@article { author = {Chen, Tao and Zou, Xingmei and Xu, Zuo and Wang, Yuanfang and Wang, Ping and Peng, Hao and Liu, Delong and Lin, Jinyu and Luo, Ruiyi and Wang, Yao and Chen, Qiusan and Chen, Daixiong and Cai, Mingsheng and Li, Meili}, title = {Molecular Characterization of the Epstein-Barr Virus BGLF2 Gene, its Expression, and Subcellular Localization}, journal = {Iranian Journal of Biotechnology}, volume = {16}, number = {2}, pages = {85-96}, year = {2018}, publisher = {National Institute of Genetic Engineering and Biotechnology of Iran}, issn = {1728-3043}, eissn = {2322-2921}, doi = {10.21859/ijb.1610}, abstract = {Background: Epstein–Barr virus (EBV) is a universal herpes virus which can cause a life-long and largely asymptomatic infection in the human population. However, the exact pathogenesis of the EBV infection is not well known.Objective: A comprehensive bioinformatics prediction was carried out for investigating the molecular properties of the BGLF2 and to afford a foundation for future research of the role and instrument of BGLF2 in the course of EBV infection.Materials and Methods: A 1011-base-pair sequence of BGLF2 gene from the Epstein-Barr virus (EBV) Akata strain genome was amplified using polymerase chain reaction and was further characterized by cloning, sequencing, and subcellular localization in the COS-7 cells.Results: The bioinformatics analysis demonstrated that EBV BGLF2 gene encodes a putative BGLF2 polypeptide which contains a conservative Herpes_UL16 domain. It was established that the polypeptide shows a close relationship with the Herpes UL16 tegument protein family and is extremely conserved among its homologues proteins encoded by UL16 genes. Multiple sequence alignments of the nucleic acid and amino acid sequence showed that the gene product of EBV BGLF2 contains a comparatively higher homology with the BGLF2-like proteins of the subfamily Gammaherpesvirinae than that of other subfamilies of the herpes virus. Moreover, the phylogenetic analyses suggested that EBV BGLF2 has a close genetic relationship with the member of Gammaherpesvirinae; in particular with the members of Cercopithecine herpesvirus 15 and Callitrichine herpesvirus 3. An antigen epitope analysis indicated that BGLF2 contains several potential B-cell epitopes. In addition, the secondary structure, as well as the three dimensional structure prediction suggests that BGLF2 consists of the both α-helix and b-strand. Besides, the subcellular localization prediction revealed that BGLF2 localizes in both nucleus and cytoplasm.Conclusions: Illustrating the relevance of the molecular properties and genetic evolution of EBV, BGLF2 will offer the perspectives for further study on the role and mechanism of the BGLF2 in course of EBV infection. These works will also conduct our understanding of the EBV at the molecular level as well as enriching the herpesvirus database.}, keywords = {BGLF2,Cloning,Bioinformatics analysis,Epstein-Barr Virus,Molecular property}, url = {https://www.ijbiotech.com/article_60557.html}, eprint = {https://www.ijbiotech.com/article_60557_2170b26f2d2ddc3f92d994a89dd9f3e8.pdf} } @article { author = {Rezaei, Marzie and Ghaderi, Abbas}, title = {Monoclonal Antibody Production Against Vimentin by Whole Cell Immunization in a Mouse Model}, journal = {Iranian Journal of Biotechnology}, volume = {16}, number = {2}, pages = {97-104}, year = {2018}, publisher = {National Institute of Genetic Engineering and Biotechnology of Iran}, issn = {1728-3043}, eissn = {2322-2921}, doi = {10.21859/ijb.1802}, abstract = {Background: Pancreatic carcinoma is the fourth-leading cause of cancer death in the United States and due to its late presentation, only few patients would be candidates for the curative treatment of pancreactomy. Monoclonal antibodies have brought hope to targeted therapy.Objectives: To identify new biomarkers, a panel of monoclonal antibodies was generated against newly established cell line, Faraz-ICR from a patient with pancreatic acinar cell carcinoma.Material and Methods: Balb/c female mice were immunized with Faraz-ICR cell line