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    Downregulation of ITM2A gene expression in macrophages of patients with ankylosing spondylitis

    , Article International Archives of Allergy and Immunology ; Volume 182, Issue 11 , 2021 , Pages 1113-1121 ; 10182438 (ISSN) Lari, A ; Pourbadie, H. G ; Jafari, M ; Sharifi Zarchi, A ; Akhtari, M ; Nejatbakhsh Samimi, L ; Jamshidi, A ; Mahmoudi, M ; Sharif University of Technology
    S. Karger AG  2021
    Abstract
    Objectives: Ankylosing spondylitis (AS) is a rheumatic disorder that is mostly determined by genetic and environmental factors. Given the known importance of macrophage in AS pathogenesis, we investigated the transcriptional profile of macrophage cells in the disease. Methods and Results: Two approaches of differential expression and subsequently, weighted gene co-expression network analysis was utilized to analyze a publicly available microarray dataset of macrophages. Integral membrane protein 2A (ITM2A) was among the most significant genes with a decreased trend in the common results of both methods. In order to confirm the finding, the expression of ITM2A was evaluated in... 

    Expression of functional recombinant human tissue transglutaminase (TG2) using the bac-to-bac baculovirus expression system

    , Article Advanced Pharmaceutical Bulletin ; Volume 6, Issue 1 , 2016 , Pages 49-56 ; 22285881 (ISSN) Yazdani, Y ; Azari, S ; Kalhor, H. R ; Sharif University of Technology
    Tabriz University of Medical Sciences 
    Abstract
    Tissue transglutaminase (TG2) is a unique multifunctional enzyme. The enzyme possesses enzymatic activities such as transamidation/crosslinking and non-enzymatic functions such as cell migration and signal transduction. TG2 has been shown to be involved in molecular mechanisms of cancers and several neurodegenerative diseases such as Alzheimer's disease. The present study aimed at cloning and expression of full length human TG2 in Bac-to-Bac baculovirus expression system and evaluation of its activity. Methods: pFastBac HTA donor vector containing coding sequence of human TG2 was constructed. The construct was transformed to DH10Bac for generating recombinant bacmid. The verified bacmid was... 

    A quantum mechanical approach towards the calculation of transition probabilities between DNA codons

    , Article BioSystems ; Volume 184 , 2019 ; 03032647 (ISSN) Ghasemi, F ; Shafiee, A ; Sharif University of Technology
    Elsevier Ireland Ltd  2019
    Abstract
    The role of quantum tunneling in altering the structure of nucleotides to each other and causing a mutational event in DNA has been a topic of debate for years. Here, we introduce a new quantum mechanical approach for analyzing a typical point-mutation in DNA strands. Assuming each codon as a base state, a superposition of codon states could provide a physical description for a set of codons encoding the same amino acid and there are transition amplitudes between them. We choose the amino acids Phe and Ile as our understudy bio-systems which are encoded by two and three codons, respectively. We treat them as large quantum systems and use double- and triple-well potential models to study the... 

    Recent approaches to mRNA vaccine delivery by lipid-based vectors prepared by continuous-flow microfluidic devices

    , Article Future medicinal chemistry ; Volume 14, Issue 21 , 2022 , Pages 1561-1581 ; 17568927 (ISSN) Ghasemi Toudeshkchouei, M ; Tavakoli, A ; Mohammadghasemi, H ; Karimi, A ; Ai, J ; Rabiee, M ; Rabiee, N ; Sharif University of Technology
    NLM (Medline)  2022
    Abstract
    Advancements in nanotechnology have resulted in the introduction of several nonviral delivery vectors for the nontoxic, efficient delivery of encapsulated mRNA-based vaccines. Lipid- and polymer-based nanoparticles (NP) have proven to be the most potent delivery systems, providing increased delivery efficiency and protection of mRNA molecules from degradation. Here, the authors provide an overview of the recent studies carried out using lipid NPs and their functionalized forms, polymeric and lipid-polymer hybrid nanocarriers utilized mainly for the encapsulation of mRNAs for gene and immune therapeutic applications. A microfluidic system as a prevalent methodology for the preparation of NPs... 

    Comparative study of commercial media to improve GMP manufacturing of recombinant human interferon β-1a by CHO cells in perfusion bioreactor

    , Article Cytotechnology ; Volume 74, Issue 6 , 2022 , Pages 669-680 ; 09209069 (ISSN) Sedighikamal, H ; Karimi Mostofi, R ; Sattarzadeh, A ; Shahbazi, M ; Aghazadeh, H ; Sharif University of Technology
    Springer Science and Business Media B.V  2022
    Abstract
    Chinese hamster ovary cells are the main cellular factories for production of a wide range of recombinant proteins in biopharmaceutical industry. Recombinant human Interferon beta-1a (rh-IFN β-1a), as a cytokine is broadly used to treat multiple sclerosis. In this work, the cell line producing rh-IFN β-1a was studied to improve cell density along with the specific expression. For this reason different cell culture experiments were done using different commercial serum-free media to find the appropriate media providing higher cell density. It was shown DMEMF12, DMEM:ProCHO5, and CHO-S-SFM II led to higher cell density and shorter doubling time. Next, using these media, fed-batch, and... 

    CircWalk: a novel approach to predict CircRNA-disease association based on heterogeneous network representation learning

    , Article BMC Bioinformatics ; Volume 23, Issue 1 , 2022 ; 14712105 (ISSN) Kouhsar, M ; Kashaninia, E ; Mardani, B ; Rabiee, H. R ; Sharif University of Technology
    BioMed Central Ltd  2022
    Abstract
    Background: Several types of RNA in the cell are usually involved in biological processes with multiple functions. Coding RNAs code for proteins while non-coding RNAs regulate gene expression. Some single-strand RNAs can create a circular shape via the back splicing process and convert into a new type called circular RNA (circRNA). circRNAs are among the essential non-coding RNAs in the cell that involve multiple disorders. One of the critical functions of circRNAs is to regulate the expression of other genes through sponging micro RNAs (miRNAs) in diseases. This mechanism, known as the competing endogenous RNA (ceRNA) hypothesis, and additional information obtained from biological datasets... 

    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) Azadbakht, M ; 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... 

    Unraveling cancer metastatic cascade using microfluidics-based technologies

    , Article Biophysical Reviews ; Volume 14, Issue 2 , 2022 , Pages 517-543 ; 18672450 (ISSN) Hakim, M ; Kermanshah, L ; Abouali, H ; Hashemi, H. M ; Yari, A ; Khorasheh, F ; Alemzadeh, I ; Vossoughi, M ; Sharif University of Technology
    Springer Science and Business Media Deutschland GmbH  2022
    Abstract
    Cancer has long been a leading cause of death. The primary tumor, however, is not the main cause of death in more than 90% of cases. It is the complex process of metastasis that makes cancer deadly. The invasion metastasis cascade is the multi-step biological process of cancer cell dissemination to distant organ sites and adaptation to the new microenvironment site. Unraveling the metastasis process can provide great insight into cancer death prevention or even treatment. Microfluidics is a promising platform, that provides a wide range of applications in metastasis-related investigations. Cell culture microfluidic technologies for in vitro modeling of cancer tissues with fluid flow and the...