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Bayat H, Farahmand F, Tabatabaee SH, Shams F, Mohammadian O, Pourmaleki E, Rahimpour A. Evaluation of the paired-Cas9 nickase and RNA-guided FokI genome editing tools in precise integration of an anti-CD52 bicistronic monoclonal antibody expression construct at Chinese hamster ovary cells 18S rDNA locus. Protein Expr Purif 2024; 217:106445. [PMID: 38342386 DOI: 10.1016/j.pep.2024.106445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 01/08/2024] [Accepted: 02/08/2024] [Indexed: 02/13/2024]
Abstract
INTRODUCTION The aim of this study was to compare two CRISPR/Cas9-based orthogonal strategies, paired-Cas9 nickase (paired-Cas9n) and RNA-guided FokI (RFN), in targeting 18S rDNA locus in Chinese hamster ovary (CHO) cells and precisely integrating a bicistronic anti-CD52 monoclonal antibody (mAb) expression cassette into this locus. METHODS T7E1 and high-resolution melt (HRM) assays were used to compare the ability of mentioned systems in inducing double-strand break (DSB) at the target site. Moreover, 5'- and 3'-junction polymerase chain reactions (PCR) were used to verify the accuracy of the targeted integration of the mAb expression cassette into the 18S rDNA locus. Finally, anti-CD52 mAb gene copy number was measured and, its expression was analyzed using ELISA and western blot assays. RESULTS Our results indicated that both paired-Cas9n and RFN induced DSB at the target site albeit RFN performance was slightly more efficient in HRM analysis. We also confirmed that the anti-CD52 mAb cassette was accurately integrated at the 18S rDNA locus and the mAb was expressed successfully in CHO cells. CONCLUSION Taken together, our findings elucidated that both paired-Cas9n and RFN genome editing tools are promising in targeting the 18S rDNA locus. Site specific integration of the bicistronic anti-CD52 mAb expression cassette at this locus in the CHO-K1 cells was obtained, using RFN. Moreover, proper expression of the anti-CD52 mAb at the 18S rDNA target site can be achieved using the bicistronic internal ribosome entry site (IRES)-based vector system.
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Affiliation(s)
- Hadi Bayat
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Faranak Farahmand
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Sayed Hassan Tabatabaee
- Department of Life Science Engineering, Faculty of New Sciences and Technology, University of Tehran, Tehran, Iran
| | - Forough Shams
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Omid Mohammadian
- Department of Clinical Biochemistry, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Es'hagh Pourmaleki
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Azam Rahimpour
- Medical Nanotechnology and Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Madavani AN, Shahbazi M, Bayat H. A meta-analysis on the relationship between media with violence and aggression in Iranian sports. J Ethn Subst Abuse 2024:1-25. [PMID: 38497730 DOI: 10.1080/15332640.2023.2288823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
The present research aimed to conduct a systematic study on violence and aggression in the context of Iranian sports and perform a meta-analysis to investigate the association between the media and violence and aggression in sports. The research encompassed all relevant studies available in scientific databases within Iran (such as Magiran, Seyed, Civilica, Normagz, Humane resource study, and police publications), as well as dissertations from the information and scientific documents database. The selected timeframe for this analysis covered the years 2001 to 2018 in the Iranian context. Through this process, 209 studies related to the subject were identified, out of which 10 studies were included in the meta-analysis based on the research protocol investigating the relationship between media and violence and aggression in sports. Data analysis was performed using SPSS25 and CMA2 software. The results showed several variables played prominent roles in the researches on violence and aggression in sports, including media performance, referees' performance, stadium amenities, law enforcement and security factors, external and internal stadium environment, coach's behavior, social control, family influence, education, socio-economic factors, substance abuse, players' behavior, influence of friends, managerial aspects, and cultural and political factors. Inferential statistics indicated effect size for the relationship between media and violence and aggression, under the fixed model, was determined to be 0.259, and under the random model, it was 0.306, both of which were statistically significant. Consequently, based on the findings from the meta-analysis, a significant direct relationship between media and violence and aggression in sports was established.
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Affiliation(s)
- Abbas Nazarian Madavani
- Department of Sport Management, Faculty of Sport Sciences, Shahid Rajaee Teacher Training University, Tehran, Iran
| | - Masumeh Shahbazi
- Department of Sport Management, Faculty of Sport Sciences, Shahid Rajaee Teacher Training University, Tehran, Iran
| | - Hadi Bayat
- Department of Sport Management, Faculty of Sport Sciences, Shahid Rajaee Teacher Training University, Tehran, Iran
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Arabfard M, Tajeddin N, Alizadeh S, Salesi M, Bayat H, Khorram Khorshid HR, Khamse S, Delbari A, Ohadi M. Dyads of GGC and GCC form hotspot colonies that coincide with the evolution of human and other great apes. BMC Genom Data 2024; 25:21. [PMID: 38383300 PMCID: PMC10880355 DOI: 10.1186/s12863-024-01207-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 02/11/2024] [Indexed: 02/23/2024] Open
Abstract
BACKGROUND GGC and GCC short tandem repeats (STRs) are of various evolutionary, biological, and pathological implications. However, the fundamental two-repeats (dyads) of these STRs are widely unexplored. RESULTS On a genome-wide scale, we mapped (GGC)2 and (GCC)2 dyads in human, and found monumental colonies (distance between each dyad < 500 bp) of extraordinary density, and in some instances periodicity. The largest (GCC)2 and (GGC)2 colonies were intergenic, homogeneous, and human-specific, consisting of 219 (GCC)2 on chromosome 2 (probability < 1.545E-219) and 70 (GGC)2 on chromosome 9 (probability = 1.809E-148). We also found that several colonies were shared in other great apes, and directionally increased in density and complexity in human, such as a colony of 99 (GCC)2 on chromosome 20, that specifically expanded in great apes, and reached maximum complexity in human (probability 1.545E-220). Numerous other colonies of evolutionary relevance in human were detected in other largely overlooked regions of the genome, such as chromosome Y and pseudogenes. Several of the genes containing or nearest to those colonies were divergently expressed in human. CONCLUSION In conclusion, (GCC)2 and (GGC)2 form unprecedented genomic colonies that coincide with the evolution of human and other great apes. The extent of the genomic rearrangements leading to those colonies support overlooked recombination hotspots, shared across great apes. The identified colonies deserve to be studied in mechanistic, evolutionary, and functional platforms.
