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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...
Point-of-use rapid detection of sars-cov-2: Nanotechnology-enabled solutions for the covid-19 pandemic
, Article International Journal of Molecular Sciences ; Volume 21, Issue 14 , 2020 , Pages 1-23 ; Bagherzadeh, M ; Ghasemi, A ; Zare, H ; Ahmadi, S ; Fatahi, Y ; Dinarvand, R ; Rabiee, M ; Ramakrishna, S ; Shokouhimehr, M ; Varma, R. S ; Sharif University of Technology
MDPI AG
2020
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused the COVID-19 pandemic that has been spreading around the world since December 2019. More than 10 million affected cases and more than half a million deaths have been reported so far, while no vaccine is yet available as a treatment. Considering the global healthcare urgency, several techniques, including whole genome sequencing and computed tomography imaging have been employed for diagnosing infected people. Considerable efforts are also directed at detecting and preventing different modes of community transmission. Among them is the rapid detection of virus presence on different surfaces with which people may come in...
Advancement of sensor integrated organ-on-chip devices
, Article Sensors (Switzerland) ; Volume 21, Issue 4 , 2021 , Pages 1-44 ; 14248220 (ISSN) ; Hartse, B. X ; Niaraki Asli, A. E ; Taghavimehr, M ; Hashemi, N ; Abbasi Shirsavar, M ; Montazami, R ; Alimoradi, N ; Nasirian, V ; Ouedraogo, L. J ; Hashemi, N. N ; Sharif University of Technology
MDPI AG
2021
Abstract
Organ-on-chip devices have provided the pharmaceutical and tissue engineering worlds much hope since they arrived and began to grow in sophistication. However, limitations for their applicability were soon realized as they lacked real-time monitoring and sensing capabilities. The users of these devices relied solely on endpoint analysis for the results of their tests, which created a chasm in the understanding of life between the lab the natural world. However, this gap is being bridged with sensors that are integrated into organ-on-chip devices. This review goes in-depth on different sensing methods, giving examples for various research on mechanical, electrical resistance, and bead-based...
Porphyrin 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...
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) ; Sharifi Zarchi, A ; Kianmehr, L ; Sharif University of Technology
MDPI
2021
Abstract
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...
Metabolomics analysis of the saliva in patients with chronic hepatitis b using nuclear magnetic resonance: A pilot study
, Article Iranian Journal of Basic Medical Sciences ; Volume 22, Issue 9 , 2019 , Pages 1044-1049 ; 20083866 (ISSN) ; Mohamadkhani, A ; Chashmniam, S ; Shahnazari, P ; Amini, M ; Arjmand, B ; Malekzadeh, R ; Nobakht Motlagh Ghoochani, B. F ; Sharif University of Technology
Mashhad University of Medical Sciences
2019
Abstract
Objective(s): Hepatitis B virus infection causes chronic disease such as cirrhosis and hepatocellular carcinoma. The metabolomics investigations have been demonstrated to be related to pathophysiologic mechanisms in many disorders such as hepatitis B infection. The aim of this study was to investigate the saliva metabolic profile of patients with chronic hepatitis B infection and to identify underlying mechanisms as well as potential biomarkers associated with the disease. Materials and Methods: Saliva from 16 healthy subjects and 20 patients with chronic hepatitis B virus were analyzed by nuclear magnetic resonance (NMR). Then, multivariate statistical analysis was performed to identify...
Some natural hypomethylating agents in food, water and environment are against distribution and risks of COVID-19 pandemic: Results of a big-data research
, Article Avicenna Journal of Phytomedicine ; Volume 12, Issue 3 , 2022 , Pages 309-324 ; 22287930 (ISSN) ; Izadi, M ; Talebpour, A ; Sharif University of Technology
Mashhad University of Medical Sciences
2022
Abstract
Objective: This study analyzes the effects of lifestyle, nutrition, and diets on the status and risks of apparent (symptomatic) COVID-19 infection in Iranian families. Materials and Methods: A relatively extensive questionnaire survey was conducted on more than 20,000 Iranian families (residing in more than 1000 different urban and rural areas in the Islamic Republic of Iran) to collect the big data of COVID-19 and develop a lifestyle dataset. The collected big data included the records of lifestyle effects (e.g. nutrition, water consumption resources, physical exercise, smoking, age, gender, health and disease factors, etc.) on the status of COVID-19 infection in families (i.e. residents of...
