Sharif Digital Repository

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... 

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... 

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... 

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... 

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... 

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... 

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,... 

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... 

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... 

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,... 

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,... 

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... 

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... 

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... 

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... 

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... 

The new water-soluble derivative of pyrazino[2,3-f][1,10] phenanthroline has been synthesized and characterized by conductivity measurement, elemental analysis, FT-IR, 1H NMR, 13C NMR spectroscopic studies, as well as single crystal x-ray crystallography. Theoretical calculations have been performed using the density functional theory (DFT) in order to confirm the structure and understand the electronic structure of the synthesized compound. The DNA binding properties of the compound were investigated by absorption spectroscopy, melting temperature and viscosity measurements. The intrinsic binding constant, Kb, was determined as 7.84 × 103 M−1 at 298 K. Thermodynamic parameters showed that... 

Breast Cancer (BRCA) is the most common threat in women worldwide. Increasing death rate of diagnosed cases is the main leading cause of designing specific genosensors for BRCA − related cancer detection. In the present study, an ultrasensitive label − free electrochemical DNA (E − DNA) sensor based on conducting polymer/reduced graphene − oxide platform has been developed for the detection of BRCA1 gene. An electrochemical method was applied as a simple and controllable technique for the electrochemical reduction of graphene oxide and also, electro − polymerization of pyrrole − 3 − carboxylic acid monomer. The results of the present work show that the polymer − coated reduced graphene −... 

The highly sensitive impedimetric biosensor in label free approach for hepatitis B virus DNA (HPV DNA) detection based on tellurium doped ZnO nanowires was fabricated. The NWs were grown by hybrid thin film oxidation in the physical vapor deposition (PVD) mechanism. The morphology characterization of the synthesized NWs was performed by field emission scanning electron microscopy (FESEM) and the images demonstrated that the diameter and the length of the materialized NWs were around 50 nm and several micrometers, respectively. The high-resolution transmission electron microscopy (HRTEM) image indicated that the fabricated NWs were crystalline and their phase characterization was validated by... 

Background: Long reads provide valuable information regarding the sequence composition of genomes. Long reads are usually very noisy which renders their alignments on the reference genome a daunting task. It may take days to process datasets enough to sequence a human genome on a single node. Hence, it is of primary importance to have an aligner which can operate on distributed clusters of computers with high performance in accuracy and speed. Results: In this paper, we presented IMOS, an aligner for mapping noisy long reads to the reference genome. It can be used on a single node as well as on distributed nodes. In its single-node mode, IMOS is an Improved version of Meta-aligner (IM)...