scholarly journals Implementation of High-Throughput Sequencing (HTS) in Aptamer Selection Technology

2020 ◽  
Vol 21 (22) ◽  
pp. 8774
Author(s):  
Natalia Komarova ◽  
Daria Barkova ◽  
Alexander Kuznetsov
Keyword(s):  
Nucleic Acid ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Combinatorial Libraries ◽  
Structure And Function ◽  
Huge Number ◽  
Systematic Evolution ◽  
And Function ◽  
Exponential Enrichment

Aptamers are nucleic acid ligands that bind specifically to a target of interest. Aptamers have gained in popularity due to their high potential for different applications in analysis, diagnostics, and therapeutics. The procedure called systematic evolution of ligands by exponential enrichment (SELEX) is used for aptamer isolation from large nucleic acid combinatorial libraries. The huge number of unique sequences implemented in the in vitro evolution in the SELEX process imposes the necessity of performing extensive sequencing of the selected nucleic acid pools. High-throughput sequencing (HTS) meets this demand of SELEX. Analysis of the data obtained from sequencing of the libraries produced during and after aptamer isolation provides an informative basis for precise aptamer identification and for examining the structure and function of nucleic acid ligands. This review discusses the technical aspects and the potential of the integration of HTS with SELEX.

scholarly journals Assessment of Bioleaching Microbial Community Structure and Function Based on Next-Generation Sequencing Technologies

Minerals ◽  
2018 ◽  
Vol 8 (12) ◽  
pp. 596 ◽  
Author(s):  
Shuang Zhou ◽  
Min Gan ◽  
Jianyu Zhu ◽  
Xinxing Liu ◽  
Guanzhou Qiu
Keyword(s):  
Community Structure ◽  
Next Generation Sequencing ◽  
Microbial Ecology ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Structure And Function ◽  
Next Generation ◽  
Sequencing Technologies ◽  
And Function ◽  
Generation Sequencing

It is widely known that bioleaching microorganisms have to cope with the complex extreme environment in which microbial ecology relating to community structure and function varies across environmental types. However, analyses of microbial ecology of bioleaching bacteria is still a challenge. To address this challenge, numerous technologies have been developed. In recent years, high-throughput sequencing technologies enabling comprehensive sequencing analysis of cellular RNA and DNA within the reach of most laboratories have been added to the toolbox of microbial ecology. The next-generation sequencing technology allowing processing DNA sequences can produce available draft genomic sequences of more bioleaching bacteria, which provides the opportunity to predict models of genetic and metabolic potential of bioleaching bacteria and ultimately deepens our understanding of bioleaching microorganism. High-throughput sequencing that focuses on targeted phylogenetic marker 16S rRNA has been effectively applied to characterize the community diversity in an ore leaching environment. RNA-seq, another application of high-throughput sequencing to profile RNA, can be for both mapping and quantifying transcriptome and has demonstrated a high efficiency in quantifying the changing expression level of each transcript under different conditions. It has been demonstrated as a powerful tool for dissecting the relationship between genotype and phenotype, leading to interpreting functional elements of the genome and revealing molecular mechanisms of adaption. This review aims to describe the high-throughput sequencing approach for bioleaching environmental microorganisms, particularly focusing on its application associated with challenges.

scholarly journals Inside the Black Box: What Makes SELEX Better?

Molecules ◽  
2019 ◽  
Vol 24 (19) ◽  
pp. 3598 ◽  
Author(s):  
Natalia Komarova ◽  
Alexander Kuznetsov
Keyword(s):  
Nucleic Acid ◽  
Selection Process ◽  
Combinatorial Libraries ◽  
Black Box ◽  
Aptamer Selection ◽  
Selection Protocol ◽  
Systematic Evolution ◽  
Exponential Enrichment

Aptamers are small oligonucleotides that are capable of binding specifically to a target, with impressive potential for analysis, diagnostics, and therapeutics applications. Aptamers are isolated from large nucleic acid combinatorial libraries using an iterative selection process called SELEX (Systematic Evolution of Ligands by EXponential enrichment). Since being implemented 30 years ago, the SELEX protocol has undergone many modifications and improvements, but it remains a laborious, time-consuming, and costly method, and the results are not always successful. Each step in the aptamer selection protocol can influence its results. This review discusses key technical points of the SELEX procedure and their influence on the outcome of aptamer selection.

scholarly journals Porous Silicon-Based Aptasensors: The Next Generation of Label-Free Devices for Health Monitoring

