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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...
Core flooding tests to investigate the effects of IFT reduction and wettability alteration on oil recovery during MEOR process in an Iranian oil reservoir
, Article Applied Microbiology and Biotechnology ; Volume 97, Issue 13 , July , 2013 , Pages 5979-5991 ; 01757598 (ISSN) ; Sharifinik, M ; Niazi, A ; Hashemi, A ; Ayatollahi, S ; Sharif University of Technology
2013
Abstract
Microbial enhanced oil recovery (MEOR) refers to the process of using bacterial activities for more oil recovery from oil reservoirs mainly by interfacial tension reduction and wettability alteration mechanisms. Investigating the impact of these two mechanisms on enhanced oil recovery during MEOR process is the main objective of this work. Different analytical methods such as oil spreading and surface activity measurements were utilized to screen the biosurfactant-producing bacteria isolated from the brine of a specific oil reservoir located in the southwest of Iran. The isolates identified by 16S rDNA and biochemical analysis as Enterobacter cloacae (Persian Type Culture Collection (PTCC)...
Chain deformation in translocation phenomena
, Article Soft Matter ; Volume 9, Issue 9 , 2013 , Pages 2750-2759 ; 1744683X (ISSN) ; Maleknejad, A ; Varnik, F ; Ejtehadi, M. R ; Sharif University of Technology
2013
Abstract
Deformation of single stranded DNA in a translocation process before reaching the pore is investigated. By solving the Laplace equation in a suitable coordinate system and with appropriate boundary conditions, an approximate solution for the electric field inside and outside a narrow pore is obtained. With an analysis based on the "electrohydrodynamic equivalence" we determine the possibility of the extension of a charged polymer due to the presence of an electric field gradient in the vicinity of the pore entrance. With a multi-scale hybrid simulation (LB-MD), it is shown that an effective deformation before reaching the pore occurs, which facilitates the process of finding the entrance for...
Finding maximum edge bicliques in convex bipartite graphs
, Article Algorithmica ; Volume 64, Issue 2 , October , 2012 , Pages 311-325 ; 01784617 (ISSN) ; Pu, S ; Sack, J. R ; Uno, T ; Zarrabi Zadeh, H ; Sharif University of Technology
Springer
2012
Abstract
A bipartite graph G = (A,B,E) is convex on B if there exists an ordering of the vertices of B such that for any vertex v ? A, vertices adjacent to v are consecutive in B. A complete bipartite subgraph of a graph G is called a biclique of G. Motivated by an application to analyzing DNA microarray data, we study the problem of finding maximum edge bicliques in convex bipartite graphs. Given a bipartite graph G = (A,B,E) which is convex on B, we present a new algorithm that computes a maximum edge biclique of G in O(nlog3 n log log n) time and O(n) space, where n = |A|. This improves the current O(n 2) time bound available for the problem. We also show that for two special subclasses of convex...
Toward single-DNA electrochemical biosensing by graphene nanowalls
, Article ACS Nano ; Volume 6, Issue 4 , March , 2012 , Pages 2904-2916 ; 19360851 (ISSN) ; Ghaderi, E ; Rahighi, R ; Sharif University of Technology
2012
Abstract
Graphene oxide nanowalls with extremely sharp edges and preferred vertical orientation were deposited on a graphite electrode by using electrophoretic deposition in an Mg 2+-GO electrolyte. Using differential pulse voltammetry (DPV), reduced graphene nanowalls (RGNWs) were applied for the first time, in developing an ultra-high-resolution electrochemical biosensor for detection of the four bases of DNA (G, A, T, and C) by monitoring the oxidation signals of the individual nucleotide bases. The extremely enhanced electrochemical reactivity of the four free bases of DNA, single-stranded DNA, and double-stranded DNA (dsDNA) at the surface of the RGNW electrode was compared to electrochemical...