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Affiliation(s)
- M Arabfard
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - N Tajeddin
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
- Department of Biology, Central Tehran Branch, Islamic Azad University, Tehran, Iran
| | - S Alizadeh
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - M Salesi
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
- Research Center for Prevention of Oral and Dental Diseases, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - H Bayat
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - H R Khorram Khorshid
- Personalized Medicine and Genometabolomics Research Center, Hope Generation Foundation, Tehran, Iran
| | - S Khamse
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - A Delbari
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - M Ohadi
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
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Bayat H, Mirahmadi M, Azarshin Z, Ohadi H, Delbari A, Ohadi M. CRISPR/Cas9-mediated deletion of a GA-repeat in human GPM6B leads to disruption of neural cell differentiation from NT2 cells. Sci Rep 2024; 14:2136. [PMID: 38273037 PMCID: PMC10810867 DOI: 10.1038/s41598-024-52675-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 01/22/2024] [Indexed: 01/27/2024] Open
Abstract
The human neuron-specific gene, GPM6B (Glycoprotein membrane 6B), is considered a key gene in neural cell functionality. This gene contains an exceptionally long and strictly monomorphic short tandem repeat (STR) of 9-repeats, (GA)9. STRs in regulatory regions, may impact on the expression of nearby genes. We used CRISPR-based tool to delete this GA-repeat in NT2 cells, and analyzed the consequence of this deletion on GPM6B expression. Subsequently, the edited cells were induced to differentiate into neural cells, using retinoic acid (RA) treatment. Deletion of the GA-repeat significantly decreased the expression of GPM6B at the RNA (p < 0.05) and protein (40%) levels. Compared to the control cells, the edited cells showed dramatic decrease of the astrocyte and neural cell markers, including GFAP (0.77-fold), TUBB3 (0.57-fold), and MAP2 (0.2-fold). Subsequent sorting of the edited cells showed an increased number of NES (p < 0.01), but a decreased number of GFAP (p < 0.001), TUBB3 (p < 0.05), and MAP2 (p < 0.01), compared to the control cells. In conclusion, CRISPR/Cas9-mediated deletion of a GA-repeat in human GPM6B, led to decreased expression of this gene, which in turn, disrupted differentiation of NT2 cells into neural cells.
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Affiliation(s)
- Hadi Bayat
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Postal Code: 1985713834, Iran
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Postal Box: 331-14115, Tehran, Iran
| | - Maryam Mirahmadi
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Postal Box: 331-14115, Tehran, Iran
- Department of Exomine, PardisGene Company, Tehran, Postal Code: 1917635816, Iran
| | - Zohreh Azarshin
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Postal Box: 331-14115, Tehran, Iran
| | - Hamid Ohadi
- School of Physics and Astronomy, University of St Andrews, St Andrews, KY16 9SS, UK
| | - Ahmad Delbari
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Postal Code: 1985713834, Iran
| | - Mina Ohadi
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Postal Code: 1985713834, Iran.
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Abeyratne WMLK, Bayat H, Munasinghe-Arachchige SP, Zhang Y, Brewer CE, Nirmalakhandan N. Feasibility of ammonium sulfate recovery from wastewater sludges: Hydrothermal liquefaction pathway vs. anaerobic digestion pathway. J Environ Manage 2023; 347:119075. [PMID: 37769474 DOI: 10.1016/j.jenvman.2023.119075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/14/2023] [Accepted: 08/30/2023] [Indexed: 09/30/2023]
Abstract
This study evaluated two pathways to recover the nitrogen-content of wastewater sludges as ammonium sulfate (AmS) for use as fertilizer. The first pathway entails sludge stabilization by hydrothermal liquefaction (HTL) followed by recovery of AmS from the resulting aqueous product by gas permeable membrane (GPM) separation. The second one entails stabilization of the sludges by anaerobic digestion (AD) followed by recovery of AmS from the resulting centrate by GPM separation. A bench-scale GPM reactor is shown to be capable of recovering >90% of N in the feed. Recoveries of NH3-N in the HTL-pathway ranged 96-100% in 5.5-7.5 h at mass removal rates of 0.2-0.3 g N/day, yielding 3.3-6.0 g AmS/L of feed. Recoveries of 98% were noted in the AD-pathway in 4 h at mass removal rates of 0.06-0.97 g N/day and a yield of 1.7-2.1 g AmS/L of feed. Inductively coupled plasma optical emission spectrometer analysis confirmed that both pathways yielded AmS meeting the US EPA and European region guidelines for land application. The GPM reactor enabled higher nitrogen-recoveries in the HTL-pathway than those reported for current practice of AD followed by ammonia stripping, ion exchange, reverse osmosis, and/or struvite precipitation (96-100% vs. 50-90%). A process model for the GPM reactor is validated using performance data on three different feedstocks.
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Affiliation(s)
- W M L K Abeyratne
- Dept. of Civil Engineering New Mexico State University, Las Cruces, NM, 88003, USA
| | - H Bayat
- Dept. of Chemical & Materials Engineering, New Mexico State University, Las Cruces, NM, 88003, USA
| | | | - Y Zhang
- Dept. of Civil Engineering New Mexico State University, Las Cruces, NM, 88003, USA
| | - C E Brewer
- Dept. of Chemical & Materials Engineering, New Mexico State University, Las Cruces, NM, 88003, USA
| | - N Nirmalakhandan
- Dept. of Civil Engineering New Mexico State University, Las Cruces, NM, 88003, USA.
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Bayat H, Pourgholami MH, Rahmani S, Pournajaf S, Mowla SJ. Synthetic miR-21 decoy circularized by tRNA splicing mechanism inhibited tumorigenesis in glioblastoma in vitro and in vivo models. Mol Ther Nucleic Acids 2023; 32:432-444. [PMID: 37181451 PMCID: PMC10173299 DOI: 10.1016/j.omtn.2023.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 04/04/2023] [Indexed: 05/16/2023]
Abstract
Glioblastoma multiforme (GBM) is the deadliest primary central nervous system tumor. miRNAs (miRs), a class of non-coding RNAs, are considered pivotal post-transcriptional regulators of cell signaling pathways. miR-21 is a reliable oncogene that promotes tumorigenesis of cancer cells. We first performed an in silico analysis on 10 microarray datasets retrieved from TCGA and GEO databases to elucidate top differentially expressed miRs. Furthermore, we generated a circular miR-21 decoy, CM21D, using the tRNA-splicing mechanism in GBM cell models, U87 and C6. The inhibitory efficacy of CM21D with that of a linear form, LM21D, was compared under in vitro conditions and an intracranial C6 rat glioblastoma model. miR-21 significantly overexpressed in GBM samples and confirmed in GBM cell models using qRT-PCR. CM21D was more efficient than LM21D at inducing apoptosis, inhibiting cell proliferation and migration, and interrupting the cell cycle by restoring the expression of miR-21 target genes at RNA and protein levels. Moreover, CM21D suppressed tumor growth more effectively than LM21D in the C6-rat GBM model (p < 0.001). Our findings validate miR-21 as a promising therapeutic target for GBM. The introduced CM21D by sponging miR-21 reduced tumorigenesis of GBM and can be considered a potential RNA-base therapy to inhibit cancers.
