University of TehranJournal of Sciences, Islamic Republic of Iran1016-110430320190701Synthesis a New Viral Base Vector Carrying Single Guide RNA (sgRNA) and Green Florescent Protein (GFP)2052097175410.22059/jsciences.2019.265567.1007316ENMahintajDaraDepartment of molecular medicine, school of advanced medical science and technology, Shiraz University of medical science, Shiraz, IranMehdiDianatpourGenetic Shiraz university of medical sciencesVahidRazbanDepartment of molecular medicine, school of advanced medical science and technology, Shiraz University of medical science, Shiraz, IranJournal Article20181002CRISPR/Cas9 system is a powerful gene editing tool <em>in vivo</em> and <em>in vitro</em>. Currently, CRISPR/Cas9 delivery cells or tissue with different vehicles are available, and Adeno- associated virus (AAV) in one of them. Due to AAV packaging size limitation, AAV base vectors that carry CRISPR/Cas9 system do not have florescent tag like GFP for simple detection and navigation of cells, containing AAV. The aim of this study was to modify and synthesis AAV base vector for CRISPR/cas9 system containing sgRNA and GFP.Px602 plasmid was double digested with NcoI and HindIII restriction enzyme. <em>Gfp </em>gene was amplified from px458 plasmid. Linear digested px602 and amplified <em>Gfp</em> gene were ligated together. After transformation and colony PCR on white colonies, plasmid was extracted and transfected to HEK-293 cell line. <em>Gfp</em> expression was monitored by florescent microscopy. After transfection of modified plasmid, florescent microscopy of HEK-293 cells showed shining green florescent cells, which indicate that <em>Gfp</em> gene, was replaced in the correct place according to our design.We modified an AAV base vector carrying CRISPR/Cas9 system, and synthesized a new vector carrying <em>Gfp</em> gene and sgRNA that can be packaged as reporter AAV for navigation and detection of cells, containing AAV.https://jsciences.ut.ac.ir/article_71754_172ed6bc92e80783fead98b84dc7cc48.pdfUniversity of TehranJournal of Sciences, Islamic Republic of Iran1016-110430320190701Chemotaxonomy, Morphology and Chemo Diversity of Scutellaria (Lamiaceae) Species in Zagros, Iran2112267175510.22059/jsciences.2019.257708.1007261ENFarzanehJafari DehkordiDepartment of Botany, Faculty of Sciences, Shahrekord UniversityNavazKharazianDepartment of Botany, Faculty of Sciences, Shahrekord universityJournal Article20180602This study concerns to evaluate the morphological and flavonoid variations, and chemotaxonomy among seven <em>Scutellaria</em> species. The limits of <em>Scutellaria</em> species were disturbed by different factors including hybridization and polymorphism. For this purpose, 39 <em>Scutellaria</em> accessions were collected from different natural habitats of Zagros region, Iran. A total of 15 quantitative and 20 qualitative morphological characters were studied. Leaf flavonoids were extracted using MeOH solution. The flavonoid classes were investigated using thin layer chromatography, column chromatography, <em>UV</em>-spect and <em>LC-MS/MS</em> (liquid chromatography mass spectrometry). To detect the taxonomic status of <em>Scutellaria </em>species, statistical analyses such as cluster, dissimilarity tree, and ordination methods were applied. The results of this research showed five flavonoid classes in different <em>Scutellaria </em>species including isoflavone, flavone, flavanone, flavonol and chalcone. Based on the cluster analysis of flavonoid and morphological data, the members of <em>Scutellaria</em> section <em>Scutellaria</em> were accurately separated from those of <em>Scutellaria</em> section <em>Lupulinaria</em>. Our study revealed a relationship between<em> Scutellaria patonii</em> and <em>Scutellaria multicaulis</em>. Moreover, the trichomes such as strigose, lanate, tomentose, pannous in leaf and stem, petiole, calyx, the form of leaf apex, and inflorescence length were found as diagnostic characters. Based on our results, the flavonoid and morphological markers display the taxonomic status of inter and intra-specific levels in <em>Scutellaria</em>. https://jsciences.ut.ac.ir/article_71755_48300fb9203ffb3ac54ed0098f051e53.pdfUniversity of TehranJournal of Sciences, Islamic Republic of Iran1016-110430320190701Phenol Based RNA Isolation is the Optimum Method for Study of Gene Expression in Human Urinary Sediment2272317175610.22059/jsciences.2019.268338.1007332ENHootanYazdani1Department of Biology, Faculty of Basic Science, Islamic Azad University, Science and Research Branch, Tehran, Iran.ShivaKalantariChronic Kidney Disease Research Center, Shahid