Shiraz University PressMolecular Biology Research Communications2322-181X5420161201In silico prediction of B cell epitopes of the extracellular domain of insulin-like growth factor-1 receptor201214383210.22099/mbrc.2016.3832ENVahidBayramiDepartment of Biotechnology, Faculty of Advanced Sciences and Technologies, University of Isfahan, Isfahan, IranMehrnazKeyhanfarDepartment of Biotechnology, Faculty of Advanced Sciences and Technologies, University of Isfahan, Isfahan, IranHassanMohabatkarDepartment of Biotechnology, Faculty of Advanced Sciences and Technologies, University of Isfahan, Isfahan, IranManijehMahdaviDepartment of Pharmaceutical Biotechnology, Faculty of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, IranViolaineMoreauCentre de Biochimie Structurale, CNRS UMR 5048, UM 1 & 2- INSERM U 1054, 29 rue de Navacelles, 34090, Montpellier, FranceJournal Article20160225The insulin-like growth factor-1 receptor (IGF-1R) is a transmembrane receptor with tyrosine kinase activity. The receptor plays a critical role in cancer. Using monoclonal antibodies (MAbs) against the IGF-1R, typically blocks ligand binding and enhances down-regulation of the cell-surface IGF-1R. Some MAbs such as cixutumumab are under clinical trial investigation. Targeting multiple distinct epitopes on IGF-1R, might be an effective strategy to inhibit IGF-1R pathway in cancer. In this study, new linear B cell epitopes for the extracellular domains of IGF-1R were predicted by in silico methods using a combination of linear B cell epitope prediction web servers such as ABCpred, Bepired, BCPREDs, Bcepred and Elliprro. Moreover, Discotope, B-pred and PEPOP web server tools were employed to predict new conformational B cell epitopes. In contrast to previously reported epitopes from extracellular region of the IGF-1R, we predicted new linear P8: (RQPQDGYLYRHNYCSK) and conformational Pc4: (HYYYAGVCVPACPPNTYRFE), Ppc6: (KMCPSTGKRENNESAPDNDT) and Ppc20: (ANILSAESSDSEFMQEPSGFI) epitopes. These epitopes are useful for further study as peptide antigens to actively immune host animals to develop new MAbs. Furthermore, the epitopes can be used in peptide-based cancer vaccines design.https://mbrc.shirazu.ac.ir/article_3832_83706b8a3fd0efa02ea5715d2357366e.pdfShiraz University PressMolecular Biology Research Communications2322-181X5420161201Isolation and identification of Legionella spp. from different aquatic sources in south-west of Iran by molecular &culture methods215223385810.22099/mbrc.2016.3858ENMohammadTabatabaeiDepartment of Pathobiology, School of Veterinary Medicine, Shiraz University, Shiraz, IranZahraHemmatiDepartment of Pathobiology, School of Veterinary Medicine, Shiraz University, Shiraz, IranMaryam-o-sadatMoezziDepartment of Pathobiology, School of Veterinary Medicine, Shiraz University, Shiraz, IranNegarAzimzadeDepartment of Pathobiology, School of Veterinary Medicine, Shiraz University, Shiraz, IranJournal Article20160305<em>Legionella pneumophila</em>, the causative agent of Legionnaires’ diseases (LD) is usually transmitted to humans via inhalation of aerosols from contaminated natural and manmade water sources. These organisms may become fatal especially in immunocompromised patients and LD is the one of the important disease from a public health perspective. This survey investigated the frequency of <em>Legionella </em>spp. including <em>L. pneumophila</em><em>,</em> in some cold and warm water systems in South-West of Iran by culture and PCR methods. Thirty four water samples were collected from diverse water supply systems. After acid and heat treatments of samples, inoculated onto buffered charcoal yeast extract agar. Isolated colonies were confirmed by morphological and biochemical tests. Then the isolates were examined for <em>icmO</em>, <em>sidA</em> and <em>lidA</em> genes by PCR assay. This study showed that frequency of <em>L. pneumophila</em> was 4 by culture and 14 by PCR. PCR method to be efficient and sensitive test for rapid detection of these organisms in environmental water sources. This study emphasizes the need for effective infection control and prevention strategies to minimize the risk from exposure to potential pathogens such as <em>Legionella </em>spp. and to create a safe working environment.https://mbrc.shirazu.ac.ir/article_3858_b47a7cfffbcd772d816690d39e69035a.pdfShiraz University