ORIGINAL_ARTICLE
L-asparaginase production in the pseudomonas pseudoalcaligenes strain JHS-71 isolated from Jooshan Hot-spring
L-asparaginase has lots of medical and industrial applications. Ever since L-asparaginase anti-tumor activity was first demonstrated, its production using microbial systems has attracted considerable attention owing to their cost-effective and eco-friendly nature. The aim of this study is to obtain L-asparaginase producing bacteria and determining the enzyme activity. Samples were picked up from Jooshan hot springs located in the Sirch, Kerman. The L-asparaginase producing bacteria were screened on the agar medium supplied with L-asparagine and phenol red indicator dye (pH-7.0). L-asparaginase activity was detected on the basis of pink color around the colony. Enzyme production was also performed based on ammonia detection by Nessler method. Among 24 strains, there were 7 strains which could produce L-asparaginase.Sequencing of 16S rRNA showed that, the best isolates producing L-asparaginase belongs to the Pseudomonas genus. Enzyme activity after 24 and 48 h of incubation showed that Pseudomonas pseudoalcaligenes strain JHS-71was the best strain that produced L-Asparaginase about 240 (U/ml) after 48h of incubation. Results showed that, L-Asparaginase activity enhanced about 27% in the presence of Co+2. L-asparaginase JHS-71 retained more than 50% of its initial activity in the presence of Cu+2, Mn+2, Zn+2, Mg+2 and Fe+2. Because of various applications of L-asparaginase in biotechnology, P. pseudoalcaligenes strain JHS-71 can be used as a suitable candidate in these fields.
https://mbrc.shirazu.ac.ir/article_3379_2c2ffbf4c8ac1d5477a5c213093f5dac.pdf
2016-02-01
1
10
10.22099/mbrc.2016.3379
L-Asparaginase
Pseudomonas
Sirch hot-spring
Screening
Identification
Arastoo
Badoei-Dalfard
badoei@uk.ac.ir
1
Assistant Professors of Biochemistry, Department of Biology, Faculty of sciences, Shahid Bahonar University of Kerman, Kerman, Iran.
LEAD_AUTHOR
Arif HM, Hussain Z. Important sources and medicinal applications of L-asparaginase. Int J Pharm Sci Rev 2014;3:35-45.
1
Ciesarova Z, Kiss E, Boegl P. Impact of L-asparaginase on acrylamide content in potato products. J Food Nutr Res 2006;45:141-146.
2
Tareke E, Rydberg P, Karlsson P, Eriksson S, Törnqvist M. Analysis of acrylamide, a carcinogen formed in heated foodstuffs. J Agr Food Chem 2002;50:4998-5006.
3
Anese M, Quarta B, Frias J. Modelling the effect of asparaginase in reducing acrylamide formation in biscuits. Food Chem 2011;126:435-40.
4
Elshafei MA, Mohamed HM, Abd-Elmontasr AM, Mahmoud DA, Elghonemy DH. Purification, characterization and antitumor activity of L-asparaginase from Penicillium brevicompactum NRC 829. Br Microb Res J 2012;2:158-174.
5
El-Bessoumy AA, Sarhan M, Mansour J. Production, isolation, and purification of L-asparaginase from Pseudomonas aeruginosa 50071 using solid-state fermentation. J Biochem Mol Biol 2004;37:387-393.
6
Han S, Jung J, Park W. Biochemical characterization of L-asparaginase in NaCl-tolerant staphylococcus sp. OJ82 isolated from fermented seafood. J Microbiol Biotechnol 2014;24:1096-1104.
7
Mahajan RV, Kumar V, Rajendran V, Saran S, Ghosh PC, Saxena RK. Purification and characterization of a novel and robust L-asparaginase having low glutaminase activity from Bacillus licheniformis: In vitro evaluation of anti-cancerous properties. PLoS ONE 2014;9:1-8.
8
Dash C, Mohapatra SB, Maiti PK. Optimization, purification and characterization of L-asparaginase from Actinomycetales bacterium BkSoiiA. Prep Biochem Biotechnol 2014;6:1-7.
9
Huang L, Liu Y, Sun Y, Yan Q, Jiang Z. Biochemical characterization of a novel L-Asparaginase with low glutaminase activity from Rhizomucor miehei and its application in food safety and leukemia treatment. Appl Environ Microbiol 2014 80:1561-1569.
10
Singh Y, Gundampati RK, Jagannadham MV, Srivastava SK. Extracellular L-asparaginase from a protease-deficient Bacillus aryabhattai ITBHU02: purification, biochemical characterization, and evaluation of antineoplastic activity in vitro. Appl Biochem Biotechnol 2013;17:1759-1774.
11
Clementi A. Presence of L-asparaginase in animals and its significance. Arch Int Physiol 1922;19:369-398.
12
Kidd JG. Regression of transplanted lymphomas induced in vivo by means of normal Guinea pig serum II. Studies on the nature of the active serum constituent: Histological mechanism of the regression: Tests for effects of guinea pig serum on lymphoma cells in vitro: Discussion. J Exp Med 1953;98:583-606.
13
Fisher SH, Wray LV. Bacillus subtilis 168 contains two differentially regulated genes encoding L-asparaginase. J Bacteriol 2002;184:2148-2154.
14
Warangkar SC, Khobragade CN. Purification, characterization, and effect of thiol compounds on activity of the Erwinia carotovora L-asparaginase. Enzyme Res 2010;1:1-10.
15
Deokar VD, Vetal MD, Rodrigues L. Production of intracellular L-asparaginase from Erwinia carotovora and its statistical optimization using response surface methodology (RSM). Int J Chem Sci 2010;1:25-36.
16
Howard C, James, HS. Production of L-asparaginase II by Escherichia coli. J Bacteriol 1968;96:2043-2048.
17
Prista AA, Kyridio DA. L-asparaginase of Thermus thermophilus: purification, properties and identification of essential amino acids for catalytic activity. Mol Cell Biochem 2001;216:93-101.
18
Abdel-Fattah YR, Olama ZA. L-asparaginase production by Pseudomonas aeruginosa in Solid-State culture: evaluation and optimization of culture conditions using factorial designs. Process Biochem 2002;38:115-122.
19
Mukherjee J, Majumdar S, Scheper T. Studies on nutritional and oxygen requirements for production of L-asparaginase by Enterobacter aerogenes. Appl Microbiol Biotechnol 2002;53:180-184.
20
Pinheiro IO, Araujo JM, Ximenes ECPA, Pinto JCS. Production of L-asparaginase by Zymomonas mobilisstrain CP4. Biomater Diagnostic 2001;6:243-244.
21
Mesas JM, Gil JA, Martin JF. Characterization and partial purification of L-asparaginase from Corynebacterium glutamicum. J Gen Microbiol 1990;136:515-519.
22
Georgia AK, Nikolaos EL. L-asparaginase from Erwinia Chrysanthemi 3937: cloning, expression and characterization. J Biotechnol 2007;127:657-669.
23
Aghaiypour K, Wlodawer A, Lubkowski J. Structural basis for the activity and substrate specificity of Erwinia chrysanthemi L-asparaginase. Biochemistry 2001;40:5655-5664.
24
Kelo E, Noronkoski T, Stoineva IB, Petkov DD, Mononen I. Beta-aspartyl peptides as substrates of L-asparaginases from Escherichia coli and Erwinia chrysanthemi. FEBS Lett 2002;528:130-132.
25
Asselin BL, Lorenson MY, Whitin JC. Comparative pharmacokinetic studies of three asparaginase preparations. J Clin Oncol 1993;11:1780-1786.
26
Moorthy V, Ramalingam A, Sumantha A, Shankaranaya RT. Production, purification and characterisation of extracellular L-asparaginase from a soil isolate of Bacillus sp. Afr J Microbiol Res 2010;4:1862-1867.
27
Sambrook J, Russell D. Molecular Cloning: A Laboratory Manual, Cold Spring Harbor, New York. 2001.
28
Badoei-Dalfard A, Karami Z. Screening and isolation of an organic solvent tolerant protease from Bacillus sp. JER02: Activity optimization by response surface methodology. J Mol Catal B: Enz 2013;89:15-23.
29
Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Bio Evol 2007;24:159-199.
30
Imada A, Igarasi S, Nakahama K, Isono M. Asparaginase and glutaminase activities of microorganisms. J Gen Microbiol 1973;76:85-99.
31
Makky EA, Loh YC, Karim MR. Purification and partial characterization of a low molecular weight L-asparaginase produced from corn cob waste. Biocatal Agric Biotechnol 2014;3:265-270.
