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polymerase-chain-reaction
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Total 66 records
PCR Amplification Prediction using Machine Learning
, M.Sc. Thesis Sharif University of Technology ; Hossein Khalaj, Babak (Supervisor)
Abstract
Polymerase Chain Reaction (PCR) is a laboratory method for amplifying a part of DNA. This method is used in determining the sequence of genes, detecting pathogenic agents in epidemics, creating genetic changes in bacteria, diseases, plants and even animals. Many factors affect the quality of the reaction. Each of these factors can be effective in amplifying the target in DNA. If we can predict the result of PCR using the factors involved in the reaction, it will save a lot of money and time. The aim of this research is to predict the result of PCR amplification using machine learning methods. For this purpose, two methods are proposed: feature-based method and string-based method. In the...
Design of a Microfluidic Digital Droplet PCR
, M.Sc. Thesis Sharif University of Technology ; Saeedi, Mohammad Saeed (Supervisor)
Abstract
Polymerase chain reaction, abbreviated as PCR, is a method of amplifying the number of copies of a desired DNA sequence through special protocols. The rapid advance of microfluidic devices and the emerging concept of digital microfluidics has resulted into the development of digital droplet PCR (ddPCR) systems with their significant uses in the detection of rare mutations, cancer diagnosis, and surveillance. A large number of micron-sized droplets are required to perform ddPCR. in this study, To investigate the gradient of confinements induced droplet self-breakup mechanism, we carried out the computational fluid dynamics (CFD) simulations for the two-phase flow using a commercial software...
Design, Simulation and Construction of a Rapid Gene Amplification Microfluidic Device Using Polymerase Chain Reaction (PCR) Method
, M.Sc. Thesis Sharif University of Technology ; Shamloo, Amir (Supervisor)
Abstract
Polymerase chain reaction method is a conventional method for obtaining multiple copies of a specified segment in the DNA molecule and to amplify the DNA molecule itself. Therefore, 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. Although efforts have been made in order to reduce...
Design and Fabrication of a Microfluidic Digital PCR
, M.Sc. Thesis Sharif University of Technology ; Saeedi, Mohammad Saeed (Supervisor) ; Firouzabadi, Bahar (Supervisor)
Abstract
Polymerase chain reaction, abbreviated as PCR, is a method of amplifying the number of copies of a desired DNA sequence through special protocols. The rapid advance of microfluidic devices and the emerging concept of digital microfluidics has resulted into the development of digital droplet PCR (ddPCR) systems with their significant uses in the detection of rare mutations, cancer diagnosis, and surveillance. In this study, an integrated ddPCR microfluidic chip alongside its thermoelectric thermal cycler and optical analysis systems have been designed, fabricated and their performance has been tested and evaluated. It was shown that the effect of master mold’s surface quality, the material of...
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...
Creating Random Mutations on The Human Transglutaminase 2 Gene and Lysozyme Gene to Increase The Solubility of the Enzymes in order to Perform Promiscuous Organic Reactions Using The Recombinant Enzymes
, M.Sc. Thesis Sharif University of Technology ; Kalhor, Hamid Reza (Supervisor)
Abstract
Transglutaminase 2 enzyme is expressed in various parts of the human body and is present in almost all tissue cells. The function of this enzyme is multiple and it catalyzes different reactions depending on where it is located in the cell. The most important activities of this enzyme are: isopeptide bond formation between the side chains of two proteins (transamidation reaction), diamidation reaction (hydrolysis of amide bond), esterification, kinase activity. The hen egg white lysozyme protein is another natural antimicrobial protein that has been extensively studied. The muramidase activity of egg white lysozyme against highly gram-positive bacteria is well known, and this property has...
Cloning and Production of the Flavin Reductase Enzyme in Order to Perform Organic Reaction and Synthesis of Cation Exchange Column for Protein Purification
, M.Sc. Thesis Sharif University of Technology ; Kalhor, Hamid Reza (Supervisor)
Abstract
The reductase enzymes perform an important function in the cell. These enzymes are usually coupled with other enzymes and participate in reactions such as halogenation, reduction of alkene, and carboxylic acids. These reactions are carried out by reproducing cofactors such as FADH2 and NAD+; however, there is no evidence that this enzyme alone can perform an organic reaction. In this work, we aim to examine whether recombinant flavin reductase can carry out organic reactions. In order to amplify the flavin reductase enzyme gene from the E. coli genome by PCR (Polymerase Chain Reaction) method, two synthetic primers were designed; The forward primer of the gene contained a cleavage site for...
