It is well established that DNA base modifications play a key role in gene regulation during development and in response to environmental stress. This type of epigenetic control of development and ...environmental responses has been intensively studied over the past few decades. Similar to DNA, various RNA species also undergo modifications that play important roles in, for example, RNA splicing, protein translation, and the avoidance of immune surveillance by host. More than 160 different types of RNA modifications have been identified. In addition to base modifications, RNA modification also involves splicing of pre-mRNAs, leading to as many as tens of transcript isoforms from a single pre-RNA, especially in higher organisms. However, the function, prevalence and distribution of RNA modifications are poorly understood. The lack of a suitable method for the reliable identification of RNA modifications constitutes a significant challenge to studying their functions. This review focuses on the technologies that enable de novo identification of RNA base modifications and the alternatively spliced mRNA transcripts.
para-Phenylenediamine quinones (PPD-Qs) are a newly discovered class of transformation products derived from para-phenylenediamine (PPD) antioxidants. These compounds are prevalent in runoff, ...roadside soil, and particulate matter. One compound among these, N-1,3-dimethylbutyl-n′-phenyl-p-phenylenediamine quinone (6PPD-Q), was found to induce acute mortality of coho salmon, rainbow trout, and brook trout, with the median lethal concentrations even lower than its appearance in the surface and receiving water system. However, there was limited knowledge about the occurrence and fate of these emerging environmental contaminants in wastewater treatment plants (WWTPs), which is crucial for effective pollutant removal via municipal wastewater networks. In the current study, we performed a comprehensive investigation of a suite of PPD-Qs along with their parent compounds across the influent, effluent, and biosolids during each processing unit in four typical WWTPs in Hong Kong. The total concentrations of PPDs and PPD-Qs in the influent were determined to be 2.7–90 and 14–830 ng/L. In the effluent, their concentrations decreased to 0.59–40 and 2.8–140 ng/L, respectively. The median removal efficiency for PPD-Qs varied between 53.0 and 91.0% across the WWTPs, indicating that a considerable proportion of these contaminants may not be fully eliminated through the current processing technology. Mass flow analyses revealed that relatively higher levels of PPD-Qs were retained in the sewage sludge (20.0%) rather than in the wastewater (16.9%). In comparison to PPDs, PPD-Qs with higher half-lives exhibited higher release levels via effluent wastewater, which raises particular concerns about their environmental consequences to aquatic ecosystems.
A simple, rapid and high-throughput approach was developed for authentication of red wine for the first time, by combining spectral results from matrix-assisted laser desorption/ionization mass ...spectrometry (MALDI-MS) and direct analysis in real time mass spectrometry (DART-MS). By coupling with orthogonal partial least squares discrimination analysis (OPLS-DA), this approach enabled successful classification of 535 wines from 8 countries, with the correct classification rates of 100% on the calibration set and over 90% on the validation set for almost all countries, and 26 potential characteristic markers selected. Compared to one single technique, this approach allowed detection of more compound ions, and with better fitting and predictive performances. The satisfactory differentiation results of vintages and grape varieties further verified the robustness of the approach. This study demonstrated the feasibility of combining multiple mass spectrometric techniques for wine analysis, which can be extended to other fields or to combinations of other analytical techniques.
Plastic pollution is recognized as a major threat to ecosystems in the 21st century. Large plastic objects undergo biotic and abiotic degradation to generate micro- and nano-sized plastic pieces. ...Despite tremendous efforts to evaluate the adverse effects of microplastics, a comprehensive understanding of the toxicity of nanoplastics remains elusive, especially at the protein level. To this end, we used isobaric-tag-for-relative-and-absolute-quantitation-based quantitative proteomics to investigate the proteome dynamics of the soil nematode Caenorhabditis elegans in response to exposure to 100 nm polystyrene nanoplastics (PS-NPs). After 48 h of exposure to 0.1, 1, or 10 mg/L PS-NPs, 136 out of 1684 proteins were differentially expressed and 108 of these proteins were upregulated. These proteins were related to ribosome biogenesis, translation, proteolysis, kinases, protein processing in the endoplasmic reticulum, and energy metabolism. Remarkably, changes in proteome dynamics in response to exposure to PS-NPs were consistent with the phenotypic defects of C. elegans. Collectively, our findings demonstrate that disruption of proteome homeostasis is a biological consequence of PS-NPs accumulation in C. elegans, which provides insights into the molecular mechanisms underlying the toxicology of nanoplastics.
