National Institute of Genetic Engineering and Biotechnology of IranIranian Journal of Biotechnology1728-30438120100101Detection of Polymorphism in Ancient Tempranillo Clones (Vitis vinifera L.) Using Microsatellite and Retrotransposon Markers167121ENClaudia CarcamoINIA-CBGP, Dpto. Biotecnología, Campus Montegancedo (Autovia M40-Km38), Pozuelo de Alarcón, 28223 Madrid, SpainIgnacio ProvedoViveros Provedo, Logroño, SpainRosa Arroyo-GarcíaINIA-CBGP, Dpto. Biotecnología, Campus Montegancedo (Autovia M40-Km38), Pozuelo de Alarcón, 28223 Madrid, SpainJournal Article20150420Tempranillo is one of the most widely cultivated grapevine varieties in Spain. After several years of clone selection, some highly recommended old clones have been identified in terms of both their qualitative and production characteristics. This study was designed to discriminate among 28 ancient clones of the cultivar Tempranillo (Vitis vinifera). DNA samples from clones were analysed using two different molecular markers; microsatellites or simple sequence repeats (SSR) and retrotransposons. The results of this study indicate that one variant genotype was expressed as three alleles. Further analysis revealed the presence of a chimera, in which the third allele was present in the leaf but not root or wood tissue, indicating a functionally double-layered apical meristem. The present research also showed that one of the retrotranposon marker was able to discriminate one grapevine clone (VP1) from the remaining clones.National Institute of Genetic Engineering and Biotechnology of IranIranian Journal of Biotechnology1728-30438120100101The Phylogeny of Calligonum and Pteropyrum (Polygonaceae) Based on Nuclear Ribosomal DNA ITS and Chloroplast trnL-F Sequences7157122ENSolmaz TavakkoliDepartment of Plant Biology, Faculty of Biological Sciences, Tarbiat Modares University, P.O. Box 14115-175,Tehran, IranShahrokh Kazempour OsalooDepartment of Plant Biology, Faculty of Biological Sciences, Tarbiat Modares University, P.O. Box 14115-175,Tehran, IranAli Asghar MaassoumiDepartment of Botany, Research Institute of Forests and Rangelands, P.O. Box 13185-116, Tehran, IranJournal Article20150420This study represents phylogenetic analyses of two woody polygonaceous genera Calligonum and Pteropyrum using both chloroplast fragment (trnL-F) and the nuclear ribosomal internal transcribed spacer (nrDNA ITS) sequence data. All inferred phylogenies using parsimony and Bayesian methods showed that Calligonum and Pteropyrum are both monophyletic and closely related taxa. They have no affinity with Atraphaxis, instead allied with a clade in which the genus is nested. Infrageneric relationships in Calligonum, due to the paucity of informative nucleotide sites in both DNA regions are not resolved.National Institute of Genetic Engineering and Biotechnology of IranIranian Journal of Biotechnology1728-30438120100101Genetic Similarities Among Iranian Populations of Festuca, Lolium, Bromus and Agropyron Using Amplified Fragments Length Polymorphism (AFLP) Markers16237123ENMohammad Mahdi MajidiDepartment of Agronomy and Plant Breeding, College of Agriculture, Isfahan University of Technology, Isfahan, P.O. Box 84156-8311, I.R. IranAghafakhr MirlohiDepartment of Agronomy and Plant Breeding, College of Agriculture, Isfahan University of Technology, Isfahan, P.O. Box 84156-8311, I.R. IranJournal Article20150420The study of genetic variation and phylogenetic relationships is essential for the efficient selection of superior plant material and conducting introgression breeding programs. In Iran, despite the wide geographical distribution of grasses no report is available on the genetic diversity and relationships of cool season grass populations. In this study amplified fragment length polymorphism (AFLP) was used to study 42 populations from eight species of Festuca arundinacea Schereb., Festuca. pratensis Huds., Festuca. rubra L., Festuca. ovina L., Lolium perenne L., L. rigidum Gaud., Bromus tomentellus Boiss. and Agropyron cristatum (L) Gaertn. The number of amplified products ranged from 11 to 78 per primer combination and a total of 497 markers were scored. Jaccard’s genetic similarity coefficients among populations ranged from 0.15 to 0.88 showing high levels of inter and intra-specific genetic diversity. The cluster analysis and principle coordinate analysis (PCOA) reflected