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Affiliation(s)
- Hadi Bayat
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-111, Iran
| | | | - Saeid Rahmani
- School of Computer Science, Institute for Research in Fundamental Sciences (IPM), Tehran 19538-33511, Iran
| | - Safura Pournajaf
- Department of Physiology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran 14115-111, Iran
| | - Seyed Javad Mowla
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-111, Iran
- Corresponding author: Seyed Javad Mowla, Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-111, Iran.
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Shams F, Moravvej H, Hosseinzadeh S, Mostafavi E, Bayat H, Kazemi B, Bandehpour M, Rostami E, Rahimpour A, Moosavian H. Overexpression of VEGF in dermal fibroblast cells accelerates the angiogenesis and wound healing function: in vitro and in vivo studies. Sci Rep 2022; 12:18529. [PMID: 36323953 PMCID: PMC9630276 DOI: 10.1038/s41598-022-23304-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 10/29/2022] [Indexed: 12/13/2022] Open
Abstract
Fibroblasts are the main cells of connective tissue and have pivotal roles in the proliferative and maturation phases of wound healing. These cells can secrete various cytokines, growth factors, and collagen. Vascular endothelial growth factor (VEGF) is a unique factor in the migration process of fibroblast cells through induces wound healing cascade components such as angiogenesis, collagen deposition, and epithelialization. This study aimed to create VEGF165 overexpressing fibroblast cells to evaluate angiogenesis function in wound healing. In vitro, a novel recombinant expression vector, pcDNA3.1(-)-VEGF, was produced and transfected into the fibroblast cells. Following selecting fibroblast cells with hygromycin, recombinant cells were investigated in terms of VEGF expression by quantifying and qualifying methods. Mechanical, physical, and survival properties of polyurethane-cellulose acetate (PU-CA) scaffold were investigated. Finally, in vivo, the angiogenic potential was evaluated in four groups containing control, PU-CA, PU-CA with fibroblast cells, and VEGF-expressing cells on days 0, 2, 5, 12 and 15. Wound biopsies were harvested and the healing process was histopathologically evaluated on different days. qRT-PCR showed VEGF overexpression (sevenfold) in genetically-manipulated cells compared to fibroblast cells. Recombinant VEGF expression was also confirmed by western blotting. Manipulated fibroblast cells represented more angiogenesis than other groups on the second day after surgery, which was also confirmed by the antiCD31 antibody. The percentage of wound closure area on day 5 in genetically-manipulated Hu02 and Hu02 groups showed a significant reduction of wound area compared to other groups. These findings indicate that overexpression of VEGF165 in fibroblast cells results in enhanced angiogenesis and formation of granulated tissue in the early stage of the healing process, which can show its therapeutic potential in patients with impaired wound healing and also provide functional support for gene therapy.
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Affiliation(s)
- Forough Shams
- grid.411600.2Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamideh Moravvej
- grid.411600.2Skin Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Simzar Hosseinzadeh
- grid.411600.2Medical Nanotechnology and Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran ,grid.411600.2Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ebrahim Mostafavi
- grid.168010.e0000000419368956Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA USA ,grid.168010.e0000000419368956Department of Medicine, Stanford University School of Medicine, Stanford, CA USA
| | - Hadi Bayat
- grid.411600.2Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran ,grid.412266.50000 0001 1781 3962Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Bahram Kazemi
- grid.411600.2Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mojgan Bandehpour
- grid.411600.2Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Elnaz Rostami
- grid.412502.00000 0001 0686 4748Department of Animal Sciences and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Azam Rahimpour
- grid.411600.2Medical Nanotechnology and Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran ,grid.411600.2Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamidreza Moosavian
- grid.46072.370000 0004 0612 7950Department of Clinical Pathology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
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Shams F, Bayat H, Mohammadian O, Mahboudi S, Vahidnezhad H, Soosanabadi M, Rahimpour A. Advance trends in targeting homology-directed repair for accurate gene editing: An inclusive review of small molecules and modified CRISPR-Cas9 systems. Bioimpacts 2022; 12:371-391. [PMID: 35975201 PMCID: PMC9376165 DOI: 10.34172/bi.2022.23871] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 11/21/2021] [Accepted: 11/21/2021] [Indexed: 11/25/2022]
Abstract
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Introduction: Clustered regularly interspaced short palindromic repeat and its associated protein (CRISPR-Cas)-based technologies generate targeted modifications in host genome by inducing site-specific double-strand breaks (DSBs) that can serve as a substrate for homology-directed repair (HDR) in both in vitro and in vivo models. HDR pathway could enhance incorporation of exogenous DNA templates into the CRISPR-Cas9-mediated DSB site. Owing to low rate of HDR pathway, the efficiency of accurate genome editing is diminished. Enhancing the efficiency of HDR can provide fast, easy, and accurate technologies based on CRISPR-Cas9 technologies.
Methods: The current study presents an overview of attempts conducted on the precise genome editing strategies based on small molecules and modified CRISPR-Cas9 systems.
Results: In order to increase HDR rate in targeted cells, several logical strategies have been introduced such as generating CRISPR effector chimeric proteins, anti-CRISPR proteins, modified Cas9 with donor template, and using validated synthetic or natural small molecules for either inhibiting non-homologous end joining (NHEJ), stimulating HDR, or synchronizing cell cycle. Recently, high-throughput screening methods have been applied for identification of small molecules which along with the CRISPR system can regulate precise genome editing through HDR.
Conclusion: The stimulation of HDR components or inhibiting NHEJ can increase the accuracy of CRISPR-Cas-mediated engineering systems. Generating chimeric programmable endonucleases provide this opportunity to direct DNA template close proximity of CRISPR-Cas-mediated DSB. Small molecules and their derivatives can also proficiently block or activate certain DNA repair pathways and bring up novel perspectives for increasing HDR efficiency, especially in human cells. Further, high throughput screening of small molecule libraries could result in more discoveries of promising chemicals that improve HDR efficiency and CRISPR-Cas9 systems.