Ultra-sensitive detection of leukemia by graphene
, Article Nanoscale ; Vol. 6, issue. 24 , Dec , 2014 , p. 14810-14819 ; Ghaderi, E ; Hashemi, E ; Rahighi, R ; Sharif Universit of Technology
Abstract
Graphene oxide nanoplatelets (GONPs) with extremely sharp edges (lateral dimensions ∼20-200 nm and thicknesses <2 nm) were applied in extraction of the overexpressed guanine synthesized in the cytoplasm of leukemia cells. The blood serums containing the extracted guanine were used in differential pulse voltammetry (DPV) with reduced graphene oxide nanowall (rGONW) electrodes to develop fast and ultra-sensitive electrochemical detection of leukemia cells at leukemia fractions (LFs) of ∼10-11 (as the lower detection limit). The stability of the DPV signals obtained by oxidation of the extracted guanine on the rGONWs was studied after 20 cycles. Without the guanine extraction, the DPV peaks...
Colorimetric assay for exon 7 SMN1/SMN2 single nucleotide polymorphism using gold nanoprobes
, Article BioImpacts ; Volume 3, Issue 4 , 2013 , Pages 185-194 ; 22285652 (ISSN) ; Hormozi Nezhad, M. R ; Abadi, A ; Sanati, M. H ; Kazemi, B ; Sharif University of Technology
2013
Abstract
Introduction: Proximal spinal muscular atrophy (SMA) is one of the most significant neurodegenerative diseases amongst the autosomal-recessive genetic disorders which is caused by the absence of protein survival of motor neuron (SMN). A critical nucleotide difference in SMN2 compared to SMN1 gene leads to an inefficient protein. Hence, homozygous lack of SMN1 provides a progressive disease. Due to the high prevalence, up to now, several molecular diagnostic methods have been used which most of them are lengthy, expensive, and laborious. Methods: In the present study, we exploited a gold nanoprobe-based method for semi-quantitative SMN1 gene dosage analysis compared to SMN2. The assay was...
Novel high-performance nanocomposite proton exchange membranes based on poly (ether sulfone)
, Article Renewable Energy ; Volume 35, Issue 1 , 2010 , Pages 226-231 ; 09601481 (ISSN) ; Dashtimoghadam, E ; Ghaffarian, S.R ; Hasani Sadrabadi, M.H ; Heidari, M ; Moaddel, H ; Sharif University of Technology
2010
Abstract
In the present research, proton exchange membranes based on partially sulfonated poly (ether sulfone) (S-PES) with various degrees of sulfonation were synthesized. It was found that the increasing of sulfonation degree up to 40% results in the enhancement of water uptake, ion exchange capacity and proton conductivity properties of the prepared membranes to 28.1%, 1.59 meq g -1, and 0.145 S cm -1, respectively. Afterwards, nanocomposite membranes based on S-PES (at the predetermined optimum sulfonation degree) containing various loading weights of organically treated montmorillonite (OMMT) were prepared via the solution intercalation technique. X-ray diffraction patterns revealed the...
Biodesulfurization of dibenzothiophene by a newly isolated Rhodococcus erythropolis strain
, Article Bioresource Technology ; Volume 101, Issue 3 , 2010 , Pages 1102-1105 ; 09608524 (ISSN) ; Vosoughi, M ; Ziaee, A. A ; Sharif University of Technology
2010
Abstract
A new dibenzothiophene (DBT) desulfurizing bacterium was isolated from oil-contaminated soils in Iran. HPLC analysis and PCR-based detection of the presence of the DBT desulfurization genes (dszA, dszB and dszC) indicate that this strain converts DBT to 2-hydroxybiphenyl (2-HBP) via the 4S pathway. The strain, identified as Rhodococcus erythropolis SHT87, can utilize DBT, dibenzothiophene sulfone, thiophene, 2-methylthiophene and dimethylsulfoxide as a sole sulfur source for growth at 30 °C. The maximum specific desulfurization activity of strain SHT87 resting cells in aqueous and biphasic organic-aqueous systems at 30 °C was determined to be 0.36 and 0.47 μmol 2-HBP min-1 (g dry cell)-1,...
