Search for: metabolism
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    Metabolic load comparison between the quarters of a game in elite male basketball players using sport metabolomics

    , Article European Journal of Sport Science ; Volume 21, Issue 7 , 2021 , Pages 1022-1034 ; 17461391 (ISSN) Khoramipour, K ; Gaeini, A. A ; Shirzad, E ; Gilany, K ; Chashniam, S ; Sandbakk, Ø ; Sharif University of Technology
    Taylor and Francis Ltd  2021
    Purpose: A basketball match is characterized by intermittent high-intensity activities, thereby relying extensively on both aerobic and anaerobic metabolic pathways. Here, we aimed to compare the metabolic fluctuations between the four 10-min quarters of high-level basketball games using metabolomics analyses. Methods: 70 male basketball players with at least 3 years of experience in the Iran national top-league participated. Before and after each quarter, saliva samples were taken for subsequent untargeted metabolomics analyses, where Principal component analysis (PCA) and Partial least squares-discriminant analysis (PLS-DA) were employed for statistical analysis. Results: Quarters 1 and 3... 

    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
    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... 

    Opposite trends of GAS6 and GAS6-AS expressions in breast cancer tissues

    , Article Experimental and Molecular Pathology ; Volume 118 , 2021 ; 00144800 (ISSN) Lavasani, A ; Hussen, B. M ; Taheri, F ; Sattari, A ; Yousefi, H ; Omrani, M. D ; Nazer, N ; Ghafouri Fard, S ; Taheri, M ; Sharif University of Technology
    Academic Press Inc  2021
    Growth arrest-specific gene 6 (GAS6) is a growth factor-like cytokine whose function is related with vitamin K. This protein interacts with receptor tyrosine kinase proteins such as Tyro3, Axl, and TAM Receptor family, therefore affecting the tumorigenic processes via different mechanisms. GAS6-antisense 1 (GAS6-AS1) is a long non-coding RNAs (lncRNAs) that is transcribed from a genomic regions nearby GAS6. This lncRNA is also implicated in the pathobiology of cancer. We intended to judge the role of GAS6 and GAS6-AS1 in the pathogenesis of breast cancer through appraisal of their expression levels in breast cancer tissues and their paired neighboring non-cancerous samples. Expression of... 

    Defining microRNA signatures of hair follicular stem and progenitor cells in healthy and androgenic alopecia patients

    , Article Journal of Dermatological Science ; Volume 101, Issue 1 , 2021 , Pages 49-57 ; 09231811 (ISSN) Mohammadi, P ; Nilforoushzadeh, M. A ; Youssef, K. K ; Sharifi Zarchi, A ; Moradi, S ; Khosravani, P ; Aghdami, R ; Taheri, P ; Hosseini Salekdeh, G ; Baharvand, H ; Aghdami, N ; Sharif University of Technology
    Elsevier Ireland Ltd  2021
    Background: The exact pathogenic mechanism causes hair miniaturization during androgenic alopecia (AGA) has not been delineated. Recent evidence has shown a role for non-coding regulatory RNAs, such as microRNAs (miRNAs), in skin and hair disease. There is no reported information about the role of miRNAs in hair epithelial cells of AGA. Objectives: To investigate the roles of miRNAs affecting AGA in normal and patient's epithelial hair cells. Methods: Normal follicular stem and progenitor cells, as well as follicular patient's stem cells, were sorted from hair follicles, and a miRNA q-PCR profiling to compare the expression of 748 miRNA (miRs) in sorted cells were performed. Further, we... 