Molecules ◽  
2019 ◽  
Vol 24 (12) ◽  
pp. 2216 ◽  
Author(s):  
Monica Terracciano ◽  
Ilaria Rea ◽  
Nicola Borbone ◽  
Rosalba Moretta ◽  
Giorgia Oliviero ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Porous Silicon ◽  
Limit Of Detection ◽  
Combinatorial Libraries ◽  
High Sensitivity ◽  
Label Free ◽  
Great Specificity ◽  
Silicon Based ◽  
Exponential Enrichment

Aptamers are artificial nucleic acid ligands identified and obtained from combinatorial libraries of synthetic nucleic acids through the in vitro process SELEX (systematic evolution of ligands by exponential enrichment). Aptamers are able to bind an ample range of non-nucleic acid targets with great specificity and affinity. Devices based on aptamers as bio-recognition elements open up a new generation of biosensors called aptasensors. This review focuses on some recent achievements in the design of advanced label-free optical aptasensors using porous silicon (PSi) as a transducer surface for the detection of pathogenic microorganisms and diagnostic molecules with high sensitivity, reliability and low limit of detection (LoD).

scholarly journals The citrus microbiome: from structure and function to microbiome engineering and beyond

2021 ◽  
Author(s):  
Yunzheng Zhang ◽  
Pankaj Trivedi ◽  
jin xu ◽  
M. Caroline Roper ◽  
Nian Wang
Keyword(s):  
Artificial Intelligence ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Plant Root ◽  
Rapid Development ◽  
Structure And Function ◽  
Omics Technologies ◽  
Microbiome Research ◽  
Citrus Root ◽  
And Function

Individual microbes often have defined relationship with their hosts that include beneficial, commensal, and pathogenic interactions. However, at the community level, plant microbiomes are considered to play a beneficial role in protecting the plant from potential pathogens, acquiring nutrients, and improving growth and production. Citrus is a globally important perennial fruit crop and its production faces many challenges. There have been tremendous interests to explore the structure and function of citrus microbiome and engineer citrus microbiome to address various challenges. In this review, we summarized recent advances in understanding of citrus microbiome, including the composition and function of microbiome in the rhizosphere, rhizoplane, endorhiza, core members and their functional traits. We conducted comparisons of citrus root-associated microbiome with other plant root-associated microbiomes. We also present a perspective on how incoming pathogens interact with the resident microbial community and their outcomes. Despite the promising potential of the citrus microbiome to combat disease, harnessing the citrus microbiome for beneficial applications remains in its infancy. We envision that rapid development of high throughput sequencing and multi-omics technologies, artificial intelligence, consortia of microbes, genome editing technology, and high-throughput culturing present many exciting opportunities to citrus microbiome research and microbial engineering to improve citrus health and productivity.

scholarly journals Selection of aptamers against triple negative breast cancer cells using high throughput sequencing

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Débora Ferreira ◽  
Joaquim Barbosa ◽  
Diana A. Sousa ◽  
Cátia Silva ◽  
Luís D. R. Melo ◽  
...  
Keyword(s):  
Breast Cancer ◽  
High Throughput ◽  
Triple Negative Breast Cancer ◽  
High Throughput Sequencing ◽  
Triple Negative ◽  
Metastatic Breast ◽  
Target Cells ◽  
Cancer Tissue ◽  
Surface Receptors

AbstractTriple-negative breast cancer is the most aggressive subtype of invasive breast cancer with a poor prognosis and no approved targeted therapy. Hence, the identification of new and specific ligands is essential to develop novel targeted therapies. In this study, we aimed to identify new aptamers that bind to highly metastatic breast cancer MDA-MB-231 cells using the cell-SELEX technology aided by high throughput sequencing. After 8 cycles of selection, the aptamer pool was sequenced and the 25 most frequent sequences were aligned for homology within their variable core region, plotted according to their free energy and the key nucleotides possibly involved in the target binding site were analyzed. Two aptamer candidates, Apt1 and Apt2, binding specifically to the target cells with $$K_{d}$$ K d values of 44.3 ± 13.3 nM and 17.7 ± 2.7 nM, respectively, were further validated. The binding analysis clearly showed their specificity to MDA-MB-231 cells and suggested the targeting of cell surface receptors. Additionally, Apt2 revealed no toxicity in vitro and showed potential translational application due to its affinity to breast cancer tissue sections. Overall, the results suggest that Apt2 is a promising candidate to be used in triple-negative breast cancer treatment and/or diagnosis.

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