the phylogenetic relationships among species and clearly demonstrated differences in the degree of similarity among accessions. Results indicated that AFLP is a useful technique to reveal genetic diversity at different taxonomic levels of grasses and might facilitate the selective introgression of useful genes in plant breeding programs.National Institute of Genetic Engineering and Biotechnology of IranIranian Journal of Biotechnology1728-30438120100101Simple Sequence Repeats Amplification: a Tool to Survey the Genetic Background of Olive Oils24317124ENZohreh RabieiDepartment of Biotechnology, Faculty of New Technologies and Energy Engineering, Shahid Beheshti University, G.C. Tehran, I.R. Iran0000-0001-6686-3077Sattar Tahmasebi EnferadiDepartment of Molecular Genetics, National Institute of Genetic Engineering and Biotechnology, P.O. BOX 14965/161, Tehran, I.R. Iran0000-0003-1070-6392Abbas SaidiDepartment of Biotechnology, Faculty of New Technologies and Energy Engineering, Shahid Beheshti University, G.C. Tehran, I.R. IranSonia PatuiUniversità degli Studi di Udine, Dipartimento di Biologia e Protezione delle Piante, via delle Scienze 91-33100 Udine, ItalyGian Paolo VannozziUniversità degli Studi di Udine, Dipartimento di Scienze Agrarie e Ambientali, via delle Scienze 208-33100 Udine, ItalyJournal Article20150420A reliable DNA extraction method for use on extra virgin olive oil based on a commercial kit was defined, and the possibility of using this DNA for fingerprinting the original cultivar was demonstrated. The genetic traceability of single-cultivar virgin olive oil from two cultivars (Carolea and Frantoio) was achieved by identifying the varieties from which they were produced. This involved the analysis of DNA sequences using a panel of seven simple sequence repeats (SSRs) to provide genotype-specific allelic profiles. The amplified SSR fragments and the DNA profiles from the monovarietal oil corresponded to the profiles from the leaves of the same cultivar. The most reliable SSR in providing correct allele sizing in distinguishing either single-cultivar olive oil samples or the different ratios of their blends are DCA3, DCA4, DCA16, DCA17, and GAPU101, while DCA9, GAPU59 produced less concordance against data obtained by the genetic analysis of leaf samples. To have reproducible results, PCR product purification and selection of a set of markers with a highly robust amplification pattern is suggested.National Institute of Genetic Engineering and Biotechnology of IranIranian Journal of Biotechnology1728-30438120100101Inhibitory Effects of Lactobacillus salivarius and Lactobacillus crispatus Isolated from Chicken Gastrointestinal Tract on Salmonella enteritidis and Escherichia coli Growth32377125ENMehrnaz NouriDepartment of Medical Biotechnology, School of Medical Sciences, Tarbiat Modares University, P.O. Box 14115-333, Tehran, I.R. IranFatemeh RahbarizadehDepartment of Medical Biotechnology, School of Medical Sciences, Tarbiat Modares University, P.O. Box 14115-333, Tehran, I.R. IranDavoud AhmadvandDepartment of Clinical Biochemistry, School of Medical Sciences, Tarbiat Modares University, P.O. Box 14115-333, Tehran, I.R. IranFarhad MoosakhaniDepartment of Veterinary Medicine, Azad University, Karaj, I.R. Iran 4Department of Clinical Sciences, Clinical Research Centre, Lund University, Malmö, SwedenElham SadeqzadehDepartment of Medical Biotechnology, School of Medical Sciences, Tarbiat Modares University, P.O. Box 14115-333, Tehran, I.R. IranShahram LavasaniDepartment of Medical Biotechnology, School of Medical Sciences, Tarbiat Modares University, P.O. Box 14115-333, Tehran, I.R. IranVahid Khoddami VishtehDepartment of Medical Biotechnology, School of Medical Sciences, Tarbiat Modares University, P.O. Box 14115-333, Tehran, I.R. IranJournal Article20150420Probiotics are live cultures of microbes; often lactic acid bacteria, but also some other species, which when fed to animals, improve their health and growth through altering the intestinal microbial balance. In the present research, healthy chickens’ gastrointestinal (GI) tracts were screened for the presence of lactic acid bacteria with probiotic properties. The probiotic properties of the isolates taken from different parts of the GI tract were evaluated. They were examined for resistance to 2% (w/v) bile salts and acidic