Sharif Digital Repository

The novel coronavirus pandemic has rapidly spread around the world since December 2019. Various techniques have been applied in identification of SARS-CoV-2 or COVID-19 infection including computed tomography imaging, whole genome sequencing, and molecular methods such as reverse transcription polymerase chain reaction (RT-PCR). This review article discusses the diagnostic methods currently being deployed for the SARS-CoV-2 identification including optical biosensors and point-of-care diagnostics that are on the horizon. These innovative technologies may provide a more accurate, sensitive and rapid diagnosis of SARS-CoV-2 to manage the present novel coronavirus outbreak, and could be... 

The novel coronavirus pandemic has rapidly spread around the world since December 2019. Various techniques have been applied in identification of SARS-CoV-2 or COVID-19 infection including computed tomography imaging, whole genome sequencing, and molecular methods such as reverse transcription polymerase chain reaction (RT-PCR). This review article discusses the diagnostic methods currently being deployed for the SARS-CoV-2 identification including optical biosensors and point-of-care diagnostics that are on the horizon. These innovative technologies may provide a more accurate, sensitive and rapid diagnosis of SARS-CoV-2 to manage the present novel coronavirus outbreak, and could be... 

Although numerous molecular methods for spinal muscular atrophy (SMA) detection have been exploited, most of hem are laborious, time consuming and costly. Recently, gold nanoparticles (AuNPs) have attracted attention in the field of colourimetric bioanalysis, because AuNP aggregation can be tracked with the naked eye as well as ultraviolet-visible (UV-vis) peak analysis. Here, based on a non-cross linking platform, a colourimetric-based method was used to evaluate the capability of thiolated oligo-AuNPs (Au nanoprobes) to distinguish between normal individuals, carriers and those with SMA. In this platform, removal of the repulsive force of the Au nanoprobes using high salt concentration... 

The single stranded DNA can be adsorbed on the negatively charged surface of gold nanoparticles (AuNPs), but the rigid structure of double stranded DNA prevents it from adsorption. Signal of a tagged single stranded DNA will be quenched by the plasmon effect of the AuNP surface after its adsorption. This phenomenon has been used to study the DNA hybridization and interactions of two complementary 21mer oligonucleotides each tagged with a different fluorescent dye in the presence of 13 nm gold nanoparticles. The DNA strands used in this study belong to the genome of HIV. The obtained rank deficient three-way fluorescence data sets were resolved by both PARAFAC and restricted Tucker3 models.... 

In recent years, there has been increasing interest in damaged DNA and RNA nucleobases. These damaged nucleobases can cause DNA mutation, resulting in various diseases such as cancer. Alkylating agents are mutagenic and carcinogenic in a variety of prokaryotic and eukaryotic organisms. The present study employs density functional theory (DFT/B3LYP) with the 6-311++G(d,p) basis set to investigate the effect of chemical damage in O-alkyl pyrimidines such as O4-methylthymine, O2-methylcytosine and O 2-methylthymine. We compared the intrinsic properties, such as proton affinities, gas phase acidities, equilibrium tautomerization and nucleobase pair's hydrogen bonding properties, of these... 

Density functional theory (DFT) calculations were performed at the B3LYP level with a 6-311++G(d,p) basis set to systematically explore the geometrical multiplicity and binding strength for complexes formed by Li+, Na+, and K+ with cytidine and 2′-deoxycytidine. All computational studies indicate that the metal ion affinity (MIA) decreases from Li+ to Na+ and K+ for cytosine nucleosides. For example, for cytidine the affinity for the above metal ions are 79.5, 55.2, and 41.8 and for 2′-deoxycytidine, 82.8, 57.4, and 42.2 kcal/mol, respectively. It is also interesting to mention that linear correlations between calculated MIA values and the atomic numbers (Z) of the above metal ions were... 

Haplotype information has become increasingly important in analyzing fine-scale molecular genetics data, Due to the mutated form in human genome; SNPs (Single Nucleotide Polymorphism) are responsible for some genetic diseases. As a consequence, obtaining all SNPs from human populations is one of the primary goals of studies in human genomics. In this paper, a data fusion method based on multiple parallel classifiers for reconstruction of haplotypes from a given sample Single Nucleotide Polymorphism (SNP) is proposed. First, we design a single greedy algorithm for solving haplotype reconstructions. [2] is used as an efficient approach to be combined with first classification method. The... 

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... 

Analysis of cancer mutational signatures have been instrumental in identification of responsible endogenous and exogenous molecular processes in cancer. The quantitative approach used to deconvolute mutational signatures is becoming an integral part of cancer research. Therefore, development of a stand-alone tool with a user-friendly interface for analysis of cancer mutational signatures is necessary. In this manuscript we introduce CANCERSIGN, which enables users to identify 3-mer and 5-mer mutational signatures within whole genome, whole exome or pooled samples. Additionally, this tool enables users to perform clustering on tumor samples based on the proportion of mutational signatures in... 

Signal generation techniques for visual detection of analytes have received a great deal of attention in various sensing fields. These approaches are considered to be advantageous when instrumentation cannot be employed, such as for on-site assays, point-of-care tests, and he althcare diagnostics in resource-constrained areas. Amongst various visual detection approaches explored for non-invasive quantitative measurements, ratiometric fluorescence sensing has received particular attention as a potential method to overcome the limitations of intensity-based probes. This technique relies on changes in the intensity of two or more emission bands (induced by an analyte), resulting in an effective... 

