Mass Spectrometry for Investigating the Effects of Toxic Metals on Nucleic Acid Modifications

Site-specific quantification of Adenosine-to-Inosine RNA editing by Endonuclease-Mediated qPCR

RNA molecules contain diverse modified nucleobases that play pivotal roles in numerous biological processes. Adenosine-to-inosine (A-to-I) RNA editing, one of the most prevalent RNA modifications in mammalian cells, is linked to a multitude of human diseases. To unveil the functions of A-to-I RNA editing, accurate quantification of inosine at specific sites is essential. In this study, we developed an endonuclease-mediated cleavage and real-time fluorescence quantitative PCR method for A-to-I RNA editing (EM-qPCR) to quantitatively analyze A-to-I RNA editing at a single site. By employing this method, we successfully quantified the levels of A-to-I RNA editing on various transfer RNA (tRNA) molecules at position 34 (I34) in mammalian cells with precision. Subsequently, this method was applied to tissues from sleep-deprived mice, revealing a notable alteration in the levels of I34 between sleep-deprived and control mice. The proposed method sets a precedent for the quantitative analysis of A-to-I RNA editing at specific sites, facilitating a deeper understanding of the biological implications of A-to-I RNA editing.

Artisanal Gem Mining in Brazil: Evaluation of Oxidative Stress and Genotoxicity Biomarkers

This study was carried out in the district of Taquaral de Minas, in the municipality of Itinga, located in Jequitinhonha Valley, state of Minas Gerais, which is considered one of the largest yolk-producing regions in Brazil. Miners in gem extraction areas are prone to severe oxidative damage due to their increased exposure to toxic metals, as well as chemical, physical, and biological agents, resulting in diseases such as silicosis. Thus, this work aimed to evaluate occupational exposure in prospectors through biomonitoring techniques using a variety of biomarkers for oxidative stress, genotoxicity, and mutagenicity. Twenty-two miners and seventeen workers who were not occupationally exposed were recruited, totaling thirty-nine participants. The study was approved by the Research Ethics Committee of the Federal University of the Jequitinhonha and Mucuri Valleys. In this study, the levels of total peroxides, catalase activity, and microelements in plasma were evaluated. Additionally, environmental analysis was carried out through the Ames and Allium cepa tests. The results of the lipoperoxidation assessment were significant, with increased frequencies in exposed individuals compared to controls (p < 0.05), as determined by the Mann-Whitney test. Micronutrients in the blood showed lower concentrations in the group exposed to Fe and Se than in individuals not exposed to these elements. The results of the Ames test and Allium cepa test were statistically significant compared to the controls (p < 0.05), as determined by the Mann-Whitney test for genotoxicity and cytotoxicity. Thus, the results of the present study indicate possible environmental contamination and a potential risk to the health of miners, which suggests that further studies are important in the region.

Emerging Roles of N6-Methyladenosine (m6A) Epitranscriptomics in Toxicology

Epitranscriptomics, the study of chemically modified RNAs, is a burgeoning field being explored in a variety of scientific disciplines. Of the currently known epitranscriptomic modifications, N6-methyladenosine (m6A) methylation is the most abundant. The m6A modification is predominantly regulated by 3 tiers of protein modulators classified as writers, erasers, and readers. Depending upon cellular needs, these proteins function to deposit, remove, or read the methyl modifications on cognate mRNAs. Many environmental chemicals including heavy metals, pesticides, and other toxic pollutants, are all known to perturb transcription and translation machinery to exert their toxic responses. As such, we herein review how the m6A modification may be affected under different toxicological paradigms. Furthermore, we discuss how toxicants can affect the 3 tiers of regulation directly, and how these effects influence the m6A-modified mRNAs. Lastly, we highlight the disparities between published findings and theories, especially those concerning the m6A reader tier of regulation. In the far-reaching field of toxicology, m6A epitranscriptomics provides another enticing avenue to explore new mechanisms and therapies for a diverse range of environmentally linked disorders and diseases.

Quantification and mapping of DNA modifications

Apart from the four canonical nucleobases, DNA molecules carry a number of natural modifications. Substantial evidence shows that DNA modifications can regulate diverse biological processes. Dynamic and reversible modifications of DNA are critical for cell differentiation and development. Dysregulation of DNA modifications is closely related to many human diseases. The research of DNA modifications is a rapidly expanding area and has been significantly stimulated by the innovations of analytical methods. With the recent advances in methods and techniques, a series of new DNA modifications have been discovered in the genomes of prokaryotes and eukaryotes. Deciphering the biological roles of DNA modifications depends on the sensitive detection, accurate quantification, and genome-wide mapping of modifications in genomic DNA. This review provides an overview of the recent advances in analytical methods and techniques for both the quantification and genome-wide mapping of natural DNA modifications. We discuss the principles, advantages, and limitations of these developed methods. It is anticipated that new methods and techniques will resolve the current challenges in this burgeoning research field and expedite the elucidation of the functions of DNA modifications.

A three-dimensional pinwheel-shaped paper-based microfluidic analytical device for fluorescence detection of multiple heavy metals in coastal waters by rational device design

Here, we present the rational design of a pinwheel-shaped three-dimensional microfluidic paper-based analytical device (3D-μPAD) for specific, sensitive and multiplexed detection of heavy metals in coastal waters. A more homogeneous permeation of fluids along the chip than common design, even under unskilled performance, has been achieved by the elaborate chip design of the hydrostatic balancing inlet port and uniformly stressed reversible sealing. With the combination of ion imprinted polymer grafted CdTe quantum-dots and fluid accumulation pad, 4 metals (Cu²⁺, Cd²⁺, Pb²⁺, and Hg²⁺) in 1 analysis and 25-fold enrichment for each metal can be simultaneously performed within 20 min, with detection limits of 0.007-0.015 μg/L. It has the ability to selectively recognize these 4 metals in mixtures and immunizing to interferences from components found in coastal waters, which provided results that were in agreement with values gained from atomic absorption. The inexpensive and portable nature as well as the highly sensitive and flexible performance of the new developed 3D-μPAD could make it attractive as an on-site testing approach for marine environmental monitoring.

Nucleic Acids Analysis

Nucleic acids are natural biopolymers of nucleotides that store, encode, transmit and express genetic information, which play central roles in diverse cellular events and diseases in living things. The analysis of nucleic acids and nucleic acids-based analysis have been widely applied in biological studies, clinical diagnosis, environmental analysis, food safety and forensic analysis. During the past decades, the field of nucleic acids analysis has been rapidly advancing with many technological breakthroughs. In this review, we focus on the methods developed for analyzing nucleic acids, nucleic acids-based analysis, device for nucleic acids analysis, and applications of nucleic acids analysis. The representative strategies for the development of new nucleic acids analysis in this field are summarized, and key advantages and possible limitations are discussed. Finally, a brief perspective on existing challenges and further research development is provided.