Loading...
Search for:
dna
0.009 seconds
Total 173 records
A comparative overview of epigenomic profiling methods
, Article Frontiers in Cell and Developmental Biology ; Volume 9 , 2021 ; 2296634X (ISSN) ; Sepehri, M. H ; Nazer, N ; Norouzi, M. R ; Sharif University of Technology
Frontiers Media S. A
2021
Abstract
In the past decade, assays that profile different aspects of the epigenome have grown exponentially in number and variation. However, standard guidelines for researchers to choose between available tools depending on their needs are lacking. Here, we introduce a comprehensive collection of the most commonly used bulk and single-cell epigenomic assays and compare and contrast their strengths and weaknesses. We summarize some of the most important technical and experimental parameters that should be considered for making an appropriate decision when designing epigenomic experiments. © Copyright © 2021 Mehrmohamadi, Sepehri, Nazer and Norouzi
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...
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,...
Over-Expression of immune-related lncrnas in inflammatory demyelinating polyradiculoneuropathies
, Article Journal of Molecular Neuroscience ; Volume 71, Issue 5 , 2021 , Pages 991-998 ; 08958696 (ISSN) ; Ghafouri-Fard, S ; Mazdeh, M ; Nicknafs, F ; Nazer, N ; Sayad, A ; Taheri, M ; Sharif University of Technology
Humana Press Inc
2021
Abstract
Long non-coding RNAs (lncRNAs) have crucial roles in the pathogenesis of immune-related disorders. However, their role in the pathobiology of inflammatory demyelinating polyradiculoneuropathies remains unclear. In the current study, we measured peripheral expression of four lncRNAs, namely TUG1, FAS-AS1, NEAT1, and GAS5, in patients with acute/chronic inflammatory demyelinating polyradiculoneuropathies (AIDP/CIDP) compared with healthy subjects. Notably, all lncRNAs were over-expressed in patients compared with controls (P < 0.0001 for all lncRNAs). When assessing their expressions in AIDP and CIDP groups separately, TUG1 and NEAT1 were up-regulated in both patient groups compared with...
Laboratory detection methods for the human coronaviruses
, Article European Journal of Clinical Microbiology and Infectious Diseases ; Volume 40, Issue 2 , 2021 , Pages 225-246 ; 09349723 (ISSN) ; Dowlatshahi, S ; Abdekhodaie, M. J ; Sharif University of Technology
Springer Science and Business Media Deutschland GmbH
2021
Abstract
Coronaviruses are a group of envelop viruses which lead to diseases in birds and mammals as well as human. Seven coronaviruses have been discovered in humans that can cause mild to lethal respiratory tract infections. HCoV-229E, HCoV-OC43, HCoV-NL63, and HCoV-HKU1 are the low-risk members of this family and the reason for some common colds. Besides, SARS-CoV, MERS-CoV, and newly identified SARS-CoV-2, which is also known as 2019-nCoV, are the more dangerous viruses. Due to the rapid spread of this novel coronavirus and its related disease, COVID-19, a reliable, simple, fast, and low-cost detection method is necessary for patient diagnosis and tracking worldwide. Human coronaviruses detection...
Optical pattern generator for efficient bio-data encoding in a photonic sequence comparison architecture
, Article PLoS ONE ; Volume 16, Issue 1 January 2021 , 2021 ; 19326203 (ISSN) ; Dijujin, N. H ; Koohi, S ; Sharif University of Technology
Public Library of Science
2021
Abstract
In this study, optical technology is considered as SA issues’ solution with the potential ability to increase the speed, overcome memory-limitation, reduce power consumption, and increase output accuracy. So we examine the effect of bio-data encoding and the creation of input images on the pattern-recognition error-rate at the output of optical Vander-lugt correlator. Moreover, we present a genetic algorithm-based coding approach, named as GAC, to minimize output noises of cross-correlating data. As a case study, we adopt the proposed coding approach within a correlation-based optical architecture for counting k-mers in a DNA string. As verified by the simulations on Salmonella whole-genome,...
Optical pattern generator for efficient bio-data encoding in a photonic sequence comparison architecture
, Article PloS one ; Volume 16, Issue 1 , 2021 , Pages e0245095- ; 19326203 (ISSN) ; Hashemi Dijujin, N ; Koohi, S ; Sharif University of Technology
NLM (Medline)
2021
Abstract
In this study, optical technology is considered as SA issues' solution with the potential ability to increase the speed, overcome memory-limitation, reduce power consumption, and increase output accuracy. So we examine the effect of bio-data encoding and the creation of input images on the pattern-recognition error-rate at the output of optical Vander-lugt correlator. Moreover, we present a genetic algorithm-based coding approach, named as GAC, to minimize output noises of cross-correlating data. As a case study, we adopt the proposed coding approach within a correlation-based optical architecture for counting k-mers in a DNA string. As verified by the simulations on Salmonella whole-genome,...
