Demystifying EPR: A Rookie Guide to the Application of Electron Paramagnetic Resonance Spectroscopy on Biomolecules
Yaser
NejatyJahromy
Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany
author
Erik
Schubert
Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany
author
text
article
2014
eng
Electron Paramagnetic Resonance (EPR) spectroscopy, also known as Electron Spin Resonance(ESR) especially among physicists, is a strong and versatile spectroscopic method forinvestigation of paramagnetic systems, i.e. systems like free radicals and most transition metalions, which have unpaired electrons. The sensitivity and selectivity of EPR are notable andintriguing as compared to other spectroscopic methods and approaches. As a qualitative method,EPR can detect species down to the nanomolar range. On the other hand, the specificity of themethod stems from spectral features which directly depend on the types, distances, and relativeorientations of the atoms in the neighborhood of the electron spin centers. In addition tostructural information, EPR can be used to elucidate time dependent behavior of the studiedsystem and it is applicable to systems of different size, ranging from small molecules tomacromolecules. The following short review of general EPR methods is intended for anaudience with little prior knowledge about EPR. It includes examples of suitable representativesystems, techniques for the study of short lived paramagnetic species and even diamagneticmolecules, and introduces the reader to tools necessary for making sense of the spectra. Thispaper focuses only on continuous wave (cw) EPR and does not elaborate on the more advancedpulsed EPR methods.
Progress in Biological Sciences
University of Tehran Press
1016-1058
4
v.
2
no.
2014
133
152
https://pbiosci.ut.ac.ir/article_52305_5fa9f97359498cb1f5de8b8649d9044b.pdf
dx.doi.org/10.22059/pbs.2014.52305
Genetic worth and stability of selection indices in rice (Oryza sativa L.)
Mohammad
Fotokian
Crop Science and Plant Breeding Department, College of Agriculture, Shahed University, Tehran, Iran
author
Kayvan
Agahi
Crop Science and Plant Breeding Department, College of Agriculture, Shahed University, Tehran, Iran
author
text
article
2014
eng
Improvement of one trait on its own will affect the performance of other traits because ofgenotypic correlations between traits. Index selection is one of the tools used by plant breedersto overcome this problem. The purpose of this paper is to evaluate selection indices developedfor improving grain yield in rice (Oryza sativa L.). Forty-nine rice genotypes were cultivated atTonekabon Rice Research Station, Iran, in 2009 and 2010. Selection indices were developedbased on phenotypic and genotypic correlations, path coefficients, broad-sense heritability oftraits and stepwise multiple linear regression coefficients. Assessment of indices revealed thatthe stability decreased concurrently with increase in the genetic worth, and hence an inverseassociation existed between stability and genetic worth of indices. The results also suggestedthat selection for TP, GW, GP and GL and against PH using their multiple linear regressionparameters as economic weights was an effective criterion for improving grain yield in ricegenotypes. On the other hand, the most stable indices were those that were developed based onheritability of traits as well as genotypic path coefficients.
Progress in Biological Sciences
University of Tehran Press
1016-1058
4
v.
2
no.
2014
153
166
https://pbiosci.ut.ac.ir/article_52296_acdb9527b050046ea55daa1795d2ded4.pdf
dx.doi.org/10.22059/pbs.2014.52296
Appraisal of the entire mitochondrial genome for DNA barcoding in birds
Leila
Nourani
Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
author
Mansour
Aliabadian
1. 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, Iran
author
text
article
2014
eng
DNA barcoding based on a standardized region of 648 base pairs of mitochondrial DNAsequences from Cytochrome C Oxidase 1 (COX1) is proposed for animal species identification.Recent studies suggested that DNA barcoding has been effective for identifying 94% of birdspecies. The proposed threshold of 10 times the average intraspecific variation could be used forthe identification and delimitation of new species. As a different part of the mitochondrial DNAevolves at various mutation rates, they show a variety of capabilities to distinguish taxa tospecies level. In order to compare the efficiency of protein-coding genes (PCGs) in birds, thecomplete genome of 310 birds, including 12 mitochondrial genes (except ND6) and barcodingthe region of COX1, were examined. We concentrated on the intra- and inter-specific variationsand the degree of mutational saturation as criteria for our evaluations. Some genes like ATP8,ND2 and ND5 showed the greatest divergence in intra- and inter-specific variations. Theoverlap between intra- and inter-specific variability for all genes is still troublesome. Our resultsmay have been influenced by the sample size because our data were not representative of allbird species. More additional taxa may shed light more on DNA barcoding candidate genes.
