Shiraz University Press
Molecular Biology Research Communications
2322-181X
2345-2005
7
1
2018
03
01
Evaluation of prodynorphin gene polymorphisms and their association with heroin addiction in a sample of the southeast Iranian population
1
6
EN
Mohammad
Hashemi
0000-0002-6074-7101
Cellular and Molecular Research Center, Zahedan University of Medical Sciences, Zahedan, Iran
mhd.hashemi@gmail.com
Mansour
Shakiba
Department of Psychiatry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
mansoorshakiba@yahoo.com
Sara
Sanaei
Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
sarasanae7@yahoo.com
Ghazaleh
Shahkar
Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
gh.shahkar@gmail.com
Maryam
Rezaei
Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
maryamrezaee47@gmail.com
Azizolla
Mojahed
Department of Clinical Psychology, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
mojahed@zaums.ac.ir
Gholamreza
Bahari
Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
r_b_1333@yahoo.com
10.22099/mbrc.2017.27182.1294
Genetic factors are supposed to account for about 30-50% of the predisposition to cocaine and heroin addiction. This study aims at investigating the effect of rs2281285, rs2235749, rs910080 and 68bp VNTR polymorphisms of prodynorphin (<em>PDYN</em>) gene on heroin dependence risk in a sample of the southeast Iranian population. This case-control study was done on 216 heroin dependence subjects and 219 healthy subjects. Genomic DNA was extracted from peripheral blood cells using salting out method. Genotyping of <em>PDYN</em> polymorphisms were performed using polymerase chain reaction (PCR) or PCR-RFLP method. The findings showed that <em>PDYN</em> rs910080 T>C variant significantly increased the risk of heroin dependence (OR=7.91, 95%CI=3.36-18.61, P<0.0001, CC vs TT; OR=7.53, 95%CI=3.30-17.16, P<0.0001, CC vs TT+TC; OR=1.75, 95%CI=1.33-2.32, p<0.0001, C vs T). The rs2235749 C>T, rs2281285 A>G and 68bp VNTR variants of <em>PDYN</em> gene were not associated with heroin dependence. Altogether, our results provide an association between rs910080 polymorphism of <em>PDYN</em> gene and risk of heroin dependence in a sample of the southeast Iranian population.
Prodynorphin,Addiction,Heroin,Polymorphism,VNTR
https://mbrc.shirazu.ac.ir/article_4659.html
https://mbrc.shirazu.ac.ir/article_4659_ab8530e6c905a7a69b4e13fe3c6044d3.pdf
Shiraz University Press
Molecular Biology Research Communications
2322-181X
2345-2005
7
1
2018
03
01
Evaluation of genetic relationship between 15 bamboo species of North-East India based on ISSR marker analysis
7
15
EN
Thoungamba
Amom
Deparment of Biotechnology, Manipur University, India
amom.thoungam@gmail.com
Leimapokpam
Tikendra
Deparment of Biotechnology, Manipur University, India
tikenleimapokpam@gmail.com
Hamidur
Rahaman
Deparment of Biotechnology, Manipur University, India
hamidur2006@gmail.com
Angamba
Potshangbam
Deparment of Biotechnology, Manipur University, India
angambameetei@gmail.com
Potshangbam
Nongdam
Deparment of Biotechnology, Manipur University, India
purenba@rediffmail.com
10.22099/mbrc.2018.28378.1303
The classification of bamboos based on floral morphology and reproductive characters is very hard due to erratic flowering behavior and unusually long reproductive cycle. The application of reliable and effective DNA molecular markers is highly essential to address this problem. In the present investigation, inter-simple sequence repeats (ISSR) markers were employed to study phylogenetic relationship of 15 different bamboos of North-East India. The 10 ISSR primers generated 116 polymorphic loci or scorable bands with average of 11.6 bands per primer. The genetic similarity coefficient ranged from 0.41-0.76 showing high genetic polymorphism among different bamboo species. The phylogenetic tree constructed based on genetic similarity matrix revealed genetic proximity of endemic <em>Bambusa</em><em> mizorameana</em> to other five <em>Dendrocalamus</em> species by clustering into a single group, while <em>Dendrocalamus manipureanus</em> segregated from the cluster indicating its genetic divergent character. Except for <em>Schizotachyum fuchsianum,</em> the three <em>Schizotachyum </em>species viz., <em>S. dullooa, S. pergracile</em> and <em>S. munroi</em> exhibited close genetic affinity by grouping into a single minor clade. Principal coordinates analysis (PCoA) showed distribution of different bamboos species in the plot in accordance to unweighted pair-group method with arithmetic average (UPGMA) cluster analysis. Genetic relationship of 15 different bamboos as revealed from the dendrogram and PCoA analysis reasonably conformed to traditional system of classification though slight disagreement existed. This is the first report on the successful use of ISSR markers in the phylogenetic and genetic variation studies of 15 important bamboos of the region including the endemic bamboo species of <em>B. mizorameana</em>, <em>B. manipureana</em>, <em>D. sikkimensis</em> and <em>D. manipureanus</em>.