32
Monica T, Lincoln L, Niyonzima FN, Sunil SM. Isolation, purification and characterization of fungal extracellular L-asparaginase from Mucor Hiemalis. J Biocatal Biotransform 2013;2:1-9.
33
Talluri P, Bhavana M, Rajagopal SV. Isolation and screening of L-asparaginase producing bacteria from Visakhapatnam samples, Vssl. Int J Pharm Biol Sci 2013;3: 1121-1125.
34
Basha NS, Rekha R, Komala M, Ruby S. Production of extracellular anti-leukaemic enzyme L-asparaginase from marine Actinomycetes by solid state and submerged fermentation: purification and characterisation. Trop J Pharm Res 2009;8:353-360.
35
Pradhan B, Dash SK, Sahoo S. Screening and characterization of extracelluar L-asparaginase producing Bacillus subtilis strain hswx88, isolated from Taptapani hot spring of Odisha, India. Asian Pac J Trop Biomed 2013;3:936-41.
36
Kumar S, Dasu VV, Pakshirajan K. Localization and production of novel L-asparaginase from Pectobacterium carotovorum MTCC 1428. Process Biochem 2010;45:223-229.
37
Amena S, Vishalakshi N, Prabhakar M, Dayanand A, Lingappa K. Production, purification and characterization of L-asparaginase from Streptomyces gulbargensis. Brazil J Microbiol 2010;41:173-78.
38
Dhanam JG, Kannan S. Screening and characterization of L-asparaginase Producing Streptomyces isolated from soil samples of Periyar Lake, Kumily. Biosci Dis 2014;5:50-54.
39
Kumar S, Dasu V, Pakshirajan K. Purification and characterization of glutaminase-free L-asparaginase from Pectobacterium carotovorum MTCC 1428. Bioresour Technol 2011;102:2077-2082.
40
ORIGINAL_ARTICLE
Omentin-1 rs2274907 and resistin rs1862513 polymorphisms influence genetic susceptibility to nonalcoholic fatty liver disease
Nonalcoholic fatty liver disease (NAFLD) is an obesity-associated disease and dysregulation of adipokines has an important role in its development. Omentin-1 (ITLN1 protein) and resistin are two adipokine secreted from adipose tissue. Single nucleotide polymorphisms in the adipokine genes may affect expression and activity of the adipokine, and thus play a contributory role in NAFLD pathogenesis. The aim of the present study was to investigate the association between omentin-1 rs2274907 (326A/T) and resistin rs1862513 (-420 C/G) polymorphisms and risk of NAFLD in Iranian patients. This case-control study was done on 282 subjects included 94 patients with NAFLD and 188 healthy peoples. The genotypes were determined using PCR-RFLP method. The frequency of omentin-1 AT genotype in patients with NAFLD was significantly different from that in the control (OR=2.3, 95% CI: 1.3-3.8, P=0.003). A significant association was observed between NAFLD and the GG genotype regarding resistin rs1862513 polymorphism (OR=2.3, 95% CI: 1.1-4.8, P=0.03). In conclusion, Omentin-1 rs2274907 and resistin rs1862513 polymorphisms might be a candidate genetic factor for susceptibility to NAFLD.
https://mbrc.shirazu.ac.ir/article_3380_178b7e62a8eea9504675b9db8c71e7ae.pdf
2016-02-01
11
17
10.22099/mbrc.2016.3380
Non-alcoholic fatty liver disease
Polymorphism
ITLN
Resistin
Leila
Kohan
kohan@iaua.ac.ir
1
Department of Biology, Arsanjan branch, Islamic Azad University, Arsanjan, Iran
LEAD_AUTHOR
Mehrnush
Safarpur
mehrnush.safarpur@yahoo.com
2
Department of Biology, Arsanjan branch, Islamic Azad University, Arsanjan, Iran
AUTHOR
Hamed
Abdollahi
hamed.4004@yahoo.com
3
Department of Biology, Arsanjan branch, Islamic Azad University, Arsanjan, Iran
AUTHOR
Angulo P. GI epidemiology: nonalcoholic fatty liver disease. Aliment Pharmacol Ther 2007; 25: 883-889.
1
Kleiner DE, Brunt EM, Van Natta M, Behling C, Contos MJ, Cummings OW, Ferrell LD, Liu YC, Torbenson MS, Unalp-Arida A, Yeh M, McCullough AJ, Sanyal AJ. Design and validation of a histological scoring system for nonalcoholic fatty liver disease. Hepatology 2005;41:1313-1321.
2
Paschos P, Paletas K. Non-alcoholic fatty liver disease and metabolic syndrome. Hippokratia 2009;13:9-19.
3
Moore JB. Non-alcoholic fatty liver disease: the hepatic consequence of obesity and the metabolic syndrome. Proc Nutr Soc 2010;69:211-220.
4
Tilg H. Adipocytokines in non-alcoholic fatty liver disease: Key players regulating steatosis, inflammation and fibrosis. Curr Pharma Des 2010;16:1893-1895.
5
Yilmaz Y, Yonal O, Kurt R, Alahdab YO, Eren F, Ozdogan O, Celikel CA, Imeryuz N, Kalayci C, Avsar E. Serum levels of omentin, chemerin and adipsin in patients with biopsy-proven nonalcoholic fatty liver disease. Scand J Gastroenterol 2011; 46:91-97.
6
Smitka K, Marešová D. Adipose tissue as an endocrine organ: An update on pro-inflammatory and anti-inflammatory microenvironment. Prague Med Rep 2015; 116:87-111.
7
Yang RZ, Lee MJ, Hu H, Pray J, Wu HB, Hansen BC, Shuldiner AR, Fried SK, McLenithan JC, Gong DW. Identification of omentin as a novel depot-specific adipokine in human adipose tissue: possible role in modulating insulin action. Am J Physiol Endocrinol Metab 2006;290:E1253-1261.
8
Steppan CM, Brown EJ, Wright CM, Bhat S, Banerjee RR, Dai CY, Enders GH, Silberg DG, Wen X, Wu GD, Lazar MA. A family of tissue-specific resistin-like molecules. Proc Natl Acad Sci USA 2001;16:502-506.
9
Steppan CM, Bailey ST, Bhat S, Brown EJ, Banerjee RR, Wright CM, Patel HR, Ahima RS, Lazar MA. The hormone resistin links obesity to diabetes. Nature 2001; 409:307-312.
10
Guerre-Millo M. Adipose tissue and adipokines: for better or worse. Diabetes Metab 2004;30:13-19.
11
Pagano C, Soardo G, Pilon C, Milocco C, Basan L, Milan G, Donnini D, Faggian D, Mussap M, Plebani M, Avellini C, Federspil G, Sechi LA, Vettor R. Increased serum resistin in nonalcoholic fatty liver disease is related to liver disease severity and not to insulin resistance. J Clin Endocrinol Metab 2006;91:1081-1086.
12
Stojsavljević S, Gomerčić Palčić M, Virović Jukić L, Smirčić Duvnjak L, Duvnjak M. Adipokines and proinflammatory cytokines, the key mediators in the pathogenesis of nonalcoholic fatty liver disease. World J Gastroenterol 2014;20: 18070-18091.
13
Schäffler A, Zeitounl M, Wobser H, Buechler C, Aslanidis C, Herfarth H. Frequency and significance of the novel single nucleotide missense polymorphism Val109Asp in the human gene encoding omentin in Caucasian patients with type 2 diabetes mellitus or chronic inflammatory bowel diseases. Cardio vasc Diabetol 2007;6:1-8.
14
Engert JC, Vohl M-C, Williams SM, Lepage P, Loredo-Osti JC, Faith J, Doré C, Renaud Y, Burtt NP, Villeneuve A, Hirschhorn JN, Altshuler D, Groop LC, Després J-P, Gaudet D, Hudson TJ. 5′flanking variants of resistin are associated with obesity. Diabetes 2002;51:1629-1634
15
Duvnjak M, Baršić N, Tomašić V, Lerotić I. Genetic polymorphisms in non-alcoholic fatty liver disease: Clues to pathogenesis and disease progression. World J Gastroenterol 2009;15:6023-6027.
16
Willner IR, Waters B, Patil SR, Reuben A, Morelli J, Riely CA: Ninety patients with non-alcoholic steato hepatitis: insulin resistance, familial tendency, and severity of disease. Am J Gastroenterol 2001;96:2957-2961.
17
Browning JD1, Szczepaniak LS, Dobbins R, Nuremberg P, Horton JD, Cohen JC, Grundy SM, Hobbs HH. Prevalence of hepatic steatosis in an urban population in the United States: impact of ethnicity. Hepatology 2004;40:1387-1395.
