A Comprehensive Comparison of Rapid RNA Extraction Methods for Detection of SARS-CoV-2 as the Infectious Agent of the Upper Respiratory Tract using Direct RT-LAMP Assay.

Background: The current COVID-19 pandemic has highlighted the need for faster and more cost-effective diagnostic methods. The RNA extraction step in current diagnostic methods, such as real-time qPCR, increases the cost and time required for testing. Reverse-transcription loop-mediated isothermal amplification (RT-LAMP) is a promising technique for developing diagnostic tests with desired sensitivity and specificity without the need for RNA extraction.

An intelligent DNA nanorobot for detection of MiRNAs cancer biomarkers using molecular programming to fabricate a logic-responsive hybrid nanostructure.

Herein, we designed a DNA framework-based intelligent nanorobot using toehold-mediated strand displacement reaction-based molecular programming and logic gate operation for the selective and synchronous detection of miR21 and miR125b, which are known as significant cancer biomarkers. Moreover, to investigate the applicability of our design, DNA nanorobots were implemented as capping agents onto the pores of MSNs. These agents can develop a logic-responsive hybrid nanostructure capable of specific drug release in the presence of both targets.

CRISPR/Cas9-Mediated Disruption of ZNF543 Gene: An Approach Toward Discovering Its Relation to TRIM28 Gene in Parkinson's Disease.

Genetic studies of familial forms of Parkinson's disease (PD) have shown that the ZNF543 gene is a candidate gene that operates relevant to this disease. However, until now, there is no evidence for ZNF543 gene function in PD, and mechanisms resulting from its mutation have not been elucidated. Given the same genetic location of the ZNF543 gene with TRIM28 and their effects on PD pathogenesis, we surmised that ZNF543 might act as a transcription factor for TRIM28 gene expression.

Binary detection of protein and nucleic acid enabled cancer diagnosis through branched hybridization chain reaction.

Developing isothermal bio-analyzers for amplified detection of multi-factor diseases like cancer biomarkers (nucleic acid and protein) has facilitated the early diagnosis and clinical theranostics. In light of that, a sensitive detection system was developed assisted by the recognition capability of a functional aptamer followed by cyclic self-assembly of three auxiliary hairpins via branched hybridization chain reaction (b-HCR) performance. In the downstream process, in the presence of hemin, split sequences of a DNAzyme brought in close proximity to facilitate the color alteration of the solution to a green appearance.

Borderline Boolean states improve the biosensing applications of DNA circuits.

Molecular circuits have been used in a wide range of diagnosis applications, from the detection of chemical molecules in solution to the complex processing of cell surface receptors. One of the most important challenges of these systems is the lack of distinguishability between different circuit states when each circuit state represents a specific disease. In this work, we designed a molecular amplification circuit with borderline Boolean states that each state can be distinguished with different color intensity.

Developing a colorimetric nucleic acid-responsive DNA hydrogel using DNA proximity circuit and catalytic hairpin assembly.

The development of powerful techniques for sensitive detection of nucleic acids has attracted much attention for fabricating accurate biosensors in various fields, such as genomics, clinical diagnostics, and forensic sciences. Up to now, different systems have been introduced, the majority of which are expensive, time-consuming, and relatively low selectivity/limit of detection. These limitations caught our attention to fabricate a nucleic acid responsive system by combining three layers of signal amplification strategy, namely a split proximity circuit (SPC), a catalytic hairpin assembly (CHA), and a DNA hydrogel.

Multiplex monitoring of Alzheimer associated miRNAs based on the modular logic circuit operation and doping of catalytic hairpin assembly.

In recent years, DNA logic gates have been extensively applied in developing multiplex processing platforms to provide an accurate decision on the diagnosis of multi-factor diseases. In this work, we presented a new cascaded logical operator by combining different modules for computational monitoring of four miRNAs related to Alzheimer disease (has-miR-143-3p, has-miR-18b-5p, has-miR-424-5p, and has-miR-93-5p). Herein, three sequential logic gates were programed that upon entering the miRNA inputs, delivered the trigger strand of CHA (catalytic hairpin assembly) reaction through a cyclic amplification.

Colorimetric nanoplatform for visual determination of cancer cells via target-catalyzed hairpin assembly actuated aggregation of gold nanoparticles.

According to aptamer-mediated hairpin DNA cascade amplifier and gold nanoparticles aggregation, an optical platform for cancer cells determination has been proposed. High-affinity chimeric aptamers were used for cancer cell detection and also as an initiator for beginning hairpin assembly to construct three-way junction (3WJ) nanostructures. These three hairpins were modified at 3' ends with biotin.