Improving the performance of a photonic PCR system using TiO2 nanoparticles
, Article Journal of Industrial and Engineering Chemistry ; 2020 ; Ghazimirsaeed, E ; Shamloo, A ; Dizani, M ; Sharif University of Technology
Korean Society of Industrial Engineering Chemistry
2020
Abstract
Nucleic acid amplification using polymerase chain reaction (PCR) method has been widely used in different fields such as agricultural science, medicine, pathogen identification, and forensics to name a few. Today, it seems inevitable to have a robust, simple PCR system for diagnostics at the point-of-care (POC) level. Many photonic PCR systems have been proposed in the literature that benefit from plasmonic photothermal heating to achieve the common PCR thermal cycling. However, non-homogeneous temperature distribution is a challenge in some of them. In the present work, to achieve more efficient gene amplification, the effect of adding TiO2 nanoparticles has been investigated in a photonic...
Theoretical simulation of surface-enhanced resonance Raman spectroscopy of cytosine and its tautomers
, Article Journal of Raman Spectroscopy ; Volume 51, Issue 1 , 2020 , Pages 55-65 ; Mohammadpour, M ; Ramazani, S ; Jamshidi, Z ; Sharif University of Technology
John Wiley and Sons Ltd
2020
Abstract
The primary challenge of spectroscopic techniques in selective detection and characterization of tautomeric structures of DNA and RNA bases, and moreover, the accurate interpretation and explanation of the experimental results are the main motives of theoretical studies. Surface-enhanced Raman spectroscopy (SERS) can be a powerful approach to distinguish cytosine in the presence of its tautomers. For this respect, herein, the theoretical simulation of the SERS spectra of cytosine and its three most stable tautomers adsorbed on silver clusters is carried out. The calculations of SERS spectra is based on the excited-state energy gradient approximation as a well-established approach that gives...
Poly-L-lysine/hyaluronan nanocarriers as a novel nanosystem for gene delivery
, Article Journal of Microscopy ; Volume 287, Issue 1 , 2022 , Pages 32-44 ; 00222720 (ISSN) ; Bagherzadeh, M. A ; Mofazzal Jahromi, M. A ; Mohammad-Beigi, H ; Abdoli, A ; Mir, H ; Roustazadeh, A ; Pirestani, M ; Sahandi Zangabad, P ; Kiani, J ; Bakhshayesh, A ; Jahani, M ; Joghataei, M. T ; Karimi, M ; Sharif University of Technology
John Wiley and Sons Inc
2022
Abstract
The present research comes up with a novel DNA-loaded poly-L-lysine (PLL)/hyaluronan (HA) nanocarrier (DNA-loaded PLL/HA NCs) for gene delivery applications, as a promising candidate for gene delivery into diverse cells. A straightforward approach was employed to prepare such a nanosystem through masking DNA-loaded PLL molecules by HA. Fourier-transform infrared (FTIR) spectroscopy, dynamic light scattering (DLS), field emission-scanning electron microscopy (FE-SEM) and transmission electron microscopy (TEM) were used to analyse the interaction of the molecules as well as the physicochemical properties of the NCs. The NCs showed a negative charge of –24 ± 3 mV, with an average size of 138 ±...
Association between human leukocyte antigens and cutaneous adverse drug reactions to antiepileptics and antibiotics in the Iranian population
, Article Dermatologic Therapy ; Volume 35, Issue 5 , 2022 ; 13960296 (ISSN) ; Rostami, A ; Firooz, A ; Esmaili, N ; Ghiasi, M ; Lajevardi, V ; Amirzargar, A. A ; Sheykhi, I ; Khamesipour, A ; Akhdar, M ; Sharif University of Technology
John Wiley and Sons Inc
2022
Abstract
In this case–control study, class І and ІІ human leukocyte antigen (HLA) alleles in Iranian patients with benign and severe cutaneous adverse drug reactions (CADRs) due to aromatic anticonvulsants and antibiotics were evaluated. Patients diagnosed with CADRs (based on clinical and laboratory findings) with a Naranjo score of ≥ 4 underwent blood sampling and HLA-DNA typing. The control group comprised 90 healthy Iranian adults. Alleles with a frequency of more than two were reported. Deviations from Hardy–Weinberg equilibrium were not observed. Eighty patients with CADRs including 54 females and 26 males with a mean age of 41.49 ± 16.08 years were enrolled in this study. The culprit drugs...