pH, capability to adhere to the intestinal epithelium and inhibitory effects on the growth of Salmonella enteritidis and Escherichia coli. Fermentation profile analyses and sequencing data of the conserved 16S rRNA genes showed that from a total of five selected clones, four clones isolated from the duodenum and caeca were Lactobacillus salivarius and the fifth clone, isolated from the duodenum, was Lactobacillus crispatus. All the selected clones were able to adhere to the chicken’s epithelial cells. The lactobacilli isolated from different parts of the GI tract had probiotic properties suitable for use in animal feed. Due to the inhibitory effects of the isolated lactic acid bacteria on the growth of pathogenic microbiota, it can be concluded that these bacteria are good candidates for treatment of chicken GI infectious diseases.National Institute of Genetic Engineering and Biotechnology of IranIranian Journal of Biotechnology1728-30438120100101Effect of Whey Permeate and Yeast Extract on Metabolic Activity of Bifidobacterium Animalis Subsp. Lactis Bb 1238457126ENHasan JaliliDepartmant of Food Science, Technology and Engineering, Faculty of Agricultural Engineering and Technology, Agricultural Campus, University of Tehran, P.O. Box 4111, Karaj, I.R. IranHadi RazaviDepartmant of Food Science, Technology and Engineering, Faculty of Agricultural Engineering and Technology, Agricultural Campus, University of Tehran, P.O. Box 4111, Karaj, I.R. IranMohammad SafariDepartmant of Food Science, Technology and Engineering, Faculty of Agricultural Engineering and Technology, Agricultural Campus, University of Tehran, P.O. Box 4111, Karaj, I.R. IranJournal Article20150420In fermented products containing Bifidobacteria, factors such as organic acid concentration and b-galactosidase activity are important in the development of flavor and texture of final products. Both the process conditions and medium components have significant effects on fluctuation of such factors. The effects of whey permeate powder and yeast extract concentrations, as nitrogen sources was investigated, on metabolic activity of Bifidobacterium animalis subsp. lactis Bb 12 in skim milk based media. Development of organic acids, growth rate and b-galactosidase activity under uncontrolled pH conditions was also monitored. Media with high concentrations of nitrogen sources showed maximum viable counts of B. animalis. The activity of b-galactosidase increased during the logarithmic phase and the initial stage of the stationary phase of growth and then decreased thereafter. Increasing the yeast extract concentration resulted in an increase in the specific sugar consumption rate with concomitant reduction in formation of acetic acid and formic acid. Consequently, the molar ratio of acetic acid to lactic acid was decreased. Using limited amounts of nitrogen sources resulted in more organic acid production in the tested microorganism. During the early hours of fermentation in which the amounts of nitrogen levels were limited, the specific rate of b-glactosidase activity was very high. Therefore, by evaluating the activity of this enzyme we can estimate the amount nutrient components in the medium.The production of succinic acid was observed during logarithmic and stationary phase in all fermentation media. Citric acid that naturally exists in whey and skim milk powder was consumed during the stationary phase of growth by B. animalis and its consumption correlated significantly with the production of succinic acid at this stage.National Institute of Genetic Engineering and Biotechnology of IranIranian Journal of Biotechnology1728-30438120100101Molecular Detection of Lipase A gene in Putative Bacillus subtilis Strains Isolated from Soil46497095ENHamid Mir Mohammad SadeghiDepartment of Biotechnology and Isfahan Pharmaceutical Research Center, School of Pharmacy, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
