Loading...
Search for:
dna
0.008 seconds
Total 173 records
Study, Optimization and Construction of a Microfluidic Gene Amplification Device by Using Thin Film Layer Method
, M.Sc. Thesis Sharif University of Technology ; Vosoughi, Manouchehr (Supervisor) ; Alemzadeh, Iran (Co-Supervisor) ; Shamloo, Amir (Co-Supervisor)
Abstract
Polymerase Chain Reaction (PCR) is a process in which a special piece of a gene is amplified millions of times over a short period. This method has been of paramount importance in different fields of research and has been applied for different applications. PCR requires thermal cycling, or repeated temperature changes between two or three discrete temperatures to amplify specific nucleic acid target sequences. To achieve such thermal cycling, conventional bench-top thermal cyclers generally use a metal heating block powered by Peltier elements or benefit from forced convection heat transfer. Due to the fact that these methods are time consuming, it seems that design and fabrication of a fast...
Solving haplotype reconstruction problem in MEC model with hybrid information fusion
, Article EMS 2008, European Modelling Symposium, 2nd UKSim European Symposium on Computer Modelling and Simulation, Liverpool, 8 September 2008 through 10 September 2008 ; 2008 , Pages 214-218 ; 9780769533254 (ISBN) ; Moeinzadeh, M. H ; Habibi, J ; Sharifian-R, S ; Rasooli-V, A ; Najafi-A, A ; Sharif University of Technology
2008
Abstract
Single Nucleotide Polymorphisms (SNPs), a single DNA base varying from one individual to another, are believed to be the most frequent form responsible for genetic differences. Genotype is the conflated information of a pair of haplotypes on homologous chromosomes. Although haplotypes have more information for disease associating than individual SNPs and genotype, it is substantially more difficult to determine haplotypes through experiments. Hence, computational methods which can reduce the cost of determining haplotypes become attractive alternatives. MEC, as a standard model for haplotype reconstruction, is fed by fragments as input to infer the best pair of haplotypes with minimum error...
Characterization of a moderate thermophilic Nocardia species able to grow on polycyclic aromatic hydrocarbons
, Article Letters in Applied Microbiology ; Volume 45, Issue 6 , December , 2007 , Pages 622-628 ; 02668254 (ISSN) ; Vossoughi, M ; Ardestani, S. K ; Sharif University of Technology
2007
Abstract
Aims: Our goal was the characterization of a new moderate thermophilic polycyclic aromatic hydrocarbon (PAH)-utilizing Nocardia strain. Methods and Results: A thermophilic bacterium, strain TSH1, was isolated from a contaminated soil. The macroscopic and microscopic features fit well with the description of Nocardia species. The results of 16S rRNA gene analysis showed 100% match to the type strain of N. otitidiscaviarum DSM 43242T. Strain TSH1 showed the same mycolic acid pattern as the type strain of N. otitidiscaviarum but its fatty acid profile did not permit identification to the species level. The carbon utilization profile of strain TSH1 was different from N. otitidiscaviarum. The...
Comparison of Shuffling-Adaptive Neuro Fuzzy Inference System (Shuffling-ANFIS) with conventional ANFIS as feature selection methods for nonlinear systems
, Article QSAR and Combinatorial Science ; Volume 26, Issue 10 , 2007 , Pages 1046-1059 ; 1611020X (ISSN) ; Kyani, A ; Sharif University of Technology
2007
Abstract
This paper compares the Shuffling-Adaptive Neuro Fuzzy Inference System (Shuffling-ANFIS) with conventional ANFIS as the method for selecting the features of nonlinear systems. Shuffling-ANFIS technique uses the advantage of data splitting with the ANFIS as a powerful feature selection method to select the most important factors affecting nonlinear phenomena. In this technique, the features with the largest percent of frequency can be found by running the conventional ANFIS sequential forward search on the large number of training and test sets using leave-one-out validation criteria. The superiority of Shuffling-ANFIS over the conventional ANFIS was evaluated by using two synthetic and one...