The nanofibrous PAN-PANi scaffold as an efficient substrate for skeletal muscle differentiation using satellite cells
, Article Bioprocess and Biosystems Engineering ; Volume 39, Issue 7 , 2016 , Pages 1163-1172 ; 16157591 (ISSN) ; Mahmoudifard, M ; Mohamadyar Toupkanlou, F ; Dodel, M ; Hajarizadeh, A ; Adabi, M ; Soleimani, M ; Sharif University of Technology
Springer Verlag
Abstract
Among polymers, polyaniline (PANi) has been introduced as a good candidate for muscle regeneration due to high conductivity and also biocompatibility. Herein, for the first time, we report the use of electrospun nanofibrous membrane of PAN-PANi as efficient scaffold for muscle regeneration. The prepared PAN-PANi electrospun nanofibrous membrane was characterized by scanning electron microscopy (SEM), Attenuated total reflectance fourier transform infrared spectroscopy (ATR-FTIR) and tensile examination. The softer scaffolds of non-composite electrospun nanofibrous PAN govern a higher rate of cell growth in spite of lower differentiation value. On the other hand, PAN-PANi electrospun...
Expression of functional recombinant human tissue transglutaminase (TG2) using the bac-to-bac baculovirus expression system
, Article Advanced Pharmaceutical Bulletin ; Volume 6, Issue 1 , 2016 , Pages 49-56 ; 22285881 (ISSN) ; Azari, S ; Kalhor, H. R ; Sharif University of Technology
Tabriz University of Medical Sciences
Abstract
Tissue transglutaminase (TG2) is a unique multifunctional enzyme. The enzyme possesses enzymatic activities such as transamidation/crosslinking and non-enzymatic functions such as cell migration and signal transduction. TG2 has been shown to be involved in molecular mechanisms of cancers and several neurodegenerative diseases such as Alzheimer's disease. The present study aimed at cloning and expression of full length human TG2 in Bac-to-Bac baculovirus expression system and evaluation of its activity. Methods: pFastBac HTA donor vector containing coding sequence of human TG2 was constructed. The construct was transformed to DH10Bac for generating recombinant bacmid. The verified bacmid was...
The different fate of satellite cells on conductive composite electrospun nanofibers with graphene and graphene oxide nanosheets
, Article Biomedical Materials (Bristol) ; Volume 11, Issue 2 , 2016 ; 17486041 (ISSN) ; Soleimani, M ; Hatamie, S ; Zamanlui, S ; Ranjbarvan, P ; Vossoughi, M ; Hosseinzadeh, S ; Sharif University of Technology
Institute of Physics Publishing
2016
Abstract
Electrospinning of composite polymer solutions provides fantastic potential to prepare novel nanofibers for use in a variety of applications. The addition of graphene (G) and graphene oxide (GO) nanosheets to bioactive polymers was found to enhance their conductivity and biocompatibility. Composite conductive nanofibers of polyaniline (PANI) and polyacrylonitrile (PAN) with G and GO nanosheets were prepared by an electrospinning process. The fabricated membranes were investigated by physical and chemical examinations including scanning electron microscopy (SEM), Raman spectroscopy, x-ray diffraction (XRD) and tensile assay. The muscle satellite cells enriched by a pre-plating technique were...
Study of epithelial differentiation and protein expression of keratinocyte-mesenchyme stem cell co-cultivation on electrospun nylon/B. vulgaris extract composite scaffold
, Article Materials Science and Engineering C ; Volume 75 , 2017 , Pages 653-662 ; 09284931 (ISSN) ; Soleimani, M ; Vossoughi, M ; Ranjbarvan, P ; Hamedi, S ; Zamanlui, S ; Mahmoudifard, M ; Sharif University of Technology
Abstract
Employing of the composite electrospun scaffold containing herbal extract in conjugation with co-culturing of cells can open up new window to the design of efficient biomaterials for skin tissue regeneration. Here, we introduce the synergistic effect of composite electrospun nanofibrous scaffold of nylon66 loaded with Beta vulgaris (B. vulgaris) (extract of beet roots, a plants whose widely used in Iranian folk medicine as wound healing medicine) and co-culture of mesenchymal stem-cells (MSCs)-human keratinocyte (H-keratino) differentiation towards epithelial lineage. In vitro biocompatibility was examined through MTT assay and epithelial differentiation checked by real-time PCR and...
