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metabolism
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Design of amino acid- and carbohydrate-based anticancer drugs to inhibit polymerase η
, Article Scientific Reports ; Volume 12, Issue 1 , 2022 ; 20452322 (ISSN) ; Fattahi, A ; Sharif University of Technology
Nature Research
2022
Abstract
DNA polymerase η (polη) is of significant value for designing new families of anticancer drugs. This protein takes a role in many stages of the cell cycle, including DNA replication, translesion DNA synthesis, and the repairing process of DNA. According to many studies, a high level of expression of polη in most cases has been associated with low rates of patients' survival, regardless of considering the stage of tumor cells. Thus, the design of new drugs with fewer side effects to inhibit polη in cancerous cells has attracted attention in recent years. This project aims to design and explore the alternative inhibitors for polη, which are based on carbohydrates and amino acids. In terms of...
Repurposing the drug, ivermectin, in COVID-19: toxicological points of view
, Article European Journal of Medical Research ; Volume 27, Issue 1 , 2022 ; 09492321 (ISSN) ; Mirzaei, R ; Nakhaee, S ; Nejatian, A ; Ghafari, S ; Mehrpour, O ; Sharif University of Technology
BioMed Central Ltd
2022
Abstract
The global COVID-19 pandemic has affected the world’s population by causing changes in behavior, such as social distancing, masking, restricting people’s movement, and evaluating existing medication as potential therapies. Many pre-existing medications such as tocilizumab, ivermectin, colchicine, interferon, and steroids have been evaluated for being repurposed to use for the treatment of COVID-19. None of these agents have been effective except for steroids and, to a lesser degree, tocilizumab. Ivermectin has been one of the suggested repurposed medications which exhibit an in vitro inhibitory activity on SARS-CoV-2 replication. The most recommended dose of ivermectin for the treatment of...
Dopamine receptors gene expression pattern and locomotor improvement differ between female and male zebrafish during spinal cord auto repair
, Article Zebrafish ; Volume 19, Issue 4 , 2022 , Pages 137-147 ; 15458547 (ISSN) ; Mirsadeghi, S ; Rahmani, S ; Izadi, A ; Rezaei, M ; Ghodsi, Z ; Rahimi Movaghar, V ; Kiani, S ; Sharif University of Technology
Mary Ann Liebert Inc
2022
Abstract
The dopaminergic system, a spinal cord (SC) motor circuit regulator, is administrated by sexual hormones and evolutionary conserved in all vertebrates. Accordingly, we hypothesized that the dopamine receptor (DAR) expression pattern may be dissimilar in female and male zebrafish SC auto repair. We implemented an uncomplicated method to induce spinal cord injury (SCI) on fully reproductive adult zebrafish, in both genders. SCI was induced using a 28-gauge needle at 9th-10th vertebra without skin incision. Thereupon, lesioned SC was harvested for DAR gene expression analysis; zebrafish were tracked routinely for any improvement in swim distance, speed, and their roaming...
Investigation of Anticancer Drug Metabolism in Saccharomyces Cerevisiae as a Drug Resistance Model
, M.Sc. Thesis Sharif University of Technology ; Yaghmaei, Soheila (Supervisor) ; Sardari, Soroush (Supervisor)
Abstract
Cancer is a life-threatening group of diseases that arises from the uncontrolled growth and division of cells in the body. Treatment options for cancer include surgery, chemotherapy, radiation therapy, immunotherapy, targeted therapy, and hormone therapy. However, resistance to anticancer drugs can develop through a variety of mechanisms, such as the upregulation of drug efflux pumps and alterations in DNA repair mechanisms. One common mechanism of drug resistance is through changes in metabolism, where cancer cells switch to alternative metabolic pathways to survive and evade the effects of anticancer drugs. The development of new drugs targeting specific molecules and pathways involved in...