18
Hsieh CJ, Wang PW, Hu TH: Association of adiponectin gene polymorphism with nonalcoholic Fatty liver disease in taiwanese patients with type 2 diabetes. PLoS One 2015;10:e0127521.
19
Wang J, Guo XF, Yu SJ, Song J, Zhang JX, Cao Z, Wang J, Ji MY, Dong WG. Adiponectin polymorphisms and non-alcoholic fatty liver disease risk: a meta-analysis. J Gastroenterol Hepatol 2014;29:1396-1405.
20
Giannitrapani L, Soresi M, Balasus D, Licata A, Montalto G. Genetic association of interleukin-6 polymorphism (-174 G/C) with chronic liver diseases and hepatocellular carcinoma. World J Gastroenterol 2013;19:2449-2455.
21
ler R, de Luis DA, Izaola O, González Sagrado M, Conde R, Alvarez Gago T, Pacheco D, González JM, Velasco MC. G308A polymorphism of TNF-alpha gene is associated with insulin resistance and histological changes in non alcoholic fatty liver disease patients. Ann Hepatol 2010;9:439-444.
22
Sazci A1, Akpinar G, Aygun C, Ergul E, Senturk O, Hulagu S. Association of apolipoprotein E polymorphisms in patients with non-alcoholic steatohepatitis. Dig Dis Sci 2008;53:3218-3224.
23
Eisinger K1, Krautbauer S, Wiest R, Karrasch T, Hader Y, Scherer MN, Farkas S, Aslanidis C, Buechler C. Portal vein omentin is increased in patients with liver cirrhosis but is not associated with complications of portal hypertension. Eur J Clin Invest 2013;43:926-932.
24
Yaykaşli KO, Yaykaşli E, Ataoğlu S, Özşahin M, Memişoğullari R, Çelebi E, Uçgun T, Özcan ME, Uslu M Yüce H. The frequency of omentin Val109Asp polymorphism and the serum level of omentin in patients with Rheumatoid Arthritis. Acta Medica Mediterranea 2013;29:521-526.
25
Turan H1, Yaykasli KO, Soguktas H, Yaykasli E, Aliagaoglu C, Erdem T, Karkucak M, Kaya E, Ucgun T, Bahadir A. Omenin serum levels and omentin-1 gene Val109Asp polymorphism in patients with psoriasis. Int J Dermatol 2014;53:601-605.
26
Yörük U1, Yaykaşli KO, Özhan H, Memişoğullari R, Karabacak A, Bulur S, Aslantaş Y, Başar C, Kaya E. Association of omentin Val109Asp polymorphism with coronary artery disease. Anadolu Kardiyol Derg 2014;14:511-514.
27
Zhang LY1, Jin YJ, Jin QS, Lin LY, Zhang DD, Kong LL. Association between resistin +299A/A genotype and nonalcoholic fatty liver disease in Chinese patients with type 2 diabetes mellitus. Gene 2013;529:340-344.
28
Zhang CX, Guo LK, Qin YM, Li GY. Interaction of polymorphisms of resistin gene promoter -420C/G, glutathione peroxidase -1 gene Pro198Leu and cigarette smoking in nonalcoholic fatty liver disease. Chin Med J (Engl) 2015;128:2467-2473.
29
ORIGINAL_ARTICLE
Design of new potent HTLV-1 protease inhibitors: in silico study
HTLV-1 and HIV-1 are two major causes for severe T-cell leukemia disease and acquired immune deficiency syndrome (AIDS). HTLV-1 protease, a member of aspartic acid protease family, plays important roles in maturation during virus replication cycle. The impairment of these proteases results in uninfectious HTLV-1virions.Similar to HIV-1protease deliberate mutations that confer drug resistance on HTLV-1 are frequently seen in this protease. Therefore, inhibition of HTLV-1 protease activity is expected to disrupt HTLV-1’s ability to replicate and infect additional cells. In this study, we initially designed fifteen inhibitory compounds based on the conformations of a class of HIV-1 aspartyl protease inhibitors, sulfonamid-peptoid. Five compounds were chosen based on the goodness of their Drug-Likeness scoreusing “Lipinsk’s rule of five”. Here, using protein-ligand docking approach we compared the inhibitory constants of these compounds to those available in literatures and observed significantly higher inhibition for two compounds, SP-4 and SP-5. Our data suggest that the addition of two cyclic hydrocarbons to both ends of sulfonamide peptoids leads to the formation of new hydrophobic interactions due to the semi-circular form of these compounds, connecting the first chain of protease to the two ends of tested ligands via Hydrophobic interactions. We conclude that hydrophobic force plays an important role in suppressing protease activity especially for HTLV-1 protease, which in turn prevents the virus maturity. Therefore, designing and development of new ligands based on aromatic hydrocarbons in both ends of inhibitors is very promising for efficient treatment.
https://mbrc.shirazu.ac.ir/article_3483_8089b486197eb8796f63805679f4970f.pdf
2016-02-01
19
30
10.22099/mbrc.2016.3483
HTLV-1 protease
HIV protease
Molecular dynamics dimulation
Docking
Drug design
Mitra
Kheirabadi
mitrakheirabadi@yahoo.com
1
Basic Science Department, Faculty of Biology, Hakim Sabzevary University, Sabzevar, Iran
LEAD_AUTHOR
Javad
Maleki
javadmaleki394@yahoo.com
2
Basic Science Department, Faculty of Biology, Hakim Sabzevary University, Sabzevar, Iran
AUTHOR
Safieh
Soufian
s_soofian@pnu.ac.ir
3
Biology Department, Payame Noor University, Arak, Iran
AUTHOR
Samane
Hosseini
samaneh25@gmail.com
4
Department of stem cells and developmental biology at cell science research center, Royan institute for stem cell biology and technology, ACECR, Tehran, Iran
AUTHOR
Romanelli LCF, Caramelli P, Proietti ABFC. Human T-cell lymphotropic virus type 1 (htlv-1): when to suspect infection. Rev Assoc Med Bras 2010;56:340-347.
1
Kannian P, Green PL. Human T lymphotropic virus type 1 (HTLV-1): Molecular biology and oncogenesis. Viruses 2010;2:2037-2077.
2
Hinuma Y, Nagata K, Hanaoka M, Nakai M, Matsumoto T, Kinoshita KI, Shirakawa S, Miyoshi I. Adult T-cell leukemia: Antigen in an ATL cell line and detection of antibodies to the antigen in human sera. Proc Natl Acad Sci USA 1981;78:6476-80.
3
Yang YC, Hsu TY, Liu MY, Lin MT, Chen JY, Yang CS. Molecular subtyping of human T-lymphotropic virus type I (HTLV-I) by a nested polymerase chain reaction-restriction fragment length polymorphism analysis of the envelope gene: Two distinct lineages of HTLV-I in Taiwan. J Med Virol 1977;51:25-31.
4
Nguyen JT, Kato K, Hidaka K, Kumada HO, Kimura T, Kiso Y. Design and synthesis of several small-size HTLV-I protease inhibitors with different hydrophilicity profiles. Bioorg Med Chem Lett 2011;21:2425-2429.
5
Naka H, Teruya K, Bang JK, Aimoto S, Tatsumi T, Konno H, Nosaka K, Akaji K. Evaluations of substrate specificity and inhibition at PR/p3 cleavage site of HTLV-1 protease. Bioorg Med Chem Lett 2006;16:3761-3764.
6
Li M, Laco GS, Jaskolski M, Rozycki J, Alexandratos J, Wlodawer A, Gustchina A. Crystal structure of human T cell leukemia virus protease, a novel target for anticancer drug design. Proc Natl Acad Sci USA 2005;102:18332-18337.
7
Satoh T, Li M, Nguyen JT, Kisoc Y, Gustchinaa A, Wlodawera A. Crystal structures of inhibitor complexes of human T cell leukemia virus (HTLV-1) protease. J Mol Biol 2010;401:626-641.
8
Zhou J, Termin A, Wayland M, Tarby CM. Solid-phase synthesis of potential aspartic acid protease inhibitors containing a hydroxyethylamine isostere. Tetrahedron Lett 1999;40:2729-2732.
9
Ruzza, P. Peptides and Peptidomimetics in Medicinal Chemistry. INTECH 2012, ISBN 978-953-51-0513-8. DOI: 10.5772/38240.
10
Liskamp RMJ. A new application of modified peptides and peptidomimetics: potential anticancer agents. Angew Chem Int Ed Engl 1994;33:305-307.
11
Shuey SW, Delaney WJ, Shah MC, Scialdone MA. Antimicrobial b-peptoids by a block synthesis approach. Bioorg Med Chem Lett 2006;16:1245-1248.