and their spleenocytes fused with SP2/0 myeloma cell line. Highly reactive hybridoma producing antibodies against Faraz-ICR was detected using ELISA, immunofluorescence staining and flow cytometry. Western blot and 2D immunoblot were utilized for further characterization of the target antibodies.Results: Among highly reactive clones, the reactivity of 7C11 clone was assessed in comparison to other epithelial tumors. The antibody isotype was IgM that reacted with a 55 kDa protein in western blot analysis. To further characterize the target antigen, immunoproteome of the Faraz-ICR cell line was performed. By LC-MS analysis, the target of 7C11 clone was identified to be vimentin.Conclusions: Pancreatic cancer is a highly lethal malignancy with no reliable biomarker for early detection and diagnosis. In this study, by establishing a pancreatic acinar carcinoma cell line, a panel of monoclonal antibodies was generated to identify specific or associated cancer targets. Furthermore, 7C11 mAb was introduced that can specifically recognizes vimentin as a tumor marker. This antibody may serve as a new tool for prognostic and therapeutic strategies.}, keywords = {Hybridoma,Monoclonal antibody,Pancreatic acinar cell carcinoma,Vimentin}, url = {https://www.ijbiotech.com/article_60559.html}, eprint = {https://www.ijbiotech.com/article_60559_2ea22936fdc185c11f6d6b65522b449b.pdf} } @article { author = {Salehi Borujeni, Masoud and Ghaderi-Zefrehei, Mostafa and Ghanegolmohammadi, Farzan and Ansari - Mahyari, Saeid}, title = {A Novel LSSVM Based Algorithm to Increase Accuracy of Bacterial Growth Modeling}, journal = {Iranian Journal of Biotechnology}, volume = {16}, number = {2}, pages = {105-113}, year = {2018}, publisher = {National Institute of Genetic Engineering and Biotechnology of Iran}, issn = {1728-3043}, eissn = {2322-2921}, doi = {10.21859/ijb.1542}, abstract = {Background: The recent progress and achievements in the advanced, accurate, and rigorously evaluated algorithms has revolutionized different aspects of the predictive microbiology including bacterial growth.Objectives: In this study, attempts were made to develop a more accurate hybrid algorithm for predicting the bacterial growth curve which can also be applicable in predictive microbiology studies.Materials and Methods: Sigmoid functions, including Logistic and Gompertz, as well as least square support vector machine (LSSVM) based algorithms were employed to model the bacterial growth of the two important strains comprising Listeria monocytogenes and Escherichia coli. Even though cross-validation is generally used for tuning the parameters in LSSVM, in this study, parameters tuning (i.e.,‘c’ and ‘σ’) of the LSSVM were optimized using non-dominated sorting genetic algorithm-II (NSGA-II), named as NSGA-II-LSSVM. Then, the results of each approach were compared with the mean absolute error (MAE) as well as the mean absolute percentage error (MAPE).Results: Applying LSSVM, it was resulted in a precise bacterial growth modeling compared to the sigmoid functions. Moreover, our results have indicated that NSGA-II-LSSVM was more accurate in terms of prediction than LSSVM method.Conclusion: Application of the NSGA-II-LSSVM hybrid algorithm to predict precise values of ‘c’ and ‘σ’ parameters in the bacterial growth modeling resulted in a better growth prediction. In fact, the power of NSGA-II for estimating optimal coefficients led to a better disclosure of the predictive potential of the LSSVM.