A Library For Developing Optimization Algorithms In Metabolic Network Analysis
, M.Sc. Thesis Sharif University of Technology ; Tefagh, Mojtaba (Supervisor)
Abstract
In systems biology, one of the most important biological systems that is analyzed and investigated is the metabolic network. A metabolic network is a complete set of metabolic and physical processes that determine the physiological and biochemical characteristics of a cell. These networks encompass metabolic chemical reactions, metabolic pathways, and regulatory interactions that govern these reactions. Therefore, metabolic networks at the genome scale are immensely large, making even efficient algorithms time-consuming for their analysis. To address this issue, reducing metabolic networks is crucial, as it significantly decreases the execution time of algorithms and enhances computational...
Pan-cancer analysis of microRNA expression profiles highlights microRNAs enriched in normal body cells as effective suppressors of multiple tumor types: A study based on TCGA database
, Article PLoS ONE ; Volume 17, Issue 4 April , 2022 ; 19326203 (ISSN) ; Kamal, A ; Es, H. A ; Farhadi, F ; Ebrahimi, M ; Chitsaz, H ; Sharifi Zarchi, A ; Baharvand, H ; Sharif University of Technology
Public Library of Science
2022
Abstract
Background MicroRNAs (miRNAs) are frequently deregulated in various types of cancer. While antisense oligonucleotides are used to block oncomiRs, delivery of tumour-suppressive miRNAs holds great potential as a potent anti-cancer strategy. Here, we aim to determine, and functionally analyse, miRNAs that are lowly expressed in various types of tumour but abundantly expressed in multiple normal tissues. Methods The miRNA sequencing data of 14 cancer types were downloaded from the TCGA dataset. Significant differences in miRNA expression between tumor and normal samples were calculated using limma package (R programming). An adjusted p value < 0.05 was used to compare normal versus tumor miRNA...
Untargeted metabolomics based on nuclear magnetic resonance spectroscopy and multivariate classification techniques for identifying metabolites associated with breast cancer patients
, Article Chemometrics and Intelligent Laboratory Systems ; Volume 223 , 2022 ; 01697439 (ISSN) ; Khalilvand, M ; Tavakolizadeh, H ; Parastar, H ; Sharif University of Technology
Elsevier B.V
2022
Abstract
In this study, multivariate classification techniques combined with proton nuclear magnetic resonance (1HNMR) spectroscopy is proposed to identify breast cancer biomarkers that can precisely distinguish between healthy control and breast cancer (BC) patients. In this regard, first optimizing the metabolite extraction procedure was performed using Box-Behnken design (BBD). Then, data-driven soft independent modeling of class analogy (DD-SIMCA) model and partial least squares-discriminant analysis (PLS-DA) were successfully utilized for separating healthy from BC patient's classes. On this matter, both DD-SIMCA and PLS-DA models could successfully distinguish the healthy class from the BC...
A dual functional chondro-inductive chitosan thermogel with high shear modulus and sustained drug release for cartilage tissue engineering
, Article International Journal of Biological Macromolecules ; Volume 205 , 2022 , Pages 638-650 ; 01418130 (ISSN) ; Mehrjou, B ; Wang, D ; Bagheri, R ; Solouk, A ; Chu, P. K ; Wu, H ; Sharif University of Technology
Elsevier B.V
2022
Abstract
We report a chitosan-based nanocomposite thermogel with superior shear modulus resembling that of cartilage and dual pro-chondrogenic and anti-inflammatory functions. Two therapeutic agents, kartogenin (KGN) and diclofenac sodium (DS), are employed to promote chondrogenesis of stem cells and suppress inflammation, respectively. To extend the release time in a controlled manner, KGN is encapsulated in the uniform-sized starch microspheres and DS is loaded into the halloysite nanotubes. Both drug carriers are doped into the maleimide-modified chitosan hydrogel to produce a shear modulus of 167 ± 5 kPa that is comparable to that of articular cartilage (50–250 kPa). Owing to the hydrogel...
