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Editorial 2 2 Recently I was invited to attend the bi-annual Steering committee meeting of the EMGEN network, for-merly known as Eastern Mediterranean Health Genomics and Biotechnology Network (EMHGBN). This was held at the Pasteur Institute of Iran in Tehran on January 29-30, 2012. Attending this meeting as the chief editor of Avicenna Journal of Medical Biotechnology (AJMB) was very informative and I became familiar with the goals of this international organization. The EMGEN network was established in 2004 on the recom-mendation and support of WHO/EMRO and participation of representatives from selected centers of excel-lence in Molecular biology, Biotechnology, and genomics from 22 countries in the Eastern Mediterranean Re-gion including Iran. The names of these countries are listed on the website for the network (www.emgen.net). It also has useful information on the goals, membership, training programs, job opportunities, and newsletters of the organization. I recommend it to those interested in the role of biotechnology and genomics in health to visit the website and participate in the activities of the organization. As I understand, one of the major goals of EMGEN network is to increase awareness on the potentials and capacities of member countries in the fields of Biotechnology and genomics. More importantly, they aim to facilitate scientific collaborations among the scientists in the Eastern Mediterranean Region. After listening to the representatives from member countries attending the meeting, I was convinced that many more scientists from the fields of biotechnology and genomics in EMGEN network member countries ought to interact and collaborate on scientific projects before resources in member countries can be ef-fectively shared in joint projects. For my part, I encourage eminent biotech and genomic scientists from the member countries to participate in AJMB's scientific activities through submission of original articles, opinions, reviews in fields such as Medical Biotechnology, Genomics, Nanobiotechnology, Bioinformatics, and Molecular Biology. Furthermore, the chief scientists from the member countries can participate in the AJMB's scientific activities in the capacity of associate editors and reviewers in their fields of expertise. As the chief editor of AJMB, I would like to invite all the scientists in the EMGEN network countries working in the fields of Medical Biotechnology and genomics to actively participate in this network's activities. I would also like to inform those interested in obtaining research grants that funds have been made available by some member countries in the form of 50/50 contribution. 2 2 Ali M. Ardekani Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR Iran Editorial 165.pdf ####

Non-Invasive Detection of Esophageal Cancer using Genetic Changes in Circulating Cell-Free DNA 2 2 Cell free DNA (cfDNA) is a genetic biomarker that is present in serum or plasma in high concentration in many types of cancer. Identification of circu-lating cancer related DNA molecules in serum or plasma is a non-invasive tool for early diagnosis and prognosis in many cancer patients. For this review, study selection and data extraction were performed by the authors. Detection of point mutations, microsatellite alterations, DNA hypermethylations and losses of heterozygosity in circulating cell free DNA have been characterized in esophagus cancer. Application of circulating cell free DNA as a biomarker, provide the best opportunity for constructing non-invasive tests for early de-tection, prognosis and management of cancer patients, after therapy in many types of cancer. 3 13 Saeid Ghorbian Department of Biology, Science and Research Branch, Islamic Azad University Department of Biology, Science and Research Branch, Islamic Azad University Iran Ali M. Ardekani Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR Iran BiomarkersEarly detectionEsophagus neoplasmPrognosis 76.pdf Kamangar F, Dores GM, Anderson WF. Patterns of cancer incidence, mortality, and prevalence across five continents: defining priorities to reduce cancer disparities in different geographic regions of the world. J Clin Oncol 2006;24(14):2137-2150. ##Ya W, Wistuba II, Emmert-Buck MR, Erickson HS. 