Histidine-enhanced gene delivery systems: The state of the art
, Article Journal of Gene Medicine ; Volume 24, Issue 5 , 2022 ; 1099498X (ISSN) ; Jahanpeimay Sabet, M ; Hasanzadeh, A ; Kamrani Mousavi, S. M ; Haeri Moghaddam, N ; Hooshmand, S. A ; Rabiee, N ; Liu, Y ; Hamblin, M. R ; Karimi, M ; Sharif University of Technology
John Wiley and Sons Inc
2022
Abstract
Gene therapy has emerged as a promising tool for treating different intractable diseases, particularly cancer or even viral diseases such as COVID-19 (coronavirus disease 2019). In this context, various non-viral gene carriers are being explored to transfer DNA or RNA sequences into target cells. Here, we review the applications of the naturally occurring amino acid histidine in the delivery of nucleic acids into cells. The biocompatibility of histidine-enhanced gene delivery systems has encouraged their wider use in gene therapy. Histidine-based gene carriers can involve the modification of peptides, dendrimers, lipids or nanocomposites. Several linear polymers, such as polyethylenimine,...
Studies of Ponceau 4R food colorant and zinc oxide nanoparticles containing it interactions with DNA and evaluation of their antimicrobial activity
, Article Journal of Food Processing and Preservation ; Volume 46, Issue 2 , 2022 ; 01458892 (ISSN) ; Shahabadi, N ; Mahmoudi Hashemi, M ; Meibodi, F. S ; Mirjafari, Z ; Sharif University of Technology
John Wiley and Sons Inc
2022
Abstract
The current study describes design and synthesis of silica-coated zinc oxide nanoparticles containing Ponceau 4R food colorant (named as ZnO@SiO2@APTMS/P4R). The interactions of Ponceau 4R and ZnO@SiO2@APTMS/P4R with calf thymus-DNA were investigated It should be noted that the competitive binding experiment revealed that both Ponceau 4R and ZnO@SiO2@APTMS/P4R could release Hoechst 33258. As inferred from the results the binding of the Ponceau 4R and ZnO@SiO2@APTMS/P4R with DNA were surface binding, mainly due to groove binding. Furthermore, antibacterial properties of ZnO, Ponceau 4R and ZnO@SiO2@APTMS/P4R samples against gram-positive bacteria and gram-negative bacteria were examined and...
HLA alleles and haplotype frequencies in Iranian population
, Article Human Antibodies ; Volume 30, Issue 2 , 2022 , Pages 79-96 ; 10932607 (ISSN) ; Hussen, B. M ; Pashmforoush, S ; Akbari, M. T ; Arsang-Jang, S ; Nazer, N ; Hamidieh, A. A ; Hajifathali, A ; Dinger, M. E ; Sayad, A ; Dehaghi, M. O ; Sharif University of Technology
IOS Press BV
2022
Abstract
BACKGROUND: HLA genotyping is a prerequisite for selection of suitable donors in the process of bone marrow transplantation. METHODS: In the current study, the frequencies of HLA-A, -B, -C and -DRB1 alleles and A-B-C-DRB1 haplotypes were assessed in 855 healthy Iranian persons using a low-resolution sequence specific primer (SSP) kit. RESULTS: Frequencies were compared between 11 subpopulations including Armani, Balouch, Bandari, Turk, Turkaman, Arab, Fars, Kurd, Gilaki, Lor and Mazani. In total, 17 HLA-A alleles were detected, one of which (HLA-A*74) was present only among Lors. HLA-A*23 and -A*26 were the most frequent HLA-A alleles among Armanis. HLA-A*23 was also common among Turkamans....
Fabrication and characterization of an injectable reinforced composite scaffold for cartilage tissue engineering: An in vitro study
, Article Biomedical Materials (Bristol) ; Volume 16, Issue 4 , 2021 ; 17486041 (ISSN) ; Mashayekhan, S ; Zarei, F ; Sayyahpour, F. A ; Taghiyar, L ; Eslaminejad, M. B ; Sharif University of Technology
IOP Publishing Ltd
2021
Abstract
There are limitations in current medications of articular cartilage injuries. Although injectable bioactive hydrogels are promising options, they have decreased biomechanical performance. Researchers should consider many factors when providing solutions to overcome these challenges. In this study, we created an injectable composite hydrogel from chitosan and human acellular cartilage extracellular matrix (ECM) particles. In order to enhance its mechanical properties, we reinforced this hydrogel with microporous microspheres composed of the same materials as the structural building blocks of the scaffold. Articular cartilage from human donors was decellularized by a combination of physical,...