Colorimetric detection of miRNA-21 by DNAzyme-coupled branched DNA constructs.

Fluctuation of nucleic acid expression and ultrasensitive and specific detection of these variations in expression is a crucial subject in molecular medicine and clinical theranostics. A novel DNAzyme-coupled branched hybridization chain reaction (b-HCR) assay is reported for efficient signal-amplified detection of miRNA in this study. This assay was composed of a translator (T) hybridized with miR-21 to initiate the first HCR by hairpin 1 (H) and hairpin 2 (H).

Dual catalytic DNA circuit-induced gold nanoparticle aggregation: An enzyme-free and colorimetric strategy for amplified detection of nucleic acids.

An enzyme-free dual catalytic DNA circuit for amplified detection of nucleic acids has been developed. The system functions based on a cyclic self-assembly of two auxiliary hairpins (H1 and H2) and three biotinylated hairpin oligonucleotides (H3, H4 and H5), in the format of two molecular circuits. In the upstream circuit, a target initiator (I) besides H1 and H2 hairpins constructs H1-H2 duplexes that trigger the operation of a subsequent circuit.

DNA hydrogel-empowered biosensing.

DNA hydrogels as special members in the DNA nanotechnology have provided crucial prerequisites to create innovative gels owing to their sufficient stability, biocompatibility, biodegradability, and tunable multifunctionality. These properties have tailored DNA hydrogels for various applications in drug delivery, tissue engineering, sensors, and cancer therapy. Recently, DNA-based materials have attracted substantial consideration for the exploration of smart hydrogels, in which their properties can change in response to chemical or physical stimuli.

DNAzyme-embedded hyperbranched DNA dendrimers as signal amplifiers for colorimetric determination of nucleic acids.

A DNAzyme-embedded hyperbranched DNA dendrimer is used as a colorimetric signal amplifier in an ultrasensitive detection scheme for nucleic acids. The hyperbranched DNA dendrimers were constructed by single-step autonomous self-assembly of three structure-free DNA monomers. A cascade of self-assembly reactions between the first and second strands leads to the formation of linear DNA concatemers containing overhang flank fragments.

Target-triggered three-way junction in conjugation with catalytic concatemers-functionalized nanocomposites provides a highly sensitive colorimetric method for miR-21 detection.

With the great advances in DNA nanotechnology, scientists have shown interest in developing dynamic nanostructures for theranostic applications, analyte sensing and cargo delivery. Here, we present a specific enzyme-free ultrasensitive platform based on a multilayer coupled signal amplification strategy to quantify miR-21 molecule. The biosensor was integrated based on three signal amplification gadgets, namely a translator-mediated catalytic hairpin assembly (CHA), a multilayer DNA concatemer on the surface of gold decorated magnetic nanoparticle (GMNP), and a DNAzyme-mediated catalytic signal amplification.

Aptamer-integrated DNA nanoassembly: A simple and sensitive DNA framework to detect cancer cells.

The development of powerful techniques to detect cancer cells at early stages plays a notable role in diagnosing and prognosing cancer patients and reducing mortality. This paper reports on a novel functional DNA nanoassembly capable of detecting cancer cells based on structural DNA nanotechnology. DNA nanoassemblies were constructed by the self-assembly of a DNA concatemer to a plenty of sticky-ended three-way junctions.

Protective Effect of Neuropeptide Apelin-13 on 6-Hydroxydopamine-Induced Neurotoxicity in SH-SY5Y Dopaminergic Cells: Involvement of Its Antioxidant and Antiapoptotic Properties.

Parkinson's disease (PD) is a severe neurodegenerative disorder characterized by the loss of brain dopaminergic neurons. Beside pharmacologic and symptomatic treatment of PD the neuroprotective therapy has recently attracted more attention. Apelin, a novel neuropeptide, and its receptors have numerous reported roles in regulating brain functions.

Signal Amplification Technologies for the Detection of Nucleic Acids: from Cell-Free Analysis to Live-Cell Imaging.

Due to their unique properties, such as programmability, ligand-binding capability, and flexibility, nucleic acids can serve as analytes and/or recognition elements for biosensing. To improve the sensitivity of nucleic acid-based biosensing and hence the detection of a few copies of target molecule, different modern amplification methodologies, namely target-and-signal-based amplification strategies, have already been developed. These recent signal amplification technologies, which are capable of amplifying the signal intensity without changing the targets' copy number, have resulted in fast, reliable, and sensitive methods for nucleic acid detection.

