فهرست مطالب

  • Volume:3 Issue:3, 2014
  • تاریخ انتشار: 1393/07/06
  • تعداد عناوین: 6
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  • Sajjad Ahrari, Navid Mogharrab* Pages 149-164
    Microtubule Affinity-Regulating Kinase 2 (MARK2) protein has a substantial role in regulation of vital cellular processes like induction of polarity, regulation of cell junctions, cytoskeleton structure and cell differentiation. The abnormal function of this protein has been associated with a number of pathological conditions like Alzheimer disease, autism, several carcinomas and development of virulent effects of Helicobacter pylori. Here we tried to verify the structural changes induced in MARK2 by T208E activating mutation using molecular modeling and molecular dynamics simulation. Our results show that the enzyme structure shifts toward the active state due to T208E mutation, but this process is not a uniform change in all through the expected regions. Within the N-lobe of the protein, those functional regions having little or no interaction with the UBA domain, like N-half of 2, 4 strands and C-helix, go through activating motions and those having close interactions with UBA domain like C-half of 1,3 and 5 strands are comparatively held in-place and don’t accompany. Within the C-lobe, only activation segment has noticeable displacements. Free energy calculations also indicate higher affinity of UBA domain for protein N-lobe in mutant structure (ΔΔG = -9 kJ/mol) which is suggestive of a more intimate interaction between the UBA domain and protein N-lobe in mutant structure.
    Keywords: MARK2, Kinase protein regulation, UBA domain, Auto, inhibition, Molecular dynamics simulation, Molecular modeling
  • Vahid Goodarzi, Hajar Zamani, Leila Bajuli, Ali Moradshahi* Pages 165-174
    The green synthesis of metallic nanoparticles is an active research area in nanotechnology. In the present study, antioxidant potential, total reducing capacity and silver nanoparticles (Ag NPs) synthetic potential of methanolic leaf extracts of seven plant species were evaluated and compared. Antioxidant capacity, expressed as μmol Trolox equivalents g-1 DW (μmol TE g-1 DW), ranged from 116.0 to 1.80. The plants Rosmarinus sp. and Zataria Multiflora showed highest antioxidant capacities with IC50 of 1.07 and 1.22 mg ml-1, respectively. Total reducing capacity ranged from 7.6 to 0.17 mg gallic acid equivalent to g-1 DW (mg GAE g-1 DW). Plants with high antioxidant potentials also showed higher total reducing capacity. In fact, the order of the plants reducing capacity was similar to that of their antioxidant potential. The same two plant species, i.e., Zataria Multiflora and Rosmarinus sp. with high reducing capacities, showed higher potentials for Ag NPs synthesis. It is concluded that reducing substances in the extracts contribute significantly to the antioxidant potential of the tested plant species and plants with a high reducing capacity are excellent sources for the green synthesis of metallic nanoparticles. In addition, synthetic antioxidants have adverse effects on human health; therefore, to benefit more from the health promoting properties of plant species, evaluating their novel natural antioxidants is recommended.
    Keywords: Antioxidant potential, Reduction capacity, DPPH, Folin, Ciocalteu, Silver nanoparticles
  • Bahman Bahramnejad* Pages 175-185
    P. atlantica subsp. Kurdica, with the local name of Baneh, is a wild medicinal plantwhich grows in Kurdistan, Iran. The identification of resistance gene analogs holdsgreat promise for the development of resistant cultivars. A PCR approach withdegenerate primers designed according to conserved NBS-LRR (nucleotide bindingsite-leucine rich repeat) regions of known disease-resistance (R) genes was used toamplify and clone homologous sequences from P. atlantica subsp. Kurdica. A DNAfragment of the expected 500-bp size was amplified. The nucleotide sequence of thisamplicon was obtained through sequencing and the predicted amino acid sequencecompared to the amino acid sequences of known R-genes revealed significant sequencesimilarity. Alignment of the deduced amino acid sequence of P. atlantica subsp.Kurdica resistance gene analog (RGA) showed strong identity, ranging from 68% to77%, to the non-toll interleukin receptor (non-TIR) R-gene subfamily from other plants.A P-loop motif (GMMGGEGKTT), a conserved and hydrophobic motif GLPLAL, akinase-2a motif (LLVLDDV), when replaced by IAVFDDI in PAKRGA1 and a kinase-3a (FGPGSRIII) were presented in all RGA. A phylogenetic tree, based on the deducedamino-acid sequences of PAKRGA1 and RGAs from different species indicated thatthey were separated in two clusters, PAKRGA1 being on cluster II. The isolated NBSanalogs can be eventually used as guidelines to isolate numerous R-genes in Pistachio.