MicroRNAs 29, 150, 155, 223 level and their relation to viral and immunological markers in HIV-1 infected naive patients
, Article Future Virology ; Volume 13, Issue 9 , 2018 , Pages 637-645 ; 17460794 (ISSN) ; Bokharaei Salim, F ; Esghaei, M ; Keyvani, H ; Honardoost, M ; Mostafaei, S ; Ghasemi, A ; Tavakoli, A ; Javanmard, D ; Babaei, F ; Garshasbi, S ; Monavari, S. H ; Sharif University of Technology
Abstract
Aim: The aim of this study was to assess the relationship between microRNAs and viral and immunological markers in HIV-1 infection. Materials & methods: The expression level of miRNAs was evaluated in 60 HIV-1 patients and 20 healthy controls using real-time PCR assays. Results: The results showed that among all miRNAs, miR-29 and miR-150 were significantly downregulated in HIV-1 patients compared with healthy controls, while miR-155 and miR-223 were significantly upregulated compared with healthy controls (p < 0.001 for all comparisons). Conclusion: The mentioned miRNAs seem to influence the clinical progression of HIV-1 infection in naive patients. Moreover, determining the profiles of...
Multifunctional core-shell nanoplatforms (gold@graphene oxide) with mediated NIR thermal therapy to promote miRNA delivery
, Article Nanomedicine: Nanotechnology, Biology, and Medicine ; Volume 14, Issue 6 , 2018 , Pages 1891-1903 ; 15499634 (ISSN) ; Akhavan, O ; Adeli, M ; Razzazan, S ; Dinarvand, R ; Zanganeh, S ; Soleimani, M ; Dinarvand, M ; Atyabi, F ; Sharif University of Technology
Elsevier Inc
2018
Abstract
Recent insights into the nanomedicine have revealed that nanoplatforms enhance the efficacy of carrier in therapeutic applications. Here, multifunctional nanoplatforms were utilized in miRNA-101 delivery and NIR thermal therapy to induce apoptosis in breast cancer cells. Au nanorods (NRs) or nanospheres (NSs) covered with graphene oxide (GO) were prepared and functionalized with polyethylene glycol as a stabilizer and poly-L-arginine (P-L-Arg) as a targeting agent. In nanoplatforms, coupling Au@GO prepared stable structures with higher NIR reactivity. P-L-Arg substantially enhanced the cellular uptake and gene retardation of stuffs coated by them. However, rod-shape nanoplatforms indicated...
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...
Engineering of mature human induced pluripotent stem cell-derived cardiomyocytes using substrates with multiscale topography
, Article Advanced Functional Materials ; Volume 28, Issue 19 , 2018 ; 1616301X (ISSN) ; Garbern, J. C ; Behzadi, S ; Hill, M. J ; Tresback, J. S ; Heydari, T ; Ejtehadi, M. R ; Ahmed, N ; Copley, E ; Aghaverdi, H ; Lee, R. T ; Farokhzad, O. C ; Mahmoudi, M ; Sharif University of Technology
Wiley-VCH Verlag
2018
Abstract
Producing mature and functional cardiomyocytes (CMs) by in vitro differentiation of induced pluripotent stem cells (iPSCs) using only biochemical cues is challenging. To mimic the biophysical and biomechanical complexity of the native in vivo environment during the differentiation and maturation process, polydimethylsiloxane substrates with 3D topography at the micrometer and sub-micrometer levels are developed and used as cell-culture substrates. The results show that while cylindrical patterns on the substrates resembling mature CMs enhance the maturation of iPSC-derived CMs, sub-micrometer-level topographical features derived by imprinting primary human CMs further accelerate both the...
Prevalence of influenza a infection in the middle-east: a systematic review and meta-analysis
, Article Clinical Respiratory Journal ; Volume 12, Issue 5 , 2018 , Pages 1787-1801 ; 17526981 (ISSN) ; Monavari, H. R ; Mostafaei, S ; Hadifar, S ; Ghasemi, A ; Babaei, F ; Kavosi, H ; Tavakoli, A ; Javanmard, D ; Esghaei, M ; Khodabandehlou, N ; Sharif University of Technology
Blackwell Publishing Ltd
2018
Abstract
Objective: This systematic review and meta-analysis was performed to determine the prevalence rate of influenza virus from different parts of Middle East region, and present an overall relative frequency (RF) for this region. Methods: The authors performed a systematic literature review from several reliable databases such as PubMed, ISI Web of Science and Scopus during 2000–2016. Furthermore, the keywords of this research were ‘Influenza’, ‘Subtype’, ‘Seroprevalence’, ‘Incidence’, ‘Seroepidemiology’, ‘H1N1’, ‘H3N2’, ‘H5N1’, ‘H9N2’, ‘Middle-East’ and ‘Meta-analysis’. The reported data were selected according to inclusion and exclusion criteria. Results: The authors selected 71 studies out of...