12
Goodman M, Zapf C, Rew Y. New reagents reactions and peptidomimetics for drug design. Biopolymers 2001;60:229-245.
13
Hodgson DR, Sanderson JM. The synthesis of peptides and proteins containing non-natural amino acids. Chem Soc Rev 2004;33:422-430.
14
Shuker SB, Mariani VL, Herger BE, Dennison KJ. Understanding HTLV-I protease. Chem Biol 2003;10:373-380.
15
Kádas J, Weber IT, Bagossi P, Miklóssy G, Boross P, Oroszlan S, Tözsér J. Narrow substrate specificity and sensitivity towards ligand binding site mutations of human T-cell leukemia virus type-1 protease. J Biol Chem 2004;279:27148-27157.
16
Geller M, Miller M, Swanson SM, Maizel J. Analysis of the structure of HIV-1 protease complexed with a hexapeptide inhibitor. Part II: Molecular dynamic studies of the active site region. Proteins 1997;27:195-203.
17
Satoha T, Li M, Nguyen J,T, Kiso Y, Gustchina A, Wlodawer A. Crystal structures of inhibitor complexes of human T-cell leukemia virus (HTLV-1) protease. J Mol Biol 2010;401:626-641.
18
Kuhnert M, Steuber H, Diederich WE. Structural basis for HTLV-1 protease inhibition by the HIV-1 protease inhibitor indinavir. J Med Chem 2014;57:6266-6272.
19
Viste A. Laboratory Exercises Using HyperChem (Caffery, Mary L.; Dobosh, Paul A.; Richardson, Diane M. (J Chem Educ 1999;76(8):1065).
20
Lipinski CA, Lombardo F, Dominy BW, Feeney PJ. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv Drug Deliv Rev 2012;64:4-17.
21
Maunz A, Gütlein M, Rautenberg M, Vorgrimmler D, Gebele D, Helma C. Lazar: a modular predictive toxicology framework. Front Pharmacol 2013;4:1-12.
22
http://wwwrcsborg/pdb/home/homedo
23
De Voss JJ, Ortiz de Montellano PR. Substrate docking algorithms and the prediction of substrate specificity. Methods Enzymol 1996;272:336-347.
24
Atilgan E, Hu J. Improving protein docking using sustainable genetic algorithms. Int J Compu Inoform Sys Ind Manag App 2011;3:248-255.
25
Alonso H, Bliznyuk AA, Gready JE. Combining docking and molecular dynamic simulations in drug design. Med Res Rev 2006;26:531-568.
26
Berendsen HJC, Postma JPM. Vangunsteren WF, Dinola A, Haak JR. Molecular-dynamics with coupling to an external bath. J Chem Phys 1984;81:3684-3690.
27
Berendsen HJC, Grigera JR, Straatsma TP. The missing term in effective pair potentials. J Phys Chem 1987; 91:6269-6271.
28
Darden T, York D, Pedersen L. Particle mesh Ewald - an N Log(N) method for Ewald sums in large systems. J Chem Phys 1993;98:10089-10092.
29
Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG. A smooth particle mesh Ewald method. J Chem Phys 1995;103:8577-8593.
30
Tözsér J, Weber IT. The protease of human T-cell leukemia virus type-1 is a potential therapeutic target. Curr Pharm Des 2007;13:1285-1294.
31
Li M, Laco GS, Jaskolski M, Rozycki J, Alexandratos J, Wlodawer A, Gustchina A. Crystal structure of human T cell leukemia virus protease a novel target for anticancer drug design. Proc Natl Acad Sci USA 2005;102:18332-18337.
32
Maleki J, Kheirabadi M, Soufian S, Sabaghzadeh R. Design the new virus HTLV-1 protease peptide inhibitors based on Benzene functional group by computational methods. J Sabzevar Uni Med Sci 2014;21:637-645.
33
Gustchina A, Sansom C, Prevost M, Richelle J, Wodak SY, Wlodawer A, Weber IT.. Energy calculations and analysis of HIV-1 protease-inhibitor crystal structures. Protein Eng 1994;7:309-317.
34
Zhang H, Wang YF, Shen CH, Agniswamy J, Rao KV, Xu CX, Ghosh AK, Harrison RW, Weber IT. Novel P2 tris-tetrahydrofuran group in antiviral compound 1 (GRL-0519) fills the S2 binding pocket of selected mutants of HIV-1 protease. J Med Chem 2013;56:1074-1083.
35
ORIGINAL_ARTICLE
Design, simplified cloning, and in-silico analysis of multisite small interfering RNA-targeting cassettes
Multiple gene silencing is being required to target and tangle metabolic pathways in eukaryotes and researchers have to develop a subtle method for construction of RNA interference (RNAi) cassettes. Although, several vectors have been developed due to different screening and cloning strategies but still some potential limitations remain to be dissolved. Here, we worked out a simple cloning strategy to develop multisite small interfering RNA (siRNA) cassette from different genes by two cloning steps. In this method, effective siRNA sites in the target messenger RNAs (mRNAs) were determined using in silico analysis and consecutively arranged to reduce length of inverted repeats. Here, we used one-step (polymerase chain reaction) PCR by designed long primer sets covering the selected siRNA sites. Rapid screening, cost-effective and shorten procedure are advantages of this method compare to PCR classic cloning. Validity of constructs was confirmed by optimal centroid secondary structures with high stability in plants.
https://mbrc.shirazu.ac.ir/article_3484_195a8f89de92345a4b285b51d493fa07.pdf
2016-02-01
31
43
10.22099/mbrc.2016.3484
Cloning strategy
Computational modeling
One-step PCR method
siRNA-targeting cassette
Bahram
Baghban-Kohnehrouz
bahramrouz@yahoo.com
1
Department of Plant Breeding & Biotechnology, University of Tabriz, Tabriz, Iran.
LEAD_AUTHOR
Shahnoush
Nayeri
shahnoush.nayeri@yahoo.com
2
Department of Plant Breeding & Biotechnology, University of Tabriz, Tabriz, Iran.
AUTHOR
Escobedo-Bonilla CM. Application of RNA interference (RNAi) against viral infections in shrimp: a review. J Antivir Antiretrovir2011; Article ID S9, doi:10.4172/jaa.s9-001.
1
Rosso MN, Jones JT, Abad P. RNAi and functional genomics in plant parasitic nematodes. Annu Rev Phytopathol 2009;47:207-232.
2
Obbard DJ, Gordon KHJ, Buck AH, Jiggins FM. The evolution of RNAi as a defense against viruses and transposable elements. Philos Trans R Soc B2009;346: 99-115.
3
Huvenne H, Smagghe G. Mechanisms of dsRNA uptake in insects and potential of RNAi for pest control: A review. J Insect Physiol 2010;56:227-235.
4
Kim DH, Rossi JJ. RNAi mechanisms and applications. Biotechniques 2009,44:613-616.
5
Mohr SE, Perrimon N. RNAi screening: new approaches, understandings and organisms. Wiley Interdiscip Rev RNA 2012;3:145-158.
6
Panwar V, McCallum B, Bakkeren G. Endogenous silencing of Puccinia triticina pathogenicity genes through in planta-expressed sequences leads to the suppression of rust diseases on wheat. Plant J 2012; Article ID 12047.
7
Ntui VO, Kong K, Azadi P, Sher Khan R, Chin DP, Igawa T, Mii M, Nakamura I. RNAi-mediated resistance to cucumber mosaic virus (CMV) in genetically engineered tomato. Am J Plant Sci 2014;5:554-572.
8
Arunraj R, Sree GB, Parani M. Desiccation and topping induced silencing of putrescine N-methyl transferase2 regulate nicotine biosynthesis in Nicotiana tabacum cv. Petite Havana. Aust J Crop Sci2014;8:109-118.
9
Gil-Humanes J, Piston F, Tollefsen S, Sollid LM, Barro F. Effective shutdown in the expression of celiac disease-related wheat gliadin T-cell epitopes by RNA interference. Proc Natl Acad Sci USA 2010;107:17023-17028.
10
Tyler AM, Bhandari DG, Poole M, Napier JA, Jones HD, Lu C, Lycett GW. Gluten quality of bread wheat is associated with activity of RabD GTPases. Plant Biotechnol J 2014;13:163-176..
11
Wang XB, Wua Q, Ito T, Cillo F, Li WX, Chen X, Yu JL, Ding SW. RNAi-mediated viral immunity requires amplification of virus-derived siRNAs in Arabidopsis thaliana. Proc Natl Acad Sci USA 2010;107:484-489.
12
Hoffera P, Ivashuta S, Pontes O, Vitins A, Pikaard C, Mroczka A, Wagner N, Voelkera T. Posttranscriptional gene silencing in nuclei. Proc Natl Acad SciUSA 2011;108:409-414.