Progress in Biological Sciences
University of Tehran Press
1016-1058
4
v.
2
no.
2014
167
178
https://pbiosci.ut.ac.ir/article_52297_d6945a8d6a6e83e3e4d86054906fe551.pdf
dx.doi.org/10.22059/pbs.2014.52297
Alterations in antioxidant defence in the early life stages of silver carp, Hypophthalmichthys molitrix
Fatemeh
Liravi
Department of Fisheries, Pardis Campus, Khorramshahr University of Marine Science and Technology,
Khorramshahr, Iran
author
Amir Parviz
Salati
Department of Fisheries, Faculty of Marine Natural Resources, Khorramshahr University of Marine Science and
Technology, Khorramshahr, Iran
author
Farzad
Asadi
Department of Biochemistry, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
author
Hossein
Pasha-Zanoosi
Department of Physical Oceanography, Faculty of Marine Sciences, Khorramshahr University of Marine Science
and Technology, Khorramshahr, Iran
author
text
article
2014
eng
Fish larvae experience major cellular and biochemical changes during their early life stages.The aim of the present study was to evaluate alterations in the antioxidant status and values oflipid peroxidation and vitamin C content during the different life developmental stages ofHypophthalmichthys molitrix. Eggs and larvae were sampled at fertilization, organogenesis,eyed egg, hatch, active feeding, and 14 and 21 days after active feeding. An age dependentsignificant variation in SOD activity was seen during the period of study as the highest activityrecorded at the eyed egg stage (P<0.05). Meanwhile, the activity of GPX and CAT did not showany significant changes in this study (P>0.05). The overall trend of MDA concentration showedsignificant increase from fertilization toward 21 days after fertilization (P<0.05). Vitamin Ccontent showed an opposite pattern and decreased during the period of study (P<0.05). It can beconcluded that vitamin C plays a crucial role in the antioxidant defence system during the earlylife stages of H. molitrix as could prevent from increase of MDA content till active feeding.
Progress in Biological Sciences
University of Tehran Press
1016-1058
4
v.
2
no.
2014
179
187
https://pbiosci.ut.ac.ir/article_52298_ee375710c979fea958121ad71d6c2c12.pdf
dx.doi.org/10.22059/pbs.2014.52298
Silicon alleviates salt stress in pistachio plants
Ghader
Habibi
Department of Biology, Payame Noor University, I. R. of Iran
author
Fahimeh
Norouzi
Department of Plant Science, University of Tabriz, 51666-14779 Tabriz, Iran
author
Roghieh
Hajiboland
Department of Plant Science, University of Tabriz, 51666-14779 Tabriz, Iran
author
text
article
2014
eng
In this work, the effects of silicon (Si) supplementation were studied in pistachio (Pistacia veraL. cv Ahmadaghaii) plants exposed to high salinity stress. Plants were grown in pots undercontrol and salt (EC=15 dS m-1) conditions without or with Si treatment (0.35 g Na2SiO3 Kg-1soil) under field conditions. Salt stress reduced the plants’ growth significantly in both –Si and+Si plants; however, Si-supplied plants had a higher root and shoot dry weight as compared tothose without Si supply under salinity conditions. Salt stress caused a significant reduction ofleaf photochemical activities; however, Si application ameliorated these effects. The reductionof the net CO2 assimilation rate under salinity stress was alleviated by Si application,accompanied by an increase in water-use-efficiency. The concentration of Na in the leaves androots was significantly reduced by Si, while root K and leaf Ca concentrations were higher inSi-treated plants under salt stress compared with –Si ones. The activity of antioxidativeenzymes increased under salt stress and Si application caused a further increase, beingsignificant for superoxide dismutase (SOD). Salt stress induced membrane damage, as wasindicated by a higher malondialdehyde (MDA) concentration. In Si-supplemented plants,however, the MDA amount did not increase under salt stress. The results indicated that the Simediatedalleviation of salt stress in pistachio plants is related to higher photosynthesis andwater-use efficiency, a reduction of Na uptake and transport, and the stimulation of the plant’santioxidative defence capacity.
Progress in Biological Sciences
University of Tehran Press
1016-1058
4
v.
2
no.