PressMolecular Biology Research Communications2322-181X5420161201Influence of heparin molecular size on the induction of C-terminal unfolding in β2-microglobulin225232386610.22099/mbrc.2016.3866ENKanonFukasawaDepartment of Chemistry, Kurume University School of Medicine, Kurume, Fukuoka, JapanYuichiroHigashimotoDepartment of Chemistry, Kurume University School of Medicine, Kurume, Fukuoka, JapanYoshihiroMotomiyaSuiyukai Clinic, Kashihara, Nara, JapanYoshinoriUjiDepartment of Medical Technology and Sciences, School of Health Sciences at Fukuoka, International University of Health and Welfare, Okawa, Fukuoka, JapanYukioAndoDepartment of Neurology, Graduate School of Medical Sciences, Kumamoto University, Honjo, Kumamoto, JapanJournal Article20160823Dialysis-related amyloidosis (DRA) is characterized by accumulation of amyloid β<sub>2</sub>-microglobulin (β<sub>2</sub>m) in the interstitial matrix. Matrix substances such as heparin have reportedly been strongly implicated in the pathogenesis of dialysis-related amyloidosis. In clinical setting of hemodialysis, two types of heparin, i.e., high and low molecular heparin (H.M.H. and L.M.H.) have been routinely used. Still commonly used is H.M.H., followed by L.M.H. preparations with distinct advantages. Here, we studied that the interaction of native and two amyloidogenic β<sub>2</sub>m variants: ΔN6β<sub>2</sub>m and D76N β<sub>2</sub>m with H.M.H. and L.M.H. We also investigated whether heparin could induce β<sub>2</sub>m to have an amyloidogenic conformation.Biolayer interferometry revealed that ΔN6β<sub>2</sub>m had a strong reaction and D76N β<sub>2</sub>m had a moderate reaction with H.M.H.. Furthermore, H.M.H. induced the C-terminal unfolding in a native β<sub>2</sub>m. By contrast, L.M.H. showed no reaction even with ΔN6β<sub>2</sub>m.This study showed firstly a direct binding of β<sub>2</sub>m with H.M.H.. H.M.H. would provoked a C-terminal unfolding of β<sub>2</sub>m, which indicated production of an amyloidogenic intermediate, i.e., β<sub>2</sub>m92-99. In addition, our findings also suggest that L.M.H. may provide beneficial effects against the development of the DRA.https://mbrc.shirazu.ac.ir/article_3866_e3deb7382c93556b2b8e5e1c43d317e1.pdfShiraz University PressMolecular Biology Research Communications2322-181X5420161201In silico identification of miRNAs and their target genes and analysis of gene co-expression network in saffron (Crocus sativus L.) stigma233246387510.22099/mbrc.2016.3875ENZahraZinatiAgroecology Department, College of Agriculture and Natural Resources of Darab, Shiraz University, IranRoohollahShamloo-DashtpagerdiCrop Production and Plant Breeding Department, College of Agriculture, Shiraz University, IranAliBehpouriAgroecology Department, College of Agriculture and Natural Resources of Darab, Shiraz University, IranJournal Article20160312As an aromatic and colorful plant of substantive taste, saffron (<em>Crocus sativus</em> L.) owes such properties of matter to growing class of the secondary metabolites derived from the carotenoids, apocarotenoids. Regarding the critical role of microRNAs in secondary metabolic synthesis and the limited number of identified miRNAs in <em>C. sativus</em>, on the other hand, one may see the point how the characterization of miRNAs along with the corresponding target genes in <em>C. sativus </em>might expand our perspectives on the roles of miRNAs in carotenoid/apocarotenoid biosynthetic pathway. A computational analysis was used to identify miRNAs and their targets using EST (Expressed Sequence Tag) library from mature saffron stigmas. Then, a gene co-expression network was constructed to identify genes which are potentially involved in carotenoid/apocarotenoid biosynthetic pathways. EST analysis led to the identification of two putative miRNAs (miR414 and miR837-5p) along with the corresponding stem-looped precursors. To our knowledge, this is the first report on miR414 and miR837-5p in<em> C. sativus</em>. Co-expression network analysis indicated that miR414 and miR837-5p may play roles in <em>C</em><em>. sativus</em> metabolic pathways and led to identification of candidate genes including six transcription factors and one protein kinase probably involved in carotenoid/apocarotenoid biosynthetic pathway. Presence of transcription factors, miRNAs and protein kinase in the network