13
Xiong Y, Zeng H, Zhang Y, Xu D, Qiu D, Silencing the HaHR3 gene by transgenic plant-mediated RNAi to disrupt Helicoverpa armigera development. Int J Biol Sci 2013;9:370-381.
14
Das S, Marwal A, Choudhary DK, Gupta VK, Gaur RK. Mechanism of RNA interference (RNAi): current concept. Int Proc Chem Biol Environ Eng 2011;9: 240-245.
15
Barba M, Haddi A. RNA silencing and viroids. J Plant Pathol2009;91:243-247.
16
Nicolas FE, Torres-Martinez S, Ruiz-Vazquaz RM. Loss and retention of RNA interference in fungi and parasites. Pathogens2013;9:e1003089.
17
Kemp C, Mueller S, Goto A, Barbier V, Paro S, Bonnay F, Dostert C, Troxler L, Hetru C, Meignen C, Pfeffer S, Hoffmann JA, Imler JL. Broad RNA interference- mediated antiviral immunity and virus-specific inducible responses in Drosophila. J Immun2013;190:650-658.
18
Cohen HC, Xiong MP. Non-cell-autonomous RNA interference in mammalian cells: Implications for in vivo cell-based RNAi delivery. J RNAi Gene Silencing2011;7: 456-463.
19
Wang X, Li Y, Huang H, Zhang X, Xie P, Hu W, Li D, Wang S. A simple and robust vector-based shRNA expression system used for RNA interference. PLOS One2013;8:e56110.
20
Yu N, Christiaens O, Liu J, Cappelle K, Caccia S, huvenne H, Smagghe G. Delivery of dsRNA for RNAi in insects: an overview and future directions. Insect Sci2013; 20:4-14.
21
Nejepinska J, Malik R, Wagner S, Svoboda P. Reporters transiently transfected into mammalian cells are highly sensitive to translational repression induced by dsRNA expression. PLOS One 2014;9:e87517.
22
Zhuang JJ, Hunter CP. RNA interference in Caenorhabditis elegans: Up take, mechanism and regulation. Parasitology 2012;139:560-573.
23
Grishok A. Endogenous RNAi and adaptation to environments in C. elegans. Worm 2012;1:129-133.
24
Edmens AL, Waterhouse PM. Vectors and methods for hairpin RNA and artificial microRNA-mediated gene silencing in plants. Plant Chromosome Eng 2011;701: 179-197.
25
Hirai S, Kodama H. RNAi vectors for manipulation of gene expression in higher plants. Open Plant Sci J 2008;2:21-30.
26
Yan P, Shen W, Gao XZ, Li X, Zhou P, Duan J. High-throughput construction of intron-containing hairpin RNA vectors for RNAi in plants. PLOS One 2012;7: e38186.
27
Chen S, Songkumarn P, Liu J, Wang GL. A versatile zero background T-vector system for gene cloning and functional genomics. Plant Physiol2009;150:1111-1121.
28
Xu G, Sui N, Tang Y, Xie K, Lai Y, Liu Y. One-step, zero-back ground, ligation-independent cloning intron-containing hairpin RNA constructs for RNAi in plants. New Phytol 2010;187:240-250.
29
Yan P, Shen W, Gao XZ, Duan J, Zhou P. Rapid one-step construction of hairpin RNA. Biochem Biophys Res Commun 2009;383:464-468.
30
Xu J,Zeng JQ, Wan G, Hu GB, Yan H, Ma LX. Construction of siRNA/miRNA expression vectors based on a one-step PCR process. BMC Biotechnol2009; 9: 53.
31
Brown D, Jarvis R, Pallotta V, Byrom M, Ford L. RNA interference in mammalian cell culture: design, execution and analysis of the siRNA effects. Ambion Technical Notes 2002;9:3-5.
32
Khvorova A, Reynolds A, Jayasena SD. Functional siRNAs and miRNAs exhibit strand bias. Cell 2003;115:209-216.
33
Life technologies, Using siRNA for gene silencing is a rapidly evolving tool in molecular biology, technical bulletin #506. Http//:www.lifetechnologies.com/ir/en/ home/technical reference library/ RNA technical resources from Ambion/ RNAi/ siRNA/ general articles/ siRNA design guidelines/ technical bulletin #506/, 2014.
34
Reynolds A, Leake D, Boase Q, Scaringe S, Marshall WS, Khovorova A. Rational siRNA design for RNA interference. Natl Biotechnol 2004;22:326-330.
35
Schwartz DS, Hutvagner G, Du T, Xu Z, Aronin N, Zamore PD. Asymmetry in the assembly of the RNAi enzyme complex. Cell 2003;115:199-208.
36
Ui-Tei K, Naito Y, Takahashi F, Haraguchi T, Ohki-Hamazaki H, Juni A, Uedo R, Saigo K. Guidelines for the selection of highly effective siRNA sequences for mammalian and chick RNA interference. Nucleic Acids Res2004;32:936-948.
37
Dai X, Zhao PX. psRNA target: a plant small RNA target analysis server. Nucleic Acids Res 2011;39:155-159.
38
Ding Y, Chan CY, Lawrence CE. Sfold web server for statically folding and rational design of nucleic acids. Nucleic Acids Res 2004;32:135-141.
39
Ding Y, Lawrence CE. Astatically sampling algorithm for RNA secondary structure prediction. Nucleic Acid Res 2001;31:7280-7301.
40
Mathews DH, Disney MD, Childs JL, Schroeder SJ, Zuker M, Turner DH. Incorporating chemical modification concentrates in to dynamic programming algorithm for prediction of RNA secondary structure. Proc Natl Acad Sci USA 2004;101:7287-7292.
41
Ding Y, Chan CY, Lawrence CE. RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble. Bioinformatics 2005;11:1157-1166.
42
Chan CY, Lawrence CE, Ding Y. Structure clustering features on the Sfold web server. Bioinformatics 2005;21:3926-3928.
43
Elhefnawi M, Hassan N, Kamar M, Siam R, Remoli AL, El-Azab I, Alaid G, Sgarbanti M. The design of therapeutic small interfering RNA molecules targeting diverse strains of influenza a virus. Bioinformatics 2011;27:3364-3370.
44
ORIGINAL_ARTICLE
Analysis of IL-33 gene polymorphism (rs11792633 C/T) and risk of schizophrenia
Recently, inflammation has been found to be a significant factor in the development of Schizophrenia (SCZ). The aim of the present research was to investigate whether interleukin-33 (IL-33, OMIM: 608678) gene polymorphism (rs11792633, C/T) is associated with the development of SCZ or not.DNA was isolated from the serum of 70 patients with SCZ and 70 healthy controls. The PCR based method was used for detection of the IL-33 polymorphism. The CT (OR=0.05, 95% CI: 0.003-0.057, P<0.001) andTT(OR=0.12, 95% CI: 0.028-0.46, P<0.001) genotypes significantly decreased the risk of SCZ. Our present findings indicate that the IL-33 polymorphism associated with the risk of SCZ.
https://mbrc.shirazu.ac.ir/article_3485_014c2cf0db6a88aa6897cf7d4f5a2dab.pdf
2016-02-01
45
48
10.22099/mbrc.2016.3485
IL-33
Polymorphism
Schizophrenia
DorMohammad
Kordi-Tamandani
dor_kordi@yahoo.com
1
University of sistan and Baluchestan
LEAD_AUTHOR
Ahmad Reza
Bahrami
ar-bahrami@ferdowsi.um.ac.ir
2
university of Ferdowssi,Mashhad, Iran
AUTHOR
Raziye
Sabbaghi-ghale-no
raziyesabagh@yahoo.com
3
university of Ferdowssi,Mashhad, Iran
AUTHOR
Hanieh
Soleimani
haniehsoleimani33@gmail.com
4
University of sistan and Baluchestan
AUTHOR
Tayebe
Baranzehi
kiana8588@gmail.com
5
University of sistan and Baluchestan
AUTHOR
Saha S, Chant D, Welham J, McGrath J. A systematic review of the prevalence of schizophrenia. PLoS Med 2005;2:e141.
1
Maes M, Bosmans E, Calabrese J, Smith R, Meltzer HY. Interleukin-2 and interleukin-6 in schizophrenia and mania: effects of neuroleptics and mood stabilizers. J Psychiatr Res 1995;29:141-152.
2
Fila-Danilow A, Kucia K, Kowalczyk M, Owczarek A, Paul-Samojedny M, Borkowska Suchanek R, Kowalski JP. Association study of interleukin-4 polymorphisms with paranoid schizophrenia in the Polish population: a critical approach. Mol Biol Rep 2012;39:7941-7947.