    StrongestPath: a Cytoscape application for protein-protein interaction analysis

    , Article BMC bioinformatics ; Volume 22, Issue 1 , 2021 , Pages 352- ; 14712105 (ISSN) Mousavian, Z ; Khodabandeh, M ; Sharifi Zarchi, A ; Nadafian, A ; Mahmoudi, A ; Sharif University of Technology
    NLM (Medline)  2021
    BACKGROUND: StrongestPath is a Cytoscape 3 application that enables the analysis of interactions between two proteins or groups of proteins in a collection of protein-protein interaction (PPI) network or signaling network databases. When there are different levels of confidence over the interactions, the application is able to process them and identify the cascade of interactions with the highest total confidence score. Given a set of proteins, StrongestPath can extract a set of possible interactions between the input proteins, and expand the network by adding new proteins that have the most interactions with highest total confidence to the current network of proteins. The application can... 

    Polymer-Coated NH2-UiO-66 for the codelivery of DOX/pCRISPR

    , Article ACS Applied Materials and Interfaces ; Volume 13, Issue 9 , 2021 , Pages 10796-10811 ; 19448244 (ISSN) Rabiee, N ; Bagherzadeh, M ; Heidarian Haris, M ; Ghadiri, A. M ; Matloubi Moghaddam, F ; Fatahi, Y ; Dinarvand, R ; Jarahiyan, A ; Ahmadi, S ; Shokouhimehr, M ; Sharif University of Technology
    American Chemical Society  2021
    Herein, the NH2-UiO-66 metal organic framework (MOF) has been green synthesized with the assistance of high gravity to provide a suitable and safe platform for drug loading. The NH2-UiO-66 MOF was characterized using a field-emission scanning electron microscope, transmission electron microscope (TEM), X-ray diffraction, and zeta potential analysis. Doxorubicin was then encapsulated physically on the porosity of the green MOF. Two different stimulus polymers, p(HEMA) and p(NIPAM), were used as the coating agents of the MOFs. Doxorubicin was loaded onto the polymer-coated MOFs as well, and a drug payload of more than 51% was obtained, which is a record by itself. In the next step, pCRISPR was... 

    S494 O-glycosylation site on the SARS-CoV-2 RBD affects the virus affinity to ACE2 and its infectivity; a molecular dynamics study

    , Article Scientific Reports ; Volume 11, Issue 1 , 2021 ; 20452322 (ISSN) Rahnama, S ; Azimzadeh Irani, M ; Amininasab, M ; Ejtehadi, M. R ; Sharif University of Technology
    Nature Research  2021
    SARS-CoV-2 is a strain of Coronavirus family that caused the ongoing pandemic of COVID-19. Several studies showed that the glycosylation of virus spike (S) protein and the Angiotensin-Converting Enzyme 2 (ACE2) receptor on the host cell is critical for the virus infectivity. Molecular Dynamics (MD) simulations were used to explore the role of a novel mutated O-glycosylation site (D494S) on the Receptor Binding Domain (RBD) of S protein. This site was suggested as a key mediator of virus-host interaction. By exploring the dynamics of three O-glycosylated models and the control systems of unglcosylated S4944 and S494D complexes, it was shown that the decoration of S494 with elongated O-glycans... 

    Dna-Rna hybrid (R-loop): From a unified picture of the mammalian telomere to the genome-wide profile

    , Article Cells ; Volume 10, Issue 6 , 2021 ; 20734409 (ISSN) Rassoulzadegan, M ; Sharifi Zarchi, A ; Kianmehr, L ; Sharif University of Technology
    MDPI  2021
    Local three-stranded DNA/RNA hybrid regions of genomes (R-loops) have been detected either by binding of a monoclonal antibody (DRIP assay) or by enzymatic recognition by RNaseH. Such a structure has been postulated for mouse and human telomeres, clearly suggested by the identification of the complementary RNA Telomeric repeat-containing RNA “TERRA”. However, the tremendous disparity in the information obtained with antibody-based technology drove us to investigate a new strategy. Based on the observation that DNA/RNA hybrids in a triplex complex genome co-purify with the double-stranded chromosomal DNA fraction, we developed a direct preparative approach from total protein-free cellular... 

