Sharif Digital Repository

Herein, we present a novel, simple, and ultrasensitive electrochemical DNA (E-DNA) sensor based on hollow carbon spheres (HCS) decorated with polyaniline (PANI). A thiolated 21-mer oligonucleotide, characteristic of HBV DNA, is immobilized via electrodeposited gold nanoparticles on HCS-PANI. Cyclic voltammetry (CV), differential pulse voltammetry (DPV), and electrochemical impedance spectroscopy (EIS) are used to characterize the electrochemical properties of the prepared nanocomposite. Scanning electron microscopy is employed to investigate the morphological texture of the fabricated modifier. An enhanced intrinsic signal of PANI is probed to evaluate the biosensing ability of the prepared... 

DNA sequencing has faced a huge demand since it was first introduced as a service to the public. This service is often offloaded to the sequencing companies who will have access to full knowledge of individuals' sequences, a major violation of privacy. To address this challenge, we propose a solution, which is based on separating the process of reading the fragments of sequences, which is done at a sequencing machine, and assembling the reads, which is done at a trusted local data collector. To confuse the sequencer, in a pooled sequencing scenario, in which multiple sequences are going to be sequenced simultaneously, for each target individual, we add fragments of one non-target individual,... 

Several evidences support the idea that a small population of tumour cells representing self-renewal potential are involved in initiation, maintenance, metastasis, and outcomes of cancer therapy. Elucidation of microRNAs/genes regulatory networks activated in cancer stem cells (CSCs) is necessary for the identification of new targets for cancer therapy. The aim of the present study was to predict the miRNAs pattern, which can target both metastasis and self-renewal pathways using integration of literature and data mining. For this purpose, mammospheres derived from MCF-7, MDA-MB231, and MDA-MB468 were used as breast CSCs model. They had higher migration, invasion, and colony formation... 

An impedimetric human papilloma virus (HPV) DNA biosensor based on gold nanotubes (AuNTs) in label free detection was materialized. The AuNTs decorated nanoporous polycarbonate (AuNTs-PC) template as biosensor electrode was fabricated by electrodeposition method. The single strand DNA (ss-DNA) probe was covalently immobilized onto the AuNTs-PC electrode. The hybridization of target sequences with the ss-DNA probe was observed by the electrochemical impedance spectroscopy (EIS). The biosensor showed high selectivity and could differentiate between the complementary, mismatch and non-complementary DNA sequences. The EIS measurements were matched to Randle's equivalent circuit. The... 

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)... 

Genome-Wide Association Study (GWAS) addresses the problem of associating subsequences of individuals' genomes to the observable characteristics called phenotypes. In a genome of length G, it is observed that each characteristic is only related to a specific subsequence of it with length L, called the causal subsequence. The objective is to recover the causal subsequence, using a dataset of N individuals' genomes and their observed characteristics. Recently, the problem has been investigated from an information theoretic point of view in [1]. It has been shown that there is a threshold effect for reliable learning of the causal subsequence at Gh ( N L/G ) by characterizing the capacity of... 

Background: Breast cancer is currently the most common neoplasm diagnosed in women globally. There is a growing body of evidence to suggest that human papillomavirus (HPV) infection may play a key role in invasiveness of breast cancer. The aim of this study was to determine the presence of HPV in patients with breast cancer and its possible association with cancer progression. Methods: Breast specimens were collected from 72 patients with breast cancer and 31 healthy controls. The presence of HPV was investigated by polymerase chain reaction (PCR) and genotyping was performed for positive cases. We also evaluated the viral factors such as E6, E2, and E7 in HPV positive cases. Enzyme-linked... 

With the passage of time and more advanced societies, there is a greater emergence and incidence of disease and necessity for improved treatments. In this respect, nowadays, aptamers, with their better efficiency at diagnosing and treating diseases than antibodies, are at the center of attention. Here, in this review, we first investigate aptamer function in various fields (such as the detection and remedy of pathogens, modification of nanoparticles, antibiotic delivery and gene delivery). Then, we present aptamer-conjugated nanocomplexes as the main and efficient factor in gene delivery. Finally, we focus on the targeted co-delivery of genes and drugs by nanocomplexes, as a new exciting... 

Nucleic acid amplification using polymerase chain reaction (PCR) method has been widely used in different fields such as agricultural science, medicine, pathogen identification, and forensics to name a few. Today, it seems inevitable to have a robust, simple PCR system for diagnostics at the point-of-care (POC) level. Many photonic PCR systems have been proposed in the literature that benefit from plasmonic photothermal heating to achieve the common PCR thermal cycling. However, non-homogeneous temperature distribution is a challenge in some of them. In the present work, to achieve more efficient gene amplification, the effect of adding TiO2 nanoparticles has been investigated in a photonic... 

