@article { author = {Qujeq, Durdi and Tatar, Mohsen and Feizi, Farideh and Parsian, Hadi and Halalkhor, Sohrab}, title = {Effects of Teucrium polium aerial parts extracts on malonyl-CoA decarboxylase level}, journal = {Molecular Biology Research Communications}, volume = {2}, number = {4}, pages = {101-107}, year = {2013}, publisher = {Shiraz University Press}, issn = {2322-181X}, eissn = {2345-2005}, doi = {10.22099/mbrc.2013.1751}, abstract = {Malonyl-CoA decarboxylase (MCD) is an enzyme involved in the decarboxylation of malonyl-CoA to acetyl-CoA. In order to explore the hypothesis that the changing plant materials’ MCD activity level can serve as therapy to diabetics, the effect of Teucrium polium compounds was studied in a diabetic rat model. In this experimental study, two groups of rats, a control and a diabetic group, each including six rats, were used. At the end of the experiment, all rats were exterminated by ether anesthesia, their pancreases removed and dissected. Isolated rat pancreas was cultured in buffers with or without 100-500µg/l T. polium aerial parts extracts containing arginine and leucine. MCD and insulin levels were measured after culture at 37°C and 5% CO2, for 1, 3 and 5 days. Results showed that T. polium aqueous and the alcoholic extract decreased MCD activity. Present data also indicate that incubation of pancreatic tissue at a concentration of 2.8 and 16.7 mmol/L glucose stimulated insulin release. For the first time it seems that aqueous and alcoholic extracts of this plant decreased MCD activity. }, keywords = {Aerial parts,Teucrium polium,malonyl-CoA decarboxylase,MCD,Insulin}, url = {https://mbrc.shirazu.ac.ir/article_1751.html}, eprint = {https://mbrc.shirazu.ac.ir/article_1751_2fc27ab19c8164922fd835e15f1455dd.pdf} } @article { author = {Azari, Nooshin and Dayer, Mohammad and Razmi, Nematollah and Dayer, Mohammad Saaid}, title = {Mechanistic prospective for human PrPC conversion to PrPSc: Molecular dynamic insights}, journal = {Molecular Biology Research Communications}, volume = {2}, number = {4}, pages = {109-122}, year = {2013}, publisher = {Shiraz University Press}, issn = {2322-181X}, eissn = {2345-2005}, doi = {10.22099/mbrc.2013.1819}, abstract = {PrPC conversion to PrPSc isoform is the main known cause for prion diseases including Crutzfeldt-Jakob, Gerstmann-Sträussler-Sheinker syndrome and fatal familial insomnia in human. The precise mechanism underling this conversion is yet to be well understood. In the present work,  using the coordinate file of PrPC (available on the Protein Data Bank) as a starting structure, separate molecular dynamic simulations were carried out at neutral and acidic pH in an explicit water box at 37°C and 1 atmosphere pressure for 10ns second period. Results showed that the acidic pH accelerates PrPC conversion to PrPSc by decreasing the protein gyration radius, flexibility and protein-solvent hydrogen bonds. In acidic conditions, PrPC attains a more folded and less flexible tertiary structure compared to its native structure at neutral pH; otherwise, the decrease of protein-solvent hydrogen bonds at acidic pH will enhance the hydrophobic character of PrPC that may exhibit association as multimeric assemblies. It can also lower water solubility and increase resistance to proteolytic degradations. Data indicated that there was no sensible protein denaturation during this conversion. It is hypothesized that the formation of slightly misfolded conformations with minor structural changes in secondary and/or tertiary structures are enough to menace scrapie formation in PrPC. Our findings show that scrapie formation seems to be a theoretically reversible process. }, keywords = {Human Prion Protein,Prion Disease,pH,Misfolded Structure,Molecular Dynamic Simulation}, url = {https://mbrc.shirazu.ac.ir/article_1819.html}, eprint = {https://mbrc.shirazu.ac.ir/article_1819_ae90e7a71d5f61955cbd142c91d7e1c6.pdf} } @article { author = {Mousavy, Seyed Jafar and Rostamian, Mosayeb and Ebrahimi, Firouz and Dayer, Mohammad Reza}, title = {The effect of pH on recombinant C-terminal domain of Botulinum Neurotoxin type E (rBoNT/E-HCC)}, journal = {Molecular Biology Research Communications}, volume = {2}, number = {4}, pages = {123-132}, year = {2013}, publisher = {Shiraz University Press}, issn = {2322-181X}, eissn = {2345-2005}, doi = {10.22099/mbrc.2013.1820}, abstract = {Recombinant proteins are tending to be the most favorable vaccine-candidates against botulism. Recombinant Carboxy-terminal of botulinum neurotoxin serotype E (rBoNT/E-HCC) has been introduced as an efficient vaccine against botulism type E. In this report, we made an effort to investigate the effect of different pH on protein structure to assess if rBoNT/E-HCC could be used as a vaccine for oral administration. Initially, rBoNT/E-HCC was expressed and purified. Structural changes of rBoNT/E-HCC at several pH conditions were studied by various techniques including circular dichroism (CD), fluorescence, aggregation and UV-Vis spectroscopy. The results showed the more compact and more stable structure for rBoNT/E-HCC at acidic pH, and loosely folded structure at alkaline pH. Our finding as the first step of rBoNT/E-HCC evaluation, hopefully introduce it as a suitable vaccine candidate for oral administration.