University of Tehran PressProgress in Biological Sciences1016-10584220141201Demystifying EPR: A Rookie Guide to the Application of Electron Paramagnetic Resonance Spectroscopy on Biomolecules1331525230510.22059/pbs.2014.52305ENYaserNejatyJahromyInstitute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, GermanyErikSchubertInstitute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, GermanyJournal Article20140615Electron Paramagnetic Resonance (EPR) spectroscopy, also known as Electron Spin Resonance<br />(ESR) especially among physicists, is a strong and versatile spectroscopic method for<br />investigation of paramagnetic systems, i.e. systems like free radicals and most transition metal<br />ions, which have unpaired electrons. The sensitivity and selectivity of EPR are notable and<br />intriguing as compared to other spectroscopic methods and approaches. As a qualitative method,<br />EPR can detect species down to the nanomolar range. On the other hand, the specificity of the<br />method stems from spectral features which directly depend on the types, distances, and relative<br />orientations of the atoms in the neighborhood of the electron spin centers. In addition to<br />structural information, EPR can be used to elucidate time dependent behavior of the studied<br />system and it is applicable to systems of different size, ranging from small molecules to<br />macromolecules. The following short review of general EPR methods is intended for an<br />audience with little prior knowledge about EPR. It includes examples of suitable representative<br />systems, techniques for the study of short lived paramagnetic species and even diamagnetic<br />molecules, and introduces the reader to tools necessary for making sense of the spectra. This<br />paper focuses only on continuous wave (cw) EPR and does not elaborate on the more advanced<br />pulsed EPR methods.<br /> https://pbiosci.ut.ac.ir/article_52305_5fa9f97359498cb1f5de8b8649d9044b.pdfUniversity of Tehran PressProgress in Biological Sciences1016-10584220141201Genetic worth and stability of selection indices in rice (Oryza sativa L.)1531665229610.22059/pbs.2014.52296ENMohammadFotokianCrop Science and Plant Breeding Department, College of Agriculture, Shahed University, Tehran, IranKayvanAgahiCrop Science and Plant Breeding Department, College of Agriculture, Shahed University, Tehran, IranJournal Article20131220Improvement of one trait on its own will affect the performance of other traits because of<br />genotypic correlations between traits. Index selection is one of the tools used by plant breeders<br />to overcome this problem. The purpose of this paper is to evaluate selection indices developed<br />for improving grain yield in rice (Oryza sativa L.). Forty-nine rice genotypes were cultivated at<br />Tonekabon Rice Research Station, Iran, in 2009 and 2010. Selection indices were developed<br />based on phenotypic and genotypic correlations, path coefficients, broad-sense heritability of<br />traits and stepwise multiple linear regression coefficients. Assessment of indices revealed that<br />the stability decreased concurrently with increase in the genetic worth, and hence an inverse<br />association existed between stability and genetic worth of indices. The results also suggested<br />that selection for TP, GW, GP and GL and against PH using their multiple linear regression<br />parameters as economic weights was an effective criterion for improving grain yield in rice<br />genotypes. On the other hand, the most stable indices were those that were developed based on<br />heritability of traits as well as genotypic path coefficients.<br /> https://pbiosci.ut.ac.ir/article_52296_acdb9527b050046ea55daa1795d2ded4.pdfUniversity of Tehran PressProgress in Biological Sciences1016-10584220141201Appraisal of the entire mitochondrial genome for DNA barcoding in birds1671785229710.22059/pbs.2014.52297ENLeilaNouraniDepartment of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, IranMansourAliabadian1. Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
2. Research Department of Zoological Innovations, Institute of Applied Zoology, Faculty of Sciences, Ferdowsi
University of Mashhad, Mashhad, IranJournal Article20140105DNA barcoding based on a standardized region of 648 base pairs of mitochondrial DNA<br />sequences from Cytochrome C Oxidase 1 (COX1) is proposed for animal species identification.