Smartphone image analysis-based fluorescence detection of tetracycline using machine learning.

Tetracycline (TC) is vastly used as a veterinary drug, making its detection highly important. We have aimed to develop a rapid detection method for TC. For this, BSA-protected Au/Ag bimetallic nanoclusters (BSA-BMNCs) were synthesized for the detection of TC in water and milk. The interaction of TC with BSA shifted the emission of the BMNCs from red to yellow as concentrations of TC increased. Images of the sensing platform were captured with various smartphones and the color and texture information was extracted to generate training datasets for water and milk samples. The datasets were used to train machine learning (ML) algorithms. A model using bagging and artificial neural networks (R2 = 0.994, NRMSE = 0.078) for water samples and one using bagging and decision trees (R2 = 0.999, NRMSE = 0.027) for milk samples were developed. This study shows the ability of ML algorithms for the development of rapid sensors for the detection of food analytes.

Development of sandwich electrochemiluminescence immunosensor for COVID-19 diagnosis by SARS-CoV-2 spike protein detection based on Au@BSA-luminol nanocomposites.

Coronavirus disease (COVID-19) is a new and highly contagious disease posing a threat to global public health and wreaking havoc around the world. It's caused by the Coronavirus that causes severe acute respiratory syndrome (SARS-CoV-2). In the current pandemic situation, rapid and accurate SARS-CoV-2 diagnosis on a large scale is critical for early-stage diagnosis. Early detection and monitoring of viral infections can aid in controlling and preventing infection in large groups of people. Accordingly, we developed a sensitive and high-throughput sandwich electrochemiluminescence immunosensor based on antigen detection for COVID-19 diagnosis (the spike protein of SARS-CoV-2). For the spike protein of SARS-CoV-2, the ECL biosensor had a linear range of 10 ng mL-1 to 10 µg mL-1 with a limit of detection of 1.93 ng mL-1. The sandwich ECL immunosensor could be used in early clinical diagnosis due to its excellent recovery in detecting SARS-CoV-2, rapid analysis (90 min), and ease of use.

hsa-miR-766-5p as a new regulator of mitochondrial apoptosis pathway for discriminating of cell death from cardiac differentiation.

Dispose of unnecessary cells in multicellular organism take place through apoptosis as a mode of programmed cell death (PCD). This process is triggered through two main pathway including extrinsic pathway or death receptor pathway and intrinsic or mitochondrial pathway. An alternative role for mitochondrial pathway of cell death is its involvement in cell differentiation. Biochemistry of cell differentiation indicates a common origin for differentiation and apoptosis. miRNAs are a group of small non coding mediator RNAs in regulation of many routes such as apoptosis and differentiation. By using bioinformatics tools hsa-miR-766-5p was predicted to target the BAX, BAK and BOK genes involved in mitochondrial apoptosis pathway. RT-qPCR and dual luciferase assay showed targeting of BAX, BAK and BOK 3'UTRs via hsa-miR-766, detected in SW480 and HEK293T cell lines. Caspases 3/7 and 9 activity assay revealed the involvement of hsa-miR-766-5p in mitochondrial apoptosis pathway regulation detected following overexpression and downregulation of this miRNA, detected in SW480 cells treated with 1 µM doxorubicin. Flow cytometry and MTT assay indicated cell death reduction and viability elevation effect of hsa-miR-766 in SW480 cells after its overexpression. Endogenous expression of hsa-miR-766 during the course of human embryonic stem cells (hESCs) differentiation into cardiomyocytes revealed an inverse expression status of this miRNA with BOK. However, the expression of this miRNA was inversely related to BAX and BAK for some time points of differentiation. Overall this results show the involvement of hsa-miR-766 in regulation of mitochondrial apoptosis pathway.

A new fluorescence turn-on nanobiosensor for the detection of micro-RNA-21 based on a DNA-gold nanocluster.

In this study, DNA/gold nanoclusters (AuNCs) were used to develop an AuNC-based turn-on fluorescence probe for the analysis of mi-RNA-21, which is a potential screening biomarker for cancer detection. AuNCs on a DNA scaffold were prepared through a one-pot wet-chemical route and evaluated by transmission electron microscopy and dynamic light scattering. Experiments revealed that the fluorescence intensity of the DNA-AuNCs showed a gradual increase with the addition of the target species in a concentration range from 1pM to 10 nM. The method had a detection limit of 0.7 pM and was able to discriminate the target species from mismatched mi-RNAs very efficiently. The method was used for the determination of mi-RNA spiked human plasma samples, and was evaluated as a promising nanobiosensor for application in the selective detection of mi-RNA in various biomedical and clinical tests.

Label free colorimetric and fluorimetric direct detection of methylated DNA based on silver nanoclusters for cancer early diagnosis.

Epigenetic changes such as DNA methylation of CpG islands located in the promoter region of some tumor suppressor genes are very common in human diseases such as cancer. Detection of aberrant methylation pattern could serve as an excellent diagnostic approach. Recently, the direct detection of methylated DNA sequences without using chemical and enzymatic treatments or antibodies has received great deal of attentions. In this study, we report a colorimetric and fluorimetric technique for direct detection of DNA methylation. Here, the DNA is being used as an effective template for fluorescent silver nanoclusters formation without any chemical modification or DNA labeling. The sensitivity test showed that upon the addition of target methylated DNA, the fluorescence intensity is decreased in a linear range when the concentration of methylated DNA has increased from 2.0×10(-9) to 6.3 ×10(-7) M with the detection limit of 9.4×10(-10) M. The optical and fluorescence spectral behaviors were highly reproducible and clearly discriminated between unmethylated, methylated and even partially methylated DNA in CpG rich sequences. The results were also reproducible when the human plasma was present in our assay system.

A theoretical study on interactions between mitoxantrone as an anticancer drug and DNA: application in drug design.

This research is an effort to further understand the physicochemical interaction between the novel drug, mitoxantrone (MTX) and its biologic receptor, DNA. The ultimate goal is to design drugs that interact more with DNA. Understanding the physicochemical properties of the drug as well as the mechanism by which it interacts with DNA, it should ultimately allow the rational design of novel anti-cancer or anti-viral drugs. Molecular modelling on the complex formed between MTX and DNA presented that this complex was indeed fully capable of participating in the formation of a stable intercalation site. Furthermore, the molecular geometries of MTX and the DNA bases (adenine, guanine, cytosine and thymine) were optimized with the aid of the B3LYP/6-31G* method. The properties of the isolated intercalator and its stacking interactions with the adenine...thymine (AT) and guanine...cytosine (GC) nucleic acid base pairs were studied with the DFTB method (density functional tight-binding), an approximate version of the DFT method, that was extended to cover the London dispersion energy. The B3LYP/6-31G* stabilization energies of the intercalator...base pair complexes were found 10.06 kcal/mol and 21.64 kcal/mol for AT...MTX and GC...MTX, respectively. It was concluded that the dispersion energy and the electrostatic interaction contributed to the stability of the intercalator.DNA base pair complexes. The results concluded from the comparison of the DFTB method and the Hartree-fock method point out that these methods show close results and support each other.