bamboos,Genetic diversity,ISSR markers,Bambusa,Dendrocalamus
https://mbrc.shirazu.ac.ir/article_4775.html
https://mbrc.shirazu.ac.ir/article_4775_a900ae1608f73d0c545829a9e5eba412.pdf
Shiraz University Press
Molecular Biology Research Communications
2322-181X
2345-2005
7
1
2018
03
01
The association between NFKB1 -94ATTG ins/del and NFKB1A -826C/T genetic variations and coronary artery disease risk
17
24
EN
Abbas
Seidi
Department of Genetic, Faculty of Basic Sciences, Islamic Azad University, Zanjan Branch, Zanjan, Iran
a_seidi@yahoo.com
Sina
Mirzaahmadi
Department of Genetic, Faculty of Basic Sciences, Islamic Azad University, Zanjan Branch, Zanjan, Iran
sinacanmirr@yahoo.com
Khalil
Mahmoodi
Department of Cardiology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
khalil_mahmoodi@yahoo.com
Mohammad
Soleiman Soltanpour
Department of Medical Laboratory Sciences, School of Paramedical Sciences, Zanjan University of Medical Sciences, Zanjan, Iran
soltanpourm@zums.ac.ir
10.22099/mbrc.2018.28261.1302
Coronary artery disease (CAD) is considered as a chronic inflammatory disease initiated from early childhood. Nuclear factor κB (NF κB) and κB1A (NF κB1A) are the key regulators of inflammatory responses. The <em>NFKB1</em> -94ATTG ins/del and <em>NFKB1A</em> -826C/T polymorphisms may contribute to the development of CAD. The aim of the present study was to investigate the association of these polymorphisms with the risk of CAD. The study population included 120 patients with angiographically confirmed CAD and 100 matched controls. Genotyping of <em>NFKB1</em> -94ATTG ins/del and <em>NFKB1A</em> -826C/T polymorphism was performed using PCR-RFLP method. Lipid level was determined by routine colorimetric methods. Statistical analysis was done by SPSS 16 software. Results indicated that the genotypic (P=0.041) and allelic (P=0.009) distribution of the NFKB1-94ATTG ins/del polymorphism was significantly different between the two groups. In the univariate analysis (ins/ins genotype as reference), the del/del genotype (OR=2.88, 95% CI=1.21-6.84, P=0.015) but not ins/del genotype (OR=1.48, 95% CI=0.83-2.64, P=0.191) was significantly associated with the increased risk of CAD. In the multiple binary logistic regression analysis, diabetes, hypertension, smoking, LDL-cholesterol, total cholesterol, HDL-cholesterol and <em>NFKB1</em> -94ATTG del/del genotype were identified as significant and independent risk factors for CAD development. The distribution of genotypes and alleles of <em>NFKB1A</em> -826C/T polymorphism was not significantly different between the two groups. In conclusion the present study identified <em>NFKB1</em> -94ATTG ins/del polymorphism but not <em>NFKB1A</em> -826C/T polymorphism as a significant and independent risk factor for development and severity of CAD.
Coronary artery disease,Nuclear factor κB,Polymorphism
https://mbrc.shirazu.ac.ir/article_4780.html
https://mbrc.shirazu.ac.ir/article_4780_e47b02532fc901bfd0d9e7f1946aaed1.pdf
Shiraz University Press
Molecular Biology Research Communications
2322-181X
2345-2005
7
1
2018
03
01
Apoptosis induction in acute promyelocytic leukemia cells through upregulation of CEBPα by miR-182 blockage
25
33
EN
Mohammadreza
Sharifi
0000-0002-1538-9034
Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
mo_sharifi@med.mui.ac.ir
Mahdi
Fasihi-Ramandi
Molecular Biology Research Center, Baqiyatallah University of Medical
Sciences, Tehran, Iran
fasihi.m@gmail.com
Abdolkarim
Sheikhi
Department of Immunology, School of Medicine, Dezful University of Medical Sciences, Dezful, Iran
sheikhi@queensu.ca
Abbas
Moridnia
Department of Immunology, School of Medicine, Dezful University of Medical Sciences, Dezful, Iran
moridnia.a@dums.ac.ir
Maryam
Saneipour
Department of Immunology, School of Medicine, Dezful University of Medical Sciences, Dezful, Iran
sanei_0412@yahoo.com
10.22099/mbrc.2018.27625.1297
MicroRNAs (miRNAs) involved in regulation of the genes. The CCAAT/enhancer-binding protein-α (<em>CEBPα</em>) is a crucial transcription factor for normal hematopoiesis and cell cycle that frequently disrupted in human acute myeloid leukemia (AML). The miR-182 up-regulation in several malignant diseases such as AML was reported, in the other hand bioinformatics analysis revealed <em>CEBPα</em> targeted by miR-182.miR-182-5p inhibition in human acute promyelocytic leukemia (APL) cell line was performed by using locked nucleic acid (LNA) and subsequently miR-182-5p and <em>CEBPα </em>expression, apoptosis, necrosis and cell proliferation were measured.After LNA-anti-miR-182-5p transfection to cells at different time points, miR-182-5p down regulation and <em>CEBPα</em> overexpression was revealed in the LNA-anti-miR group compared to the control groups. The cell viability was meaningfully varied between LNA-anti-miR and control groups. Increasing of the apoptotic ratio was linked to miR-182-5p inhibition in the LNA-anti-miR group rather than other groups. Similarly, the necrotic ratio in the LNA-anti-miR group was higher.Our results supported the hypothesis that miR-182-5p inhibition can reduce the cell viability predominantly due to induces apoptosis and necrosis. The present results can apply in translational medicine for investigation of antisense therapy and drug development in leukemia.