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Ligation Independent Cloning of Polycistronic, Genetically Modified, HuMAb4D5-8 F (ab') 2, in Bacterial Plasmid 2 2 In recent years, recombinant monoclonal antibodies and their derivatives have emerged as important targeted therapy agents. Monoclonal antibodies are ex-tremely difficult to produce. So, the cost of production is very high and many people cannot afford these drugs. In this regard, choosing inexpensive and easy ways to manipulate production systems such as bacterial hosts to reduce the cost of manufacturing these critical components are considered as vital step for developmental issues in recombinant expression systems. We, therefore, at-tempted to generate a polycistronic construct of anti HER-2 F(ab')2 fragment antibody for insertion in an expression bacterial plasmid. Also some modifica-tions were made in the hinge region to express antibody F(ab')2 fragment in its authentic form preventing from multiple varieties of disulfide bond formation. Finally, synthesized construct was cloned in pET-32 Ek/LIC vector without using restriction enzyme digestion or ligation reactions. The results of this study show-ed that modified F(ab')2 fragment was simply and successfully inserted in Escherichia coli (E.coli) using the Ligation Independent Cloning technology. 15 22 Leila Farahmand Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Biotechnology Research Center, Tehran University of Medical SciencesIranian Center for Breast Cancer (ICBC), Academic Center for Education, Culture and Research (ACECR) Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Biotechnology Research Center, Tehran University of Medical Sciences IranIran Keivan Majidzadeh Iranian Center for Breast Cancer (ICBC), Academic Center for Education, Culture and Research (ACECR)AJA University of Medical Science AJA University of Medical Science IranIran Zargham Sepehrizadeh Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Biotechnology Research Center, Tehran University of Medical Sciences Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Biotechnology Research Center, Tehran University of Medical Sciences Iran Mohammad Reza Mofid Isfahan University of Medical Sciences Isfahan University of Medical Sciences Iran Rezvan Esmaeili Iranian Center for Breast Cancer (ICBC), Academic Center for Education, Culture and Research (ACECR) Iran Mojtaba Tabatabaei Yazdi Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Biotechnology Research Center, Tehran University of Medical Sciences Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Biotechnology Research Center, Tehran University of Medical Sciences Iran <i>Escherichia coli</i>Monoclonal antibodiesPlasmids 77.pdf Fang L, Barekati Z, Zhang B, Liu Z, Zhong X. 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In silico Evaluation of Crosslinking Effects on Denaturant meq values and ΔCp upon Protein Unfolding 2 2 Important thermodynamic parameters including denaturant equilibrium m values (meq) and heat capacity changes (ΔCp) can be predicted based on changes in Solvent Accessible Surface Area (SASA) upon unfolding. Crosslinks such as disulfide bonds influence the stability of the proteins by decreasing the entropy gain as well as reduction of SASA of unfolded state. The aim of the study was to develop mathematical models to predict the effect of crosslinks on ΔSASA and ultimately on meq and ΔCp based on in silico methods. Changes of SASA upon computationally simulated unfolding were calculated for a set of 45 proteins with known meq and ΔCp values and the effect of crosslinks on ΔSASA of unfolding was investigated. The results were used to predict the meq of denaturation for guanidine hydrochloride and urea, as well as ΔCp for the studied proteins with overall error of 20%, 31% and 17%, re-spectively. The results of the current study were in close agreement with those obtained from the previous studies. 23 34 Maryam Hamzeh-Mivehroud Biotechnology Research Center, Tabriz University of Medical Sciences, Daneshgah Street Biotechnology Research Center, Tabriz University of Medical Sciences, Daneshgah Street Iran Ali Akbar Alizade Biotechnology Research Center, Tabriz University of Medical Sciences, Daneshgah StreetSchool of Pharmacy, Tabriz University of Medical Sciences Biotechnology Research Center, Tabriz University of Medical Sciences, Daneshgah StreetSchool of Pharmacy, Tabriz University of Medical Sciences IranIran Monire Ahmadifar Biotechnology Research Center, Tabriz University of Medical Sciences, Daneshgah StreetSchool of Pharmacy, Tabriz University of Medical Sciences Biotechnology Research Center, Tabriz University of Medical Sciences, Daneshgah StreetSchool of Pharmacy, Tabriz University of Medical Sciences IranIran Siavoush Dastmalchi Biotechnology Research Center, Tabriz University of Medical Sciences, Daneshgah StreetSchool of Pharmacy, Tabriz University of Medical Sciences Biotechnology Research Center, Tabriz University of Medical Sciences, Daneshgah StreetSchool of Pharmacy, Tabriz University of Medical Sciences IranIran CrosslinksDisulfidesProtein stabilityThermodynamics 78.pdf Uhlen M, Ponten F. 