3
Oboki K, Ohno T, Kajiwara N, Saito H, Nakae S. IL-33 and IL-33 receptors in host defense and diseases. Allergol Int 2010;59:143-160.
4
Talabot-Ayer, Calo N, Vigne S, Lamacchia C, Gabay C, Palmer G. The mouse interleukin (IL) 33 gene is expressed in a cell type- and stimulus-dependent manner from two alternative promoters. J Leukoc Biol 2012;91:119-125.
5
Rogala B, Gluck J. The role of interleukin-33 in rhinitis. Curr Allergy Asthma Rep 2013;13:196-202.
6
Miller AM. Role of IL-33 in inflammation and disease. J Inflamm (Lond) 2011; 8:22.
7
Nakae S, Morita H, Ohno T, Arae K, Matsumoto K, Saito H. Role of interleukin-33 in innate-type immune cells in allergy. Allergol Int 2013;62:13-20.
8
Yu JT, Song JH, Wang ND, Wu ZC, Zhang Q, Zhang N, Zhang W, Xuan SY, Tan L. Implication of IL-33 gene polymorphism in Chinese patients with Alzheimer's disease. Neurobiol Aging 2012;33:e11-14.
9
Lin CC, Chang CM, Chang PY, Huang TL. Increased interleukin-6 level in Taiwanese schizophrenic patients. Chang Gung Med J 2011;34:375-3781.
10
Chapuis J, Hot D, Hansmannel F, Kerdraon O, Ferreira S, Hubans C, Maurage CA, Huot L, Bensemain F, Laumet G, Ayral AM, Fievet N, Hauw JJ, DeKosky ST, Lemoine Y, Iwatsubo T, Wavrant-Devrieze F, Dartigues JF, Tzourio C, Buee L, Pasquier F, Berr C, Mann D, Lendon C, Alperovitch A, Kamboh MI, Amouyel P, Lambert JC. Transcriptomic and genetic studies identify IL-33 as a candidate gene for Alzheimer's disease. Mol Psychiatry 2009;14:1004-1016.
11
Miller AM, Xu D, Asquith DL, Denby L, Li Y, Sattar N, Baker AH, McInnes IB, Liew FY. IL-33 reduces the development of atherosclerosis. J Exp Med 2008;205: 339-346.
12
ORIGINAL_ARTICLE
Epigenetics in diagnosis of colorectal cancer
Colorectal cancer (CRC) is a third most common epithelial carcinoma. CRC is known to develop from the early precancerous lesion to full blown malignancy via definite phases due to cumulative mutations and aberrant methylation of number of genes. The use of serum biomarkers that is non-invasive to discriminate cancer patients from healthy persons will prove to be an important tool to improve the early diagnosis of CRC. This will serve as the boon to the clinical management of the disease.
https://mbrc.shirazu.ac.ir/article_3495_0da8688fc4f72d968631ea1a98b55659.pdf
2016-02-01
49
57
10.22099/mbrc.2016.3495
Colorectal cancer
Epigenetics
Hypermethylation
Biomarkers
Aga
Sameer
mousvi786@gmail.com
1
Basic Medical Sciences Department, College of Medicine- Jeddah,
King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, National Guard Health Affairs, Jeddah, 21423.
Kingdom of Saudi Arabia.
LEAD_AUTHOR
Saniya
Nissar
syedmousvi@gmail.com
2
Department of Biochemistry, Kashmir University, Hazratbal, Srinagar, Kashmir, INDIA. 190006.
AUTHOR
Migliore L, Igheli F, Spisni R, Coppede F. Genetics, Cytogenetics and Epigenetics of colorectal cancer. J Biomed Biotech 2011; 792362. doi:10.1155/2011/792362.
1
Grady WM, Ulrich CM. DNA alkylation and DNA methylation: cooperating mechanisms driving the formation of colorectal adenomas and adenocarcinomas? Gut 2007;56:318-320.
2
Vogelstein B, Fearon ER, Hamilton SR, Kern SE, Preisinger AC, Leppert M, Nakamura Y, White R, Smits AM, Bos JL. Genetic alterations during colorectal-tumor development. N Engl J Med 1988;319:525-532.
3
Fearon ER and Vogelstein B. A genetic model for colorectal tumorigenesis. Cell 1990;61:759-767.
4
Cunningham D, Atkin W, Lenz HJ, Lynch HT, Minsky B, Nordlinger B, Starling N. Colorectal cancer. Lancet 2010;375:1030-1047.
5
Perea J, Lomas M, Hidalgo M. Molecular basis of colorectal cancer: Towards an individualized management? Rev Esp Enferm Dig 2011;103:29-35.
6
Sameer AS. Colorectal cancer: molecular mutations and polymorphisms. Front Oncol 2013;3:114.
7
Toyota M, Ahuja N, Ohe-Toyota M, Herman JG, Baylin SB, Issa JP. CpG island methylator phenotype in colorectal cancer. Proc Natl Acad Sci USA 1999;96:8681-8686
8
Toyota M, Ho C, Ahuja N, Jair KW, Li Q, Ohe-Toyota M, Baylin SB, Issa JP. Identification of differentially methylated methylated sequences in colorectal cancer by methylated CpG island amplification. Cancer Res 1999;59: 2307-2312.
9
Lao VV, Grady MW. Epigenetics and colorectal cancer. Nat Rev Gastroenterol Hepatol 2011;8:686-700.
10
Wong JJL, Hawkins NJ, Ward RL. Colorectal cancer: a model for epigenetic tumorigenesis. Gut 2007;56:140-148.
11
Jass JR, Iino H, Ruszkiewicz A, Painter D, Solomon MJ, Koorey DJ, Cohn D, Furlong KL, Walsh MD, Palazzo J, Edmonston TB, Fishel R, Young J, Leggett BA. Neoplastic progression occurs through mutator pathways in hyperplastic polyposis of the colorectum. Gut 2000;47:43-49.
12
Migheli F, Migliore L. Epigenetics of colorectal cancer. Clin Genet 2012;81: 312–318.
13
Snover DC. Update on serrated pathway to colorectal carcinoma. Hum Pathol 2011; 42:1-10.
14
Vaiopoulos AG, Athanasoula KC, Papavassiliou AG. Epigenetic modifications in colorectal cancer: Molecular insights and therapeutic challenges. Biochim Biophys Acta 2014;1842:971-980.
15
Carmona FJ, Azuara D, Berenguer-Llergo A, Fernández AF, Biondo S, de Oca J, Rodriguez-Moranta F, Salazar R, Villanueva A, Fraga MF, Guardiola J, Capellá G,Esteller M, Moreno V. DNA methylation biomarkers for noninvasive diagnosis of colorectal cancer. Cancer Prev Res 2013;6:656-665.
16
Fung KYC, Nice E, Priebe I, Belobrajdic D, Phatak A, Purins L, Tabor B, Pompeia C, Lockett T, Adams TE, Burgess A, Cosgrove L. Colorectal cancer biomarkers: To be or not to be? Cautionary tales from a road well travelled. World J Gastroenterol2014;20:888-898.
17
Gyparaki MT, Basdra EK, Papavassiliou AG. DNA methylation biomarkers as diagnostic and prognostic tools in colorectal cancer. J Mol Med 2013;91:1249-1256.
18
Kim YH, Lee HC, Kim SY, Yeom YI, Ryu KJ, Min BH, Kim DH, Son HJ, Rhee PL, Kim JJ, Rhee JC, Kim HC, Chun HK, Grady WM, Kim YS. Epigenomic analysis of aberrantly methylated genes in colorectal cancer identifies genes commonly affected by epigenetic alterations. Ann Surg Oncol 201118:2338-2347.
19
Levin B. Molecular screening testing for colorectal cancer. Clin Cancer Res 2006; 12:5014-5017.
20
Lange CP, Laird PW. Clinical applications of DNA methylation biomarkers in colorectal cancer. Epigenomics 2013;5:105-108.
21
Hardt PD, Toepler M, Ngoumou B, Rupp J, Kloer HU. Measurement of fecal pyruvate kinase type M2 (tumor M2-PK) concentrations in patients with gastric cancer, colorectal cancer, colorectal adenomas and controls. Anticancer Res 2003; 23:851-853.
