Effects of T208E activating mutation on MARK2 protein structure and dynamics: Modeling and simulation
Sajjad
Ahrari
Department of Biology, College of Sciences, Shiraz University
author
Navid
Mogharrab
Department of Biology, College of Sciences, Shiraz University
author
text
article
2014
eng
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 b2, b4 strands and aC-helix, go through activating motions and those having close interactions with UBA domain like C-half of b1, b3 and b5 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 (∆∆G = -9 kJ/mol) which is suggestive of a more intimate interaction between the UBA domain and protein N-lobe in mutant structure.
Molecular Biology Research Communications
Shiraz University Press
2322-181X
3
v.
3
no.
2014
149
164
https://mbrc.shirazu.ac.ir/article_2195_081fd7900bd78eca8d2c38a16015c0df.pdf
dx.doi.org/10.22099/mbrc.2014.2195
Evaluation of antioxidant potential and reduction capacity of some plant extracts in silver nanoparticle synthesis
Vahid
Goodarzi
Biology Department, Shiraz University
author
Hajar
Zamani
Biology Department, Shiraz University
author
Leila
Bajuli
Biology Department, Shiraz University
author
Ali
Moradshahi
Department of Biology, Collage of Sciences, Shiraz University, Shiraz,Iran
author
text
article
2014
eng
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.
Molecular Biology Research Communications
Shiraz University Press
2322-181X
3
v.
3
no.
2014
165
174
https://mbrc.shirazu.ac.ir/article_2196_7c048deb5920f18169cc547d68ff7c77.pdf
dx.doi.org/10.22099/mbrc.2014.2196
Identification and characterization of a NBS–LRR class resistance gene analog in Pistacia atlantica subsp. Kurdica
Bahman
Bahramnejad
Department of Agricultural Biotechnology, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
author
text
article
2014
eng
P. atlantica subsp. Kurdica, with the local name of Baneh, is a wild medicinal plant which grows in Kurdistan, Iran. The identification of resistance gene analogs holds great promise for the development of resistant cultivars. A PCR approach with degenerate primers designed according to conserved NBS-LRR (nucleotide binding site-leucine rich repeat) regions of known disease-resistance (R) genes was used to amplify and clone homologous sequences from P. atlantica subsp. Kurdica. A DNA fragment of the expected 500-bp size was amplified. The nucleotide sequence of this amplicon was obtained through sequencing and the predicted amino acid sequence compared to the amino acid sequences of known R-genes revealed significant sequence similarity. Alignment of the deduced amino acid sequence of P. atlantica subsp. Kurdica resistance gene analog (RGA) showed strong identity, ranging from 68% to 77%, 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, a kinase-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 deduced amino-acid sequences of PAKRGA1 and RGAs from different species indicated that they were separated in two clusters, PAKRGA1 being on cluster II. The isolated NBS analogs can be eventually used as guidelines to isolate numerous R-genes in Pistachio.
Molecular Biology Research Communications
Shiraz University Press
2322-181X
3
v.
3
no.
2014
175
185
https://mbrc.shirazu.ac.ir/article_2372_bb01f9410f9b01feda46c534e708c2a6.pdf
dx.doi.org/10.22099/mbrc.2014.2372
Comparison of genetic variation of wild and farmed Bream (Abramis brama orientalis; berg, 1905) using microsatellite markers
Zeinab
Hosseinnia
Department of Fisheries, Faculty of Fisheries and Environmental Sciences, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran
author
Ali
Shabany
Department of Fisheries, Faculty of Fisheries and Environmental Sciences, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran
author
Hamed
Kolangi-Miandare
Department of Fisheries, Faculty of Fisheries and Environmental Sciences, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran
author
text
article
2014
eng
Bream (Abramis brama orientalis) is one of the most commercially valuable fish in the Caspian Sea. The aim of this study was to compare levels of genetic polymorphism between wild and farmed Bream populations using seven microsatellite loci. Genetic diversity was investigated by studying samples collected from two regions; Chaboksar and the Artificial Propagation Center of Guilan province. Allele frequency was found to have declined in wild and cultured fish due to inbreeding and genetic drift. Significant population differentiation (Fst) was observed between wild and farmed populations, which could be explained by the low number of alleles in two populations. Significant deviations from the Hardy-Weinberg equilibrium were found at more loci. Beyond the null alleles' hypothesis, heterozygote deficiency may have arisen due to inbreeding. Both populations showed lowest genetic diversity according to the number of alleles and genotypes per each locus. This approach was carried out for the first time and could provide information regarding the genetic variability of farmed and wild abramis brama fish using microsatellite markers. Results could be used for the management and conservation of artificial Bream propagation programs.