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Affiliation(s)
- Forough Shams
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hadi Bayat
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Omid Mohammadian
- Medical Nano-Technology and Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Somayeh Mahboudi
- Department of Food Science and Technology, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Hassan Vahidnezhad
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
- Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA, USA
| | - Mohsen Soosanabadi
- Department of Medical Genetics, Semnan University of Medical Sciences, Semnan, Iran
| | - Azam Rahimpour
- Medical Nano-Technology and Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Torkamandi S, Bahrami S, Ghorashi T, Dehani M, Bayat H, Hoseini SM, Rezaei S, Soosanabadi M. Dysregulation of long noncoding RNA MEG3 and NLRC5 expressions in patients with relapsing-remitting multiple sclerosis: is there any correlation? Genes Immun 2021; 22:322-326. [PMID: 34782775 DOI: 10.1038/s41435-021-00154-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/27/2021] [Accepted: 11/02/2021] [Indexed: 12/14/2022]
Abstract
Long noncoding RNA MEG3 and NLRC5 genes are both involved in the immune system and the regulation of NLRC5 by MEG3 is documented in rheumatoid arthritis. Therefore, we intended to evaluate the association between the expressions of MEG3 and NLRC5 in multiple sclerosis (MS). Forty relapsing and remitting MS (RRMS) patients (20 in each group) and twenty healthy individuals were enrolled. The expression level of MEG3 and NLRC5 was assessed in peripheral blood mononuclear cells. Sub-group analysis demonstrated that the expression level of MEG3 is reduced in the relapse patient group compared to remission and healthy groups (p < 0.001). The expression level of NLRC5 was higher in whole patients compared with healthy controls (p < 0.05). Moreover, a negative correlation was observed between the expression of these two genes (r = -0.73, p < 0.0001). To conclude, our findings showed the dysregulation of MEG3 and NLRC5 expressions in RRMS patients. Also, the converse association of MEG3 and NLRC5 reflects that the role of MEG3 in MS development is probably mediated by modulation of NLRC5.
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Affiliation(s)
- Shahram Torkamandi
- Department of Medical Genetics and Immunology, Faculty of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Shima Bahrami
- Department of Medical Genetics, Semnan University of Medical Sciences, Semnan, Iran
| | - Tahereh Ghorashi
- Department of Medical Genetics, Semnan University of Medical Sciences, Semnan, Iran
| | - Mohammad Dehani
- Department of Medical Genetics, Semnan University of Medical Sciences, Semnan, Iran
| | - Hadi Bayat
- Medical Nano-Technology & Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Molecular genetics, Faculty of biological sciences, Tarbiat modares university, Tehran, Iran.,Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Somaye Rezaei
- Department of Neurology, Imam Khomeini Hospital, Urmia University of Medical Sciences, Urmia, Iran.,Department of Neurology, Imam Hossein Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohsen Soosanabadi
- Department of Medical Genetics, Semnan University of Medical Sciences, Semnan, Iran.
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Hassani M, Dehani M, Zare Rafie M, Esmaeilzadeh E, Davar S, Pakzad B, Mosallaei M, Hoseini SM, Bayat H, Soosanabadi M. Investigation of rs531564 Polymorphism in the Primary MicroRNA-124 Gene in Patients with Systemic Lupus Erythematosus and Rheumatoid Arthritis: Association with Disease Susceptibility and Clinical Characteristics. Iran J Allergy Asthma Immunol 2021; 20:303-313. [PMID: 34134452 DOI: 10.18502/ijaai.v20i3.6336] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 05/19/2021] [Indexed: 11/24/2022]
Abstract
MicroRNA-124 (miR-124) is known as an important regulator of the immune system and inflammatory response. Studies have reported that this miRNA is dysregulated in autoimmune disorders such as systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA). A functional analysis demonstrated that rs531564 (C>G) affects the biogenesis of primary microRNA transcript-124 (pri-miR-124) and changes the expression of mature miR-124. In the present study, for the first time, we intended to evaluate the possible association between rs531564 polymorphism with SLE and RA risk. In this case-control study, 110 patients with SLE, 115 patients with RA, and 120 healthy subjects were enrolled to evaluate rs531564 genotypes with real-time polymerase chain reaction (PCR) high resolution melting method. Our findings demonstrated that frequency of GC genotype and G allele were considerably higher in the control group than RA patients, demonstrating that that GC genotype and G allele have a protective effect for healthy individuals (GC vs CC; OR: 0.29; 95%CI [0.12,0.67] and G vs C; OR: 0.42; 95%CI [0.23,0.78]). However, no significant correlation was confirmed between allele and genotype frequencies of rs531564 with SLE risk (p>0.05). However, the G allele in rs531564 polymorphism was associated with serum level of C-reactive protein (CRP), erythrocyte sedimentation rate (ESR), anti-dsDNA antibody, C3, C4, and creatinine, and frequency of renal involvements in SLE patients (p<0.05). Moreover, in RA patients, the G was correlated with lower concentration ESR and CRP (p<0.001). Our findings propose a considerable association between rs531564 polymorphism in the pri-miR-124 gene with susceptibility and clinical characteristics of RA and SLE in the Iranian population.
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Affiliation(s)
- Mehdi Hassani
- School of Medicine, Aja University of Medical Science, Tehran, Iran.
| | - Mohammad Dehani
- School of Medicine, Aja University of Medical Science, Tehran, Iran.
| | - Maryam Zare Rafie
- School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran.
| | | | - Saeideh Davar
- Department of Epidemiology and Biostatistics, School of Medicine, Urmia University of Medical Sciences, Urmia, Iran.
| | - Bahram Pakzad
- Division of Rheumatology, Department of Internal Medicine, School of Medicine, Isfahan University of Medical Science, Isfahan, Iran..
| | - Meysam Mosallaei
- School of Medicine, Aja University of Medical Science, Tehran, Iran.
| | | | - Hadi Bayat
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran AND Medical Nano-Technology and Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mohsen Soosanabadi
- Department of Medical Genetics, Semnan University of Medical Sciences, Semnan, Iran.