    Keywords: Pistacia atlantica subsp. Kurdica, Resistance gene analog (RGA), cloning
  • Zeinab Hosseinnia*, Ali Shabany, Hamed Kolangi-Miandare Pages 187-195
    Bream (Abramis brama orientalis) is one of the most commercially valuable fish inthe Caspian Sea. The aim of this study was to compare levels of genetic polymorphismbetween wild and farmed Bream populations using seven microsatellite loci. Geneticdiversity was investigated by studying samples collected from two regions; Chaboksarand the Artificial Propagation Center of Guilan province. Allele frequency was found tohave declined in wild and cultured fish due to inbreeding and genetic drift. Significantpopulation differentiation (Fst) was observed between wild and farmed populations,which could be explained by the low number of alleles in two populations. Significantdeviations from the Hardy-Weinberg equilibrium were found at more loci. Beyond thenull alleles'' hypothesis, heterozygote deficiency may have arisen due to inbreeding.Both populations showed lowest genetic diversity according to the number of allelesand genotypes per each locus. This approach was carried out for the first time and couldprovide information regarding the genetic variability of farmed and wild abramis bramafish using microsatellite markers. Results could be used for the management andconservation of artificial Bream propagation programs.
    Keywords: Microsatellite, Abramis brama, Polymorphism, Hardy, Weinberg equilibrium
  • Hamed Kolangi-Miandare, Ghasem Askari* Pages 197-204
    This study was carried out to investigate the genetic diversity and populationstructure of 90 specimens of Oxynoemacheilus argyrogramma collected fromSepidbarg, Gamasiab and Ghaleji rivers, in the west of Iran. Analyses using threemicrosatellite loci indicated that the average number of alleles in the population was 12,which was well above the reported values for freshwater fishes. The expected (He) andobserved (Ho) heterozygosity means were 0.865 and 0.576, respectively. Almost all locishowed deviation from the Hardy-Weinberg equilibrium (HWE). The resultsdemonstrated that Oxynoemacheilus argyrogramma had desirable genetic diversity inthe investigated regions.
    Keywords: Oxynoemacheilus argyrogramma, Genetic diversity, Microsatellite, Iran
  • Farhad Nazarian, Firouzabadi*, Ahmad Ismaili, Sayed Mahmoud Zabeti Pages 205-313
    Extraction of intact quality DNA from plant tissues, especially those rich insecondary metabolites, is often challenging. Literally, hundreds of different DNAisolation protocols from various plant species have been published over the last decades.Although many commercial DNA isolation kits are convenient and designed to be safe,their cost and availability cause limitations in small molecular labs in many developingcountries. In nearly all protocols and DNA isolation kits, phenol and chloroform areused to precipitate various classes of impurities. However, phenol is partially soluble inwater, resulting in the co-existence of proteins in upper (aqueous) phases. Thisphenomenon results in the contamination of the nucleic acids and low quality DNA.Nanotechnology advances have helped many areas of molecular biology such as thedevelopment of new diagnosis and purification kits. In this study, for the first time, wereport a different approach to isolate DNA from plants based on carbon nanotubes(CNTs). The results show that the phenol reagent stack on CNTs can effectively removeproteins, polysaccharides and other polyphenol constituents. The A260/A280nmabsorbance ratios of isolated DNA samples were 1.9 and 1.8 for chamomile and opiumplants, respectively, indicating the high purity of the isolated DNA. DNA yield wasmore than two times the standard Doyle and Doyle method. Furthermore, the isolatedDNA proved amenable to PCR amplification, using Random Amplified PolymorphicDNA (RAPD) analysis.
    Keywords: DNA isolation, Carbon nanotube, Phenol, Plants