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Toxicity Study of Silver Nanoparticles Synthesized from Suaeda monoica on Hep-2 Cell Line 2 2 Recently there has been fabulous excitement in the nano-biotechnological area for the study of nanoparticles synthesis using some natural biological system, which has led the growth advanced nanomaterials. This intention made us to assess the biologically synthesized silver nanoparticles from the leaf of Suaeda monoica (S.monoica) using 1 mM silver nitrate. The leaf extract of S.monoica incubated with 1 mM silver nitrate solution and characterized by UV- spectrometer and AFM. The effect of synthesized silver nanoparticles on Human Epidermoid Larynx Carcinoma cell line was evaluated by the MTT colorimetric technique. As a result we observed gradual change in the colour of extract from greenish to brown. The synthesized silver nanoparticles con-firmed by UV at 430 nm and spherical shape identified in the range of 31 nm under AFM. The effect of silver nanoparticles on Human Epidermoid Larynx Carcinoma cell line exhibits a dose-dependent toxicity for the cell tested and the viability of Hep-2 cells decreased to 50% (IC50) at the concentration of 500 nM. Further findings will be determined the exact mechanisms of this cost effective Nano-treatments. 35 39 Kaliyamurthi Satyavani Marine Medicinal Plant Biotechnology Laboratory, Faculty of Marine Sciences, Annamalai University, Parangipettai Marine Medicinal Plant Biotechnology Laboratory, Faculty of Marine Sciences, Annamalai University, Parangipettai India Selvaraj Gurudeeban Marine Medicinal Plant Biotechnology Laboratory, Faculty of Marine Sciences, Annamalai University, Parangipettai Marine Medicinal Plant Biotechnology Laboratory, Faculty of Marine Sciences, Annamalai University, Parangipettai India Thiruganasambandam Ramanathan Marine Medicinal Plant Biotechnology Laboratory, Faculty of Marine Sciences, Annamalai University, Parangipettai Marine Medicinal Plant Biotechnology Laboratory, Faculty of Marine Sciences, Annamalai University, Parangipettai India Thangavel Balasubramanian Marine Medicinal Plant Biotechnology Laboratory, Faculty of Marine Sciences, Annamalai University, Parangipettai Marine Medicinal Plant Biotechnology Laboratory, Faculty of Marine Sciences, Annamalai University, Parangipettai India Cytotoxicity testNanomaterialsPlant leavesSilver nanoparticle 79.pdf Bandaranayake WM. 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Construction and Stable Expression of a Truncated Human Receptor Tyrosine Kinase Ror1 (Ror1-ECD) 2 2 Expression of receptor tyrosine kinase Ror1 in a wide variety of cancers has emerged as a new era focusing on targeting this receptor in cancer therapy. Our preliminary re-sults indicate the presence of a truncated transcript of Ror1 in tumor cells. The trun-cated Ror1 encompasses extracellular and transmembrane domains, lacking catalytic kinase domain (Ror1-ECD). As enzyme activity is highly dependent on the catalytic domain, we were wondering how this transcript and its encoded protein could play a possible role in tumorigenesis. To understand the function of this truncated transcript and whether or not the encoded protein translocates to the cell surface, we construct-ed a mammalian expression vector containing exon 1 to exon 8 of human Ror1 gene as a model system. The encoded protein by this construct covers the entire extracellular and transmembrane domains of Ror1. The Chinese Hamster Ovary Cell line (CHO) was used for transfection. Our results showed that this construct could express Ror1-ECD at protein level and also the protein could effectively translocate to the surface of transfected cells. Such model may suggest that a proportion of Ror1 molecules ex-pressed by tumor cells are not full-length Ror1. This notion may be considered when applying flow cytometry using antibodies against Ror1 for screening of tumor cells in order to avoid any miscalculation in the number of Ror1 molecules expressed by tumor cells. Furthermore, such expression may bring about assumptions on functional roles of Ror1-ECD in tumorigenesis, which requires extensive functional studies. 