Designing a polymerase chain reaction device working with radiation and convection heat transfer
, Article 2017 International Conference on Nanomaterials and Biomaterials, ICNB 2017, 11 December 2017 through 13 December 2017 ; Volume 350, Issue 1 , 2018 ; 17578981 (ISSN) ; Kalan, K ; Shamloo, A ; Sharif University of Technology
Institute of Physics Publishing
2018
Abstract
Gene proliferation is vital for infectious and genetic diseases diagnosis from a blood sample, even before birth. In addition, DNA sequencing, genetic finger-print analyzing, and genetic mutation detecting can be mentioned as other procedures requiring gene reproduction. Polymerase chain reaction, briefly known as PCR, is a convenient and effective way to accomplish this task; where the DNA containing sample faces three temperature phases alternatively. These phases are known as denaturation, annealing, and elongation/extension which in this study -regarding the type of the primers and the target DNA sequence- are set to occur at 95, 58, and 72 degrees of Celsius. In this study, a PCR device...
Recovery from random samples in a big data set
, Article IEEE Communications Letters ; Volume 19, Issue 11 , September , 2015 , Pages 1929-1932 ; 10897798 (ISSN) ; Gohari, A ; Sharif University of Technology
Institute of Electrical and Electronics Engineers Inc
2015
Abstract
Consider a collection of files, each of which is a sequence of letters. One of these files is randomly chosen and a random subsequence of the file is revealed. This random subsequence can be the result of a random sampling of the file. The goal is to recover the identity of the file, assuming a simple greedy matching algorithm to search the file collection. We study the fundamental limits on the maximum size of the file collection for reliable recovery in terms of the length of the random subsequence. The sequence of each file is assumed to follow a hidden Markov model (HMM), which is a common model for many data structures such as voice or DNA sequences. The connection between this problem...
Performance characterization of a low-cost dual-channel camera-based microarray scanner
, Article 24th Iranian Conference on Electrical Engineering, ICEE 2016, 10 May 2016 through 12 May 2016 ; 2016 , Pages 1534-1538 ; 9781467387897 (ISBN) ; Ghobeh, M ; Ghiasvand, E ; Akbari Roshan, K ; Motahari, S. A ; Sharif University of Technology
Institute of Electrical and Electronics Engineers Inc
2016
Abstract
In this paper, we have proposed, designed, implemented, and characterized a low-cost camera-based microarray scanner which is capable of imaging fluorescently-labeled DNA or Protein microarrays. The proposed system is designed to simultaneously measure two different fluorescent dyes using two parallel channels which increase the overall scan speed. We have shown that the wide dynamic range of system makes it able to detect fluorophore densities from 100-106 molecule/μm2. In each capture, a 5.6 mm × 3.7 mm field is imaged on a 22.3 mm × 14.9 mm (18 megapixels) CMOS sensor. Therefore, the microarray can be scanned with ∼ 1μm2 spatial resolution which is high enough to distinguish borders of...
Mining DNA sequences based on spatially coded technique using spatial light modulator
, Article IWCIT 2016 - Iran Workshop on Communication and Information Theory, 3 May 2016 through 4 May 2016 ; 2016 ; 9781509019229 (ISBN) ; Abdollahramezani, S ; Bahrani, S ; Chizari, A ; Jamali, M. V ; Khorramshahi, P ; Tashakori, A ; Shahsavari, S ; Salehi, J. A ; Sharif University of Technology
Institute of Electrical and Electronics Engineers Inc
2016
Abstract
In this paper, we present an optical computing method for string data alignment applicable to genome information analysis. By applying moire technique to spatial encoding patterns of deoxyribonucleic acid (DNA) sequences, association information of the genome and the expressed phenotypes could more effectively be extracted. Such moire fringes reveal occurrence of matching, deletion and insertion between DNA sequences providing useful visualized information for prediction of gene function and classification of species. Furthermore, by applying a cylindrical lens, a new technique is proposed to map two-dimensional (2D) association information to a one-dimensional (1D) column of pixels, where...
Genome-Wide Association Studies: Information Theoretic Limits of Reliable Learning
, Article 2018 IEEE International Symposium on Information Theory, ISIT 2018, 17 June 2018 through 22 June 2018 ; Volume 2018-June , 2018 , Pages 2231-2235 ; 21578095 (ISSN); 9781538647806 (ISBN) ; Maddah Ali, M. A ; Motahari, A. S ; Sharif University of Technology
Institute of Electrical and Electronics Engineers Inc
2018
Abstract
In the problems of Genome-Wide Association Study (GWAS), the objective is to associate subsequences of individual's genomes to the observable characteristics called phenotypes. The genome containing the biological information of an individual can be represented by a sequence of length G. Many observable characteristics of the individuals can be related to a subsequence of a given length L, called causal subsequence. The environmental affects make the relation between the causal subsequence and the observable characteristics a stochastic function. Our objective in this paper is to detect the causal subsequence of a specific phenotype using a dataset of N individuals and their observed...