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Applied Physiology Research Center, Isfahan University of Medical Sciences, Isfahan, I.R. Iran0000-0002-4834-4502Mohammad RabbaniDepartment of Biotechnology and Isfahan Pharmaceutical Research Center, School of Pharmacy, Isfahan University of Medical Sciences, Isfahan, I.R. IranFatemeh MoazenDepartment of Biotechnology and Isfahan Pharmaceutical Research Center, School of Pharmacy, Isfahan University of Medical Sciences, Isfahan, I.R. IranSareh HomamiDepartment of Biotechnology and Isfahan Pharmaceutical Research Center, School of Pharmacy, Isfahan University of Medical Sciences, Isfahan, I.R. IranJournal Article20150420The present study was undertaken to screen the soil samples collected in Iran for the presence of the Bacillus subtilis lipase A gene. The bacterial colonies obtained from the collected soil samples were examined by physical appearance, biochemical tests and the polymerase chain reaction (PCR). Only four colonies were identified as putative B. subtilis strains and all contained the lipase A gene. However, the intensities of the DNA bands were different and correlated with the differences obtained from the biochemical tests. Polymorphism of the lipase gene was also determined in samples using SSCP assay. In conclusion, this study demonstrates an easy and reliable method for detection of the lipase gene in B. subtilis strains. Further screening of the soil by this method will enable the detection and identification of industrially more favorable lipases.National Institute of Genetic Engineering and Biotechnology of IranIranian Journal of Biotechnology1728-30438120100101Comparison of Four Different Purification Methods for Isolation of Anti Echis carinatus Antivenom Antibodies from Immunized Chicken Egg Yolk50557102ENSubramani MeenatchisundaramDepartment of Microbiology, Nehru Arts and Science College, Coimbatore, IndiaAntonysamy MichaelDepartment of Microbiology, PSG College of Arts and Science, Coimbatore, IndiaJournal Article20150420Egg-laying hens were immunized with the Echis carinatus venom and the resulting antibodies were extracted from egg yolk by four different purification methods. The chicken egg yolk antibodies were purified by the water dilution method, polyethylene glycol (PEG) and ammonium sulphate precipitation method, chloroform extraction and the Lithium sulphate precipitation method. These methods were compared in terms of total protein content, immunospecific anti E. carinatus immunoglobulin Y (IgY) activity and in vitro and in vivo neutralizing capacity of IgY against the E. carinatus venom. Total IgY concentrations varied from 1.6 to 7.0 mg per ml of egg yolk. In neutralization studies, IgY purified by PEG and ammonium sulphate precipitation (PEG-AS) showed better results when compared to other purification methods. Approximately 1.25 mg of IgY (PEG-AS) was able to neutralize 2Lethal Dose50 of the E. carinatus venom. Purification of IgY by PEG and ammonium sulphate yielded very pure IgY at high quantities (93% ± 5% of total egg yolk protein), which was also capable of neutralizing toxic and lethal components of the E. carinatus venom.National Institute of Genetic Engineering and Biotechnology of IranIranian Journal of Biotechnology1728-30438120100101Investigation of Culture Conditions for Biosynthesis of Silver Nanoparticles Using Aspergillus fumigatus56617105ENZahra Ranjbar NavaziEnvironmental Group, Department of Energy, Materials and Energy Research Center, Karaj, I.R. IranMohammad PazoukiEnvironmental Group, Department of Energy, Materials and Energy Research Center, Karaj, I.R. IranFarah Sadat HalekEnvironmental Group, Department of Energy, Materials and Energy Research Center, Karaj, I.R. IranJournal Article20150420In this study, silver nanoparticles were synthesized using the fungus, Aspergillus fumigatus. The effects of three independent variables including glucose content of culture media, initial pH and initial spore concentration on biosynthesis of silver nanoparticles were investigated. These variables affect cell morphology, cell mass, size and morphology of silver nanoparticles and degree of silver ion reduction. The formation of silver nanoparticles was confirmed spectrophotomterically. Size and morphology of silver nanoparticles were investigated using transmission electron microscopy (TEM). The effects of culture conditions on cell mass concentration as well as the amount and size of synthesized silver nanoparticles were studied. As a result, the optimum culture condition for biosynthesis of silver nanoparticles consisted of a glucose concentration of 16 g/l, pH of 4.5 and spore concentration of 1.5×107 spore/l. TEM micrographs showed that the size of nanoparticles in the sample synthesized under optimized condition was in the range of 7-19 nm.