Background: Flagellin of Salmonella enterica serovar Enteritidis (SEF) stimulates immune responses to both itself and coapplied antigens. It is therefore used in vaccine development and immunotherapy. Removal of pathogenic S. enterica ser. Enteritidis from SEF production process is advantageous due to the process safety improvement. The protein solubility analysis using SDS-PAGE indicated that 53.49% of SEF expressed in Escherichia coli formed inclusion bodies. However, the protein recovery from inclusion bodies requires a complex process with a low yield. Objective: We thus aim to study possibility of enhancing SEF expression in E. coli in soluble form using chemical and molecular... 

Background: Unique properties of graphene and its derivatives make them attractive in the field of nanomedicine. However, the mass application of graphene might lead to side effects, which has not been properly addressed in previous studies, especially with regard to its effect on the cell cycle. Methods: The effect of two concentrations (100 and 200 μg/mL) of nano-and microsized graphene oxide (nGO and mGO) on apoptosis, cell cycle, and ROS generation was studied. The effect of both sizes on viability and genotoxicity of the embryonic fibroblast cell cycle was evaluated. MTT and flow cytometry were applied to evaluate the effects of graphene oxide (GO) nanosheets on viability of cells.... 

Nowadays, the accelerated expansion of genetic data challenges speed of current DNA sequence alignment algorithms due to their electrical implementations. Essential needs of an efficient and accurate method for DNA variant discovery demand new approaches for parallel processing in real time. Fortunately, photonics, as an emerging technology in data computing, proposes optical correlation as a fast similarity measurement algorithm; while complexity of existing local alignment algorithms severely limits their applicability. Hence, in this paper, employing optical correlation for global alignment, we present an optical processing approach for local DNA sequence alignment to benefit both... 

Cancer immunotherapy has been emerged as a promising strategy for treatment of a broad spectrum of malignancies ranging from hematological to solid tumors. One of the principal approaches of cancer immunotherapy is transfer of natural or engineered tumor-specific T-cells into patients, a so called "adoptive cell transfer", or ACT, process. Construction of allogeneic T-cells is dependent on the employment of a gene-editing tool to modify donor-extracted T-cells and prepare them to specifically act against tumor cells with enhanced function and durability and least side-effects. In this context, CRISPR technology can be used to produce universal T-cells, equipped with recombinant T cell... 

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused the COVID-19 pandemic that has been spreading around the world since December 2019. More than 10 million affected cases and more than half a million deaths have been reported so far, while no vaccine is yet available as a treatment. Considering the global healthcare urgency, several techniques, including whole genome sequencing and computed tomography imaging have been employed for diagnosing infected people. Considerable efforts are also directed at detecting and preventing different modes of community transmission. Among them is the rapid detection of virus presence on different surfaces with which people may come in... 

The primary challenge of spectroscopic techniques in selective detection and characterization of tautomeric structures of DNA and RNA bases, and moreover, the accurate interpretation and explanation of the experimental results are the main motives of theoretical studies. Surface-enhanced Raman spectroscopy (SERS) can be a powerful approach to distinguish cytosine in the presence of its tautomers. For this respect, herein, the theoretical simulation of the SERS spectra of cytosine and its three most stable tautomers adsorbed on silver clusters is carried out. The calculations of SERS spectra is based on the excited-state energy gradient approximation as a well-established approach that gives... 

Semiconducting single-walled carbon nanotubes (SWCNTs) are among the few photostable optical emitters that are ideal for sensing, imaging, drug delivery, and monitoring of protein activity. These applications often require strategies for immobilizing proteins onto the nanotube while preserving the optical properties of the SWCNTs. Site-specific and oriented immobilization strategies, in particular, offer advantages for improving sensor and optical signaling responses. In this study, we demonstrate site-specific protein immobilization of a model of enhanced yellow fluorescent protein with a single engineered cysteine residue, using either single-stranded DNA or a pyrene-containing linker to... 

We present a perturbation theory to find the response of an anisotropic DNA to the external tension. It is shown that the anisotropy has a nonzero but small contribution to the force-extension curve of the DNA. Thus an anisotropic DNA behaves like an isotropic one with an effective bending constant equal to the harmonic average of its soft and hard bending constants. © 2008 American Institute of Physics