indicated multiple layers of regulation in saffron stigma. The candidate genes from this study may help unraveling regulatory networks underlying the carotenoid/apocarotenoid biosynthesis in saffron and designing metabolic engineering for enhanced secondary metabolites.https://mbrc.shirazu.ac.ir/article_3875_87c248ee1eac36fe4cfcafdd87e2e48d.pdfShiraz University PressMolecular Biology Research Communications2322-181X5420161201Partial and complete microdeletions of Y chromosome in infertile males from South of Iran247255389310.22099/mbrc.2016.3893ENRahelehMasoudiBiology Department, College of Sciences, Shiraz University, Shiraz, IranLiusaMazaheri AsadiBiology Department, College of Sciences, Shiraz University, Shiraz, IranShahryarKhorasaniBiology Department, College of Sciences, Shiraz University, Shiraz, IranJournal Article20160509Y chromosome microdeletions are the second genetic cause of male infertility. The incidence of Y chromosome microdeletions can vary considerably depending on several factors, including patient selection criteria, population composition, and diagnostic protocols. They are associated with spermatogenic failure and lead to azoospermia or oligozoospermia. The advance in assisted reproductive technology and intracytoplasmic sperm injection, and the possibility of genetic defect transmission to the next generation make it necessary to improve our knowledge about the various factors leading to spermatogenic impairment. This study was designed to determine the frequency of microdeletions of Y chromosome in a population from South of Iran. 81 infertile males with non-obstructive azoospermia or oligozoospermia were selected. Multiplex PCR using several STS markers was carried out to detect the complete or partial microdeletions. The frequency of both complete and partial microdeletions in men with azoospermia or severe oligozoospermia was 7.4%. All microdeletions were observed in AZFc region. There was 1.25% complete microdeletions and after excluding complete microdeletions, we detected 5% gr/gr and 1.25% b2/b3 microdeletions. In our control group of fertile males, 4% gr/gr microdeletions was detected while there was no b2/b3 microdeletions. We concluded that there is a low frequency of Y chromosome microdeletions in a population of infertile males from South of Iran. b2/b3 microdeletions was detected only in infertile males and not in the control group. Screening a population with larger sample size is necessary to determine the involvement of this partial microdeletion in infertility of this population.https://mbrc.shirazu.ac.ir/article_3893_ac453e5eec75fa36e0797d74c9d22839.pdfShiraz University PressMolecular Biology Research Communications2322-181X5420161201Impact of heat shock step on bacterial transformation efficiency257261391510.22099/mbrc.2016.3915ENMaralRahimzadehDepartment of Nanobiotechnology, School of Biological Sciences, Tarbiat Modares University, Tehran, IranMajidSadeghizadehDepartment of Molecular Genetics, School of Biological Sciences, Tarbiat Modares University, Tehran, IranFarhoodNajafiDepartment of Resin and Additives, Institute for Color Science and Technology, Tehran, IranShahriarArabDepartment of Biophysics, School of Biological Sciences, Tarbiat Modares University, Tehran, IranHamidMobasheriLaboratory of Membrane Biophysics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, IranJournal Article20160901CaCl<sub>2</sub> treatment followed by heat shock is the most common method for artificial transformation. Here, the cells were transformed using CaCl<sub>2 </sub>treatment either with heat shock (standard protocol) or without heat shock (lab protocol) to comprehend the difference in transformation efficiency. The BL21 strain of <em>Escherichia coli</em> (<em>E. coli</em>) was being susceptible using CaCl<sub>2 </sub>treatment. Some Cells were kept at -80 <sup>o</sup>C while the others were kept at 4 ̊C. Afterwards the susceptible cells were transformed using either standard or lab protocol. The transformation efficiency between cells experienced heat shock and those were not influenced by heat shock was almost the same. Moreover, regardless of transformation protocol, the cells kept at 4 ̊C were transformed more efficiently in compared to those were kept at -80 <sup>o</sup>C.https://mbrc.shirazu.ac.ir/article_3915_c33553c369e007f356bf1a28e6f7df87.pdf