2014
189
202
https://pbiosci.ut.ac.ir/article_52299_6769a7a3930224321cabb3ff1e31ceec.pdf
dx.doi.org/10.22059/pbs.2014.52299
Flavonoid Patterns and their Diversity in ten Stachys L. (Lamiaceae) Species from Iran
Navaz
kharazian
Department of Botany, Faculty of Sciences, University of Shahrekord, 115, Shahrekord, Iran
author
Mojgan
Mohammadi
Department of Botany, Faculty of Sciences, University of Shahrekord, 115, Shahrekord, Iran
author
text
article
2014
eng
Stachys genus with medicinal properties and high polymorphic features has been considered oneof the largest genera of Lamiaceae. The aim of this study was to determine the flavonoid patternvariations and flavonoid groups in ten Stachys species belonging to two sections; Fragilicaulis,and Aucheriana. The studied species were collected from natural habitats in Iran and analysedfor their flavonoid constituents using thin layer chromatography with silica gel. The purificationof the flavonoid compounds of each species was carried out using column chromatography withsephadex LH20. The identification of flavonoid class was confirmed by spectral data. In orderto study the flavonoid variations, cluster analysis was used with SPSS ver.20 software. Theresults of this study showed that the highest variations were found in Stachys pilifera Benth.,Stachys aucheri Benth., Stachys ballotiformis Vatke and Stachys benthamiana Boiss. Based onthe results, six flavonoid classes were identified. Most of the flavonoid classes were found to beflavones. The flavones and isoflavones were observed in section Fragilicaulis and flavanones,flavonols, isoflavones, dihydroflavonol, chalcones and flavones were in section Aucheriana. Itcan be concluded that the flavonoid compounds are appropriate markers in chemotaxonomicstudies of the Stachys genus.
Progress in Biological Sciences
University of Tehran Press
1016-1058
4
v.
2
no.
2014
203
218
https://pbiosci.ut.ac.ir/article_52300_9b3beaf80d153ae8c28e79fae945c0fa.pdf
dx.doi.org/10.22059/pbs.2014.52300
Re-assessment of subspecific taxa in Astragalus section Anthylloidei (Fabaceae) based on molecular evidence
Kosar
Naderi Safar
Department of Plant Biology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14155-154, Iran
author
Shahrokh
Kazempour Osaloo
Department of Plant Biology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14155-154, Iran
author
Ali Asghar
Maasoumi
Department of Botany, Research Institute of Forests and Rangelands, Tehran 13185-116, Iran
author
text
article
2014
eng
The taxonomic and phylogenetic status of several taxa previously recognized as subspecies inAstragalus sect. Anthylloidei is re-assessed based on DNA sequences and morphologicalfeatures. We focused on Astragalus ebenoides (subsp. ebenoides and subsp. naghadehensis),Astragalus murinus (subsp. murins and subsp. bornmuelleri), Astragalus remotiflorus (subsp.remotiflorus and subsp. melanogramma), Astragalus nigrohirsutus (=Astragalus remotiflorussubsp. nigrohirsutus), Astragalus submitis (=Astragalus submitis subsp. submitis) andAstragalus yushensis (=Astragalus submitis subsp. maassoumii). A total of 15 accessionsrepresenting 14 ingroups and one outgroup were analysed for nrDNA ITS and plastid DNA,rpl32 gene and rpl32-trnL(UAG) intergenic spacer. Phylogenetic trees were constructed usingneighbour joining, Bayesian and maximum parsimony methods. The phylogenetic analyses ofboth datasets revealed that the subspecies described formerly under each of the studied speciesare distinct and should be elevated to specific rank. The nucleotide sequence variationsobserved among different subspecies, along with morphological characters, providedappropriate criteria in setting the species boundaries. The new combinations and a diagnostickey to the studied species are provided.
Progress in Biological Sciences
University of Tehran Press
1016-1058
4
v.
2
no.
2014
219
234
https://pbiosci.ut.ac.ir/article_52301_ec3e26d9b601992f7d64ff6a765e359e.pdf
dx.doi.org/10.22059/pbs.2014.52301
A quantitative competitor PCR assay to detect genetically modified roundup-ready soybeans in commercially sold foods in Iran
Elham
Ghazizadeh
1. Department of Plant Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB),
Tehran, Iran
2. Department of Biology, Faculty of Science, Lorestan University, Khoramabad, Iran
author
Amir
Mousavi
Department of Plant Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB),
Tehran, Iran
author
Faranak
Hadi
Department of Biology, Faculty of Science, Lorestan University, Khoramabad, Iran
author
text
article
2014
eng
Due to ever-increasing global diffusion and related socio-economic implications, the detectionof genetically modified organisms (GMOs) is very important. In this study, we design a plasmidcontaining two genes in mutated form as construct-specific (cp4 epsps) and event-specific(pd35S). It is applied for quantitative-competitor (QC) PCR as a simple and reliable method forthe detection of GM food. This plasmid is calibrated with the external standard of the IRMM(The Institute for Reference Materials and Measurements), and then used to detect the presenceof cp4 epsps and pd35S sequences in five foods derived from GM round-ready (RR) soya soldcommercially in Iran. The results indicate the presence of GM RR soya in these products,quantitatively. In order to detect whether they contain more or less than 1% RR soya DNA, QCPCRwith various amounts of DNA plasmids as a standard was performed. The results showthat this plasmid can be used as a calibrator for 1% cp4 epsps and pd35S, and that it can also beapplied instead of 1% IRMM genomics.
