournal Article20140201Androgenesis via anther culture or microspore culture is one of the current methods for producing haploid and double haploid plants in maize. To use of this method in maize breeding program it should be able to regenerate enough plantlets. Anthers culture usually is carried out indirectly via callus induction and regeneration on at least two different media. In this study a responsive genotype, ETH-M82, using a new single culture medium was used for embryogenesis and regeneration. We tested different growth regulators (2,4-D; kinetin; NAA & IAA) in modified YP medium. After6-week, direct regeneration on some treatments was observed. The highest frequency of direct formation of plantlets (in 100 anthers) occurred on medium supplemented with 2mgl<sup>-1 </sup>IAA and 2mgl<sup>-1 </sup>kinetin (4%).Best results with an average of 3.1plantlets in replication were obtained with the medium solidified with agar, while in difcobactoagar only 1.4 of plantlets in replication was produced. This experiment suggested that agar and plant growth regulators in the medium were beneficial for producing embryo and plantlet from maize anthers.https://www.biotechrep.ir/article_68938_ca66b4e89c3a64fcedefe6360e974862.pdfBaqiyatallah University of Medical SciencesJournal of Applied Biotechnology Reports2322-11861120140301Microarray Data Analysis for Detection and Classification of Viral Infection222768939ENKhadijehNazariFaculty of Mathematics, Sharif University of Technology, Tehran, IranAliKaramiResearch Center of Molecular Biology, Baqiyatallah University of Medical Sciences, Tehran, IranNezameddinMahdavi AmiriFaculty of Mathematics, Sharif University of Technology, Tehran, IranFatemePouraliResearch Center of Molecular Biology, Baqiyatallah University of Medical Sciences, Tehran, IranJournal Article20140210DNA microarrays consist of collection of DNA microscopic spots that In order to form an array attached to a solid surface such as glass, plastic or silicon chip. The pieces of fixed DNA considered as a searcher. In this technology it is possible to test sample against thousands probes for specific genes. With this ability, arrays accelerate the biological investigations, gene finding, molecular detection and disease diagnosis. Microarray technology can be seen as a continued development of southern blotting. The most important stage in this technology is data analysis. To analysis such large data whit high degree of confidence and reliability needs reliable bioinformatics tools. Infectious diseases still is major problem for human. One of the most important application of microarray technology is the possibility of testing for the presence of thousands micro-organism in environmental and clinical samples only in a single excrement. Thereby we take an important step in rapid and accurate detection of infectious diseases. Here, we present E-Predict algorithm and DetectiV package that is based on species identification in microarray. We demonstrate the application of E-Predict and DetectiV for viral detection in a large publicly available dataset and show that DetectiV performs better than E-Predict. DetectiV is implemented as a package for R - powerful, open source software for statistical programming - that containing visualization, normalization and significance testing functions.https://www.biotechrep.ir/article_68939_a5bff26f8f2adb1ec19661b4c4bc9f86.pdfBaqiyatallah University of Medical SciencesJournal of Applied Biotechnology Reports2322-11861120140301Enhancing iron oxidation efficiency by a native strain of Acidithiobacillus ferrooxidans via response surface methodology, and characterization of proteins involved in metal resistance by proteomic approach283868940ENFahimehNematiIslamic Azad University, Pharmaceutical Sciences Branch, Tehran, IranDaryoushArabianDepartment of Bioscience and Biotechnology, Malek Ashtar University of Technology, Tehran, IranRasoolKhalilzadehDepartment of Bioscience and Biotechnology, Malek Ashtar University of Technology, Tehran, IranFazinAbbaspour AghdamFaculty of Chemical Engineering, Sahand University of Technology, Tabriz, IranJournal Article20140209The effects of different factors on growth and bio-oxidation efficiency of a native strain of <em>Acidithiobacillus ferrooxidans</em> have been evaluated by the utilization of response surface methodology, RSM. Medium pH and iron concentration were found to be the most significant factors while temperature and ammonia concentrations had the least weight within the ranges investigated. Optimum operational conditions for maximizing Fe<sup>2+</sup> oxidation were found to be 31 <sup>o</sup>C, 7 g/Liron concentration, 4.5 g/Ltotal ammonium salt concentration and medium pH 1.85. Maximum recovery of 98% of Zinc is the main outcome of results as observed at 7 g/Lof Fe<sup>2+</sup>, under optimized experimental conditions. The response of a bacterial strain to metals toxicity also studied. The isolate showed good resistance to most of the toxic metals. The proteomics approach was used to identify the differentially expressed proteins under heavy metal stress. Four of the differentially expressed proteins were