22
Holten-Andersen MN, Christensen IJ, Nielsen HJ, Stephens RW, Jensen V, Nielsen OH, Sørensen S, Overgaard J, Lilja H, Harris A, Murphy G, Brünner N. Total levels of tissue inhibitor of metalloproteinases 1 in plasma yield high diagnostic sensitivity and specificity in patients with colon cancer. Clin Cancer Res 2002;8:156-164
23
Tóth K, Sipos F, Kalmár A, Patai AV, Wichmann B, Stoehr R, Golcher H, Schellerer V, Tulassay Z, Molnár B. Detection of methylated SEPT9 in plasma is a reliable screening method for both left- and right-sided colon cancers. PLoS One 2012;7:e46000.
24
Warren JD, Xiong W, Bunker AM, Vaughn CP, Furtado LV, Roberts WL, Fang JC, Samowitz WS, Heichman KA. Septin 9 methylated DNA is a sensitive and specific blood test for colorectal cancer. BMC Med 2011;9:133.
25
Ahlquist DA, Taylor WR, Mahoney DW, Zou H, Domanico M, Thibodeau SN, Boardman LA, Berger BM, Lidgard GP. The stool DNA test is more accurate than the plasma septin 9 test in detecting colorectal neoplasia. Clin Gastroenterol Hepatol 2012; 10:272-277.
26
Ned RM, Melillo S, Marrone M. Fecal DNA testing for colorectal cancer screening: the ColoSureTM test. PLoS Curr 2011; 3: RRN1220.
27
Church TR, Wandell M, Lofton-Day C, Mongin SJ, Burger M, Payne SR, Castaños-Vélez E, Blumenstein BA, Rösch T, Osborn N, Snover D, Day RW, Ransohoff DF. Prospective evaluation of methylated SEPT9 in plasma for detection of asymptomatic colorectal cancer. Gut 2014;63:317-325.
28
Lee BB, Lee EJ, Jung EH, Chun HK, Chang DK, Song SY, Park J, Kim DH. Aberrant methylation of APC, MGMT, RASSF2A, and Wif1 genes in plasma as a biomarker for early detection of colorectal cancer. Clin Cancer Res 2009;15:6185-6191
29
Wasserkort R, Kalmar A, Valcz G, Spisak S, Krispin M, Toth K, Tulassay Z, Sledziewski AZ, Molnar B. Aberrant septin 9 DNA methylation in colorectal cancer is restricted to a single CpG island. BMC Cancer 2013;13:398.
30
Imperiale TF, Ransohoff DF, Itzkowitz SH, Levin TR, Lavin P, Lidgard GP, Ahlquist DA, Berger BM. Multitarget Stool DNA Testing for Colorectal-Cancer Screening. N Engl J Med 2014;370:1287-1297.
31
Melotte V, Lentjes MHFM, van den Bosch SM, Hellenbrekers DMEI, de Hoon JPJ, Wouters KAD, Daenen KLJ, Partouns- Hendriks IEJM, Stressels F, Louwagie J, Smits KM, Weijenberg MP, Sanduleanu S, Khalid-de Bakker CA, Oort FA, Meijer GA, Jonkers DM, Herman JG, de Bruïne AP, van Engeland M. N-Myc downstream-regulated gene 4 (NDRG4): a candidate tumor suppressor gene and potential biomarker for colorectal cancer. J Natl Cancer Inst 2009;101:916-927.
32
Glöckner SC, Dhir M, Yi JM, McGarvey KE, Van Neste L, Louwagie J, Chan TA, Kleeberger W, de Bruïne AP, Smits KM, Khalid-de Bakker CA, Jonkers DM, Stockbrügger RW, Meijer GA, Oort FA, Iacobuzio-Donahue C, Bierau K, Herman JG, Baylin SB, van Engeland M, Schuebel KE, Ahuja N. Methylation of TFPI2 in stool DNA: a potential novel biomarker for the detection of colorectal cancer. Cancer Res 2009;69:4691-4699.
33
Hibi K, Goto T, Kitamura YH, Yokomizo K, Sakuraba K, Shirahata A, Mizukami H, Saito M, Ishibashi K, Kigawa G, Nemoto H, Sanada Y. Methylation of TFPI2 gene is frequently detected in advanced well differentiated colorectal cancer. Anticancer Res 2010; 30:1205-1207.
34
Hibi K, Goto T, Shirahata A, SaitoM, Kigawa G, Nemoto H, Sanada Y. Detection of TFPI2 methylation in the serum of colorectal cancer patients. Cancer Lett 2011; 311:96-100.
35
Silva TD, Vidigal VM, Felipe AV, DE Lima JM, Neto RA, Saad SS, Forones NM. DNA methylation as an epigenetic biomarker in colorectal cancer. Oncol Lett 2013; 6:1687-1692.
36
Ogino S, Kawasaki T, Kirkner GJ, Kraft P, Loda M, Fuchs CS. Evaluation of markers for CpG island methylator phenotype (CIMP) in colorectal cancer by a large population-based sample. J Mol Diagn 2007;9:305-314.
37
Wallner M, Herbst A, Behrens A, Crispin A, Stieber P, Göke B, Lamerz R, Kolligs FT. Methylation of serum DNA is an independent prognostic marker in colorectal cancer. Clin Cancer Res 2006;12:7347-7352.
38
Philipp AB, Stieber P, Nagel D, Neumann J, Spelsberg F, Jung A, Lamerz R, Herbst A, Kolligs FT. Prognostic role of methylated free circulating DNA in colorectal cancer. Int J Cancer 2012;131:2308-2319.
39
Tanzer M, Balluff B, Distler J, Hale K, Leodolter A, Röcken C, Molnar B, Schmid R, Lofton-Day C, Schuster T, Ebert MP. Performance of epigenetic markers SEPT9 and ALX4 in plasma for detection of colorectal precancerous lesions. PLoS One 2010;5:e9061.
40
Lofton-Day C, Model F, Devos T, Tetzner R, Distler J, Schuster M, Song X, Lesche R, Liebenberg V, Ebert M, Molnar B, Grützmann R, Pilarsky C, Sledziewski A. DNA methylation biomarkers for blood-based colorectal cancer screening. Clin Chem 2008;54:414-423.
41
Vedeld HM, Skotheim RI, Lothe RA, Lind GE. The recently suggested intestinal cancer stem cell marker DCLK1 is an epigenetic biomarker for colorectal cancer. Epigenetics 2014;9:346-350.
42
Mitchell SM, Ross JP, Drew HR, Ho T, Brown GS, Saunders NF, Duesing KR, Buckley MJ, Dunne R, Beetson I, Rand KN, McEvoy A, Thomas ML, Baker RT, Wattchow DA, Young GP, Lockett TJ, Pedersen SK, Lapointe LC, Molloy PL. A panel of genes methylated with high frequency in colorectal cancer. BMC Cancer 2014;14:54.
43
Roperch JP, Incitti R, Forbin S, Bard F, Mansour H, Mesli F, Baumgaertner I, Brunetti F, Sobhani I. Aberrant methylation of NPY, PENK, and WIF1 as a promising marker for blood-based diagnosis of colorectal cancer. BMC Cancer 2013;13:566.
44
Ahn JB, Chung WB, Maeda O, Shin SJ, Kim HS, Chung HC, Kim NK, Issa JP. DNA methylation predicts recurrence from resected stage III proximal colon cancer. Cancer 2011; 117:1847-185.
45
Lind GE, Danielsen SA, Ahlquist T, Merok MA, Andresen K, Skotheim RI, Hektoen M, Rognum TO, Meling GI, Hoff G, Bretthauer M, Thiis-Evensen E, Nesbakken A, Lothe RA. Identification of an epigenetic biomarker panel with high sensitivity and specificity for colorectal cancer and adenomas. Mol Cancer 2011;10: 85-99.
46
Warton K, Samimi G. Methylation of cell-free circulating DNA in the diagnosis of cancer. Front Mol Biosci 2015;2:13.
47
Tanaka T, Tanaka M, Tanaka T, Ishigamori R. Biomarkers for colorectal cancer. Int J Mol Sci 2010;11:3209-3225.