Progress in Biological Sciences
University of Tehran Press
1016-1058
4
v.
2
no.
2014
235
243
https://pbiosci.ut.ac.ir/article_52302_240f2c87eedef6187899ee77599ea345.pdf
dx.doi.org/10.22059/pbs.2014.52302
Automatic classification of highly related Malate Dehydrogenase and L-Lactate Dehydrogenase based on 3D-pattern of active sites
Amir
Rahimi
Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
author
Armin
Madadkar-Sobhani
Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran;
Department of Life Sciences, Barcelona Supercomputing Center, Barcelona, Spain
author
Rouzbeh
Touserkani
School of Computer Sciences ,Institute for Research in Fundamental Sciences (IPM), Tehran, Iran
author
Bahram
Goliaei
Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
author
text
article
2014
eng
Accurate protein function prediction is an important subject in bioinformatics, especially wheresequentially and structurally similar proteins have different functions. Malate dehydrogenaseand L-lactate dehydrogenase are two evolutionary related enzymes, which exist in a widevariety of organisms. These enzymes are sequentially and structurally similar and sharecommon active site residues, spatial patterns and molecular mechanisms. Here, we studyvarious features of the active site cavity of 229 PDB chain entries and try to classify themautomatically by various classifiers including the support vector machine, k nearest neighbourand random forest methods. The results show that the support vector machine yields the highestpredictive performance among mentioned classifiers. Despite very close and conserved patternsamong Malate dehydrogenases and L-lactate dehydrogenases, the SVM predicts the functionefficiently and achieves 0.973 Matthew’s correlation coefficient and 0.987 F-score. The sameapproach can be used in other enzyme families for automatic discrimination betweenhomologous enzymes with common active site elements, however, acting on differentsubstrates.
Progress in Biological Sciences
University of Tehran Press
1016-1058
4
v.
2
no.
2014
245
260
https://pbiosci.ut.ac.ir/article_52303_4aaa914ca443366efcc2744ae7f23622.pdf
dx.doi.org/10.22059/pbs.2014.52303
Apoptotic protease-activating factor 1 (Apaf-1) as a liable gene for spontaneous mutations in vitro
Taha
Azad
Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
author
Amin
Tashakor
Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
author
Mina
Ghahremani
Department of Plant Biology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
author
Roohullah
Hemmati
Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
author
Farangis
Ataei
Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
author
Saman
Hosseinkhani
Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
author
text
article
2014
eng
The apoptotic protease-activating factor 1 (Apaf-1) receives the death signal in the intrinsic ormitochondrial pathway of apoptosis. Upon the releasing of cytochrome c from theintermembrane space of mitochondria and binding to Apaf-1 molecules, a heptamericapoptosome complex is formed and triggers the downstream cascade of caspases. Here, for thefirst time we present spontaneous mutations and recombinations of the Apaf-1 gene and itsneighbouring sequences. We sequence 48 colonies containing pcDNA3.1 vector withNluc/Apaf1 and Cluc/Apaf1 obtained through the quick-change site-directed mutagenesismethod, transforming to DH5-α and XL10-Gold at two temperatures, 18 and 37ºC. In 21 ofthese cases, we found 38 different mutations. Our data suggest that there is a direct relationshipbetween bacterial incubation temperatures and the number of unwanted spontaneous mutations.During our experiment we found that the Apaf-1 gene is much less susceptible to spontaneousmutations when it is transformed into XL10-Gold at 18 ºC . In contrast, a large number ofspontaneous mutations were found when the gene of interest transformed into DH5α at 37ºC .
Progress in Biological Sciences
University of Tehran Press
1016-1058
4
v.
2
no.
2014
261
273
https://pbiosci.ut.ac.ir/article_52304_ce8f33ace899b4c12db1452d67f5fe75.pdf
dx.doi.org/10.22059/pbs.2014.52304