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Salmaninejad A, Jafari Abarghan Y, Bozorg Qomi S, Bayat H, Yousefi M, Azhdari S, Talebi S, Mojarrad M. Common therapeutic advances for Duchenne muscular dystrophy (DMD). Int J Neurosci 2020; 131:370-389. [DOI: 10.1080/00207454.2020.1740218] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Arash Salmaninejad
- Halal Research Center of IRI, FDA, Tehran, Iran
- Medical Genetics Research Center, Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Yousef Jafari Abarghan
- Medical Genetics Research Center, Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Saeed Bozorg Qomi
- Medical Genetics Research Center, Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hadi Bayat
- Medical Nano-Technology & Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Meysam Yousefi
- Department of Medical Genetics Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Sara Azhdari
- Department of Anatomy and Embryology, School of Medicine, Bam University of Medical Sciences, Bam, Iran
| | - Samaneh Talebi
- Medical Genetics Research Center, Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Majid Mojarrad
- Medical Genetics Research Center, Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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Mohammadian O, Rajabibazl M, Pourmaleki E, Bayat H, Ahani R, Rahimpour A. Development of an improved lentiviral based vector system for the stable expression of monoclonal antibody in CHO cells. Prep Biochem Biotechnol 2019; 49:822-829. [PMID: 31156045 DOI: 10.1080/10826068.2019.1621893] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Therapeutic monoclonal antibodies (mAbs) have become the dominant products in biopharmaceutical industry. Mammalian cell expression systems including Chinese hamster ovary (CHO) cells are the most commonly used hosts for the production of complex recombinant proteins. However, development of stable, high producing CHO cell lines suffers from the low expression level and instability of the transgene. The increasing efforts in the development of novel therapeutic antibodies and the advent of biosimilars have revealed the necessity for the development of improved platforms for rapid production of products for initial characterization and testing. In line with this premise, vector design and engineering has been applied to improve the expression level and stability of the transgene. This study reports the application of an improved lentiviral vector system containing the human interferon-β scaffold attachment region (IFN-SAR) for the development of antibody producing stable CHO cells. mAb expressing clones producing 1100 µg/L of IgG1 monoclonal antibody were isolated without extensive screening of a large number of clones. Our results here indicate the positive effects of IFN-SAR on stable mAb expression using lentiviral based expression vectors. We also observed that although IFN-SAR can improve light chain (LC) and heavy chain (HC) gene copy numbers in stable cell pools, mAb expression in single cell clones was not affected by the transgene copy number.
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Affiliation(s)
- Omid Mohammadian
- a Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences , Tehran , Iran
| | - Masoumeh Rajabibazl
- a Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences , Tehran , Iran.,b Nano-Technology and Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences , Tehran , Iran
| | - Es'hagh Pourmaleki
- b Nano-Technology and Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences , Tehran , Iran.,c Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences , Tehran , Iran
| | - Hadi Bayat
- b Nano-Technology and Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences , Tehran , Iran.,d Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University , Tehran , Iran
| | - Roshanak Ahani
- b Nano-Technology and Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences , Tehran , Iran
| | - Azam Rahimpour
- b Nano-Technology and Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences , Tehran , Iran.,c Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences , Tehran , Iran
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Bayat H, Naderi F, Khan AH, Memarnejadian A, Rahimpour A. The Impact of CRISPR-Cas System on Antiviral Therapy. Adv Pharm Bull 2018; 8:591-597. [PMID: 30607331 PMCID: PMC6311650 DOI: 10.15171/apb.2018.067] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 09/08/2018] [Accepted: 09/29/2018] [Indexed: 12/16/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein nuclease (Cas) is identified as an adaptive immune system in archaea and bacteria. Type II of this system, CRISPR-Cas9, is the most versatile form that has enabled facile and efficient targeted genome editing. Viral infections have serious impacts on global health and conventional antiviral therapies have not yielded a successful solution hitherto. The CRISPR-Cas9 system represents a promising tool for eliminating viral infections. In this review, we highlight 1) the recent progress of CRISPR-Cas technology in decoding and diagnosis of viral outbreaks, 2) its applications to eliminate viral infections in both pre-integration and provirus stages, and 3) various delivery systems that are employed to introduce the platform into target cells.
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Affiliation(s)
- Hadi Bayat
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Fatemeh Naderi
- Department of Molecular Genetics, Tehran Medical Sciences Branch, Islamic Azad University, Tehran, Iran
| | - Amjad Hayat Khan
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Penang, Malaysia
| | | | - Azam Rahimpour
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Naderi F, Hashemi M, Bayat H, Mohammadian O, Pourmaleki E, Etemadzadeh MH, Rahimpour A. The Augmenting Effects of the tDNA Insulator on Stable Expression of Monoclonal Antibody in Chinese Hamster Ovary Cells. Monoclon Antib Immunodiagn Immunother 2018; 37:200-206. [DOI: 10.1089/mab.2018.0015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Fatemeh Naderi
- Department of Genetics, Tehran Medical Branch, Islamic Azad University, Tehran, Iran
| | - Mehrdad Hashemi
- Department of Genetics, Tehran Medical Branch, Islamic Azad University, Tehran, Iran
| | - Hadi Bayat
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Omid Mohammadian
- Department of Clinical Biochemistry, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Es'hagh Pourmaleki
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Azam Rahimpour
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Abstract
Background: Monoclonal antibodies (mAbs) are considered the most important and financially successful category of the biopharmaceuticals. Extensive optimization of the expression vector, host system and culture parameters are required for the successful production of active monoclonal antibodies in mammalian cells. In this regards, transient expression enables rapid and cost-effective production of recombinant proteins for initial characterization. Methods: In the present study, an internal ribosome entry site (IRES) based bicistronic expression system has been evaluated for the transient expression of an anti-CD52 monoclonal antibody in mammalian cells. The IRES based bicistronic vector was generated through sequential cloning of the Light chain (LC), IRES, and Heavy chain (HC) in an intermediate vector and transfer of the resulting fragment to the expression vector. Transfection of the HEK293T cells was performed and antibody expression was analyzed in cell culture supernatant. Results: Restriction enzyme analysis indicated successful cloning of the antibody coding unit in the expression vector. Analysis of EGFP expression indicated successful transfection of the HEK293T cells. Production levels of 220 µg/L of antibody were achieved in HEK293T cells during three days of culture. Conclusion: Our results show the convenience and efficiency of the bicistronic expression system for transient expression of the whole monoclonal antibodies in mammalian cells.