}, keywords = {Bacterial growth curve,Hybrid algorithm,LSSVM,NSGA-II,Modeling}, url = {https://www.ijbiotech.com/article_60555.html}, eprint = {https://www.ijbiotech.com/article_60555_7f1fada0fe637ed532d1ffb9fcd19d16.pdf} } @article { author = {Li, Qunliang and Zhang, Xin and Guo, Xiaobo and Yao, Pingjia and Wei, Yuanan}, title = {Enzymatic Synthesis of Sucrose-6-acetate by a Novel Immobilized Fructosyltransferase From Aspergillus sp. GX-0010}, journal = {Iranian Journal of Biotechnology}, volume = {16}, number = {2}, pages = {114-119}, year = {2018}, publisher = {National Institute of Genetic Engineering and Biotechnology of Iran}, issn = {1728-3043}, eissn = {2322-2921}, doi = {10.21859/ijb.1380}, abstract = {Background: Sucralose is an ideal food sweetener and sucrose-6-acetate (s-6-a) is a key intermediate for synthesis of sucralose. Synthesis of s-6-a was studied by free fructosyltransferase (FTase) from Aspergillus oryzae. Because of the limitations of free enzyme in stability and reusability, a FTase obtained from the new isolated Aspergillus sp. GX-0010 was immobilized and investigated for the potential of s-6-a synthesis.Objectives: The synthesis of s-6-a with sucrose and glucose-6-acetate (g-6-a) by immobilized fructosyltransferase (IFTase) from a novel Aspergillus sp. GX-0010 was studied, and its synthesis conditions were also optimized.Materials and Methods: Aspergillus sp. GX-0010 was isolated. The effects of reaction time, ratio of g-6-a to sucrose, pH, substrate (sucrose and g-6-a) concentrations, IFTase concentration and temperature on the synthesis of s-6-a were investigated.Results: IFTase was able to catalyze sucrose and g-6-a to synthesize the s-6-a. Thermal and pH stability of IFTase were promoted once compared to the FTase. The optimal condition for IFTase catalysis was obtained at 50 °C, 60 min reaction time, pH 6.5, 1:2 ratio of g-6-a to sucrose and 35.0 g.L-1 concentration of enzyme. Under this optimal condition, a g-6-a conversion rate of 24.96% was reached.Conclusions: This study showed IFTase has a great potential in the biosynthesis of s-6-a, a key intermediate of sucralose synthesis.}, keywords = {Aspergillus sp. GX-0010,Immobilized fructosyltransferase,Sucralose,Sucrose-6-acetate}, url = {https://www.ijbiotech.com/article_60553.html}, eprint = {https://www.ijbiotech.com/article_60553_29b60185613139607c280e2403bf0617.pdf} } @article { author = {Esmailzadeh Mianlengeh, Zeinab and Soltani Najafabadi, Masood and Saidi, Abbas and Askari, Hossein}, title = {Monitoring Response of a Few bZip Transcription Factors in Response to Osmotic Stress in Sunflower}, journal = {Iranian Journal of Biotechnology}, volume = {16}, number = {2}, pages = {120-131}, year = {2018}, publisher = {National Institute of Genetic Engineering and Biotechnology of Iran}, issn = {1728-3043}, eissn = {2322-2921}, doi = {10.21859/ijb.1422}, abstract = {Background: Sunflower (Helianthus annuus L.) is one of the important vegetable oil supplies in the world and in Iran, as well. It is classified as a drought semi-tolerant crop; however, its yield is adversely affected by drought stress. Understanding the initial events in sensing stress and the related physiologic and biochemical events thereafter, is crucial in designing drought stress breeding programs. Transcription factors are master molecules directly involved in the plant responses under drought stress, from signal perception and transduction to the regulation of physiologic processes.Objective: The expression pattern of some bZip transcription factors in response to osmotic stress was investigated in sunflower.Material and Methods: Employing real-time PCR to monitor, the response of 10 bZIP transcription factors was performed under different osmotic stress conditions including -0.3, 0.9, and 1.2 MPa. Whole seedling was sampled at 6, 12, and 24 h after the osmotic condition application.Results: Exposure to osmotic potential of 0.9 MPa for 24 h caused a reduction in the fresh weight of the seedling. Among the evaluated genes, eight genes, bz-497, bz-502, bz-485, bz-499, bz-492, bz-504, bz-505, and bz-509 appeared as the osmotic stress responsive transcription factor. Changes in the expression of the genes under 0.3 MPa was observed for four genes. Most of the osmotic responsive genes appeared to be up-regulated. Most of responsiveness in the gene expression was happened under 0.9 MPa of the osmotic stress which is corresponding to fresh weight reduction in the seedlings. Among the investigated genes, two genes was identified to have possible roles in sensitive response of sunflower against drought stress.Conclusions: It was a focus to have systemic view on the complex response of the plant to abiotic stress, and avoidance of the single gene analysis. Also, the importance of molecular data in molecular breeding procedures toward achievement of the stress tolerant lines was highlighted.