Dose-dependent effects of nanoscale graphene oxide on reproduction capability of mammals
, Article Carbon ; Volume 95 , December , 2015 , Pages 309-317 ; 00086223 (ISSN) ; Ghaderi, E ; Hashemi, E ; Akbari, E ; Sharif University of Technology
Elsevier Ltd
2015
Abstract
In vivo dose-dependent effects of nanoscale graphene oxide (NGO) sheets on reproduction capability of Balb/C mice were investigated. Biodistribution study of the NGO sheets (intravenously injected into male mice at dose of ∼2000 μg/mL or 4 mg/kg of body weight) showed a high graphene uptake in testis. Hence, in vivo effects of the NGO sheets on important characteristics of spermatozoa (including their viability, morphology, kinetics, DNA damage and chromosomal aberration) were evaluated. Significant in vivo effects was found at the injected concentrations ≥200 μg/mL after (e.g., ∼45% reduction in sperm viability and motility at 2000 μg/mL). Observation of remarkable DNA fragmentations and...
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...
Toward chemical perfection of graphene-based gene carrier via ugi multicomponent assembly process
, Article Biomacromolecules ; Volume 17, Issue 9 , 2016 , Pages 2963-2971 ; 15257797 (ISSN) ; Akhavan, O ; Hashemi, E ; Shamsara, M ; Sharif University of Technology
American Chemical Society
Abstract
The graphene-based materials with unique, versatile, and tunable properties have brought new opportunities for the leading edge of advanced nanobiotechnology. In this regard, the use of graphene in gene delivery applications is still at early stages. In this study, we successfully designed a new complex of carboxylated-graphene (G-COOH) with ethidium bromide (EtBr) and used it as a nanovector for efficient gene delivery into the AGS cells. G-COOH, with carboxyl functions on its surface, in the presence of EtBr, formaldehyde, and cyclohexylisocyanide were participated in Ugi four component reaction to fabricate a stable amphiphilic graphene-EtBr (AG-EtBr) composite. The coupling reaction was...
Smart micro/nanoparticles in stimulus-responsive drug/gene delivery systems
, Article Chemical Society Reviews ; Volume 45, Issue 5 , 2016 , Pages 1457-1501 ; 03060012 (ISSN) ; Ghasemi, A ; Sahandi Zangabad, P ; Rahighi, R ; Moosavi Basri, S. M ; Mirshekari, H ; Amiri, M ; Shafaei Pishabad, Z ; Aslani, A ; Bozorgomid, M ; Ghosh, D ; Beyzavi, A ; Vaseghi, A ; Aref, A. R ; Haghani, L ; Bahrami, S ; Hamblin, M. R ; Sharif University of Technology
Royal Society of Chemistry
2016
Abstract
New achievements in the realm of nanoscience and innovative techniques of nanomedicine have moved micro/nanoparticles (MNPs) to the point of becoming actually useful for practical applications in the near future. Various differences between the extracellular and intracellular environments of cancerous and normal cells and the particular characteristics of tumors such as physicochemical properties, neovasculature, elasticity, surface electrical charge, and pH have motivated the design and fabrication of inventive "smart" MNPs for stimulus-responsive controlled drug release. These novel MNPs can be tailored to be responsive to pH variations, redox potential, enzymatic activation, thermal...
The characterization of proteins involved in toxic metal resistance of a bacterial strain isolated from mine site using a proteomic approach
, Article Pollution Research ; Volume 28, Issue 3 , 2009 , Pages 337-343 ; 02578050 (ISSN) ; Arabian, D ; Roostaazad, R ; Gade, W. N ; Shitole, M. G ; Sharif University of Technology
Abstract
We investigated the response of a bacterial strain isolated from low grade complex zinc and lead sulfide mines to metals toxicity (i.e., zinc, manganese, nickel, cobalt, copper, arsenate, chromium, lead, and mercury). The bacterium was identified as a strain of Aciditiobacillus ferrooxidans. The isolate showed good resistance to most of the toxic metals. The proteomics approach was used to identify the differentially expressed proteins under heavy metal stress in this strain. Four of the differentially expressed proteins were identified as major outer membrane protein of A. ferrooxidans, ribulose bisphosphate carboxylase large subunit of A. ferrooxidans, putative DNA restriction methylase,...