48
ORIGINAL_ARTICLE
No association between GSTM1 and GSTT1 genetic polymorphisms and susceptibility to opium sap dependence
Glutathione S-transferases (GSTs; EC: 2.5.1.18) are a ubiquitous family of eukaryotic and prokaryotic phase II metabolic isozymes. Genes encoding GSTM1 (OMIM: 138350), and GSTT1 (OMIM: 600436) are members of class mu and theta, respectively. The most common polymorphism in the GSTM1 is a deletion of the whole GSTM1 gene with a lack of enzyme activity. A homozygous deletion in the GSTT1 has also been reported (null genotypes of GSTT1). The aim of the present study was to investigate the association between GSTM1 and GSTT1 polymorphisms and risk of dependency to opium sap. The present study was performed in Shiraz (southern Iran). In total, 71 males dependent to opium sap and 590 healthy males (as a control group) were included in this study. The genotypes of GSTM1 and GSTT1 polymorphisms were determined by PCR. Our data indicate that neither GSTM1 (OR=0.78, 95% CI: 0.47-1.27, P=0.325) nor GSTT1 (OR=1.25, 95% CI: 0.70-2.21, P=0.442) null genotypes significantly associated with the risk of opium sap dependence. There is no additive effect of the null genotypes of GSTT1 and GSTM1 in relation to the risk of dependency to opium sap. The present study indicated that the null genotypes of GSTT1 and GSTM1 are not risk factor for opium sap dependence.
https://mbrc.shirazu.ac.ir/article_3503_c5ea2feb933b8a62cbffe03b04a4ee90.pdf
2016-02-01
59
64
10.22099/mbrc.2016.3503
GSTM1
GSTT1
Opium sap dependence
Polymorphism
Khyber
Saify
khaibar.saify@yahoo.com
1
Department of Biology, College of Sciences, Shiraz University, Shiraz 71467-13565, Iran
AUTHOR
Mohammad Rashid
Khalighinasab
msaadat41@yahoo.cm
2
Department of Biology, College of Sciences, Shiraz University, Shiraz 71467-13565, Iran
AUTHOR
Mostafa
Saadat
msaadat41@yahoo.com
3
Department of Biology, College of Sciences, Shiraz University, Shiraz 71467-13565, Iran
LEAD_AUTHOR
Agrawal A, Lynskey MT. Are there genetic influences on addiction: evidence from family, adoption and twin studies? Addiction 2008;103:1069-1081.
1
Gelernter J, Kranzler HR. Genetics of drug dependence. Dialogues Clin Neurosci 2010;12:77-84.
2
Sun Y, Meng S, Li J, Shi J, Lu L. Advances in genetic studies of substance abuse in China. Shanghai Arch Psychiatry 2013;25:199-211.
3
Ducci F, Goldman D. Genetic approaches to addiction: genes and alcohol. Addiction 2008;103:1414-1428.
4
Dusinska M, Staruchova M, Horska A, Smolkova B, Collins A, Bonassi S, Volkovova K. Are glutathione S transferases involved in DNA damage signalling? Interactions with DNA damage and repair revealed from molecular epidemiology studies. Mutat Res 2012;736:130-137.
5
Harada S, Misawa S, Nakamura T, Tanaka N, Ueno E, Nozoe M. Detection of GST1 gene deletion by the polymerase chain reaction and its possible correlation with stomach cancer in Japanese. Hum Genet 1992;90:62-64.
6
Pemble S, Schroeder KR, Spencer SR, Meyer DJ, Hallier E, Bolt HM, Ketterer B, Taylor JB. Human glutathione S-transferase theta (GSTT1): cDNA cloning and the characterization of a genetic polymorphism. Biochem J 1994;300:271-276.
7
Kelada SN, Kardia SL, Walker AH, Wein AJ, Malkowicz SB, Rebbeck TR. The glutathione S-transferase-mu and –theta genotypes in the etiology of prostate cancer: genotype-environmental interaction with smoking. Cancer Epidemiol Biomarkers Prev 2000;9:1329-1334.
8
Mohammadynejad P, Saadat I, Ghanizadeh A, Saadat M. Bipolar disorder and polymorphisms of glutathione S-transferases M1 (GSTM1) and T1 (GSTT1). Psychiatry Res 2011;186:144-146.
9
Saadat I, Saadat M. Glutathione S-transferase M1 and T1 null genotypes and the risk of gastric and colorectal cancers. Cancer Lett 2001;169:21-26.
10
Cao DL, Ye DW, Dai B, Zhang HL, Shen YJ, Zhu Y, Zhu YP, Shi GH, Ma CG, Xiao WJ, Qin XJ, Lin GW. Association of glutathione S-transferase T1 and M1 polymorphisms with prostate cancer susceptibility in populations of Asian descent: a meta-analysis. Oncotarget 2015;6:35843-35850.
11
Tang J, Zhou Q, Zhao F, Wei F, Bai J, Xie Y, Huang Y. Association of glutathione S-transferase T1, M1 and P1 polymorphisms in the breast cancer risk: a meta-analysis in Asian population. Int J Clin Exp Med 2015;8:12430-12447.
12
Kim SK, Kang SW, Chung JH, Park HJ, Cho KB, Park MS. Genetic polymorphisms of glutathione-related enzymes (GSTM1, GSTT1, and GSTP1) and schizophrenia risk: A meta-analysis. Int J Mol Sci 2015;16:19602-19611.
13
Eslami S, Sahebkar A. Glutathione-S-transferase M1 and T1 null genotypes are associated with hypertension risk: a systematic review and meta-analysis of 12 studies. Curr Hypertens Rep 2014;16:432.
14
Saadat M, Saadat I, Saboori Z, Emad A. Combination of CC16, GSTM1 and GSTT1 polymorphisms is associated with asthma. J Allergy Clin Immunol 2004;113:996-998.
15
Liang S, Wei X, Gong C, Wei J, Chen Z, Chen X, Wang Z, Deng J. Significant association between asthma risk and the GSTM1 and GSTT1 deletion polymorphisms: an updated meta-analysis of case-control studies. Respirology 2013;18:774-783.
16
Saadat M. Null genotypes of glutathione S-transferase M1 (GSTM1) and T1 (GSTT1) polymorphisms increased susceptibility to type 2 diabetes mellitus, a meta-analysis. Gene 2013;532:160-162.
17
Wilson MH, Grant PJ, Hardie LJ, Wild CP. Glutathione S-transferase M1 null genotype is associated with a decreased risk of myocardial infraction. FASEB J 2000; 14:791-796.
18
Juronen E, Tasa G, Uuskula M, Pooga M, Mikelsaar AV. Purification, characterization and tissue distribution of human class theta glutathione S-transferase T1-1. Biochem Mol Biol Int 1996;39:21-29.
19
Listowsky I, Rowe JD, Patskovsky YV, Tchaikovskaya T, Shintani N, Novikova E, Nieves E. Human testicular glutathione S-transferases: insights into tissue-specific expression of the diverse subunit classes. Chemico-Biol Interact 1998;111-112:103-112.
20
Saify K, Saadat M. Expression patterns of antioxidant genes in human SH-SY5Y cells after treatment with methadone. Psychiatry Res 2015;230:116-119.
21
Koizumi H, Hashimoto K, Kumakiri C, Shimizu E, Sekine Y, Ozaki N, Inada T, Harano M, Komiyama T, Yamada M, Sora I, Ujike H, Takei N, Iyo M. Association between the glutathione S-transferase M1 gene deletion and female methamphetamine abusers. Am J Med Genet B Neuropsychiatr Genet 2004;126B: 43-45.
22
Khalighinasab MR, Saify K, Saadat M. Association between GSTM1 and GSTT1 polymorphisms and susceptibility to methamphetamine dependence. Mol Biol Res Commun 2015;4:25-32.
23
Khalighinasab MR, Saify K, Saadat M. Association between null alleles of GSTM1 and GSTT1 and dependence to heroin and opium. Psychiatry Res 2015;228:977-978.
24
Ghazavi A, Mosayebi G, Solhi H, Rafiei M, Moazzeni SM. Serum markers of inflammation and oxidative stress in chronic opium (Taryak) smokers. Immunol Lett 2013;153:22-26.
25
Soykut B, Eken A, Erdem O, Akay C, Aydın A, Çetin MK, Dilbaz N. Oxidative stress enzyme status and frequency of micronuclei in heroin addicts in Turkey. Toxicol Mech Methods 2013;23:684-688.
26
Rafiee L, Saadat I, Saadat M. Glutathione S-transferase genetic polymorphisms (GSTM1, GSTT1 and GSTO2) in three Iranian populations. Mole Biol Rep 2010;37: 155-158.
27
Saadat M. Distribution of ACE insertion/deletion (I/D) polymorphism in Iranian populations. Mol Biol Res Commun 2015;4:63-66.
28
Saify K, Saadat I, Saadat M. Down-regulation of antioxidant genes in human SH-SY5Y cells after treatment with morphine. Life Sci 2016;144:26-29.
29
Nakatome M, Miyaji A, Mochizuki K, Kishi Y, Isobe I, Matoba R. Association between the GST genetic polymorphisms and methamphetamine abusers in the Japanese population. Leg Med (Tokyo) 2009;11 Suppl 1:S468-470.
30
Newton CR (1995). Mutational analysis: known mutations, in: M.J. McPherson, D. Hames, G.R. Taylor (Eds.), PCR2. A Practical Approach, IRL Press, Oxford, pp. 219–222.
31