miR-182-5p,Locked Nucleic Acid,Acute Promyelocytic Leukemia,CEBPα
https://mbrc.shirazu.ac.ir/article_4790.html
https://mbrc.shirazu.ac.ir/article_4790_7d1c9d82e95a650cfb15026144197423.pdf
Shiraz University Press
Molecular Biology Research Communications
2322-181X
2345-2005
7
1
2018
03
01
Prediction of T-cell epitopes for designing a reverse vaccine against streptococcal bacteria
35
41
EN
Samira
Ebrahimi
Department of Biotechnology, Faculty of Advanced Sciences and Technologies, University of Isfahan, Isfahan, Iran
s.ebrahimi@ast.ui.ac.ir
Hassan
Mohabatkar
Department of Biotechnology, Faculty of Advanced Sciences and Technologies, University of Isfahan, Isfahan, Iran
h.mohabatkar@ast.ui.ac.ir
10.22099/mbrc.2018.28775.1308
Streptococcal bacteria are among dangerous human pathogens with major prevalence worldwide. A good vaccine against streptococcal bacteria should have epitopes that confer protection from infection by different streptococcal bacteria types. we aimed was to recognize the most immunogenic and conserved epitopes of streptococcal bacteria, which could be a potential candidate for vaccine development. Nineteen different M proteins of different streptococcal bacteria were chosen and analyzed. Nine-mer epitopes able to simulate both cells mediate and humoral immunity were predicted. Molecular docking was applied in order to measure free binding energy of selected epitopes. Final epitopes were analyzed if they were conserved among different streptococcal bacteria. The identified epitopes require experimental validation for their potential use in peptide vaccines.
Epitope prediction,Molecular docking,M protein,Streptococcal bacteria,Vaccine design
https://mbrc.shirazu.ac.ir/article_4791.html
https://mbrc.shirazu.ac.ir/article_4791_31cef331a5acfc37ec5de337bc23e457.pdf
Shiraz University Press
Molecular Biology Research Communications
2322-181X
2345-2005
7
1
2018
03
01
Evolutionary features of 8K (KDa) silencing suppressor protein of Potato mop-top virus
43
50
EN
Aminalah
Tahmasebi
Plant Virology Research Center, College of Agriculture, Shiraz University, Shiraz, Iran
tahmasebi.info@yahoo.com
Alireza
Afsharifar
Plant Virology Research Center, College of Agriculture, Shiraz University, Shiraz, Iran
afshari@shirazu.ac.ir
Ahmad
Heydari
Firoozabad Center for Higher Education, Iran
a.heidar140@fabad-ihe.ac.ir
Mohammad
Mehrabadi
Department of Entomology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran.
m.mehrabadi@modares.ac.ir
10.22099/mbrc.2018.28458.1304
The cysteine-rich 8K protein of Potato mop-top virus (PMTV) suppresses host RNA silencing. In this study, evolutionary analysisof 8K sequences of PMTV isolates was studied on the basis of nucleotide and amino acid sequences. Twenty-one positively selected sites were identified in 8K codingregions. Recombination events were found in the 8K of PMTV isolates with a rate of 1.8. Totally 30 haplotypes were detected with haplotype diversity ranging from 0.8 to 1.0 and nucleotide diversity from 7.58 to 13.62. The positions 33 and 30 indicated the highly positive and negative selection (with the highest and the lowest dN-dS values), respectively. Tajima’s D test suggested that 8K is evolving with a strong positive selection for worldwide isolates. High frequency of segregating sites was identified along 204 positions of <em>8K</em>. Moreover, in this study, we used Shannon entropy-based approach to evaluate the variability of each site of nucleotide and corresponding amino acid. Based on Shannon entropy method, 139 and 97 nucleotide sites had the highest entropy value, while 47 and 33 amino acid sites showed the most diversity along 8K sequences. Our findings suggest that 8K as an RNA silencing suppressor evolves rapidly. Taken together, its variability might play a big threat to infect other plants or overcome resistant cultivars.
Genetic Variation,8K,Potato mop-top virus,RNA silencing suppressor
https://mbrc.shirazu.ac.ir/article_4793.html
https://mbrc.shirazu.ac.ir/article_4793_da30eb9689ede8c72ac0d8530eed0a60.pdf