SVNN: an efficient PacBio-specific pipeline for structural variations calling using neural networks
, Article BMC Bioinformatics ; Volume 22, Issue 1 , 2021 ; 14712105 (ISSN) ; Hadadian Nejad Yousefi, M ; Goudarzi, M ; Sharif University of Technology
BioMed Central Ltd
2021
Abstract
Background: Once aligned, long-reads can be a useful source of information to identify the type and position of structural variations. However, due to the high sequencing error of long reads, long-read structural variation detection methods are far from precise in low-coverage cases. To be accurate, they need to use high-coverage data, which in turn, results in an extremely time-consuming pipeline, especially in the alignment phase. Therefore, it is of utmost importance to have a structural variation calling pipeline which is both fast and precise for low-coverage data. Results: In this paper, we present SVNN, a fast yet accurate, structural variation calling pipeline for PacBio long-reads...
Optical pattern generator for efficient bio-data encoding in a photonic sequence comparison architecture
, Article PLoS ONE ; Volume 16, Issue 1 , 2021 ; 19326203 (ISSN) ; Dijujin, N. H ; Koohi, S ; Sharif University of Technology
Public Library of Science
2021
Abstract
In this study, optical technology is considered as SA issues’ solution with the potential ability to increase the speed, overcome memory-limitation, reduce power consumption, and increase output accuracy. So we examine the effect of bio-data encoding and the creation of input images on the pattern-recognition error-rate at the output of optical Vander-lugt correlator. Moreover, we present a genetic algorithm-based coding approach, named as GAC, to minimize output noises of cross-correlating data. As a case study, we adopt the proposed coding approach within a correlation-based optical architecture for counting k-mers in a DNA string. As verified by the simulations on Salmonella whole-genome,...
Optical pattern generator for efficient bio-data encoding in a photonic sequence comparison architecture
, Article PloS one ; Volume 16, Issue 1 , 2021 , Pages e0245095- ; 19326203 (ISSN) ; Hashemi Dijujin, N ; Koohi, S ; Sharif University of Technology
NLM (Medline)
2021
Abstract
In this study, optical technology is considered as SA issues' solution with the potential ability to increase the speed, overcome memory-limitation, reduce power consumption, and increase output accuracy. So we examine the effect of bio-data encoding and the creation of input images on the pattern-recognition error-rate at the output of optical Vander-lugt correlator. Moreover, we present a genetic algorithm-based coding approach, named as GAC, to minimize output noises of cross-correlating data. As a case study, we adopt the proposed coding approach within a correlation-based optical architecture for counting k-mers in a DNA string. As verified by the simulations on Salmonella whole-genome,...
SVNN: an efficient PacBio-specific pipeline for structural variations calling using neural networks
, Article BMC Bioinformatics ; Volume 22, Issue 1 , 2021 ; 14712105 (ISSN) ; Hadadian Nejad Yousefi, M ; Goudarzi, M ; Sharif University of Technology
BioMed Central Ltd
2021
Abstract
Background: Once aligned, long-reads can be a useful source of information to identify the type and position of structural variations. However, due to the high sequencing error of long reads, long-read structural variation detection methods are far from precise in low-coverage cases. To be accurate, they need to use high-coverage data, which in turn, results in an extremely time-consuming pipeline, especially in the alignment phase. Therefore, it is of utmost importance to have a structural variation calling pipeline which is both fast and precise for low-coverage data. Results: In this paper, we present SVNN, a fast yet accurate, structural variation calling pipeline for PacBio long-reads...
Genetic risk variants for class switching recombination defects in ataxia-telangiectasia patients
, Article Journal of Clinical Immunology ; 2021 ; 02719142 (ISSN) ; Mehrmohamadi, M ; Ranjouri, M. R ; Akrami, M ; Rezaei, N ; Saberi, A ; Yazdani, R ; Abolhassani, H ; Aghamohammadi, A ; Sharif University of Technology
Springer
2021
Abstract
Background: Ataxia-telangiectasia (A-T) is a rare autosomal recessive disorder caused by mutations in the ataxia telangiectasia mutated (ATM) gene. A-T patients manifest considerable variability in clinical and immunological features, suggesting the presence of genetic modifying factors. A striking heterogeneity has been observed in class switching recombination (CSR) in A-T patients which cannot be explained by the severity of ATM mutations. Methods: To investigate the cause of variable CSR in A-T patients, we applied whole-exome sequencing (WES) in 20 A-T patients consisting of 10 cases with CSR defect (CSR-D) and 10 controls with normal CSR (CSR-N). Comparative analyses on modifier...