Beheshti University of Medical Sciences, Tehran, IranMohsenNafarChronic Kidney Disease Research Center, Shahid Beheshti University of Medical Sciences, Tehran, IranMohammadNajiUrology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.Journal Article20181027Evaluation of gene expression in urinary sediment has been considered as a promising non-invasive approach for biomarker identification of kidney diseases. Nonetheless, there are several challenges in extraction of RNA from this valuable source of biomarkers, mostly because of the factors that have influence on quality of isolated RNA such as low cellular content. Accordingly, we compared the quality of RNA from urine sediment samples that was isolated by four different methods. TRIzol reagent with basic protocol (method 1), modified procedure of TRIzol (method 2), a column-based protocol (method 3) and combination of method 1 and 3 (method 4) were applied for isolation of RNA from identical aliquots of five healthy urine samples. The quality and yield of isolated RNA were evaluated based on concentration and purity. Expression levels of GAPDH and miR-21 were studied by quantitative RT-PCR. Methods 1 and 2 showed the highest RNA yield while no difference in purity of RNA in different methods was noticed. Quantitative RT-PCR findings indicated that Ct values in samples of method 1 had the lowest level. Although higher concentrations of RNA were isolated by method 2, the declined Ct values in this method might indicate degradation of isolated RNA. Column based protocols (method 3 and 4) were failed to show significant recovery of RNA. It seems that isolation procedure using TRIzol, as a phenol based method, is the most efficient, robust and reliable procedure for RNA isolation from urinary sediment cells.https://jsciences.ut.ac.ir/article_71756_bcc67a182c236dd7369237776859e88f.pdfUniversity of TehranJournal of Sciences, Islamic Republic of Iran1016-110430320190701Electropolymerization of Glycine at Carbon Paste Electrode and its Application for the Determination of Methyl Orange2332407175710.22059/jsciences.2019.267743.1007328ENC.RarilDepartment of Chemistry, FMKMC College, Madikeri, Mangalore University Constituent College, Karnataka, IndiaJ.G.ManjunathaDepartment of Chemistry, FMKMC College, Madikeri, Mangalore University Constituent College, Karnataka, India0000-0002-0393-2474Journal Article20180814A recently constructed polyglycine modified carbon paste electrode (PGMCPE) was employed to evaluate the electrochemical behavior of methyl orange (MO). The developed electrode was characterized by FESEM to understand the morphology of the modified electrode and bare carbon paste electrode (BCPE). The modified electrode exhibits an excellent electrochemical activity towards the oxidation of MO. Through the cyclic voltammetry (CV) measurement it was found that MO oxidized at the potential of 651 mV. The peak current obtained for the electrode which was modified with glycine was 4.2 times higher than that exhibited for BCPE. The influence of the experimental parameter on electrochemical oxidation of MO like pH, scan rate, and concentration was studied. Simultaneous analysis (with indigo carmine) was also studied by Differential pulse voltammetry (DPV) technique. Under optimized condition, the linear calibration curve obtained for MO is in the concentration range 1.5×10<sup>-5</sup> to 1.8×10<sup>-4</sup> M, leading to the detection limit of 7.4×10<sup>-6</sup> M.https://jsciences.ut.ac.ir/article_71757_2418b46dc484d50e0d3aa47276730a86.pdfUniversity of TehranJournal of Sciences, Islamic Republic of Iran1016-110430320190701Role of Hydrogen Transfer and Ionic Bonding on RR, SS and RS Medetomidine Conglomerates/Acids Stability: A Theoretical Study2412507175810.22059/jsciences.2019.256301.1007248ENVahidZareiDepartment of Chemistry,factually of science,Shiraz University, Shiraz, IranNabiJavadiDepartment of Chemistry,factualy of science, Imam Hossein University, TehranZainalGhahramaniDepartment of chemistry,Firouzabad Branch, Islamic Azad UniversityHosseinFakhraianDepartment of chemistry,factualy of science, Imam hossein University,TehranJournal Article20180613This study focuses on RR, SS and RS medetomidine (MM) and inclusion of several achiral acids to distinguish which acid can help conglomerate formation instead of crystallizating racemic mixtures by defining the low-lying energy of their structures. Favorable orientation of acids was determined in interaction with the MM enantiomers after optimization. The most noticeable interactions include hydrogen transfer from acids to nitrogen (N) atom of the MM enantiomers, which