Thermodynamic studies on the complexation of cobalt(II) with dopamine in a cosolvent system
, Article Journal of Solution Chemistry ; Volume 36, Issue 5 , 2007 , Pages 595-604 ; 00959782 (ISSN) ; Boghaei, D. M ; Sharif University of Technology
2007
Abstract
Equilibrium constants for formation of a cobalt(II) complex with the bidentate ligand dopamine have been studied with spectrophotometric methods in water + ethanol cosolvent systems at 15, 25, and 35 (±0.1)∈°C and an ionic strength of 0.2 mol·dm-3. The ionic strength was maintained using sodium chloride and a phosphate buffer. The stability constants of the complex and the resulting Gibbs energy changes are obtained. The results are discussed in terms of the effect of solvent on protonation and complexation. © Springer Science+Business Media, LLC 2007
Simulation of DNA electrophoresis through microstructures
, Article Electrophoresis ; Volume 28, Issue 3 , 2007 , Pages 301-308 ; 01730835 (ISSN) ; Sarbolouki, M. N ; Rouhani, S ; Sharif University of Technology
2007
Abstract
The dependence of the mobility of DNA molecules through an hexagonal array of micropillars on their length and the applied electric field was investigated and it was found that mobility is a nonmonotonic function of their length. Results also revealed that the size dependence of the DNA mobility depends on the applied electric field and there is a crossover around E ≈ 25 V/cm for the mobility of λ-DNA and T4-DNA. These observations are explained in terms of the diffusion process inside the structure affected by the solvent and are modeled using the Langevin and its corresponding Fokker-Planck equations. The phenomenon is generalized under three regimes in a phase diagram relating the...
Effect of pesticides on erythrocytes of indigenous fish Labeo rohita
, Article Journal of King Saud University - Science ; Volume 33, Issue 7 , 2021 ; 10183647 (ISSN) ; Nadeem, A ; Maalik, S ; Mushtaq, S ; Iqbal, N ; Khan, A. K ; Shabbir, A ; Imran, M ; Niaz, S ; Yasin, M ; Qayyum, M. A ; Ahmad, B ; Skalicky, M ; Alharbi, S. A ; Alfarraj, S ; Sharif University of Technology
Elsevier B.V
2021
Abstract
Single cell gel electrophoresis was used to observe the effect of bifenthrin and chlorpyrifos on Labeo rohita. The present work was planned to study the genotoxic effect of pesticide mixture on the major indian carp, L. rohita at sub-lethal concentration 33% LC50. First of all, 96-hr LC50 was determined for L. rohita, then fish was given sub-lethal environment for 70 days. Erythrocytes from blood were taken after each fortnight for the assessment of time dependent DNA damage (% damage), aggregate tail length of comets and genomic destruction. There was increase in damage up to 56 days and after that a slight decrease was observed in next fourteen days. After statistical analysis, it was...
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...
Homozygous mutations in C14orf39/SIX6OS1 cause non-obstructive azoospermia and premature ovarian insufficiency in humans
, Article American Journal of Human Genetics ; Volume 108, Issue 2 , 2021 , Pages 324-336 ; 00029297 (ISSN) ; Jiao, Y ; Khan, R ; Jiang, X ; Javed, A. R ; Ali, A ; Zhang, H ; Zhou, J ; Naeem, M ; Murtaza, G ; Li, Y ; Yang, G ; Zaman, Q ; Zubair, M ; Guan, H ; Zhang, X ; Ma, H ; Jiang, H ; Ali, H ; Dil, S ; Shah, W ; Ahmad, N ; Zhang, Y ; Shi, Q ; Sharif University of Technology
Cell Press
2021
Abstract
Human infertility is a multifactorial disease that affects 8%–12% of reproductive-aged couples worldwide. However, the genetic causes of human infertility are still poorly understood. Synaptonemal complex (SC) is a conserved tripartite structure that holds homologous chromosomes together and plays an indispensable role in the meiotic progression. Here, we identified three homozygous mutations in the SC coding gene C14orf39/SIX6OS1 in infertile individuals from different ethnic populations by whole-exome sequencing (WES). These mutations include a frameshift mutation (c.204_205del [p.His68Glnfs∗2]) from a consanguineous Pakistani family with two males suffering from non-obstructive...
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...
Design and Fabrication of Microfluidic System for Cell Lysis and DNA Purification
, M.Sc. Thesis Sharif University of Technology ; Shamloo, Amir (Supervisor) ; Hosseini, Vahid (Supervisor)
Abstract
Nowadays, intracellular studies have been widely developed in biological applications. Intracellular analysis requires direct experiments on cells such as cell separation, purification, lysis and DNA extraction. The process of cell lysis and the resulting DNA purification is a crucial step in diagnostic processes. Since, the basis of many genetic studies is the information existed in double-stranded DNA structures.In this project, a microfluidic system is presented which performs integrated chemical cell lysis and DNA extraction. The cell used in this study is L-929. In order to increase cell lysis, the serpentine micromixer in combination with internal and external barriers at the beginning...
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,...