A nonlocal harmonic elastic rod model is proposed to describe the elastic behavior of short DNA molecules. We show that the nonlocal interactions contribute to effective bending energy of the molecule and affect its apparent persistence length. It is also shown that the anomalous behavior which has been observed in all-atom molecular dynamic simulations [A. K. Mazur, Biophys. J. 134, 4507 (2006)] can be a consequence of both nonlocal interactions between DNA base pairs and the intrinsic curvature of DNA  

In this paper we consider the anharmonic corrections to the anisotropic elastic rod model for DNA. Our model accounts for the difference between the bending energies of positive and negative rolls, which comes from the asymmetric structure of the DNA molecule. We will show that the model can explain the high flexibility of DNA at small length scales, as well as kink formation at high deformation limit. © 2009 The American Physical Society  

The majority of eukaryotic DNA, about three quarter, is wrapped around histone proteins forming so-called nucleosomes. To study nucleosomal DNA we introduce a coarse-grained molecular dynamics model based on sequence-dependent harmonic rigid base pair step parameters of DNA and nucleosomal binding sites. Mixed parametrization based on all-atom molecular dynamics and crystallographic data of protein-DNA structures is used for the base pair step parameters. The binding site parameters are adjusted by experimental B-factor values of the nucleosome crystal structure. The model is then used to determine the energy cost for placing a twist defect into the nucleosomal DNA which allows us to use... 

In this paper, we present an optical computing method for string data alignment applicable to genome information analysis. By applying moire technique to spatial encoding patterns of deoxyribonucleic acid (DNA) sequences, association information of the genome and the expressed phenotypes could more effectively be extracted. Such moire fringes reveal occurrence of matching, deletion and insertion between DNA sequences providing useful visualized information for prediction of gene function and classification of species. Furthermore, by applying a cylindrical lens, a new technique is proposed to map two-dimensional (2D) association information to a one-dimensional (1D) column of pixels, where... 

As a B group vitamins, vitamin B9 is a Water-soluble vitamin which is produced by plants and microorganisms (bacteria and yeasts). Vitamin B9 plays an important role in the production of proteins and nucleic acids in body and also is one of the substances that prevents the development of neural tube defects in the fetus. Methods: Electrochemical behavior of vitamin B9 was studied using a potentiostat/galvanostat SAMA 500, electroanalyzer system, I. R. Iran. A three-electrode system was used, including a glassy carbon working electrode (d = 2.0 mm, purchased from Azar Electrode Co., Urmia, I.R. Iran), an Ag/AgCl (saturated KCl) reference electrode and a Pt wire auxiliary electrode.... 

Gene therapy has emerged as a promising tool for treating different intractable diseases, particularly cancer or even viral diseases such as COVID-19 (coronavirus disease 2019). In this context, various non-viral gene carriers are being explored to transfer DNA or RNA sequences into target cells. Here, we review the applications of the naturally occurring amino acid histidine in the delivery of nucleic acids into cells. The biocompatibility of histidine-enhanced gene delivery systems has encouraged their wider use in gene therapy. Histidine-based gene carriers can involve the modification of peptides, dendrimers, lipids or nanocomposites. Several linear polymers, such as polyethylenimine,... 

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... 

Background: Nutrigenomic has revolutionized our understanding of nutrition. As plants make up a noticeable part of our diet, in the present study we chose microRNAs of edible plants and investigated if they can perfectly match human genes, indicating potential regulatory functionalities. Methods: miRNAs were obtained using the PNRD database. Edible plants were separated and microRNAs in common in at least four of them entered our analysis. Using vmatchPattern, these 64 miRNAs went through four steps of refinement to improve target prediction: Alignment with the whole genome (2581 results), filtered for those in gene regions (1371 results), filtered for exon regions (66 results) and finally... 

Super-paramagnetic iron oxide nanoparticles (SPIONs) are recognized as powerful biocompatible materials for use in various biomedical applications, such as drug delivery, magnetic-resonance imaging, cell/protein separation, hyperthermia and transfection. This study investigates the impact of high concentrations of SPIONs on cytotoxicity and cell-cycle effects. The interactions of surfacesaturated (via interactions with cell medium) bare SPIONs and those coated with poly(vinyl alcohol) (PVA) with adhesive mouse fibroblast cells (L929) are investigated using an MTT assay. The two SPION formulations are synthesized using a co-precipitation method. The bare and coated magnetic nanoparticles with... 

Superparamagnetic iron oxide nanoparticles (SPION) are being increasingly used in various biomedical applications such as hyperthermia, cell and protein separation, enhancing resolution of magnetic resonance imaging, and drug delivery. However, the toxicity data for SPION are limited. In this study, uncoated and single polyvinyl alcohol coated SPION with high chemical reactivity (due to the bigger surface area) were synthesized using a coprecipitation method. Cytotoxicity of these magnetic nanoparticles and their ability to cause arrest in cell life-cycles was investigated. Interaction of these nanoparticles with adhesive mouse fibroblast cell line (L929) was probed using MTT assay. High...