<br />Recent studies suggested that DNA barcoding has been effective for identifying 94% of bird<br />species. The proposed threshold of 10 times the average intraspecific variation could be used for<br />the identification and delimitation of new species. As a different part of the mitochondrial DNA<br />evolves at various mutation rates, they show a variety of capabilities to distinguish taxa to<br />species level. In order to compare the efficiency of protein-coding genes (PCGs) in birds, the<br />complete genome of 310 birds, including 12 mitochondrial genes (except ND6) and barcoding<br />the region of COX1, were examined. We concentrated on the intra- and inter-specific variations<br />and the degree of mutational saturation as criteria for our evaluations. Some genes like ATP8,<br />ND2 and ND5 showed the greatest divergence in intra- and inter-specific variations. The<br />overlap between intra- and inter-specific variability for all genes is still troublesome. Our results<br />may have been influenced by the sample size because our data were not representative of all<br />bird species. More additional taxa may shed light more on DNA barcoding candidate genes.<br /> https://pbiosci.ut.ac.ir/article_52297_d6945a8d6a6e83e3e4d86054906fe551.pdfUniversity of Tehran PressProgress in Biological Sciences1016-10584220141201Alterations in antioxidant defence in the early life stages of silver carp, Hypophthalmichthys molitrix1791875229810.22059/pbs.2014.52298ENFatemehLiraviDepartment of Fisheries, Pardis Campus, Khorramshahr University of Marine Science and Technology,
Khorramshahr, IranAmir ParvizSalatiDepartment of Fisheries, Faculty of Marine Natural Resources, Khorramshahr University of Marine Science and
Technology, Khorramshahr, IranFarzadAsadiDepartment of Biochemistry, Faculty of Veterinary Medicine, University of Tehran, Tehran, IranHosseinPasha-ZanoosiDepartment of Physical Oceanography, Faculty of Marine Sciences, Khorramshahr University of Marine Science
and Technology, Khorramshahr, IranJournal Article20140105Fish larvae experience major cellular and biochemical changes during their early life stages.<br />The aim of the present study was to evaluate alterations in the antioxidant status and values of<br />lipid peroxidation and vitamin C content during the different life developmental stages of<br />Hypophthalmichthys molitrix. Eggs and larvae were sampled at fertilization, organogenesis,<br />eyed egg, hatch, active feeding, and 14 and 21 days after active feeding. An age dependent<br />significant variation in SOD activity was seen during the period of study as the highest activity<br />recorded at the eyed egg stage (P<0.05). Meanwhile, the activity of GPX and CAT did not show<br />any significant changes in this study (P>0.05). The overall trend of MDA concentration showed<br />significant increase from fertilization toward 21 days after fertilization (P<0.05). Vitamin C<br />content showed an opposite pattern and decreased during the period of study (P<0.05). It can be<br />concluded that vitamin C plays a crucial role in the antioxidant defence system during the early<br />life stages of H. molitrix as could prevent from increase of MDA content till active feeding.<br /> https://pbiosci.ut.ac.ir/article_52298_ee375710c979fea958121ad71d6c2c12.pdfUniversity of Tehran PressProgress in Biological Sciences1016-10584220141201Silicon alleviates salt stress in pistachio plants1892025229910.22059/pbs.2014.52299ENGhaderHabibiDepartment of Biology, Payame Noor University, I. R. of IranFahimehNorouziDepartment of Plant Science, University of Tabriz, 51666-14779 Tabriz, IranRoghiehHajibolandDepartment of Plant Science, University of Tabriz, 51666-14779 Tabriz, IranJournal Article20140201In this work, the effects of silicon (Si) supplementation were studied in pistachio (Pistacia vera<br />L. cv Ahmadaghaii) plants exposed to high salinity stress. Plants were grown in pots under<br />control and salt (EC=15 dS m-1) conditions without or with Si treatment (0.35 g Na2SiO3 Kg-1<br />soil) under field conditions. Salt stress reduced the plants’ growth significantly in both –Si and<br />+Si plants; however, Si-supplied plants had a higher root and shoot dry weight as compared to<br />those without Si supply under salinity conditions. Salt stress caused a significant reduction of<br />leaf photochemical activities; however, Si application ameliorated these effects. The reduction<br />of the net CO2 assimilation rate under salinity stress was alleviated by Si application,<br />accompanied by an increase in water-use-efficiency. The concentration of Na in the leaves and<br />roots was significantly reduced by Si, while root K and leaf Ca concentrations were higher in<br />Si-treated plants under salt stress compared with –Si ones. The activity of antioxidative<br />enzymes increased under salt stress and Si application caused a further increase, being<br />significant for superoxide dismutase (SOD). Salt stress induced membrane damage, as was<br />indicated by a higher malondialdehyde (MDA) concentration. In Si-supplemented plants,<br />however, the MDA amount did not increase under salt stress. The results indicated that the Simediated<br />alleviation of salt stress in pistachio plants is related to higher photosynthesis and<br />water-use efficiency, a reduction of Na uptake and transport, and the stimulation of the plant’s<br />antioxidative defence capacity.