Shiraz University PressMolecular Biology Research Communications2322-181X9320200901Using two retrotransposon-based marker systems (SRAP and REMAP) for genetic diversity analysis of Moroccan Argan tree93103567910.22099/mbrc.2020.36390.1478ENOuafae PakhrouLaboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University, Rabat, MoroccoLeila MedraouiLaboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University, Rabat, MoroccoBouchra BelkadiLaboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University, Rabat, MoroccoFarid RachidiLaboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University, Rabat, MoroccoHasnaa ErrahmaniLaboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University, Rabat, MoroccoMohammed AlamiLaboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University, Rabat, MoroccoAbdelkarim Filali-MaltoufLaboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University, Rabat, Morocco0000-0002-2727-3389Journal Article20200209The Argania is an endemic genetic resource in Morocco holding an important ecological and socio-economical benefit. However, overgrazing and overharvesting lead to a serious downturn in the number of trees. To characterize genetic diversity within and among 24 populations, represented by 240 argan trees, four combinations of SRAP primers and eight combinations of REMAP primers were used. A total of 338 REMAP and 146 SRAP markers were amplified with a polymorphism of 100%. The average polymorphism information content value was 0.20 and 0.17 for SRAP and REMAP markers, respectively. The analysis of molecular variance showed that 26% of the genetic variation was partitioned among populations. The coefficient of gene differentiation was 0.2875 and gene flow was 1.2391. The average parameter diversity was: observed number of alleles (Na)=0.729, effective number of alleles (Ne)=1.131, Shannon’s information index (I)=1.143; Nei’s gene diversity (H)=0.093 and Percentage of Polymorphic Loci=35.68. The STRUCTURE and principal coordinate analysis revealed that the <em>Argania spinosa</em> L. populations were aggregated into 2 genetic groups. To detect outlier, baysecan software was used and 21 were detected (7 under selection, 14 under balancing selection) presenting posterior probability higher than 0.79. The current results can be explored in the design of management programs and to comprehend the adaptation mechanism of Argan tree.https://mbrc.shirazu.ac.ir/article_5679_b51db5f452f7865f55c48dd5fe588186.pdfShiraz University PressMolecular Biology Research Communications2322-181X9320200901Sequence variants of CYP345a1 and CYP6a14 gene regions in Tribolium castaneum (Coleoptera: Tenebrionidae) adults treated with the novel characterızed Bolanthus turcicus (Caryophyllaceae) extract105110572210.22099/mbrc.2020.35861.1472ENFahriye Sümer ErcanDepartment of Plant Protection, Faculty of Agriculture, Ahi Evran University, Kırşehir, TurkeySerap Yalçın AzarkanDepartment of Molecular Biology and Genetic, Faculty of Science and Art, Ahi Evran University, Kırşehir, TurkeyNuri ErcanFaculty of Agriculture, Ahi Evran University, Kırşehir, TurkeyMurat KocPublic Health Institute, Department of Traditional, Complementary and Integrative Medicine, Yıldırım Beyazıt University, Ankara, TurkeyJournal Article20191225In this study, various doses of plant extracts that obtained from <em>Bolanthus turcicus</em> was applied to an important storage pest <em>Tribolium castaneum</em> adults. <em>Bolanthus turcicus</em> is an endemic species and spreads on the Hasan Mountain above Karkın town (Turkey, Aksaray province). The plant species was collected from June to July with the field study to be carried out in this region. Obtained extract of plant was analyzed by gas chromatography mass spectrometry (GC-MS) method. The doses were defined during the study and the concentrations that kill 50% <em>and 99% of </em>the population were determined after applications. After 24 h, DNA was isolated from live and dead individuals that obtained from LC<sub>50</sub> and LC<sub>99</sub> concentration applications and analyzed for Cytochrome P450-mediated detoxification resistance genes, <em>CYP345A1 </em>and <em>CYP6A14</em> gene regions, by polymerase chain reaction (PCR). CYP genes in insects are known to be rapidly regulated when exposed to insecticides. In the study, in order to screen for 206 bp and 353 bp fragments of <em>CYP345A1</em> and <em>CYP6A14 </em>genes in <em>T. castaneum</em> adults were amplified using specific primers, respectively. DNA direct sequencing was performed on each template using the forward primer. When compared to the control, it is believed that mutation differences in live and dead individuals according to the sequencing results obtained from survival and dead adults, may allow these genes to play a protective role against the