The association of clinicopathological characterizations of colorectal cancer with membrane-bound mucins genes and LncRNAs
, Article Pathology Research and Practice ; Volume 233 , 2022 ; 03440338 (ISSN) ; Entezari, M ; Rejali, L ; Nazemalhosseini-Mojarad, E ; Maghsoudloo, M ; Asadzadeh Aghdaei, H ; Zali, M. R ; Hushmandi, K ; Rabiee, N ; Makvandi, P ; Ashrafizadeh, M ; Hashemi, M ; Sharif University of Technology
Elsevier GmbH
2022
Abstract
Background: Colorectal cancer (CRC) is one of the most common malignancies in the world and has a high mortality rate. It is believed that dysfunction in the expression of mucins and aberrant expression of some lncRNAs are associated with the occurrence and development of CRC. Therefore, the aim of the present study was to investigate the expression of MUC15, MUC16, MUC20, PCAT1, CCAT1 and HOTAIR genes in colorectal cancer and its relationship with clinicopathological variables. Materials and methods: This research was prospective case-control study. Tumors from CRC patients were collected from the Taleghani Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran. RNA...
The influence of carrier material on the dominance of polyphosphate-accumulating organism metabolism in the biofilm-based biological phosphorus removal process
, Article Chemical Engineering Journal ; Volume 450 , 2022 ; 13858947 (ISSN) ; Raie, M ; Borghei, S. M ; Appels, L ; Dewil, R ; Sharif University of Technology
Elsevier B.V
2022
Abstract
This study reveals that the type of carrier material affects the stoichiometry of the anaerobic conversion and the metabolism in cultures enriched with polyphosphate-accumulating organisms (PAOs) and helps increase the biological phosphorus removal performance. PAO-enriched biofilms were cultivated in two identical lab-scale sequencing batch reactors containing different carrier types: a typical moving bed bioreactor carrier (MBBR) and a novel carbon-based moving carrier type (CBMC) coated by activated carbon particles. The experiments were conducted at various influent PO43- concentrations (14, 17, 20 mg-PO43--P/L) and two aeration periods (220 and 460 min) under similar operating...
Label-Free real-time detection of HBsAg using a QCM immunosensor
, Article Clinical Laboratory ; Volume 68, Issue 4 , 2022 , Pages 707-720 ; 14336510 (ISSN) ; Ghavidel, A ; Ahangari Cohan, R ; Hamidi Fard, M ; Khoobi, M ; Aghasadeghi, M ; Norouzian, D ; Sharif University of Technology
Verlag Klinisches Labor GmbH
2022
Abstract
Background: Hepatitis B virus surface antigen (HBsAg) is an important protein in both diagnosis and prevention of hepatitis B infection. In the current study, a piezoelectric immunosensor based on antibody-antigen interaction was designed to detect HBsAg. A quartz crystal microbalance system was employed to detect antibody-antigen interaction. Methods: At first, an oscillator was designed to measure the resonant frequency affected by the reactants using IC 74LVC1GX04. Antibody against HBsAg was immobilized on 10 MHz AT-cut quartz crystal. The surface modifications were monitored by atomic force microscopy (AFM) and contact angle measurements. Different concentrations of antibody were used...
Crystalline polysaccharides: A review
, Article Carbohydrate Polymers ; Volume 275 , 2022 ; 01448617 (ISSN) ; Yazdi, M. K ; Jouyandeh, M ; Habibzadeh, S ; Munir, M. T ; Vahabi, H ; Bagheri, B ; Rabiee, N ; Zarrintaj, P ; Saeb, M. R ; Sharif University of Technology
Elsevier Ltd
2022
Abstract
The biodegradability and mechanical properties of polysaccharides are dependent on their architecture (linear or branched) as well as their crystallinity (size of crystals and crystallinity percent). The amount of crystalline zones in the polysaccharide significantly governs their ultimate properties and applications (from packaging to biomedicine). Although synthesis, characterization, and properties of polysaccharides have been the subject of several review papers, the effects of crystallization kinetics and crystalline domains on the properties and application have not been comprehensively addressed. This review places focus on different aspects of crystallization of polysaccharides as...