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Affiliation(s)
- Omid Mohammadian
- Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Masoumeh Rajabibazl
- Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hadi Bayat
- Nano-Technology and Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Azam Rahimpour
- Nano-Technology and Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Bayat H, Hossienzadeh S, Pourmaleki E, Ahani R, Rahimpour A. Evaluation of different vector design strategies for the expression of recombinant monoclonal antibody in CHO cells. Prep Biochem Biotechnol 2018; 48:160-164. [DOI: 10.1080/10826068.2017.1421966] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Hadi Bayat
- Medical Nano-Technology and Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Saghar Hossienzadeh
- Medical Nano-Technology and Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Eśhagh Pourmaleki
- Medical Nano-Technology and Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Roshanak Ahani
- Department of Virology, Pasteur Institute of Iran, Tehran, Iran
| | - Azam Rahimpour
- Medical Nano-Technology and Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Salmaninejad A, Valilou SF, Bayat H, Ebadi N, Daraei A, Yousefi M, Nesaei A, Mojarrad M. Duchenne muscular dystrophy: an updated review of common available therapies. Int J Neurosci 2018; 128:854-864. [PMID: 29351004 DOI: 10.1080/00207454.2018.1430694] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
BACKGROUND AND PURPOSE Duchenne muscular dystrophy (DMD) is a lethal progressive pediatric muscle disorder and genetically inherited as an X-linked disease that caused by mutations in the dystrophin gene. DMD leads to progressive muscle weakness, degeneration, and wasting; finally, follows with the premature demise in affected individuals due to respiratory and/or cardiac failure typically by age of 30. For decades, scientists tried massively to find an effective therapy method, but there is no absolute cure currently for patients with DMD, nevertheless, recent advanced progressions on the treatment of DMD will be hopeful in the future. Several promising gene therapies are currently under investigation. These include gene replacement, exon skipping, suppression of stop codons. More recently, a promising gene editing tool referred to as CRISPR/Cas9 offers exciting perspectives for restoring dystrophin expression in patients with DMD. This review intents to briefly describe these methods and comment on their advances. Since DMD is a genetic disorder, it should be treated by replacing the deficient DMD copy with a functional one. However, there are different types of mutations in this gene, so such therapeutic approaches are highly mutation specific and thus are personalized. Therefore, DMD has arisen as a model of genetic disorder for understanding and overcoming of the challenges of developing personalized genetic medicines, consequently, the lessons learned from these approaches will be applicable to many other disorders. CONCLUSIONS This review provides an update on the recent gene therapies for DMD that aim to compensate for dystrophin deficiency and the related clinical trials.
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Affiliation(s)
- Arash Salmaninejad
- a Drug Applied Research Center , Tabriz University of Medical Sciences , Tabriz , Iran.,b Student Research Committee, Department of Medical Genetics, Faculty of Medicine , Mashhad University of Medical Sciences , Mashhad , Iran.,c Medical Genetics Research Center, Faculty of Medicine , Mashhad University of Medical Sciences , Mashhad , Iran
| | - Saeed Farajzadeh Valilou
- d Medical Genetics Network (MeGeNe) , Universal Scientific Education and Research Network (USERN) , Tehran , Iran
| | - Hadi Bayat
- e Department of Tissue Engineering, School of Advanced Technologies in Medicine , Shahid Beheshti University of Medical Sciences , Tehran , Iran
| | - Nader Ebadi
- f Department of Medical Genetics, Faculty of Medicine , Tehran University of Medical Science , Tehran , Iran
| | - Abdolreza Daraei
- g Genetic Department, Faculty of Medicine , Babol University of Medical Sciences , Babol , Iran
| | - Meysam Yousefi
- b Student Research Committee, Department of Medical Genetics, Faculty of Medicine , Mashhad University of Medical Sciences , Mashhad , Iran.,c Medical Genetics Research Center, Faculty of Medicine , Mashhad University of Medical Sciences , Mashhad , Iran
| | - Abolfazl Nesaei
- h Department of Basic Sciences, Faculty of Medicine , Gonabad University of Medical Sciences , Gonabad , Iran
| | - Majid Mojarrad
- b Student Research Committee, Department of Medical Genetics, Faculty of Medicine , Mashhad University of Medical Sciences , Mashhad , Iran.,c Medical Genetics Research Center, Faculty of Medicine , Mashhad University of Medical Sciences , Mashhad , Iran
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Bayat H, Omidi M, Rajabibazl M, Sabri S, Rahimpour A. The CRISPR Growth Spurt: from Bench to Clinic on Versatile Small RNAs. J Microbiol Biotechnol 2017; 27:207-218. [DOI: 10.4014/jmb.1607.07005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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Khan AH, Bayat H, Rajabibazl M, Sabri S, Rahimpour A. Humanizing glycosylation pathways in eukaryotic expression systems. World J Microbiol Biotechnol 2016; 33:4. [DOI: 10.1007/s11274-016-2172-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Accepted: 11/04/2016] [Indexed: 01/27/2023]
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20
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Soosanabadi M, Bayat H, Kamali K, Saliminejad K, Banan M, Khorram Khorshid HR. Association Study of IL-4 -590 C/T and DDX39B -22 G/C Polymorphisms with the Risk of Late-Onset Alzheimer's Disease in Iranian Population. Curr Aging Sci 2016; 8:276-81. [PMID: 26265379 DOI: 10.2174/187460980803151027125919] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2014] [Revised: 06/13/2015] [Accepted: 07/14/2015] [Indexed: 11/22/2022]
Abstract
Interleukin-4 (IL-4), an important anti-inflammatory cytokine, is elucidated to regulate amyloid β-induced production of the inflammatory cytokines such as IL-1 and IL-6. It is assumed that IL-4 may involve in the inflammation pathology of surrounding senile plaques in Alzheimer's disease (AD) patients. DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B (DDX39B), appears to be involved in regulation of the inflammatory cytokines which are in correlation with AD pathology. This study was conducted to investigate the two single nucleotide polymorphisms (SNPs), IL-4 -590 C/T and DDX39B -22 G/C, association with the risk of late-onset AD (LOAD) in Iranian population. In the present study, therefore, a cohort of 153 LOAD cases and 153 age-matched unrelated, non-dementia control subjects were analyzed for the two polymorphisms by polymerase chain reaction- restriction fragment length polymorphism (PCR-RFLP). Our results successfully demonstrate a protective association between the IL-4 -590 T allele, IL-4 -590 C/T heterozygous genotype (P= 0.01, OR= 0.53 and P= 0.041; OR= 0.56, respectively) and LOAD in Iranian population. A resemblance significant association was detected in female population when subjects were stratified by sex: the IL-4 -590 T allele (P= 0.02, OR= 0, 40) and the heterozygous genotype (P= 0.009, OR= 0.29). However, no significant association was observed between the DDX39B -22 G/C polymorphism in the cases and controls. Furthermore, it is clarified that the protective effect of IL-4 -590 is independent from APOE protective genotypes. Accordingly, the IL-4 -590 T allele may be applied as a protective marker in the development of LOAD in Iranian population.
