scholarly journals Efficient Screening of Pesticide Diazinon-Binding Aptamers Using The Sol-Gel Coated Nanoporous Membrane-Assisted SELEX Process and Next-Generation Sequencing

2021 ◽  
Author(s):  
Min-Cheol Lim ◽  
Eun Seob Lim ◽  
Jeong-A Lim ◽  
Sung-Wook Choi ◽  
Hyun-Joo Chang
Keyword(s):  
Next Generation Sequencing ◽  
Binding Affinity ◽  
Low Cost ◽  
Sol Gel ◽  
Cross Reactivity ◽  
Next Generation ◽  
Anodized Aluminum ◽  
Next Generation Sequencing Ngs ◽  
Exponential Enrichment ◽  
Generation Sequencing

Abstract BackgroundAptamer-based methods for detecting pesticides are more efficient than antibody-based methods as aptamers have high thermal stability, low molecular weight, easy modification, and low cost. However, only few studies on SELEX performed in combination with next generation sequencing (NGS) to screen aptamers specific for pesticides have been reported. Therefore, this study aimed to develop the systematic evolution of ligands by exponential enrichment (SELEX) process, combined with NGS, to select aptamers specific to the pesticide, diazinon, which was fixed on a sol-gel-coated nanoporous anodized aluminum oxide membrane. Methods and resultsThe frequency of specific nucleotide sequences obtained after SELEX rounds was analyzed using NGS. Nine sequences with the highest frequency after SELEX round 10 followed by NGS were selected and tested to derive their binding affinity with the target, diazinon, through circular dichroism (CD) spectrophotometry. The CD signal difference of the aptamer candidates ranged from 0.13 to 2.242 mdeg between diazinon-only treated and diazinon-aptamer-treated samples at a wavelength near 270 nm. Aptamer D-4, which had the highest binding affinity from CD spectrophotometry analysis, showed no cross-reactivity with non-target pesticides, such as baycarb, bifenthrin, and pyridaben, but interacted with the other pesticides, fipronil and 2-phenylphenol.ConclusionsThe proposed SELEX process combined with NGS for the discovery of aptamers for new targets can shorten the SELEX cycle by reducing the number of SELEX rounds to 10 or less. Therefore, an efficiently selected aptamer is highly expected to be used for the detection of pesticides in foods in the field.

scholarly journals SNP Mining in Functional Genes from Nonmodel Species by Next-Generation Sequencing: A Case of Flowering, Pre-Harvest Sprouting, and Dehydration Resistant Genes in Wheat

2016 ◽  
Vol 2016 ◽  
pp. 1-10
Author(s):  
Zhong-Xu Chen ◽  
Mei Deng ◽  
Ji-Rui Wang
Keyword(s):  
Next Generation Sequencing ◽  
Sequence Data ◽  
Low Cost ◽  
Functional Genes ◽  
Accurate Information ◽  
Next Generation ◽  
Polynomial Fitting ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data ◽  
Generation Sequencing

As plenty of nonmodel plants are without genomic sequences, the combination of molecular technologies and the next generation sequencing (NGS) platform has led to a new approach to study the genetic variations of these plants. Software GATK, SOAPsnp, samtools, and others are often used to deal with the NGS data. In this study, BLAST was applied to call SNPs from 16 mixed functional gene’s sequence data of polyploidy wheat. In total 1.2 million reads were obtained with the average of 7500 reads per genes. To get accurate information, 390,992 pair reads were successfully assembled before aligning to those functional genes. Standalone BLAST tools were used to map assembled sequence to functional genes, respectively. Polynomial fitting was applied to find the suitable minor allele frequency (MAF) threshold at 6% for assembled reads of each functional gene. SNPs accuracy form assembled reads, pretrimmed reads, and original reads were compared, which declared that SNPs mined from the assembled reads were more reliable than others. It was also demonstrated that mixed samples’ NGS sequences and then analysis by BLAST were an effective, low-cost, and accurate way to mine SNPs for nonmodel species. Assembled reads and polynomial fitting threshold were recommended for more accurate SNPs target.

scholarly journals Is Next-Generation Sequencing Appropriate for the Clinic?

2014 ◽  
Vol 4 (2) ◽  
pp. 45-48
Author(s):  
Ramzi Hassouneh
Keyword(s):  
Next Generation Sequencing ◽  
Low Cost ◽  
Genomic Medicine ◽  
Clinical Applications ◽  
Next Generation ◽  
Apply Genetic ◽  
Health And Disease ◽  
Next Generation Sequencing Ngs ◽  
The Impact ◽  
Generation Sequencing

Next-generation sequencing (NGS) has ignited a revolution in genomic medicine by eliminating the inherent limitations of conventional sequencing methods. Due to its high throughput and low-cost, clinics can use NGS to perform targeted and genome sequencing to make diagnoses or pre-screen for risk to future disease. Despite its clinical uses, many challenges exist before NGS becomes a mainstay in the clinic. There is a lack of understanding of the impact of genetic variants on health and disease and how to best apply genetic information to patient care. Nevertheless, the translation of base pair reads to clinical applications has truly begun.

Initial Next-Generation Sequencing (NGS) Results of Alport Syndrome

2019 ◽  
Author(s):  
Altuğ Koç ◽  
Elçin Bora ◽  
Tayfun Cinleti ◽  
Gizem Yıldız ◽  
Meral Torun Bayram ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Alport Syndrome ◽  
Next Generation ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

The applications of next-generation sequencing (NGS) in drug development for cancer therapy

2020 ◽  
Vol 16 ◽  
Author(s):  
Pelin Telkoparan-Akillilar ◽  
Dilek Cevik
Keyword(s):  
Next Generation Sequencing ◽  
Drug Discovery ◽  
Cancer Therapy ◽  
Target Identification ◽  
Rapid Development ◽  
Next Generation ◽  
Biomedical Sciences ◽  
Dna And Rna ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Background: Numerous sequencing techniques have been progressed since the 1960s with the rapid development of molecular biology studies focusing on DNA and RNA. Methods: a great number of articles, book chapters, websites are reviewed, and the studies covering NGS history, technology and applications to cancer therapy are included in the present article. Results: High throughput next-generation sequencing (NGS) technologies offer many advantages over classical Sanger sequencing with decreasing cost per base and increasing sequencing efficiency. NGS technologies are combined with bioinformatics software to sequence genomes to be used in diagnostics, transcriptomics, epidemiologic and clinical trials in biomedical sciences. The NGS technology has also been successfully used in drug discovery for the treatment of different cancer types. Conclusion: This review focuses on current and potential applications of NGS in various stages of drug discovery process, from target identification through to personalized medicine.

scholarly journals Next-Generation Sequencing in Tumor Diagnosis and Treatment

Diagnostics ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 962
Author(s):  
Dario de Biase ◽  
Matteo Fassan ◽  
Umberto Malapelle
Keyword(s):  
Next Generation Sequencing ◽  
Tumor Diagnosis ◽  
Diagnosis And Treatment ◽  
Next Generation ◽  
Multiple Genes ◽  
Next Generation Sequencing Ngs ◽  
Very High ◽  
Generation Sequencing ◽  
High Depth

Next-Generation Sequencing (NGS) allows for the sequencing of multiple genes at a very high depth of coverage [...]

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