Biological activated carbon process for biotransformation of azo dye carmoisine by klebsiella spp
, Article Environmental Technology (United Kingdom) ; Volume 43, Issue 18 , 2022 , Pages 2713-2729 ; 09593330 (ISSN) ; Bagheri Lotfabad, T ; Heydarinasab, A ; Yaghmaei, S ; Mohseni, F. A ; Sharif University of Technology
Taylor and Francis Ltd
2022
Abstract
The feasibility of employing the biological activated carbon (BAC) process to debilitate azo dye Carmoisine by Klebsiella spp. was investigated. Plate assay revealed the capability of Klebsiella spp. for removal of Carmoisine via degradation. Kinetic parameters were measured for Carmoisine debilitation by Klebsiella spp. using the suspended anaerobic process. Two types of granular and rod-shaped activated carbon were used to form the biological beds in order to study the Carmoisine debilitation in batch processes. Scanning electron microscopy (SEM) and confocal laser scanning microscopy (CLSM) were used to indicate the colonization and biofilm formation of bacteria grown on activated carbon...
Glycan-mediated functional assembly of IL-1RI: structural insights into completion of the current description for immune response
, Article Journal of Biomolecular Structure and Dynamics ; Volume 40, Issue 6 , 2022 , Pages 2575-2585 ; 07391102 (ISSN) ; Ejtehadi, M. R ; Sharif University of Technology
Taylor and Francis Ltd
2022
Abstract
Interleukin 1 Receptor type I (IL-1RI) is a multi-domain transmembrane receptor that triggers the inflammatory response. Understanding its detailed mechanism of action is crucial for treating immune disorders. IL-1RI is activated upon formation of its functional assembly that occurs by binding of the IL-1 cytokine and the accessory protein (Il-1RAcP) to it. X-ray crystallography, small-Angle X-ray Scattering and molecular dynamics simulation studies showed that IL-1RI adopts two types of ‘compact’ and ‘extended’ conformational states in its dynamical pattern. Furthermore, glycosylation has shown to play a critical role in its activation process. Here, classical and accelerated atomistic...
Effect of cysteine oxidation in SARS-CoV-2 receptor-binding domain on its interaction with two cell receptors: Insights from atomistic simulations
, Article Journal of Chemical Information and Modeling ; Volume 62, Issue 1 , 2022 , Pages 129-141 ; 15499596 (ISSN) ; Privat Maldonado, A ; Yusupov, M ; Rahnama, S ; Bogaerts, A ; Ejtehadi, M. R ; Sharif University of Technology
American Chemical Society
2022
Abstract
Binding of the SARS-CoV-2 S-glycoprotein to cell receptors is vital for the entry of the virus into cells and subsequent infection. ACE2 is the main cell receptor for SARS-CoV-2, which can attach to the C-terminal receptor-binding domain (RBD) of the SARS-CoV-2 S-glycoprotein. The GRP78 receptor plays an anchoring role, which attaches to the RBD and increases the chance of other RBDs binding to ACE2. Although high levels of reactive oxygen and nitrogen species (RONS) are produced during viral infections, it is not clear how they affect the RBD structure and its binding to ACE2 and GRP78. In this research, we apply molecular dynamics simulations to study the effect of oxidation of the highly...
Role of carrier characteristics affecting microbial density and population in enhanced nitrogen and phosphorus removal from wastewater
, Article Journal of Environmental Management ; Volume 302 , 2022 ; 03014797 (ISSN) ; Raie, M ; Borghei, S. M ; Dewil, R ; Appels, L ; Sharif University of Technology
Academic Press
2022
Abstract
This research aims to improve simultaneous nitrification-denitrification and phosphorus removal (SNDPR) using novel carriers and to demonstrate the effect of carrier characteristics on nutrient removal in a biofilm reactor. For this purpose, biofilms enriched with both polyphosphate-accumulating organisms (PAOs) and nitrifiers were cultivated in two parallel sequencing batch reactors containing conventional moving bed bioreactor carriers (MBBR) and a novel type of carriers (carbon-based moving carriers (CBMC)). The new carriers were produced based on recycled waste materials via a chemical-thermal process and their specific surface area were 10.4 times higher than typical MBBR carriers of...
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) ; 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...