}, keywords = {BZip,Osmotic stress,Patchy pattern,Sunflower,Transcription factor}, url = {https://www.ijbiotech.com/article_60554.html}, eprint = {https://www.ijbiotech.com/article_60554_82d73a46e321b0b0f750def6b1178079.pdf} } @article { author = {Kazeroonian, Rezvanolsadat and Mousavi, Amir and Kalate Jari, Sepideh and Tohidfar, Masoud}, title = {Factors Influencing in Vitro Organogenesis of Chrysanthemum morifolium cv. ‘Resomee Splendid’}, journal = {Iranian Journal of Biotechnology}, volume = {16}, number = {2}, pages = {132-139}, year = {2018}, publisher = {National Institute of Genetic Engineering and Biotechnology of Iran}, issn = {1728-3043}, eissn = {2322-2921}, doi = {10.21859/ijb.1454}, abstract = {Background: Chrysanthemum; also commonly known as mums or chrysanths, is one of the most important ornamental crops worldwide. Introducing desirable traits into this valuable plant by the conventional breeding has so far been faced with some restrictions due to the limited gene pool and cross-incompatibility. Therefore, breeders have decided to exploit Agrobacterium-mediated transformation methods in order to satisfy the growing market demands. However, more efficient in vitro regeneration protocols are required for this approach.Objectives: The objective of this research was to develop an efficient protocol for an in vitro plant regeneration by the examining the effects of various combinations and concentrations of the plant growth regulators (PGRs) and different explants types.Materials and Methods: The leaf and petiole explants of the Chrysanthemum morifolium cv. ‘Resomee Splendid’ were collected from the in vitro grown plantlets. Murashige and Skooge (MS) medium was supplemented with different concentrations and combinations of benzylaminopurine (BAP), 1-naphthaleneacetic acid (NAA) and thidiazuron (TDZ). Thereafter, the effects of these hormonal treatments were investigated on shoot initiation percentage, the average number of shoots per explants, callogenesis, and the type of organogenesis in regard to both types of the explants.Results: Shoots were directly formed from leaf explants on the media that only contained BAP without callus formation. Amongst the other hormonal treatments, a combination of 4.5 mg.L-1 BAP plus 1 mg.L-1 NAA resulted in the direct organogenesis from the leaf explants, which was superior to the other combinations and concentrations. In regard to the petiole explants, direct shoot formation occurred in all the media except for the ones which were fortified with TDZ. In this case, considering the shoot initiation percentage and the mean shoot number per explants, the best results were achieved in the medium supplemented with 1.5 mg.L-1 BAP and 1 mg.L-1 NAA. Results showed that interaction of either BAP or TDZ with NAA was necessary for the callus induction.Conclusions: Significant differences in shoot initiation percentage and the average number of shoots per explants were observed both in leaves and petioles grown on different media. Moreover, the callogenesis rates, as well as organogenesis types, showed some differences among the studied explants when compared on the same media.}, keywords = {Callogenesis,Chrysanthemum morifolium,Explants types,Plant growth regulators,Regeneration}, url = {https://www.ijbiotech.com/article_58480.html}, eprint = {https://www.ijbiotech.com/article_58480_f284ab238332f4a083e12be27dc1bbd8.pdf} } @article { author = {Song, Xiaoqing and weng, Qiaoyun and Zhao, Yanmin and Ma, Hailian and Song, Jinhui and su, lining and Yuan, Jincheng and Liu, Yinghui}, title = {Cloning and Expression Analysis of ZmERD3 Gene From Zea mays}, journal = {Iranian Journal of Biotechnology}, volume = {16}, number = {2}, pages = {140-147}, year = {2018}, publisher = {National Institute of Genetic Engineering and Biotechnology of Iran}, issn = {1728-3043}, eissn = {2322-2921}, doi = {10.21859/ijb.1593}, abstract = {Background: