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Genome Engineering of Bacillus Subtilis Using CRISPR Technology to Overproduce Protease Production
, M.Sc. Thesis Sharif University of Technology ; Roostaazad, Reza (Supervisor) ; Banaei Moghaddam, Ali Mohammad (Supervisor)
Abstract
Enzymes are an important part of detergents, they reduce the activation energy of the reaction and thus increase the efficiency of the process. Protease enzyme is one of the most common enzymes in detergents. Bacillus strain is the most important strain in the production of this enzyme and among the species of Bacillus, Bacillus subtilis is the most used. Bacillus subtilis is a gram-positive, rod-shaped bacterium. This bacterium is considered a non-pathogenic cell that has the ability to form spores and prevent death and damage in harsh conditions. In this study, CRISPR system was used to modify the genome of Bacillus subtilis ATCC 6633 in order to increase alkaline protease. To increase the...
A Study in Genome Editing with Clustered Regularly Interspaced Short Palindromic Repeats
, M.Sc. Thesis Sharif University of Technology ; Sharifi Tabar, Mohsen (Supervisor) ; Rabiee, Hamid Reza (Co-Supervisor) ; Rohban, Mohammad Hossein (Co-Supervisor)
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats, or in short, CRISPR is a relatively new technology that enables geneticists and medical researchers to edit parts of the genome by removing, adding, or altering parts of the DNA. Initially found in the genomes of prokaryotic organisms such as bacteria and archaea, this technology can cure many illnesses such as blindness and cancer. A significant issue for a practical application of CRISPR systems is accurately predicting the single guide RNA (sgRNA) on-target efficacy and off-target sensitivity. While some methods classify these designs, most algorithms are on separate data with different genes and cells. The lack of...
Increase Production of the Enzyme by Cell Genetic Modification
, M.Sc. Thesis Sharif University of Technology ; Roosta Azad, Reza (Supervisor) ; Banaei Moghaddam, Ali Mohammad (Supervisor)
Abstract
Genetic engineering of cells has been one of the most effective ways to increase protein production in wild strains. Among the various genetic engineering techniques, the CRISPR/Cas9 system that directly edits the cell chromosome, yielding greater efficiency and easier operation. In this study, we used this system to modify the genome of Bacillus subtilis ATCC 6633 to increase the production of extracellular alkaline protease enzyme. Alkaline protease enzyme has many applications in different industries, but in this study, the application of this enzyme in the detergent industry has been considered. To increase the production of this enzyme, we disrupted and prevented the gene responsible...
Improving Subtilisin Production by Engineering the Regulatory Regions of aprE in Bacillus Subtilis
, M.Sc. Thesis Sharif University of Technology ; Banaei Moghaddam, Ali Mohammad (Supervisor) ; Yaghmaei, Soheyla (Supervisor) ; Roosta Azad, Reza (Supervisor)
Abstract
Industrial enzymes can generally be classified into three groups: carbohydrases, proteases and lipases, which account for a major part of the global enzyme trade. Proteases, in particular, have always been extensively studied and investigated due to their widespread use in various industries, such as food, pharmaceutical, chemical, and agricultural sectors. Proteases are a group of proteolytic enzymes that break down proteins and peptides into their constituent amino acids by hydrolyzing peptide bonds. Among the family of proteases, alkaline serine proteases have special biocatalytic abilities in both aqueous and organic environments. Their suitable resistance in alkaline environments and...
Developmental barcoding of whole mouse via homing CRISPR
, Article Science ; Volume 361, Issue 6405 , 2018 ; 00368075 (ISSN) ; Kalhor, K ; Mejia, L ; Leeper, K ; Graveline, A ; Mali, P ; Church, G. M ; Sharif University of TechnologyPorphyrin molecules decorated on metal–organic frameworks for multi-functional biomedical applications
, Article Biomolecules ; Volume 11, Issue 11 , 2021 ; 2218273X (ISSN) ; Rabiee, M ; Sojdeh, S ; Fatahi, Y ; Dinarvand, R ; Safarkhani, M ; Ahmadi, S ; Daneshgar, H ; Radmanesh, F ; Maghsoudi, S ; Bagherzadeh, M ; Varma, R. S ; Mostafavi, E ; Sharif University of Technology
MDPI
2021
Abstract
Metal–organic frameworks (MOFs) have been widely used as porous nanomaterials for different applications ranging from industrial to biomedicals. An unpredictable one-pot method is introduced to synthesize NH2-MIL-53 assisted by high-gravity in a greener media for the first time. Then, porphyrins were deployed to adorn the surface of MOF to increase the sensitivity of the prepared nanocomposite to the genetic materials and in-situ cellular protein structures. The hydrogen bond formation between genetic domains and the porphyrin’ nitrogen as well as the surface hydroxyl groups is equally probable and could be considered a milestone in chemical physics and physical chemistry for biomedical...
Green chemistry and coronavirus
, Article Sustainable Chemistry and Pharmacy ; Volume 21 , 2021 ; 23525541 (ISSN) ; Rabiee, N ; Fatahi, Y ; Hooshmand, S. E ; Bagherzadeh, M ; Rabiee, M ; Jajarmi, V ; Dinarvand, R ; Habibzadeh, S ; Saeb, M. R ; Varma, R. S ; Shokouhimehr, M ; Hamblin, M. R ; Sharif University of Technology
Elsevier B.V
2021
Abstract
The novel coronavirus pandemic has rapidly spread around the world since December 2019. Various techniques have been applied in identification of SARS-CoV-2 or COVID-19 infection including computed tomography imaging, whole genome sequencing, and molecular methods such as reverse transcription polymerase chain reaction (RT-PCR). This review article discusses the diagnostic methods currently being deployed for the SARS-CoV-2 identification including optical biosensors and point-of-care diagnostics that are on the horizon. These innovative technologies may provide a more accurate, sensitive and rapid diagnosis of SARS-CoV-2 to manage the present novel coronavirus outbreak, and could be...