DNA Domino-Based Nanoscale Logic Circuit: A Versatile Strategy for Ultrasensitive Multiplexed Analysis of Nucleic Acids.

In recent years, the analytical application of logical nanodevices has attracted much attention for making accurate decisions on molecular diagnosis. Herein, a DNA domino-based nanoscale logic circuit has been constructed by integrating three logic gates (AND-AND-YES) for simultaneous analysis of multiple nucleic acid biomarkers. In the first AND gate, a chimeric target DNA comprising of four biomarkers was hybridized to three biomarker-specific oligonucleotides (TRs) via their 5'-end regions and to a capture probe-magnetic microparticle.

Implementing a two-layer feed-forward catalytic DNA circuit for enzyme-free and colorimetric detection of nucleic acids.

In the present study, a highly sensitive and specific bio-sensing platform for enzyme-free and colorimetric detection of nucleic acids has been developed. The biosensor is composed of two DNA nanostructures and two fuel strands that construct the foundation of a feed-forward catalytic DNA circuit. Upon binding the target strand to a specific DNA nanostructure, the circuit is run in order that at the end a hemin-binding aptamer, with the ability to convert a colorless substrate into a colored substance is released.

Isothermal RNA detection through the formation of DNA concatemers containing HRP-mimicking DNAzymes on the surface of gold nanoparticles.

An enzyme-free signal amplification strategy for colorimetric detection of RNA molecules was developed. The detecting process was started by the hybridization of the target RNA via two helper oligonucleotides to bi-functionalized (initiator and linker oligonucleotides-modified) gold nanoparticles. Afterwards, in presence of two auxiliary oligonucleotides, the nanoparticle-confined initiators triggered the formation of DNA concatemers containing hemin-binding aptamers through a modified hybridization chain reaction [HCR] strategy.

A highly specific and sensitive loop-mediated isothermal amplification method for the detection of Escherichia coli O157:H7.

E. coli O157:H7 is one of the most important foodborne pathogen that causes some human illnesses such as bloody diarrhea, hemolytic-uremic syndrome, and kidney failure. We developed a loop-mediated isothermal amplification (LAMP) assay with six special primers that target a highly specific 299-bp region of the Z3276 gene for the detection of E.

Prophylactic Effect of BIO-1211 Small-Molecule Antagonist of VLA-4 in the EAE Mouse Model of Multiple Sclerosis.

Background And Purpose: Some functional limitations and economic burden of therapeutic antibodies indicated that introducing of alternative therapeutic compounds with same or different mechanism of action could be worthwhile. In this regard small-molecule antagonists can have a wide range of impacts, so in this research, we examine the prophylactic effects of BIO-1211 [Very Late Antigen-4 (VLA4) blocker], in experimental autoimmune encephalomyelitis (EAE) mouse model of multiple sclerosis in comparison with commercial available medicine, Natalizumab (NTZ)].

Methods: EAE was induced by subcutaneous immunization of myelin oligodendrocyte glycoprotein (MOG35-55) in 8-week-old C57BL/6 mice.

Analysis of yeh Fimbrial Gene Cluster in Escherichia coli O157:H7 in Order to Find a Genetic Marker for this Serotype.

yeh fimbrial gene cluster encodes a type of putative fimbrial complex belonging to chaperone-usher assembly pathway. Recent studies have shown that yeh fimbrial gene cluster is present in 94 % of Escherichia coli isolates and responsible for adhesion to some abiotic surfaces. Our preliminary comparative genomic analysis of 96 complete genomes of different E.

Purification and characterization of a thermo- and organic solvent-tolerant alkaline protease from Bacillus sp. JER02.

Bacillus sp. JER02 is a bacterial strain that can be grown in a medium containing organic solvents and produce a protease enzyme. JER02 protease was purified with a yield of 31.

Relationship between metalloproteinase 2 and 9 concentrations and soluble CD154 expression in Iranian patients with multiple sclerosis.

Matrix metalloproteinases (MMPs) play a critical role in the blood-brain barrier permeability and in invasion of the leukocytes into the central nervous system during multiple sclerosis (MS). In this respect, in the present study, we have evaluated the possible role of MMP-9 and MMP-2 on the expression of soluble CD154 (sCD154) and membrane-bound isoform of the CD154 in Iranian MS patients. The expressions of the aforementioned protein-related genes were analyzed at the levels of messenger RNA and proteins by real-time reverse transcription polymerase chain reaction, enzyme-linked immunosorbent assay, and Western blotting.