<br /> https://pbiosci.ut.ac.ir/article_52299_6769a7a3930224321cabb3ff1e31ceec.pdfUniversity of Tehran PressProgress in Biological Sciences1016-10584220141201Flavonoid Patterns and their Diversity in ten Stachys L. (Lamiaceae) Species from Iran2032185230010.22059/pbs.2014.52300ENNavazKharazianDepartment of Botany, Faculty of Sciences, University of Shahrekord, 115, Shahrekord, IranMojganMohammadiDepartment of Botany, Faculty of Sciences, University of Shahrekord, 115, Shahrekord, IranJournal Article20140201Stachys genus with medicinal properties and high polymorphic features has been considered one<br />of the largest genera of Lamiaceae. The aim of this study was to determine the flavonoid pattern<br />variations and flavonoid groups in ten Stachys species belonging to two sections; Fragilicaulis,<br />and Aucheriana. The studied species were collected from natural habitats in Iran and analysed<br />for their flavonoid constituents using thin layer chromatography with silica gel. The purification<br />of the flavonoid compounds of each species was carried out using column chromatography with<br />sephadex LH20. The identification of flavonoid class was confirmed by spectral data. In order<br />to study the flavonoid variations, cluster analysis was used with SPSS ver.20 software. The<br />results of this study showed that the highest variations were found in Stachys pilifera Benth.,<br />Stachys aucheri Benth., Stachys ballotiformis Vatke and Stachys benthamiana Boiss. Based on<br />the results, six flavonoid classes were identified. Most of the flavonoid classes were found to be<br />flavones. The flavones and isoflavones were observed in section Fragilicaulis and flavanones,<br />flavonols, isoflavones, dihydroflavonol, chalcones and flavones were in section Aucheriana. It<br />can be concluded that the flavonoid compounds are appropriate markers in chemotaxonomic<br />studies of the Stachys genus.<br /><br />https://pbiosci.ut.ac.ir/article_52300_9b3beaf80d153ae8c28e79fae945c0fa.pdfUniversity of Tehran PressProgress in Biological Sciences1016-10584220141201Re-assessment of subspecific taxa in Astragalus section Anthylloidei (Fabaceae) based on molecular evidence2192345230110.22059/pbs.2014.52301ENKosarNaderi SafarDepartment of Plant Biology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14155-154, IranShahrokhKazempour OsalooDepartment of Plant Biology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14155-154, IranAli AsgharMaasoumiDepartment of Botany, Research Institute of Forests and Rangelands, Tehran 13185-116, IranJournal Article20131016The taxonomic and phylogenetic status of several taxa previously recognized as subspecies in<br />Astragalus sect. Anthylloidei is re-assessed based on DNA sequences and morphological<br />features. We focused on Astragalus ebenoides (subsp. ebenoides and subsp. naghadehensis),<br />Astragalus murinus (subsp. murins and subsp. bornmuelleri), Astragalus remotiflorus (subsp.<br />remotiflorus and subsp. melanogramma), Astragalus nigrohirsutus (=Astragalus remotiflorus<br />subsp. nigrohirsutus), Astragalus submitis (=Astragalus submitis subsp. submitis) and<br />Astragalus yushensis (=Astragalus submitis subsp. maassoumii). A total of 15 accessions<br />representing 14 ingroups and one outgroup were analysed for nrDNA ITS and plastid DNA,<br />rpl32 gene and rpl32-trnL(UAG) intergenic spacer. Phylogenetic trees were constructed using<br />neighbour joining, Bayesian and maximum parsimony methods. The phylogenetic analyses of<br />both datasets revealed that the subspecies described formerly under each of the studied species<br />are distinct and should be elevated to specific rank. The nucleotide sequence variations<br />observed among different subspecies, along with morphological characters, provided<br />appropriate criteria in setting the species boundaries. The new combinations and a diagnostic<br />key to the studied species are provided.<br /><br />https://pbiosci.ut.ac.ir/article_52301_ec3e26d9b601992f7d64ff6a765e359e.pdfUniversity of Tehran PressProgress in Biological Sciences1016-10584220141201A quantitative competitor PCR assay to detect genetically modified roundup-ready soybeans in commercially sold foods in Iran2352435230210.22059/pbs.2014.52302ENElhamGhazizadeh1. Department of Plant Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB),
Tehran, Iran
2. Department of Biology, Faculty of Science, Lorestan University, Khoramabad, IranAmirMousaviDepartment of Plant Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB),