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Mohammadi H, Motamedzade M, Faghih MA, Bayat H, Mohraz MH, Musavi S. Manual Material Handling Assessment Among Workers of Iranian Casting Workshops. International Journal of Occupational Safety and Ergonomics 2015; 19:675-81. [DOI: 10.1080/10803548.2013.11077021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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22
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Mohammadparast S, Bayat H, Biglarian A, Ohadi M. Exceptional expansion and conservation of a CT-repeat complex in the core promoter of PAXBP1 in primates. Am J Primatol 2014; 76:747-56. [PMID: 24573656 DOI: 10.1002/ajp.22266] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 12/28/2013] [Accepted: 01/28/2014] [Indexed: 11/11/2022]
Abstract
Adaptive evolution may be linked with the genomic distribution and function of short tandem repeats (STRs). Proximity of the core promoter STRs to the +1 transcription start site (TSS), and their mutable nature are characteristics that highlight those STRs as a novel source of interspecies variation. The PAXBP1 gene (alternatively known as GCFC1) core promoter contains the longest STR identified in a Homo sapiens gene core promoter. Indeed, this core promoter is a stretch of four consecutive CT-STRs. In the current study, we used the Ensembl, NCBI, and UCSC databases to analyze the evolutionary trend and functional implication of this CT-STR complex in six major lineages across vertebrates, including primates, non-primate mammals, birds, reptiles, amphibians, and fish. We observed exceptional expansion (≥4-repeats) and conservation of this CT-STR complex across primates, except prosimians, Microcebus murinus and Otolemur garnettii (Fisher exact P<4.1×10(-7)). H. sapiens has the most complex STR formula, and longest repeats. Macaca mulatta and Callithrix jacchus monkeys have the simplest STR formulas, and shortest repeat numbers. CT≥4-repeats were not detected in non-primate lineages. Different length alleles across the PAXBP1 core promoter CT-STRs significantly altered gene expression in vitro (P<0.001, t-test). PAXBP1 has a crucial role in craniofacial development, myogenesis, and spine morphogenesis, properties that have been diverged between primates and non-primates. To our knowledge, this is the first instance of expansion and conservation of a STR complex co-occurring specifically with the primate lineage.
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Affiliation(s)
- Saeid Mohammadparast
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
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Valipour E, Kowsari A, Bayat H, Banan M, Kazeminasab S, Mohammadparast S, Ohadi M. Polymorphic core promoter GA-repeats alter gene expression of the early embryonic developmental genes. Gene 2013; 531:175-9. [PMID: 24055488 DOI: 10.1016/j.gene.2013.09.032] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 09/05/2013] [Accepted: 09/06/2013] [Indexed: 12/20/2022]
Abstract
Protein complexes that bind to 'GAGA' DNA elements are necessary to replace nucleosomes to create a local chromatin environment that facilitates a variety of site-specific regulatory responses. Three to four elements are required for the disruption of a preassembled nucleosome. We have previously identified human protein-coding gene core promoters that are composed of exceptionally long GA-repeats. The functional implication of those GA-repeats is beginning to emerge in the core promoter of the human SOX5 gene, which is involved in multiple developmental processes. In the current study, we analyze the functional implication of GA-repeats in the core promoter of two additional genes, MECOM and GABRA3, whose expression is largely limited to embryogenesis. We report a significant difference in gene expression as a result of different alleles across those core promoters in the HEK-293 cell line. Across-species homology check for the GABRA3 GA-repeats revealed that those repeats are evolutionary conserved in mouse and primates (p<1 × 10(-8)). The MECOM core promoter GA-repeats are also conserved in numerous species, of which human has the longest repeat and complexity. We propose a novel role for GA-repeat core promoters to regulate gene expression in the genes involved in development and evolution.
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Affiliation(s)
- E Valipour
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
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Golmohammadi R, Mohammadi H, Bayat H, Habibi Mohraz M, Soltanian AR. Noise annoyance due to construction worksites. J Res Health Sci 2013; 13:201-207. [PMID: 24077480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 05/25/2013] [Accepted: 06/25/2013] [Indexed: 06/02/2023] Open
Abstract
BACKGROUND Noise pollution can contribute to adverse health effects in humans. Noise annoyance and related problems, caused by noise emission during the progress of building construction, have become increasingly important. These problems can influence the exposed workers, as well as vicinity residents. The goal of the present study was to assess the noise annoyance due to noise from construction worksites among residents of Hamadan City (west of Iran). METHODS In this cross-sectional study, 20 construction worksites and 140 near vicinity residents were selected. The main sources of construction worksite noise were diesel power generators, cutting and welding processes, heavy machinery (such as trucks) and transport of materials. Ambient noise levels were measured using a calibrated sound level meter, at each home of the residents included in the study. A noise annoyance questionnaire was employed for annoyance assessment. RESULTS The majority of subjects had very high annoyance (87.1%). The mean and SD of ambient levels were 74.57±7.12 dB (A) which exceeded the acceptable recommended level for residential areas. The most common problems among the participants were disturbance in sleep, difficulty in reading and distraction. Results showed significant relationship between noise annoyance and some factors including residing which floors had highest annoyance (F=13.22, P<0.001) and ambient noise (F=11.313, P<0.001). CONCLUSIONS High levels of noise annoyance among near vicinity residents who are affected by construction activities. This means that construction activities and other noise related sources should be regarded as the major source of ambient noise leading to noise annoyance.
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Affiliation(s)
- Rostam Golmohammadi
- Department of Occupational Hygiene, School of Public Health and Research Center for Health Sciences, Hamadan University of Medical Sciences, Hamadan, Iran.
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Bayat H, Verhoeven JTJ, Botermans M, Peters D, Hassani-Mehraban A. First Report of a 16SrIX Group ('Candidatus Phytoplasma phoenicium'-Related) Phytoplasma Associated with a Chrysanthemum Disease. Plant Dis 2013; 97:1110. [PMID: 30722519 DOI: 10.1094/pdis-01-13-0050-pdn] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In November 2010, approximately 2% of the chrysanthemum (Chrysanthemum morifolium) cv. Paniz plants showed numerous small leaves in the top and stunting in a field collection of the National Research Center of Ornamental Plants in Mahallat, Iran. Next to these plants, some plants of the same collection showed leaves with a reddish and/or chlorotic discoloration around the veins. The observed symptoms were believed to represent infection by a phytoplasma and/or a viroid. Two plants with each type of the symptoms were individually analyzed. Using a total RNA extract from diseased leaves, RT-PCR with primer pairs targeting all known pospiviroids, including Chrysanthemum stunt viroid (CSVd) (3), were negative. Purified DNA was examined for the highly conserved phytoplasma 16S rRNA gene by nested-PCR using the universal primer sets P1/P7 and R16F2n/R16R2 (2). Fragments of 1.2 kb, obtained only from the plants with the small leaves and stunting, were sequenced and one of these sequences, which were identical, was deposited in GenBank (Accession No. KC176800). BLAST analysis of the chrysanthemum phytoplasma sequence exhibited 99% identity to Candidatus Phytoplasma phoenicium (Ca. P. phoenicium) species of the 16SrIX group. Subsequently, in silico RFLP analysis of the nested PCR product with the pDRAW32 program using AluI and TaqI restriction sites used for 16SrIX subgroups A, B, C, D, and E indicated that the 16SrIX chrysanthemum isolate belonged to subgroup D (1). Recently, based on GenBank sequences, several strains of Ca. P. phoenicium have been isolated and identified from diverse host species like Lactuca serriola, L. sativa, Solanum lycopersicon, Sonchus sp. [16SrIX-E], Carthamus tinctorius, and Prunus amygdalus [16SrIX-B] (4) in Iran. The vector species transmitting Ca. P. phoenicium to C. morifolium still needs to be identified. The leafhopper Neoaliturus fenestratus may be a potential vector as it is an often encountered efficient transmitter vector of 16SrIX group phytoplasmas in Iran (2). Next to the susceptibility of chrysanthemum to members of aster yellows, stolbur, and Ca. P. aurantifolia phytoplasma groups, this is, to our knowledge, the first report of a 16SrIX group member infecting chrysanthemum. The detection of this phytoplasma in chrysanthemum can form a new threat to this crop and other ornamentals in the Mahallat flower production region. References: (1) R. E. Davis et al. New Dis. Rep. 20:35, 2010. (2) M. Salehi et al. Plant Pathol. 56:669, 2007. (3) J. Th. J. Verhoeven et al. Eur. J. Plant Pathol. 110:823, 2004. (4) M. G. Zamharir. Afr. J. Microbiol. Res. 5:6013, 2011.