High-speed all-optical DNA local sequence alignment based on a three-dimensional artificial neural network
, Article Journal of the Optical Society of America A: Optics and Image Science, and Vision ; Volume 34, Issue 7 , 2017 , Pages 1173-1186 ; 10847529 (ISSN) ; Babashah, H ; Koohi, S ; Kavehvash, Z ; Sharif University of Technology
OSA - The Optical Society
2017
Abstract
This paper presents an optical processing approach for exploring a large number of genome sequences. Specifically, we propose an optical correlator for global alignment and an extended moiré matching technique for local analysis of spatially coded DNA, whose output is fed to a novel three-dimensional artificial neural network for local DNA alignment. All-optical implementation of the proposed 3D artificial neural network is developed and its accuracy is verified in Zemax. Thanks to its parallel processing capability, the proposed structure performs local alignment of 4 million sequences of 150 base pairs in a few seconds, which is much faster than its electrical counterparts, such as the...
Noble metal nanoparticles in biosensors: Recent studies and applications
, Article Nanotechnology Reviews ; Volume 6, Issue 3 , 2017 , Pages 301-329 ; 21919089 (ISSN) ; Sahandi Zangabad, P ; Mirshekari, H ; Karimi, M ; Hamblin, M. R ; Sharif University of Technology
Walter de Gruyter GmbH
2017
Abstract
The aim of this review is to cover advances in noble metal nanoparticle (MNP)-based biosensors and to outline the principles and main functions of MNPs in different classes of biosensors according to the transduction methods employed. The important biorecognition elements are enzymes, antibodies, aptamers, DNA sequences, and whole cells. The main readouts are electrochemical (amperometric and voltametric), optical (surface plasmon resonance, colorimetric, chemiluminescence, photoelectrochemical, etc.) and piezoelectric. MNPs have received attention for applications in biosensing due to their fascinating properties. These properties include a large surface area that enhances biorecognizers...
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 ; 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,...
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...
Prediction of DNA/RNA Sequence Binding Site to Protein with the Ability to Implement on GPU
, M.Sc. Thesis Sharif University of Technology ; Koohi, Sommaye (Supervisor)
Abstract
Based on the importance of DNA/RNA binding proteins in different cellular processes, finding binding sites of them play crucial role in many applications, like designing drug/vaccine, designing protein, and cancer control. Many studies target this issue and try to improve the prediction accuracy with three strategies: complex neural-network structures, various types of inputs, and ML methods to extract input features. But due to the growing volume of sequences, these methods face serious processing challenges. So, this paper presents KDeep, based on CNN-LSTM and the primary form of DNA/RNA sequences as input. As the key feature improving the prediction accuracy, we propose a new encoding...
Denaturation of Drew-Dickerson DNA in a high salt concentration medium: Molecular dynamics simulations
, Article Journal of Computational Chemistry ; Volume 32, Issue 16 , September , 2011 , Pages 3354-3361 ; 01928651 (ISSN) ; Parsafar, G. A ; Abroshan, H ; Akbarzadeh, H ; Sharif University of Technology
2011
Abstract
We have performed molecular dynamics simulation on B-DNA duplex (CGCGAATTGCGC) at different temperatures. The DNA was immerged in a salt-water medium with 1 M NaCl concentration to investigate salt effect on the denaturation process. At each temperature, configurational entropy is estimated using the covariance matrix of atom-positional fluctuations, from which the melting temperature (T m) was found to be 349 K. The calculated configuration entropy for different bases shows that the melting process involves more peeling (including fraying from the ends) conformations, and therefore the untwisting of the duplex and peeling states form the transition state of the denaturation process. There...
Extreme bendability of DNA double helix due to bending asymmetry
, Article Journal of Chemical Physics ; Volume 143, Issue 10 , 2015 ; 00219606 (ISSN) ; Eslami Mossallam, B ; Naderi, S ; Ejtehadi, M. R ; Sharif University of Technology
American Institute of Physics Inc
2015
Abstract
Experimental data of the DNA cyclization (J-factor) at short length scales exceed the theoretical expectation based on the wormlike chain (WLC) model by several orders of magnitude. Here, we propose that asymmetric bending rigidity of the double helix in the groove direction can be responsible for extreme bendability of DNA at short length scales and it also facilitates DNA loop formation at these lengths. To account for the bending asymmetry, we consider the asymmetric elastic rod (AER) model which has been introduced and parametrized in an earlier study [B. Eslami-Mossallam and M. R. Ejtehadi, Phys. Rev. E 80, 011919 (2009)]. Exploiting a coarse grained representation of the DNA molecule...
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...