41 45 Flora Forouzesh Department of Biology, Science and Research Branch, Islamic Azad University Department of Biology, Science and Research Branch, Islamic Azad University Iran Samira Shakeri Tabarian Department of Antigen and Antibody Engineering, Monoclonal Antibody Research Center, Avicenna Research Institute, ACECR Department of Antigen and Antibody Engineering, Monoclonal Antibody Research Center, Avicenna Research Institute, ACECR Iran Shaghayegh Emami Department of Antigen and Antibody Engineering, Monoclonal Antibody Research Center, Avicenna Research Institute, ACECR Department of Antigen and Antibody Engineering, Monoclonal Antibody Research Center, Avicenna Research Institute, ACECR Iran Mahmood Jeddi-Tehrani Department of Antigen and Antibody Engineering, Monoclonal Antibody Research Center, Avicenna Research Institute, ACECR Department of Antigen and Antibody Engineering, Monoclonal Antibody Research Center, Avicenna Research Institute, ACECR Iran Reza Hadavi Department of Antigen and Antibody Engineering, Monoclonal Antibody Research Center, Avicenna Research Institute, ACECR Department of Antigen and Antibody Engineering, Monoclonal Antibody Research Center, Avicenna Research Institute, ACECR Iran Hodjattallah Rabbani Department of Antigen and Antibody Engineering, Monoclonal Antibody Research Center, Avicenna Research Institute, ACECR Department of Antigen and Antibody Engineering, Monoclonal Antibody Research Center, Avicenna Research Institute, ACECR Iran Cell lineReceptor tyrosine kinaseGene expression 80.pdf Schlessinger J. Cell signaling by receptor tyrosine ki-nases. Cell 2000;103(2):211-225.##Matsuda T, Nomi M, Ikeya M, Kani S, Oishi I, Terashima T, et al. Expression of the receptor tyrosine kinase genes, Ror1 and Ror2, during mouse development. Mech Dev 2001;105(1-2):153-156.##Masiakowski P, Yancopoulos GD. The Wnt receptor CRD domain is also found in MuSK and related orphan recep-tor tyrosine kinases. Curr Biol 1998;8(12):R407.##Oishi I, Takeuchi S, Hashimoto R, Nagabukuro A, Ueda T, Liu ZJ, et al. Spatio-temporally regulated expression of receptor tyrosine kinases, mRorl, mRor2, during mouse development: implications in development and function of the nervous system. Genes Cells 1999;4(1):41-56.##Patthy L, Trexler M, Vali Z, Banyai L, Varadi A. Kringles: modules specialized for protein binding. Homology of the gelatin-binding region of fibronectin with the kringle structures of proteases. FEBS Lett 1984;171(1):131-136.##Rehn M, Pihlajaniemi T, Hofmann K, Bucher P. The friz-zled motif: in how many different protein families does it occur? Trends Biochem Sci 1998;23(11):415-417.##Saldanha J, Singh J, Mahadevan D. Identification of a Frizzled-like cysteine rich domain in the extracellular region of developmental receptor tyrosine kinases. Pro-tein Sci 1998;7(8):1632-1635.##Masiakowski P, Carroll RD. A novel family of cell sur-face receptors with tyrosine kinase-like domain. J Biol Chem 1992;267(36):26181-26190.##Yoda A, Oishi I, Minami Y. Expression and function of the Ror-family receptor tyrosine kinases during develop-ment: lessons from genetic analyses of nematodes, mice, and humans. J Recept Signal Transduct Res 2003;23(1): 1-15.##Forrester WC. The Ror receptor tyrosine kinase family. Cell Mol Life Sci 2002;59(1):83-96.##Baskar S, Kwong KY, Hofer T, Levy JM, Kennedy MG, Lee E, et al. Unique cell surface expression of receptor tyrosine kinase ROR1 in human B-cell chronic lympho-cytic leukemia. Clin Cancer Res 2008;14(2):396-404.##Reddy UR, Phatak S, Allen C, Nycum LM, Sulman EP, White PS, et al. Localization of the human Ror1 gene (NTRKRi) to chromosome 1p31-p32 by fluorescence in situ hybridization and somatic cell hybrid analysis. Geno-mics 1997;41(2):283-285.##Klein U, Tu Y, Stolovitzky GA. Gene expression pro-filing of B cell chronic lymphocytic leukemia reveals a homogeneous phenotype related to memory B cells. J Exp Med 2001;194(11):1625-1638.##Rosenwald A, Alizadeh AA, Widhopf G, Simon R, Davis RE, Yu X, et al. Relation of gene expression phenotype to immunoglobulin mutation genotype in B cell chronic lymphocytic leukemia. J Exp Med 2001;194(11):1639-1647.##Shabani M, Asgarian-Omran H, Vossough P, Sharifian RA, Faranoush M, Ghragozlou S, et al. Expression pro-file of orphan receptor tyrosine kinase (ROR1) and Wilm's tumor gene 1 (WT1) in different subsets of B-cll acute lymphoblastic leukemia. 