Next generation sequencing methods are widely used in evaluating the structure and functioning of microbial communities, especially those centered on 16S rRNA subunit. Since Illumina Miseq, the most used sequencing platform, does not allow the full sequencing of 16S rRNA gene, this study aims to evaluate whether the choice of different target regions might affect the outcome of microbiome studies regarding soil and saliva samples. V1V3, V3V4, V4V5 and V6V8 domains were studied, finding that while some regions showed differences in the detection of certain bacterial taxa and in the calculation of alpha diversity, especially in soil samples, the overall effect did not compromise the differentiation of any sample type in terms of taxonomic analysis at the genus level. 16S rRNA target regions did affect the detection of specific bacteria related to soil quality and development, and microbial genera used as health biomarkers in saliva. V1V3 region showed the closest similarity to internal sequencing control mock community B, suggesting it might be the most preferable choice regarding data reliability. Over the last decade, there has been a rapid rise in the development of microbiome studies because of the understanding of microbial communities as one of the main factors involved in environmental processes and in human health and disease. The affordability, reliability and high-throughput yield of data provided by next-generation sequencing (NGS) technologies has led to the substitution of classical approaches, such as culture-based methods, in the characterization of microorganisms 1. Depending on the objective of the research, amplicon sequencing or whole metagenome sequencing can be used to gain insight into microbial structural and functional patterns. Sequencing analysis of 16S rRNA subunit is the most widely used and cost effective strategy to discern the structure of the microbiome in all sorts of environments 2,3. 16S rRNA is a highly conserved and universal gene, whose sequence is about 1,500 bp long and consists of nine hypervariable regions (V1-V9) separated by conserved segments, working the latter as target sequences for primer design 4. 16S rRNA sequence has been fully characterized in a great number of bacterial species and strains, and a wide variety of primers have been designed to offer a broad applicability in the analysis of microbiome structure 2,5 , especially through the use of NGS platforms such as Illumina Miseq 3. Since Illumina Miseq does not allow the full sequencing of 16S rRNA (up to 600 bp), its hypervariable regions can be used individually or can be combined to assess the structure of bacterial communities 6. It has been shown that both the use of different primers and regions affects the outcome of microbiome studies 5,7-11 , and thus, such factors should be taken into consideration when designing a sequencing analysis. There are a considerable number of studies analyzing the effect of primers choice in the profiling of microbiome communities. It is known that the analysis of the human...
Non-canonical, four-stranded nucleic acids secondary structures are present within regulatory regions in the human genome and transcriptome. To date, these quadruplex structures include both DNA and RNA G-quadruplexes, formed in guanine-rich sequences, and i-Motifs, found in cytosine-rich sequences, as their counterparts. Quadruplexes have been extensively associated with cancer, playing an important role in telomere maintenance and control of genetic expression of several oncogenes and tumor suppressors. Therefore, quadruplex structures are considered attractive molecular targets for cancer therapeutics with novel mechanisms of action. In this review, we provide a general overview about recent research on the implications of quadruplex structures in cancer, firstly gathering together DNA G-quadruplexes, RNA G-quadruplexes as well as DNA i-Motifs.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.