toxic effect of <em>B. turcicus</em> extract.https://mbrc.shirazu.ac.ir/article_5722_da83223da1f86103b82142304272840c.pdfShiraz University PressMolecular Biology Research Communications2322-181X9320200901Evaluation of the risk of lung cancer associated with NAD(P)H: quinone oxidoreductase 1 (NQO1) C609T polymorphism in male current cigarette smokers from the Eastern India111115572510.22099/mbrc.2020.36467.1481ENSantanu BanerjeeDepartment of Biotechnology and Dr B C Guha Centre for Genetic Engineering and Biotechnology,University College of Science and Technology, University of Calcutta, Kolkata -700019, Indiahttps://orcid.org/0000-0001-6989-5330Journal Article20200215NAD(P)H: quinone oxidoreductase 1 (NQO1) is an endogenous cellular defence mechanism against several carcinogenic quinones derived from cigarette smoke. <em>NQO1</em> C609T polymorphism is a strong determinant of NQO1 structure and function. The people with mutant allele for this polymorphism has significantly reduced NQO1 activity. In this study, we tried to evaluate the risk of lung cancer associated with this polymorphism in male current smokers of the Eastern India. Using PCR-RFLP method, we compared the <em>NQO1</em> C609T genotype distribution in male current smokers with (n=150) and without (n=200) lung cancer. We observed significant variation of genotypic distribution between these two groups. The allele frequency of the variant C609T allele were 40.3% and 32.7% in smokers with and without lung cancer, respectively. From the genotypic comparison between the two smoker groups, it was found that a higher risk (OR=1.64, 95% CI: 1.05-2.55, p <0.05) of lung cancer was associated with <em>NQO1</em> C609T polymorphism.https://mbrc.shirazu.ac.ir/article_5725_35d8f3777427806cef2192eaa636f94a.pdfShiraz University PressMolecular Biology Research Communications2322-181X9320200901Prevalence of Brucella species in unpasteurized dairy products consumed in Shiraz province using PCR assay117121574710.22099/mbrc.2020.37381.1506ENFargol AbdaliNutrition Research Center, Department of Food Hygiene and Quality Control, School of Nutrition and Food Sciences, Shiraz University of Medical Sciences, Shiraz, IranSaeid HosseinzadehDepartment of Food Hygiene and Public Health, School of Veterinary Medicine, Shiraz University, Shiraz, IranEnayat BeriziNutrition Research Center, Department of Food Hygiene and Quality Control, School of Nutrition and Food Sciences, Shiraz University of Medical Sciences, Shiraz, Iran0000-0001-6733-5743Maryam PourmontaseriDepartment of Food Hygiene and Public Health, School of Veterinary Medicine, Shiraz University, Shiraz, IranJournal Article20200526The consumption of milk and unpasteurized dairy products contaminated with Brucella bacteria is one of the most important ways of brucellosis transmission to humans. The principal goal of this study was to determine the prevalence of <em>Brucella abortus</em> (<em>B. abortus</em>) and <em>Brucella melitens </em>(<em>B. melitens</em>)in unpasteurized dairy products consumed in Shiraz province. In this study conducted in 2016, 238 unpasteurized dairy products including 48 raw milk, 48 yogurt, 46 cheeses, 48 dough and 48 ice cream samples, were purchased from the retail market in Shiraz province and were examined by a specific PCR assay. This study showed positive 5/04% out of 238 unpasteurized dairy products including 9 out of 48 (18/75%) raw milk samples and 3 out of 48 (6.25%) yogurt samples). Contamination was not detected in samples of dough, cheese and traditional ice cream. The results also showed that among 12 positive samples, 6 samples were contaminated with <em>B. abortus</em> (including 4 milk samples and 2 yogurt samples), 2 samples were contaminated with <em>B. melitensis</em> (including 2 Milk samples) and 4 samples were contaminated simultaneously with <em>B. abortus</em> and <em>B. melitensis</em> (including 3 milk samples and 1 yogurt sample). The present study suggests the unpasteurized dairy products as the major sources of brucellosis in Shiraz province, South of Iran; thus, to prevent brucellosis in human, the consumption of pasteurized milk and dairy products is highly recommended.https://mbrc.shirazu.ac.ir/article_5747_b2fd1d3ec85facb19db3802ffef4bd60.pdfShiraz University PressMolecular Biology Research Communications2322-181X9320200901A novel chimeric recombinant protein PDHB-P80 of Mycoplasma agalactiae as a potential diagnostic tool123128574810.22099/mbrc.2020.37684.1513ENMalihe Akbarzadeh-NiakiDepartment of Pathobiology, Biotechnology Section, School of Veterinary Medicine, Shiraz University, Shiraz, IranAbdollah DerakhshandehDepartment of Pathobiology, School of Veterinary Medicine, Shiraz University, Shiraz, Iran0000-0002-1878-1103Nasrin KazemipourDepartment of Basic Sciences, School of Veterinary Medicine, Shiraz