identified as major outer membrane protein of <em>A. ferrooxidans</em>, ribulose large bisphosphate carboxylase subunit<em>, </em>and holo synthase.https://www.biotechrep.ir/article_68940_83aa3f196953561a61735e0555f77b7e.pdfBaqiyatallah University of Medical SciencesJournal of Applied Biotechnology Reports2322-11861120140301Determination of T-2 Mycotoxin in Fusarium strains by HPLC with fluorescence detector384368941ENRezaKachueiMolecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran0000-0003-3812-5354SassanRezaieDepartment of Medical Parasitology and Mycology, Faculty of Public Health, Tehran University of Medial Sciences, IranMohammad HosseinYadegariDepartment of Medical Mycology, Faculty of Medicine Science, Tarbiat Modares University, Tehran, IranNaserSafaieDepartment of Plant Pathology, Faculty of Agriculture, Tarbiat Modares University, Tehran, IranAbdol-AmirAllamehDepartment of Biochemistry, Faculty of Medicine Science, Tarbiat Modares University, Tehran, IranMohammad-AliAref-poorDepartment of Biology, Basic Science Research, Imam Hossein University, Tehran, IranAbbas-AliImani FooladiApplied Microbiology Research Center, Baqiyatallah University of Medical Sciences, Tehran, IranMajidRiazipourDepartment of Medical Parasitology and Mycology, Faculty of Medicine, Baqiyatallah University of Medial Sciences, IranJournal Article20140123T-2 toxin is the most poisonous trichothecene produced by <em>Fusarium</em> species especially <em>F.sporotrichioides</em>. T-2 toxin is a biological contaminant in a number of agricultural commodities that can cause severe diseases among humans and animals and even lead to death. The aim of the current study is the analysis of T-2 mycotoxin in <em>Fusarium</em> species by high-performance liquid chromatography (HPLC) combined with florescence detection and derivatization with 1-antroylnitrile (1-AN). Totally, 11<em>Fusarium</em>isolates and reference strains were studied. The isolates were tested for the T-2 toxin production after growing on rice substrate followed by using specific “Multisep 225 Trich Clean up columns” purification. In this study, T-2 toxin production was ranged from 197.05ug/kg to 8503.07ug/kg. This is the first study of T-2 toxin analysis by HPLC-F in Iran.https://www.biotechrep.ir/article_68941_8e65b27334a8a52a77e02a71ab88e8d5.pdfBaqiyatallah University of Medical SciencesJournal of Applied Biotechnology Reports2322-11861120140301Biocontrol of Amaranthus retroflexus and Rumes crispus by NLP phytotoxine, a selective bioherbicide444868942ENFatemehShakeriApplied Biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, IranAli MohammadLatifiApplied Biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, IranMortezaMirzaeiApplied Biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, IranHamidBabavalianApplied Biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, IranFatemehHashemlouApplied Biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, IranStudent of Department of Agronomy, Faculty of Crop Sciences - University of Agricultural Sciences and Natural Resources, Sary, IranJournal Article20140207Non-beneficial and harmful weeds are plants that are unwanted, outside their home farms are growing and have the potential to exceed. This study was done in order to screening fungai and isolating NLP phytotoxine from them for selective biocontrol of <em>Amaranthus retroflexus</em> and <em>Rumes crispus</em> as a dicot, common and chemical herbicide resistance weeds. NLPs are effective just on dicot plants. Contaminated soil and dicotyledons plants were Collected from different regions of Iran. after collecting and culturing them, The effect of Supernatant from fungal cultures, was asseyd by spraying of 5 µl /cm3 of it mid 20 µl tween-20 on leaves of <em>Amaranthus retroflexus,Rumes crispus </em>and wheat as negative control that were cultured in MS media and pots in 3 replications with completely randomized design in laboratory and research green house of baqiatallah university. The effects were assessed according to numbering method. Finally, the <em>QAT<sub>5</sub></em>and<em> G<sub>7-1</sub></em>strains was selected from 9 top strains, because was more destructive than others on <em>Amaranthus retroflexus </em>and<em> Rumes crispus</em> respectively from necrosis to cell death with number 4 according to numbring method and has non-harmful effect on the wheat (<em>Triticum aestivum</em>). SDS-page results showed phytotoxine that was produced by <em>QAT<sub>5</sub></em> strain was a protein and this from G<sub>7-1 </sub>was non-protein. For better result on SDS-page protein was concentrated using by ammonium sulfat method, but about G<sub>7-1 </sub>again this outcomewas repeated. The protein purification of <em>QAT<sub>5</sub></em>strain using FPLC showed the presence of a protein with about 24 kDa like other family members of this protein. Considering this fact that these phytotoxines according to the result had similarity features to what founded befor about NLPs, they are recommended as biocontrol factor of these weeds insteade of chemical herbicides.https://www.biotechrep.ir/article_68942_e52bcc2a52d699ca836ccbc3e1e9b8c6.pdf