was confirmed through quantum theory of atom in molecule (QTAIM) and natural bond orbital (NBO) analysis. In addition, nature and source of change of these bonds were investigated by determination of significant donor-acceptor interactions. The results revealed for obtaining RR and SS conglomerates; oxalic acid solvent provides the optimum stability. Furthermore, application of propanoic acid solvent should be neglected since MM crystallization is nonspontaneous with this solvent. Therefore, oxalic acid is the acid of choice for preferential conglomerate formation.https://jsciences.ut.ac.ir/article_71758_1c6577f7fbe4e754f8b5f292da1cfab5.pdfUniversity of TehranJournal of Sciences, Islamic Republic of Iran1016-110430320190701Mineralogy, Geochemistry and Raman Spectroscopy of Multi-Genesis Serpentine Polymorphs of Darepahn Ophiolites2512697175910.22059/jsciences.2019.248856.1007196ENBahramBahrambeygiDepartment of Geology, Faculty of science, Shahid Bahonar University of Kerman, Kerman, Iran0000-0002-0497-5652HessamMoeinzadehdepartment of geology faculty of sience , shahid bahonar university of kermanSeyed KazemAlavipanahdepartment of Geography , University of TehranJournal Article20180117The present article pays to some Alpine-Himalayan ophiolites of Late Cretaceous age from Darepahn area in the southern part of Nain-Baft Ophiolite belt. Whole rock processed data clearly shows that the metaperidotite rocks are silica-poor with low CaO, Al<sub>2</sub>O<sub>3,</sub> and TiO<sub>2</sub> that reflect the predominance of olivine over calcic pyroxene in the protolithes. The considerable content of Co (85.6–124.6 ppm) and very low contents of Sc (4.3–15.3 ppm) and Sr (0.7-14 ppm) provided more evidence for olivine enrichment in the rock parentages. Calculating numbers of cation per formula unites based on EMPA results for distinguished Serpentine polymorphs (classified structurally via Raman spectroscopy) display that Tschermak substitution of trivalent cations for lizardite is tetrahedrally, and for chrysotile and antigorite, it is octahedrally. These chemical differentiations, lead to identifying chemical field plots in separator diagrams between SiO<sub>2</sub>, MgO, H<sub>2</sub>O, and Al<sub>2</sub>O<sub>3</sub>. Lizardite polymorphs can consider as primarily metasomatism results thru an iron-rich fluid occurrence. It has a considerable occupation of trivalent cations (especially Fe<sup>3+</sup>) and simultaneous less than 4 Si atoms in formula structure that reflected tetrahedral Tschermak substitutions. Antigorites have some deformed recrystallized textures along with high Σoct (Total Octahedral Cations) and low H<sub>2</sub>O content that could be considered as thermal originated polymorph. Chrysotiles have bimodal MgO and FeO contents that return to magnetite formations in groundmass and octahedral Tschermak substitutions on late-stage veins. The results exemplify compositional variations of Darepahn Serpentine polymorphs as a function of textural behaviors, structural position and thermodynamic condition of the formation process.https://jsciences.ut.ac.ir/article_71759_d52ee1be50a5ced3f857189d94b2d213.pdfUniversity of TehranJournal of Sciences, Islamic Republic of Iran1016-110430320190701Liu Estimates and Influence Analysis in Regression Models with Stochastic Linear Restrictions and AR (1) Errors2712857176010.22059/jsciences.2019.275988.1007375ENHodaMohammadiDepartment of Statistics, Faculty of Mathematics and Computer Sciences, Shahid Chamran University of Ahvaz, Ahvaz, Islamic Republic of IranAbdolrahmanRasekhDepartment of Statistics, Shahid Chamran University of AhvazJournal Article20190217In the linear regression models with AR (1) error structure when collinearity exists, stochastic linear restrictions or modifications of biased estimators (including Liu estimators) can be used to reduce the estimated variance of the regression coefficients estimates. In this paper, the combination of the biased Liu estimator and stochastic linear restrictions estimator is considered to overcome the effect of collinearity on the estimated coefficients. In addition, the deletion formulas for the detection of influential observations are presented for the proposed estimator. Finally, a simulation study and numerical example have been conducted to show the superiority of the proposed procedures.https://jsciences.ut.ac.ir/article_71760_85030dff5e3f5a47965027bfddd9f1c1.pdfUniversity of TehranJournal of Sciences, Islamic Republic of Iran1016-110430320190701Persian Abstract0073852ENJournal Article20190726https://jsciences.ut.ac.ir/article_73852_72141e7cce96b6cf2968ca45f3dbbd76.pdf