University, Shiraz, Iran0000-0002-2939-1776Vida EraghiDepartment of Pathobiology, Biotechnology Section, School of Veterinary Medicine, Shiraz University, Shiraz, IranFarhid HemmatzadehSchool of Animal and Veterinary Sciences, The University of Adelaide, SA, AustraliaJournal Article20200627The aim of this study was to construct, expression of a novel recombinant chimeric protein consisting of Pyruvate dehydrogenase beta subunit (PDHB) and high antigenic region of integral membrane lipoprotein P80 of <em>Mycoplasma agalactiae</em> as a potential diagnostic tool. The full-length sequence of <em>pdhb</em> and a portion of antigenic regions of P80 were selected and analyzed by CLC main workbench 5.5 software. Several linkers and three dimensional structure of PDHB-P80 were compared to the native PDHB and analyzed to select a proper one for expression. The fusion gene sequence was optimized and synthesized in pMAT cloning vector. The synthetic pMAT-<em>pdhb</em>-<em>p80</em> was digested using <em>Bam </em>HI and <em>Sal</em> I restriction enzymes and ligated into pMAL-p5X expression vector. The pMAL-<em>pdhb</em>-<em>p80 </em>construct was transfected into <em>E.coli</em> BL21 strain cells and expressed protein were purified using amylose resin. and the purified protein was analyzed in sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and Western blotting. <em>In silico</em> analysis demonstrated that fusion proteins using IgG4 middle hinge (CPSCP) with TM-score of 0.99 showed the higher similarity between three dimensional structure of PDHB before and after fusion with high antigenic region of P80. Successful cloning verified by PCR colony, double digestion and sequence analysis. Besides, SDS-PAGE analysis and Western blotting indicated and confirmed the expression of intact recombinant chimeric protein MBP-PDHB-P80 along with some truncated forms of the recombinant protein. it could be concluded that the fusion construct has a potential for serodiagnostic assay in future studies.https://mbrc.shirazu.ac.ir/article_5748_38b5917290aab0e39c20968e2105e7c6.pdfShiraz University PressMolecular Biology Research Communications2322-181X9320200901Deciphering the functional role of hypothetical proteins from Chloroflexus aurantiacs J-10-f1 using bioinformatics approach129139575510.22099/mbrc.2020.36894.1495ENChander Jyoti ThakurDepartment of Bioinformatics, GGDSD College, Sector 32-C, 160030, Chandigarh, India0000-0002-9968-3109Sandeep SainiDepartment of Bioinformatics, GGDSD College, Sector 32-C, 160030, Chandigarh, IndiaDepartment of Biophysics, Panjab University, Sector 25, 160014, Chandigarh, India0000-0001-6822-4949Aayushi NotraDepartment of Bioinformatics, GGDSD College, Sector 32-C, 160030, Chandigarh, IndiaBhawanshu ChauhanDepartment of Bioinformatics, GGDSD College, Sector 32-C, 160030, Chandigarh, IndiaSarthak AryaDepartment of Bioinformatics, GGDSD College, Sector 32-C, 160030, Chandigarh, IndiaRishabh GuptaDepartment of Bioinformatics, GGDSD College, Sector 32-C, 160030, Chandigarh, India0000-0002-6658-4390Jyotsna ThakurDepartment of Bioinformatics, GGDSD College, Sector 32-C, 160030, Chandigarh, IndiaVarinder KumarDepartment of Bioinformatics, GGDSD College, Sector 32-C, 160030, Chandigarh, India0000-0002-8912-5429Journal Article20200407<em>Chloroflexus aurantiacus </em>J-10-f1 is an anoxygenic, photosynthetic, facultative autotrophic gram negative bacterium found from hot spring at a temperature range of 50-60°C. It can sustain itself in dark only if oxygen is available thereby exhibiting a dark orange color, however display a dark green color when grown in sunlight. Genome of the organism contains total of 3853 proteins out of which 785 (~20%) proteins are uncharacterised or hypothetical proteins (HPs). Therefore in this work we have characterized the 785 hypothetical proteins of <em>Chloroflexus aurantiacus </em>J-10-f1 using bioinformatics tools and databases. HPs annotated by more than five domain prediction tools were filtered and named high confidence-hypothetical proteins (HC-HPs). These HC-HPs were further annotated by calculating their physiochemical properties, homologous, subcellular locations, signal peptides and transmembrane regions. We found most of the HC-HPs were involved in photosynthesis, carbohydrate metabolism, biofuel production and cellulose synthesis processes. Furthermore, few of these HC-HPs could provide resistance to bacteria at high temperature due to their thermophilic nature. Hence these HC-HPs have the potential to be used in industrial as well as in biomedical needs. To conclude, the bioinformatics approach used in this study provides an insight to better understand the nature and role of <em>Chloroflexus aurantiacus </em>J-10-f1hypothetical proteins.https://mbrc.shirazu.ac.ir/article_5755_f94ed07e326b7ca30f319d9ec2019a43.pdf