Stresses (such as drought, salt, viruses, and others) seriously affect plant productivity. To cope with these threats, plants express a large number of genes, including several members of ERD (early responsive to dehydration) genes to synthesize and assemble adaptive molecules. But, the function of ERD3 gene hasn’t been known so far.Objectives: The purpose of the present study was to clone the stress-resistance gene: ZmERD3, and to analyze its expression pattern in the maize plant organs at different stages and under various stress treatments.Materials and Methods: MaizeGDB database search together with the bioinformatics analysis led to the identification of ZmERD3 gene in Zea mays. The cDNA sequence and promoter of ZmERD3 gene were obtained through PCR. Bioinformatics analysis was performed through online tools. The tissue-specific expression profile of the ZmERD3 gene in maize plant was carried out using the quantitative real time PCR (qRT-PCR) technique and its expression pattern in response to stress treatments (such as PEG, NaCl, ABA, and low temperature) was also analyzed through qRT-PCR method.Results: Based on the homology alignment with AtERD3 (XP_002867953) in MaizeGDB (http://www. maizegdb.org/), the cDNA sequence and promoter region of the ZmERD3 gene were obtained. The bioinformatic analysis showed that ZmERD3 protein has one specific hit of methyltransferase and a high probability of location in the cytoplasm, and there are many cis-regulatory elements responsive to light, heat, cold, dehydration, as well as other stresses in its promoter sequence. Expression analysis revealed that the amount of ZmERD3 mRNA is different in all indicated organs of the maize plant. In addition, the ZmERD3 expression could be induced by abiotic stress treatments. Compared to the control, treatment with NaCl or PEG-6000 could significantly enhance the expression ability of ZmERD3 gene. As well, its expression level was increased about 20 times above the control after exposure to NaCl and PEG-6000 treatments for 3-6 h.Conclusions: One putative methyltransferase gene, ZmERD3 was cloned. ZmERD3 expression exhibited an obvious tissue-specificity, and its expression could make a significant response to NaCl and PEG-6000 treatments.}, keywords = {Abiotic stresses,Expression analysis,Zea mays,ZmERD3 gene}, url = {https://www.ijbiotech.com/article_60556.html}, eprint = {https://www.ijbiotech.com/article_60556_e0ce8fd0aa4a1ee2d6dc6d12249ae1b5.pdf} } @article { author = {Gholami, Morteza and Esmaeilzadeh Bahabadi, Sedigheh and Ghanati, Faeze and Yousefzadeh Borojeni, Laleh}, title = {Stereo-Specific Transcript Regulation of the Polyamine Biosynthesis Genes by Enantiomers of Ornithine in Tobacco Cell Culture}, journal = {Iranian Journal of Biotechnology}, volume = {16}, number = {2}, pages = {148-153}, year = {2018}, publisher = {National Institute of Genetic Engineering and Biotechnology of Iran}, issn = {1728-3043}, eissn = {2322-2921}, doi = {10.21859/ijb.1835}, abstract = {Background: Ornithine (Orn) plays an essential role in the metabolism of plant cells through incorporation in polyamines biosynthesis, the urea cycle and nitrogen metabolism. Physiological response of the plant cells to its two enantiomers have not been widely investigated yet.Objectives: This study aimed to evaluate effect of ornithine enantiomers on expression of certain polyamine (PAs) biosynthetic genes in tobacco cells.Materials and Methods: Suspension-cultured tobacco cells were treated with different concentrations of L- and D- Orn for 24 h. Cell viability was assayed by Evans Blue and hydrogen peroxide content. The changes of gene expression were analyzed by semi-quantitative RT-PCR.Results: Exogenous D-Orn resulted in enhancement of expression of genes involved in Orn, arginine and S-adenosyl methionine metabolism. Additionally, exogenous D-Orn treatment resulted in sustained viability of cultured tobacco cells and normal levels of hydrogen peroxide were maintained. Supplied L-Orn increased the hydrogen peroxide level and lowered viability of cells. Treatment with L-Orn had a negative effect on the transcript levels for most analyzed PA-related genes. It was also illustrated that transcription of putrescine methyl transferase, key enzyme for nicotine production, was highly upregulated by L-Orn.Conclusions: Based on the results, D-Orn was shown to have a stereo-selective function in regulation of the PAs-related genes.