    A novel metabolic disorder in the degradation pathway of endogenous methanol due to a mutation in the gene of alcohol dehydrogenase

    , Article Clinical Biochemistry ; Volume 90 , 2021 , Pages 66-72 ; 00099120 (ISSN) Razzaghy Azar, M ; Nourbakhsh, M ; Vafadar, M ; Nourbakhsh, M ; Talebi, S ; Sharifi Zarchi, A ; Salehi Siavashani, E ; Garshasbi, M ; Sharif University of Technology
    Elsevier Inc  2021
    Background: A small amount of methanol is produced endogenously in the human body but it is efficiently metabolized by alcohol dehydrogenase (ADH) and other enzymes, and the products eliminated without harm. In this study, we present a new entity of inborn error of methanol metabolism due to a mutation in the ADH1C gene coding for the γ subunit that is part of several ADH isoenzymes. Results: This disorder was discovered in an 11.58-year-old boy. During one 9-month hospital admission, he had periods of 1–4 days during which he was comatose, and between these periods he was sometimes verbose and euphoric, and had ataxia, dysarthria. Following hemodialysis treatments, he became conscious and... 

    Supported deep eutectic liquid membranes with highly selective interaction sites for efficient CO2 separation

    , Article Journal of Molecular Liquids ; Volume 342 , 2021 ; 01677322 (ISSN) Saeed, U ; Khan, A. L ; Gilani, M. A ; Bilad, M. R ; Khan, A. U ; Sharif University of Technology
    Elsevier B.V  2021
    This study demonstrates a new strategy in which deep eutectic solvents (DES), a new class of sustainable organic solvents, were impregnated into micro porous polymer support for separation of CO2 from CH4. Three different types of DESs were prepared by mixing and subsequent heating of betaine as hydrogen bond acceptor (HBA) in combination with either glycerol (G), ethylene glycol (EG) or urea (U) as hydrogen bond donors (HBD) in 1:3 stoichiometric mole ratio. The Fourier transform infrared (FTIR) spectroscopy was performed to confirm the formation of DESs. The gas permeation results showed that permeability of CO2 increased from 31.23 to 35.67 Barrer on substitution of HBD from glycerol to... 

    PFP-WGAN: Protein function prediction by discovering gene ontology term correlations with generative adversarial networks

    , Article PLoS ONE ; Volume 16, Issue 2 , 2021 ; 19326203 (ISSN) Seyyedsalehi, S. F ; Soleymani, M ; Rabiee, H. R ; Kaazempur Mofrad, M. R ; Sharif University of Technology
    Public Library of Science  2021
    Understanding the functionality of proteins has emerged as a critical problem in recent years due to significant roles of these macro-molecules in biological mechanisms. However, in-laboratory techniques for protein function prediction are not as efficient as methods developed and processed for protein sequencing. While more than 70 million protein sequences are available today, only the functionality of around one percent of them are known. These facts have encouraged researchers to develop computational methods to infer protein functionalities from their sequences. Gene Ontology is the most well-known database for protein functions which has a hierarchical structure, where deeper terms are... 

    Expression and function of c1orf132 long-noncoding rna in breast cancer cell lines and tissues

    , Article International Journal of Molecular Sciences ; Volume 22, Issue 13 , 2021 ; 16616596 (ISSN) Shafaroudi, A. M ; Sharifi Zarchi, A ; Rahmani, S ; Nafissi, N ; Mowla, S. J ; Lauria, A ; Oliviero, S ; Matin, M. M ; Sharif University of Technology
    MDPI  2021
    miR-29b2 and miR-29c play a suppressive role in breast cancer progression. C1orf132 (also named MIR29B2CHG) is the host gene for generating both microRNAs. However, the region also expresses longer transcripts with unknown functions. We employed bioinformatics and experimental approaches to decipher C1orf132 expression and function in breast cancer tissues. We also used the CRISPR/Cas9 technique to excise a predicted C1orf132 distal promoter and followed the behavior of the edited cells by real-time PCR, flow cytometry, migration assay, and RNA-seq techniques. We observed that C1orf132 long transcript is significantly downregulated in triple-negative breast cancer. We also identified a... 