Atomic scale interactions between RNA and DNA aptamers with the TNF- α protein
, Article BioMed Research International ; Volume 2021 , 2021 ; 23146133 (ISSN) ; Moosavi, A ; Alexandrakis, G ; Mofrad, M. R. K ; Sharif University of Technology
Hindawi Limited
2021
Abstract
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...
Photoluminescent carbon quantum dot/poly-L-Lysine core-shell nanoparticles: A novel candidate for gene delivery
, Article Journal of Drug Delivery Science and Technology ; Volume 61 , 2021 ; 17732247 (ISSN) ; Mofazzal Jahromi, M. A ; Abdoli, A ; Mohammad Beigi, H ; Fatahi, Y ; Nourizadeh, H ; Zare, H ; Kiani, J ; Radmanesh, F ; Rabiee, N ; Jahani, M ; Mombeiny, R ; Karimi, M ; Sharif University of Technology
Editions de Sante
2021
Abstract
Cationic polymers such as poly-L-lysine (PLL) are able to interact electrostatically with DNA to produce polymeric systems with nanometric diameters due to the neutralization and accumulation of DNA. This study integrates the outstanding properties of carbon quantum dots (CQDs) with PLL to develop a novel gene delivery vehicle with a core-shell hybrid nanostructure. The CQD/PLL core-shell nanoparticles (NPs) were, therefore, synthesized in such a way that they had narrow size distribution and an average diameter under 10 nm, both of which were confirmed by dynamic light scattering (DLS) and transmission electron microscopy (TEM). Fourier transform infrared (FTIR) spectroscopy exhibited that...
Investigation of a protein complex network
, Article European Physical Journal B ; Volume 41, Issue 1 , 2004 , Pages 113-121 ; 14346028 (ISSN) ; Ramezanpour, A ; Karimipour, V ; Sharif University of Technology
2004
Abstract
The budding yeast Saccharomyces cerevisiae is the first eukaryote whose genome has been completely sequenced. It is also the first eukaryotic cell whose proteome (the set of all proteins) and interactome (the network of all mutual interactions between proteins) has been analyzed. In this paper we study the structure of the yeast protein complex network in which weighted edges between complexes represent the number of shared proteins. It is found that the network of protein complexes is a small world network with scale free behavior for many of its distributions. However we find that there are no strong correlations between the weights and degrees of neighboring complexes. To reveal...
Expression analysis of Wnt signaling pathway related lncRNAs in periodontitis: A pilot case-control study
, Article Human Gene ; Volume 33 , 2022 ; 27730441 (ISSN) ; Dashti, S ; Gholami, L ; Badrlou, E ; Sadeghpour, S ; Hussen, B. M ; Hidayat, H. J ; Nazer, N ; Shadnoush, M ; Sayad, A ; Arefian, N ; Sharif University of Technology
Elsevier B.V
2022
Abstract
LncRNAs are involved in the modulation of several signaling pathways which have a crucial effect in the differentiation of periodontal ligament cells and the induction of cementum regeneration. Autophagy and Wnt signaling are two important pathways with a wide range of interrelationships associated with periodontitis. We chose four lncRNAs based on their potential interaction with these two pathways. We examined the expression of FOXD2-AS1, NNT-AS1, GAS8-AS1, and CCAT1 lncRNAs in tissues and blood specimens of patients with periodontitis and unaffected controls using qRT-PCR. Expression amounts of FOXD2-AS1 were lower in blood of cases compared with controls (relative expression (RE) = 0.08,...
HELIOS: High-speed sequence alignment in optics
, Article PLoS Computational Biology ; Volume 18, Issue 11 , 2022 ; 1553734X (ISSN) ; Akbari Rokn Abadi, S ; Koohi, S ; Sharif University of Technology
Public Library of Science
2022
Abstract
In response to the imperfections of current sequence alignment methods, originated from the inherent serialism within their corresponding electrical systems, a few optical approaches for biological data comparison have been proposed recently. However, due to their low performance, raised from their inefficient coding scheme, this paper presents a novel all-optical high-throughput method for aligning DNA, RNA, and protein sequences, named HELIOS. The HELIOS method employs highly sophisticated operations to locate character matches, single or multiple mutations, and single or multiple indels within various biological sequences. On the other hand, the HELIOS optical architecture exploits...
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...
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...