}, keywords = {Botulinum Neurotoxin Type E,pH,Fluorescence,Circular Dichroism,Aggregation}, url = {https://mbrc.shirazu.ac.ir/article_1820.html}, eprint = {https://mbrc.shirazu.ac.ir/article_1820_da3daf66e614b2597e2bc88fb7250900.pdf} } @article { author = {Kolangi-Miandare, Hamed and Askari, Ghasem and Fadakar, Davoud and Aghilnegad, Mostafa and Azizah, Siti}, title = {The biometric and cytochrome oxidase subunit I (COI) gene sequence analysis of syngnathus abaster (Teleostei: Syngnathidae) in Caspian sea}, journal = {Molecular Biology Research Communications}, volume = {2}, number = {4}, pages = {133-142}, year = {2013}, publisher = {Shiraz University Press}, issn = {2322-181X}, eissn = {2345-2005}, doi = {10.22099/mbrc.2013.1821}, abstract = {The black-striped pipefish, Syngnathus abaster, is a species of the Syngnathidae family. This study provides data on the morphometric, meristic and genetic structuring of the Caspian Sea pipefish, Syngnathus abaster. Eight morphometric characteristics based on total length and five morphometric characteristics based on standard length were analyzed. A total of 50 specimens were collected in brackish-water biotopes. The average of total length (LT) and standard length (LS) were 102.37 mm and 98.68 mm, respectively.  Also in this study, DNA barcodes were expanded for Caspian Sea Black-striped pipefish, hence 652 base-pair of the cytochrome oxidase I (COI) gene was sequenced in accordance with standard DNA barcoding protocols. Since Pipefish (S. abaster) is one of the most endangered fishes in the Caspian Sea, information about its phylogenetic relationships are very rare; therefore, DNA barcoding will give a more accurate picture of the future persistence of Black-striped pipefish populations. }, keywords = {Black-striped pipefish,morphometric and meristic,DNA barcoding,Caspian Sea}, url = {https://mbrc.shirazu.ac.ir/article_1821.html}, eprint = {https://mbrc.shirazu.ac.ir/article_1821_92cce282702e6427ed7340608008a3f6.pdf} } @article { author = {Derakhshandeh, Abdollah and Firouzi, Roya and Moatamedifar, Mohammad and Motamedi, Azar and Bahadori, Maryam and Naziri, Zahra}, title = {Phylogenetic analysis of Escherichia coli strains isolated from human samples}, journal = {Molecular Biology Research Communications}, volume = {2}, number = {4}, pages = {143-149}, year = {2013}, publisher = {Shiraz University Press}, issn = {2322-181X}, eissn = {2345-2005}, doi = {10.22099/mbrc.2013.1822}, abstract = {Escherichia coli (E. coli) is a normal inhabitant of the gastrointestinal tract of vertebrates, including humans. Phylogenetic analysis has shown that E. coli is composed of four main phylogenetic groups (A, B1, B2 and D). Group A and B1 are generally associated with commensals, whereas group B2 is associated with extra-intestinal pathotypes. Most enteropathogenic isolates, however, are assigned to group D. In the present study, a total of 102 E. coli strains, isolated from human samples, were used. Phylogenetic grouping was done based on the Clermont triplex PCR method using primers targeted at three genetic markers, chuA, yjaA and TspE4.C2. Group A contained the majority of the collected isolates (69 isolates, 67.64%), followed by group B2 (18 isolates, 17.64%) and D (15 isolates, 14.7%) and no strains were found to belong to group B1. The distribution of phylogenetic groups in our study suggests that although the majority of strains were commensals, the prevalence of enteropathogenic and extra-intestinal pathotypes was noteworthy. Therefore, the role of E. coli in human infections including diarrhea, urinary tract infections and meningitis should be considered.}, keywords = {Escherichia coli,Phylogenetic grouping,Triplex PCR,Human}, url = {https://mbrc.shirazu.ac.ir/article_1822.html}, eprint = {https://mbrc.shirazu.ac.ir/article_1822_119bce9ed57f4bf4c888d20856596514.pdf} } @article { author = {Fadakar, Davoud and Rezaei, Hamid and Naseri, Maryam and Mirzakhah, Masoumeh and Naderi, Saeid and Zamani, Wahid}, title = {Phylogenetic analysis of Persian Gazella, Gazella subgutturosa (Artiodactyla: Bovidae) based on cytochrome b in central Iran}, journal = {Molecular Biology Research Communications}, volume = {2}, number = {4}, pages = {151-159}, year = {2013}, publisher = {Shiraz University Press}, issn = {2322-181X}, eissn = {2345-2005}, doi = {10.22099/mbrc.2013.1839}, abstract = {Persian gazelle, Gazella subgutturosa, exists throughout arid and semiarid regions of Iran and has a key role in these frail ecosystems. Habitat degradation and population decline has placed it on the list of vulnerable species in 2008. The phylogenetic relationships of three Persian gazelle populations in the central part of Iran (i.e. Ghamishlou National Park and Wildlife Refuge, Mouteh Wildlife Refuge in Isfahan province and Kalmand-Bahadoran Protected Area in Yazd province) were investigated using parts and short fragments of mitochondrial cytochrome b gene (425 base pairs). A maximum likelihood phylogenetic tree separated the populations of Yazd and Isfahan provinces, but populations within the Isfahan province shared the same clade. All populations were classified as Persian gazelle. The studied populations are facing threats because of road construction, industrial development and urbanization. Accordingly urgent conservation plans are needed to preserve their genetic diversity and prevent them from falling into extinction.}, keywords = {Mammals,Desert ungulate,Cytochrome b,Conservation units}, url = {https://mbrc.shirazu.ac.ir/article_1839.html}, eprint = {https://mbrc.shirazu.ac.ir/article_1839_39d124f9b76adab5a398b4a25ce3c333.pdf} }