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Affiliation(s)
- H Bayat
- National Research Center of Ornamental Plants, Mahallat, Iran
| | - J Th J Verhoeven
- National Plant Protection Organization of the Netherlands, Wageningen
| | - M Botermans
- National Plant Protection Organization of the Netherlands, Wageningen
| | - D Peters
- Wageningen University, the Netherlands
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Banan M, Bayat H, Namdar-Aligoodarzi P, Azarkeivan A, Kamali K, Daneshmand P, Zaker-Kandjani B, Najmabadi H. Utility of the multivariate approach in predicting β-thalassemia intermedia or β-thalassemia major types In Iranian patients. Hemoglobin 2013; 37:413-22. [PMID: 23805990 DOI: 10.3109/03630269.2013.805418] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Recently, five genetic modifiers [β-globin mutations, coinheritance of α-thalassemia (α-thal), XmnI polymorphism and single nucleotide polymorphisms (SNPs) in the BCL11A and HBS1L-MYB loci] were used to predict the β-thal major (β-TM) or β-thal intermedia (β-TI) types in 106 French patients with 83.2% accuracy. The dichotomous grouping was based on the age when the patient received his/her first transfusion (4 years). Here, a similar study was conducted in a cohort of 306 Iranian β-thal patients having distinct β-globin mutations and minor allele frequencies of key SNPs in these loci. Multivariate regression analyses and a simple scoring system were used to predict the β-TM/β-TI types using three scenarios: 1) when considering only the severe β-TM and the mild β-TI cases, 2) using clinical parameters for β-thal typing, and 3) using age at first transfusion as the basis for classification. Using these scenarios, the β-thal types could be correctly predicted in 77.6, 75.5 and 68.0% of cases, respectively.
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Affiliation(s)
- Mehdi Banan
- Genetics Research Centre, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
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Banan M, Bayat H, Azarkeivan A, Mohammadparast S, Kamali K, Farashi S, Bayat N, Khani MH, Neishabury M, Najmabadi H. The XmnI and BCL11A single nucleotide polymorphisms may help predict hydroxyurea response in Iranian β-thalassemia patients. Hemoglobin 2012; 36:371-80. [PMID: 22686296 DOI: 10.3109/03630269.2012.691147] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Hydroxyurea (HU), a drug which can reactivate fetal hemoglobin (Hb F) production, is frequently prescribed to β-thalassemia (β-thal) patients. However, transfusion requirements of only a subset of patients are reduced upon HU treatment. Because of its potential side-effects, targeted prescription of HU is imperative. To identify genetic markers that correlate with drug response, we have carried out a retrospective association study of single nucleotide polymorphisms (SNPs) in three Hb F quantitative trait loci (QTLs): the XmnI polymorphism, BCL11A, and the HBS1L-MYB intergenic region, with the response to HU in a cohort of 81 transfusion-dependent Iranian β-thal patients. An increase in blood transfusion intervals post-therapy was used to measure drug response. Our results suggest that presence of the XmnI T/T genotype or the BCL11A rs766432 C allele correlates strongly with response to HU (p <0.001). Accordingly, these markers may be used to accurately predict the HU response of Iranian β-thal patients.
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Affiliation(s)
- Mehdi Banan
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
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Dadgar T, Asmar M, Saifi A, Mazandaran M, Bayat H, Moradi A, Bazueri M, Ghaemi E. Antibacterial Activity of Certain Iranian Medicinal Plants Against Methicillin-Resistant and Sensitive Staphylococcus aureus. ACTA ACUST UNITED AC 2006. [DOI: 10.3923/ajps.2006.861.866] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Feng Z, Bayat H, Burhan K, DeMaria A, Carrier E. 220Repair of infarcted heart by embryonic stem cells. Biol Blood Marrow Transplant 2003. [DOI: 10.1016/s1083-8791(03)80209-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Dimri GP, Rudd KE, Morgan MK, Bayat H, Ames GF. Physical mapping of repetitive extragenic palindromic sequences in Escherichia coli and phylogenetic distribution among Escherichia coli strains and other enteric bacteria. J Bacteriol 1992; 174:4583-93. [PMID: 1624447 PMCID: PMC206253 DOI: 10.1128/jb.174.14.4583-4593.1992] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Repetitive extragenic palindromic (REP) sequences are highly conserved inverted repeat sequences originally discovered in Escherichia coli and Salmonella typhimurium. We have physically mapped these sequences in the E. coli genome by using Southern hybridization of an ordered phage bank of E. coli (Y. Kohara, K. Akiyama, and K. Isono, Cell 50:495-508, 1987) with generic REP probes derived from the REP consensus sequence. The set of REP probe-hybridizing clones was correlated with a set of clones expected to contain REP sequences on the basis of computer searches. We also show that a generic REP probe can be used in Southern hybridization to analyze genomic DNA digested with restriction enzymes to determine genetic relatedness among natural isolates of E. coli. A search for these sequences in other members of the family Enterobacteriaceae shows a consistent correlation between both the number of occurrences and the hybridization strength and genealogical relationship.
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Affiliation(s)
- G P Dimri
- Department of Molecular and Cell Biology, University of California, Berkeley 94720
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