Green chemistry and coronavirus
, Article Sustainable Chemistry and Pharmacy ; Volume 21 , 2021 ; 23525541 (ISSN) ; Rabiee, N ; Fatahi, Y ; Hooshmand, S. E ; Bagherzadeh, M ; Rabiee, M ; Jajarmi, V ; Dinarvand, R ; Habibzadeh, S ; Saeb, M. R ; Varma, R.S ; Shokouhimehr, M ; Hamblin, M. R ; Sharif University of Technology
Elsevier B.V
2021
Abstract
The novel coronavirus pandemic has rapidly spread around the world since December 2019. Various techniques have been applied in identification of SARS-CoV-2 or COVID-19 infection including computed tomography imaging, whole genome sequencing, and molecular methods such as reverse transcription polymerase chain reaction (RT-PCR). This review article discusses the diagnostic methods currently being deployed for the SARS-CoV-2 identification including optical biosensors and point-of-care diagnostics that are on the horizon. These innovative technologies may provide a more accurate, sensitive and rapid diagnosis of SARS-CoV-2 to manage the present novel coronavirus outbreak, and could be...
MaxHiC: A robust background correction model to identify biologically relevant chromatin interactions in Hi-C and capture Hi-C experiments
, Article PLoS Computational Biology ; Volume 18, Issue 6 , 2022 ; 1553734X (ISSN) ; Modegh, R. G ; Rabiee, H. R ; Sarbandi, E. R ; Rezaie, N ; Tam, K. T ; Forrest, A. R. R ; Sharif University of Technology
Public Library of Science
2022
Abstract
Hi-C is a genome-wide chromosome conformation capture technology that detects interactions between pairs of genomic regions and exploits higher order chromatin structures. Conceptually Hi-C data counts interaction frequencies between every position in the genome and every other position. Biologically functional interactions are expected to occur more frequently than transient background and artefactual interactions. To identify biologically relevant interactions, several background models that take biases such as distance, GC content and mappability into account have been proposed. Here we introduce MaxHiC, a background correction tool that deals with these complex biases and robustly...
Zn-rich (GaN)1−x(ZnO)x: a biomedical friend?
, Article New Journal of Chemistry ; Volume 45, Issue 8 , 2021 , Pages 4077-4089 ; 11440546 (ISSN) ; Rabiee, N ; Fatahi, Y ; Dinarvand, R ; Sharif University of Technology
Royal Society of Chemistry
2021
Abstract
A Zn-Rich (GaN)1−x(ZnO)xnanostructure was synthesized with the assistance of a high-gravity technique in order to reduce the reaction time and temperature. The synthesized inorganic nanomaterial has been applied in both drug and gene delivery systems, and as the first fully inorganic nanomaterial, it was investigated in a comprehensive cellular investigation as well. In order to increase the potential bioavailability, as well as the interactions with the pCRISPR, the nanomaterial was enriched with additional Zn ions. The nanomaterial and the final nanocarrier were characterized at each step before and after any biological analysisviaFESEM, AFM, TEM, FTIR and XRD. The polymer coated...
CaZnO-based nanoghosts for the detection of ssDNA, pCRISPR and recombinant SARS-CoV-2 spike antigen and targeted delivery of doxorubicin
, Article Chemosphere ; Volume 306 , 2022 ; 00456535 (ISSN) ; Akhavan, O ; Fatahi, Y ; Ghadiri, A. M ; Kiani, M ; Makvandi, P ; Rabiee, M ; Nicknam, M. H ; Saeb, M. R ; Varma, R. S ; Ashrafizadeh, M ; Nazarzadeh Zare, E ; Sharifi, E ; Lima, E. C ; Sharif University of Technology
Elsevier Ltd
2022
Abstract
Overexpression of proteins/antigens and other gene-related sequences in the bodies could lead to significant mutations and refractory diseases. Detection and identification of assorted trace concentrations of such proteins/antigens and/or gene-related sequences remain challenging, affecting different pathogens and making viruses stronger. Correspondingly, coronavirus (SARS-CoV-2) mutations/alterations and spread could lead to overexpression of ssDNA and the related antigens in the population and brisk activity in gene-editing technologies in the treatment/detection may lead to the presence of pCRISPR in the blood. Therefore, the detection and evaluation of their trace concentrations are of...
CRISPRi-mediated knock-down of PRDM1/BLIMP1 programs central memory differentiation in ex vivo-expanded human T cells
, Article BioImpacts ; Volume 12, Issue 4 , 2022 , Pages 337-347 ; 22285652 (ISSN) ; Sayadmanesh, A ; Nazer, N ; Ahmadi, A ; Hemmati, S ; Mohammadzade, H ; Ebrahimi, M ; Baharvand, H ; Khalaj, B ; Aghamaali, M. R ; Basiri, M ; Sharif University of Technology
Tabriz University of Medical Sciences
2022
Abstract
Introduction: B lymphocyte-induced maturation protein 1 (BLIMP1) encoded by the positive regulatory domain 1 gene (PRDM1), is a key regulator in T cell differentiation in mouse models. BLIMP1-deficiency results in a lower effector phenotype and a higher memory phenotype. Methods: In this study, we aimed to determine the role of transcription factor BLIMP1 in human T cell differentiation. Specifically, we investigated the role of BLIMP1 in memory differentiation and exhaustion of human T cells. We used CRISPR interference (CRISPRi) to knock-down BLIMP1 and investigated the differential expressions of T cell memory and exhaustion markers in BLIMP1-deficient T cells in comparison with...