Molecular Biology Research Communications
Shiraz University Press
2322-181X
3
v.
3
no.
2014
187
195
https://mbrc.shirazu.ac.ir/article_2396_3625942fb4bdfd0bffe4a3fe0b611f33.pdf
dx.doi.org/10.22099/mbrc.2014.2396
Genetic population structure and differentiation of Western Iranian Oxynoemacheilus argyrogramma (Heckel, 1847) using SSR markers
Hamed
Kolangi-Miandare
Aquatic Ecology, Gorgan University of Agricultural Sciences and Natural Resources, Iran
author
Ghasem
Askari
Aquatic Ecology, Gorgan University of Agricultural Sciences and Natural Resources, Iran
author
text
article
2014
eng
This study was carried out to investigate the genetic diversity and population structure of 90 specimens of Oxynoemacheilus argyrogramma collected from Sepidbarg, Gamasiab and Ghaleji rivers, in the west of Iran. Analyses using three microsatellite 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) and observed (Ho) heterozygosity means were 0.865 and 0.576, respectively. Almost all loci showed deviation from the Hardy-Weinberg equilibrium (HWE). The results demonstrated that Oxynoemacheilus argyrogramma had desirable genetic diversity in the investigated regions.
Molecular Biology Research Communications
Shiraz University Press
2322-181X
3
v.
3
no.
2014
197
204
https://mbrc.shirazu.ac.ir/article_2397_87feb63c4c82b8b8324535a5e49201cc.pdf
dx.doi.org/10.22099/mbrc.2014.2397
Phenol-stacked carbon nanotubes: A new approach to genomic DNA isolation from plants
Farhad
Nazarian-Firouzabadi
Agronomy and plant breeding group, Faculty of Agriculture, Lorestan University ,P.O.Box, 465, Khorramabad, Iran
author
Ahmad
Ismaili
Agronomy and plant breeding group, Faculty of Agriculture, Lorestan University ,P.O.Box, 465, Khorramabad, Iran
author
Sayed Mahmoud
Zabeti
Agronomy and plant breeding group, Faculty of Agriculture, Lorestan University ,P.O.Box, 465, Khorramabad, Iran
author
text
article
2014
eng
Extraction of intact quality DNA from plant tissues, especially those rich in secondary metabolites, is often challenging. Literally, hundreds of different DNA isolation 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 developing countries. In nearly all protocols and DNA isolation kits, phenol and chloroform are used to precipitate various classes of impurities. However, phenol is partially soluble in water, resulting in the co-existence of proteins in upper (aqueous) phases. This phenomenon results in the contamination of the nucleic acids and low quality DNA. Nanotechnology advances have helped many areas of molecular biology such as the development of new diagnosis and purification kits. In this study, for the first time, we report 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 remove proteins, polysaccharides and other polyphenol constituents. The A260/A280nm absorbance ratios of isolated DNA samples were 1.9 and 1.8 for chamomile and opium plants, respectively, indicating the high purity of the isolated DNA. DNA yield was more than two times the standard Doyle and Doyle method. Furthermore, the isolated DNA proved amenable to PCR amplification, using Random Amplified Polymorphic DNA (RAPD) analysis.
Molecular Biology Research Communications
Shiraz University Press
2322-181X
3
v.
3
no.
2014
205
213
https://mbrc.shirazu.ac.ir/article_2425_c7e175c0c4142bca3a38fca6dd757cd1.pdf
dx.doi.org/10.22099/mbrc.2014.2425