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Optimization of the Expression of Genes Encoding Poly (3-hydroxyalkanoate) Synthase from Pseudomonas aeruginosa PTCC 1310 in Escherichia coli 2 2 Over the years, the use of plastics has complicated the problem of disposal of solid wastes. One strategy to reduce plastic waste is the use of biodegradable plastics. A group of these plastics are polyhydroxyalkanoates (PHAs). To date more than 250 different microorganisms are known to synthesize and accumulate PHA. Most Pseu-domonas strains are able to accumulate mcl-PHA. In previous studies, the phaC1 and phaC2 genes were identified in Pseudomonas aeruginosa (P.aeruginosa) PTCC 1310 and were cloned. The aim of this study was to express these genes and optimize the conditions for their expression. The inserts obtained from vectors pTZPHAC1 and pTZPHAC2 were subcloned into pET15b expression vector. After transformation of competent Escherichia coli (E.coli) BL21 (DE3) cells with recombinant plasmids, expres-sion was induced using IPTG. By changing expression conditions such as IPTG concen-tration, time and temperature of incubation with IPTG, the expression conditions for these enzymes were optimized, and the obtained results were compared using proper statistical analysis. The PHA synthase genes were induced with IPTG and the expres-sed 62 kDa protein was observed and purified. By changing expression conditions, 1 mM IPTG, 37 °C and a 2 hr incubation provided the highest level of protein pro-duction in E.coli cells. These results suggest that induction condition of PhaC genes can influence expression of PHA synthase enzymes. 47 51 Daryoush Abedi Department of Pharmaceutical Biotechnology and Isfahan Pharmaceutical Sciences Research Center School of Pharmacy, Isfahan University of Medical Science Department of Pharmaceutical Biotechnology and Isfahan Pharmaceutical Sciences Research Center School of Pharmacy, Isfahan University of Medical Science Iran Maryam Beheshti Department of Pharmaceutical Biotechnology and Isfahan Pharmaceutical Sciences Research Center School of Pharmacy, Isfahan University of Medical Science Department of Pharmaceutical Biotechnology and Isfahan Pharmaceutical Sciences Research Center School of Pharmacy, Isfahan University of Medical Science Iran Ali Jahanian Najafabadi Department of Pharmaceutical Biotechnology and Isfahan Pharmaceutical Sciences Research Center School of Pharmacy, Isfahan University of Medical Science Department of Pharmaceutical Biotechnology and Isfahan Pharmaceutical Sciences Research Center School of Pharmacy, Isfahan University of Medical Science Iran Hamid Mir Mohammad Sadeghi Department of Pharmaceutical Biotechnology and Isfahan Pharmaceutical Sciences Research Center School of Pharmacy, Isfahan University of Medical Science Department of Pharmaceutical Biotechnology and Isfahan Pharmaceutical Sciences Research Center School of Pharmacy, Isfahan University of Medical Science Iran Vajihe Akbari Department of Pharmaceutical Biotechnology and Isfahan Pharmaceutical Sciences Research Center School of Pharmacy, Isfahan University of Medical Science Department of Pharmaceutical Biotechnology and Isfahan Pharmaceutical Sciences Research Center School of Pharmacy, Isfahan University of Medical Science Iran PhaC1PhaC2PolyhydroxyalkanoateProtein expression 81.pdf Verlinden RAJ, Hill DJ, Kenward M, Williams CD, Rad-ecka I. 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PCR cloning of Pseudomonas resinovo-rans polyhydroxyalkanoate biosynthesis genes and ex-pression in Escherichia coli. Biotechnol Lett 2000;22(9): 789-794.##Andreessen B, Lange AB, Robenek H, Steinbuchel A. Conversion of glycerol to poly (3-hydroxypropionate) in recombinant Escherichia coli. Appl Environ Microbiol 2010;76(2):622-626.##Abedi D, Najafabadi AJ, Sadeghi HM, Vallian S. Cloning and partial sequencing of phac1 and phac2 genes encoding poly(3-hydroxyalkanoate) synthases from Pseu-domonas aeruginosa PTCC 1310. Biotechnology 2007;6 (4):497-504.##Sambrok J, Russell DW. Molecular Cloning a Laboratory Manual. 3rd ed. New York: Cold Spring Harbor Labora-tory Press; 2001. ##Serafim LS, Lemos PC, Levantesi C, Tandoi V, Santos H, Reis MAM. Methods for detection and visualization of intracellular polymers stored by polyphosphate-accu-mulating microorganisms. J Microbiol Methods 2002;51 (1):1-18.##Bai Y, Zhang YL, Jin JF, Wang JD, Zhang ZS, Zhou DY. Recombinant Helicobacter pylori catalase. World J Gas-troenterol 2003;9(5):1119-1122.##Wen Q, Ma L, Wang X. Culture condition optimization of engineered E. coli BL21/pET-11c/hIL-2-mGM-CSF. Nan Fang Yi Ke Da Xue Xue Bao 2006;26(4):418-420, 424.##Yang L, Yang Q, Liu PG, Li S, Li H. Optimization of the Trichoderma Harzianum Cu Zn superoxide dismutase gene expressicn in E. coli. KMITL Sci Tech J 2007;7(2): 179-184.##Ren Q, Beilen JB, Sierro N, Zinn M, Kessler B, Witholt B. Expression of PHA polymerase genes of Pseudo-monas putida in Escherichia coli and its effect on PHA formation. Antonie Van Leeuwenhoek 2005;87(2):91-100.##Aldor IS, Keasling JD. Process design for microbial plas-tic factories: metabolic engineering of polyhydroxyalka-noates. Curr Opin Biotechnol 2003;14(5):475-483.##