    Preparation of amine–modified lignin and its applicability toward online micro–solid phase extraction of valsartan and losartan in urine samples

    , Article Journal of Chromatography A ; Volume 1643 , 2021 ; 00219673 (ISSN) Taherzadeh Ghahfarrokhi, M ; Zeinali, S ; Bagheri, H ; Sharif University of Technology
    Elsevier B.V  2021
    In the present work, with the focus on an environmentally–friendly approach, some gels were prepared by synthesizing amine–modified lignin, extracted from sugarcane bagasse, and further esterification and subsequent freeze–drying. These lignin–based gels were implemented as extractive phases in an online micro–solid phase extraction (μSPE) setup in conjunction with high performance liquid chromatography (HPLC) with UV detector. The developed method was used for analytical determination of valsartan and losartan in urine samples. To study the effect of the functionalization process, the efficiency of the unmodified lignin and the functionalized lignin were compared both in the absence and the... 

    Atomic scale interactions between RNA and DNA aptamers with the TNF- α protein

    , Article BioMed Research International ; Volume 2021 , 2021 ; 23146133 (ISSN) Asadzadeh, H ; Moosavi, A ; Alexandrakis, G ; Mofrad, M. R. K ; Sharif University of Technology
    Hindawi Limited  2021
    Interest in the design and manufacture of RNA and DNA aptamers as apta-biosensors for the early diagnosis of blood infections and other inflammatory conditions has increased considerably in recent years. The practical utility of these aptamers depends on the detailed knowledge about the putative interactions with their target proteins. Therefore, understanding the aptamer-protein interactions at the atomic scale can offer significant insights into the optimal apta-biosensor design. In this study, we consider one RNA and one DNA aptamer that were previously used as apta-biosensors for detecting the infection biomarker protein TNF-α, as an example of a novel computational workflow for... 

    Review on alzheimer's disease: inhibition of amyloid beta and tau tangle formation

    , Article International Journal of Biological Macromolecules ; Volume 167 , 2021 , Pages 382-394 ; 01418130 (ISSN) Ashrafian, H ; Hadi Zadeh, E ; Hasan Khan, R ; Sharif University of Technology
    Elsevier B.V  2021
    It is reported that approximately 40 million people are suffering from dementia, globally. Dementia is a group of symptoms that affect neurons and cause some mental disorders, such as losing memory. Alzheimer's disease (AD) which is known as the most common cause of dementia, is one of the top medical care concerns across the world. Although the exact sources of the disease are not understood, is it believed that aggregation of amyloid-beta (Aβ) outside of neuron cells and tau aggregation or neurofibrillary tangles (NFTs) formation inside the cell may play crucial roles. In this paper, we are going to review studies that targeted inhibition of amyloid plaque and tau protein tangle formation,... 

    Enzyme-inspired lysine-modified carbon quantum dots performing carbonylation using urea and a cascade reaction for synthesizing 2-benzoxazolinone

    , Article ACS Catalysis ; Volume 11, Issue 17 , 2021 , Pages 10778-10788 ; 21555435 (ISSN) Hasani, M ; Kalhor, H. R ; Sharif University of Technology
    American Chemical Society  2021
    Catalysts as the dynamo of chemical reactions along with solvents play paramount roles in organic transformations in long-lasting modes. Thus, developing effective and biobased catalysts in nontoxic solvents is highly in demand. In this report, carbon quantum dots (CQDs) functionalized with-lysine (Lys-CQDs) were generated from entirely nature-derived materials; they were demonstrated to be a promising catalyst for C-N bond formation in choline chloride urea (ChCl/U), a natural deep eutectic solvent (NADES). Among a number of synthesized CQDs, Lys-CQD turned out to be a powerful catalyst in the model reaction with aniline to afford phenyl urea. This type of transformation is important...