}, keywords = {Arginine decarboxylase,D-amino acids,Nicotiana tabacum,Ornithine decarboxylase}, url = {https://www.ijbiotech.com/article_60562.html}, eprint = {https://www.ijbiotech.com/article_60562_e8da09548ad250a1f320ea0a835f8b71.pdf} } @article { author = {Sam, Mohammad Reza and Zomorodipour, Alireza and Haddad-Mashadrizeh, Aliakbar and Ghorbani, Mahdi and Kardar, Gholam Ali and Sam, Sohrab}, title = {Functions of the Heterologous Intron-Derived Fragments Intra and Extra Factor IX-cDNA Coding Region on the Human Factor IX Expression in HepG2 and Hek-293T Cells}, journal = {Iranian Journal of Biotechnology}, volume = {16}, number = {2}, pages = {154-163}, year = {2018}, publisher = {National Institute of Genetic Engineering and Biotechnology of Iran}, issn = {1728-3043}, eissn = {2322-2921}, doi = {10.21859/ijb.1753}, abstract = {Background: Human FIX (hFIX) gene transfer into hepatocytes has provided a novel approach for treatment of hemophilia B. To obtain an improved expression of hFIX, the functional hFIX-expressing plasmids with appropriate intron-derived fragments which facilitate transcription and promote an efficient 3′-end formation of mRNAs are required.Objectives: We aim to evaluate the functions of the heterologous intron-derived fragments intra and extra hFIX-cDNA coding region with respect to the hFIX expression in the hepatocytes and kidney cells.Materials and Methods: HepG2 cells as differentiated hepatocytes and Hek-293T cells as embryonic kidney cells were transfected with the different hFIX-expressing plasmids containing various combinations of the two human beta-globin (hBG) introns within the hFIX-cDNA and Kozak sequence. In the next stage, as a hepatocyte-specific sequence, the rat aldolase B intronic enhancer sequence (rABE), was isolated from the first intron of the rat aldoase B gene and inserted within the upstream CMV promoter (CMVp) and efficacies of the engineered vectors were investigated in the stably-transfected HepG2 cells.Results: Our data indicate that the intron-less construct and hBG intron-I containing construct are more effective with regard to hFIX expression compared to other constructs in Hek-293 cells. In HepG2 cells, the rABE in combination with CMVp in context of intron-less plasmid induced an increase in total expression of hFIX protein dramatically; ranging from 2.3 to 40 folds increase compared to other constructs. The rABE in combination with CMVp in the hBG intron-I, hBG intron-II, and hBG intron-I,II containing plasmids induced 3.7, 2, and 1.6-fold increase in the total expression of hFIX protein, respectively. The presence of both hBG intronic sequences within the hFIX-cDNA induced a higher secretion level of hFIX than either intron-I or II alone and provided correctly spliced hFIX transcripts in HepG2 and kidney cell lines. The intron-less construct with or without rABE induced the highest hFIX mRNA levels in HepG2 and Hek-293T cells respectively compared to other constructs.Conclusions: The embryonic kidney cells in addition to the differentiated hepatic cell lines could be successfully targeted by plasmid vectors. The intron-less and hBG intron-I containing plasmids represent a particular interest in producing recombinant hFIX in Hek-293T cells. The synergistic function on the hFIX expression that was achieved by combining the CMVp with the liver-specific rABE would be a useful approach for future designing of the expression cassettes for hepatocyte-mediated gene expression in hemophilia B.}, keywords = {Aldolase B intronic enhancer,Beta-globin introns,Hepatocyte,Hemophilia B,Human factor IX (hFIX),Plasmid}, url = {https://www.ijbiotech.com/article_60558.html}, eprint = {https://www.ijbiotech.com/article_60558_8b2de3d8c08d339dd6d56eb05b27c560.pdf} }