Tehran, IranFaranakHadiDepartment of Biology, Faculty of Science, Lorestan University, Khoramabad, IranJournal Article20140324Due to ever-increasing global diffusion and related socio-economic implications, the detection<br />of genetically modified organisms (GMOs) is very important. In this study, we design a plasmid<br />containing two genes in mutated form as construct-specific (cp4 epsps) and event-specific<br />(pd35S). It is applied for quantitative-competitor (QC) PCR as a simple and reliable method for<br />the detection of GM food. This plasmid is calibrated with the external standard of the IRMM<br />(The Institute for Reference Materials and Measurements), and then used to detect the presence<br />of cp4 epsps and pd35S sequences in five foods derived from GM round-ready (RR) soya sold<br />commercially in Iran. The results indicate the presence of GM RR soya in these products,<br />quantitatively. In order to detect whether they contain more or less than 1% RR soya DNA, QCPCR<br />with various amounts of DNA plasmids as a standard was performed. The results show<br />that this plasmid can be used as a calibrator for 1% cp4 epsps and pd35S, and that it can also be<br />applied instead of 1% IRMM genomics.<br /> https://pbiosci.ut.ac.ir/article_52302_240f2c87eedef6187899ee77599ea345.pdfUniversity of Tehran PressProgress in Biological Sciences1016-10584220141201Automatic classification of highly related Malate Dehydrogenase and L-Lactate Dehydrogenase based on 3D-pattern of active sites2452605230310.22059/pbs.2014.52303ENAmirRahimiDepartment of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, IranArminMadadkar-SobhaniDepartment of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran;
Department of Life Sciences, Barcelona Supercomputing Center, Barcelona, SpainRouzbehTouserkaniSchool of Computer Sciences ,Institute for Research in Fundamental Sciences (IPM), Tehran, IranBahramGoliaeiDepartment of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, IranJournal Article20140324Accurate protein function prediction is an important subject in bioinformatics, especially where<br />sequentially and structurally similar proteins have different functions. Malate dehydrogenase<br />and L-lactate dehydrogenase are two evolutionary related enzymes, which exist in a wide<br />variety of organisms. These enzymes are sequentially and structurally similar and share<br />common active site residues, spatial patterns and molecular mechanisms. Here, we study<br />various features of the active site cavity of 229 PDB chain entries and try to classify them<br />automatically by various classifiers including the support vector machine, k nearest neighbour<br />and random forest methods. The results show that the support vector machine yields the highest<br />predictive performance among mentioned classifiers. Despite very close and conserved patterns<br />among Malate dehydrogenases and L-lactate dehydrogenases, the SVM predicts the function<br />efficiently and achieves 0.973 Matthew’s correlation coefficient and 0.987 F-score. The same<br />approach can be used in other enzyme families for automatic discrimination between<br />homologous enzymes with common active site elements, however, acting on different<br />substrates.<br /> https://pbiosci.ut.ac.ir/article_52303_4aaa914ca443366efcc2744ae7f23622.pdfUniversity of Tehran PressProgress in Biological Sciences1016-10584220141201Apoptotic protease-activating factor 1 (Apaf-1) as a liable gene for spontaneous mutations in vitro2612735230410.22059/pbs.2014.52304ENTahaAzadDepartment of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, IranAminTashakorDepartment of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, IranMinaGhahremaniDepartment of Plant Biology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, IranRoohullahHemmatiDepartment of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, IranFarangisAtaeiDepartment of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, IranSamanHosseinkhaniDepartment of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, IranJournal Article20140910The apoptotic protease-activating factor 1 (Apaf-1) receives the death signal in the intrinsic or<br />mitochondrial pathway of apoptosis. Upon the releasing of cytochrome c from the<br />intermembrane space of mitochondria and binding to Apaf-1 molecules, a heptameric<br />apoptosome complex is formed and triggers the downstream cascade of caspases. Here, for the<br />first time we present spontaneous mutations and recombinations of the Apaf-1 gene and its<br />neighbouring sequences. We sequence 48 colonies containing pcDNA3.1 vector with<br />Nluc/Apaf1 and Cluc/Apaf1 obtained through the quick-change site-directed mutagenesis<br />method, transforming to DH5-α and XL10-Gold at two temperatures, 18 and 37ºC. In 21 of<br />these cases, we found 38 different mutations. Our data suggest that there is a direct relationship<br />between bacterial incubation temperatures and the number of unwanted spontaneous mutations.<br />During our experiment we found that the Apaf-1 gene is much less susceptible to spontaneous<br />mutations when it is transformed into XL10-Gold at 18 ºC . In contrast, a large number of<br />spontaneous mutations were found when the gene of interest transformed into DH5α at 37ºC .<br /><br />https://pbiosci.ut.ac.ir/article_52304_ce8f33ace899b4c12db1452d67f5fe75.pdf