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•Polystyrene nanoplastics elicit phenotypic defects of C. elegans.•Uptake of nanoplastics in C. elegans disrupts overall proteome homeostasis.•Proteins related to ribosome, translation, and proteolysis are up-regulated.•Proteins related to energy metabolism are up-regulated.•Post-transcriptional regulation might occur to mediate stress response.
Although next-generation sequencing technology has been used to delineate RNA modifications in recent years, the paucity of appropriate converting reactions or specific antibodies impedes the ...accurate characterization and quantification of numerous RNA modifications, especially when these modifications demonstrate wide variations across developmental stages and cell types. In this study, we developed a high-throughput analytical platform coupling ultra-performance liquid chromatograph (UPLC) with complementary mass spectrometry (MS) to identify and quantify RNA modifications in both synthetic and biological samples. Sixty-four types of RNA modifications, including positional isomers and hypermodified ribonucleosides, were successfully monitored within a 16-min single run of UPLC–MS. Two independent methods to cross-validate the purity of RNA extracted from Caenorhabditis elegans (C. elegans) were developed using the coexisting C. elegans and Escherichia coli (E. coli) as a surveillance system. To test the validity of the method, we investigated the RNA modification landscape of three model organisms, C. elegans, E. coli, and Arabidopsis thaliana (A. thaliana). Both the identity and molarity of modified ribonucleosides markedly varied among the species. Moreover, our platform is not only useful for exploring the dynamics of RNA modifications in response to environmental cues (e.g., cold shock) but can also help with the identification of RNA-modifying enzymes in genetic studies. Cumulatively, our method presents a novel platform for the comprehensive analysis of RNA modifications, which will be of benefit to both analytical chemists involved in biomarker discovery and biologists conducting functional studies of RNA modifications.
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•UPLC-MS platform was developed for monitoring 64 RNA modifications.•Purity of eukaryotic RNA samples was cross-validated by UPLC-MS and RT-qPCR assays.•Global RNA modification landscapes of model organisms were investigated.•Dynamics of RNA modification landscape in response to cold shock was monitored.•Gene tgt-1 encodes a queuosine-modifying enzyme in C. elegans genome.
Epidemiological and experimental data have associated exposure to fine particulate matter (PM2.5) with various metabolic dysfunctions and diseases, including overweight and type 2 diabetes. Adipose ...tissue is an energy pool for storing lipids, a necessary regulator of glucose homeostasis, and an active endocrine organ, playing an essential role in developing various related diseases such as diabetes and obesity. However, the molecular mechanisms underlying PM2.5-impaired functions in adipose tissue have rarely been explored. In this work, metabolomics based on liquid chromatography-mass spectrometry was performed to study the adverse impacts of PM2.5 exposure on brown adipose tissue (BAT) and white adipose tissue (WAT) in the diabetic mouse model. We found the effects of PM2.5 exposure by comparing the different metabolites in both adipose tissues of male db/db mice using real-ambient PM2.5 exposure. The results showed that PM2.5 exposure changed the purine metabolism in mice, especially the dramatic increase of xanthine content in both WAT and BAT. These changes led to significant oxidative stress. Then the results from real-time quantitative polymerase chain reaction showed that PM2.5 exposure could cause the production of inflammatory factors in both adipose tissues. Moreover, the increased reactive oxygen species (ROS) promoted triglyceride accumulation in WAT and inhibited its decomposition, causing increased WAT content in db/db mice. In addition, PM2.5 exposure significantly suppressed thermogenesis and affected energy metabolism in the BAT of male db/db mice, which may deteriorate insulin sensitivity and blood glucose regulation. This research demonstrated the impact of PM2.5 on the adipose tissue of male db/db mice, which may be necessary for public health.
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•The impacts of PM2.5 exposure on both WAT and BAT of diabetic mice were studied.•Exposure to PM2.5 increased xanthine (precursor of uric acid) and ROS production.•PM2.5 promoted lipogenesis and inhibited lipolysis in the WAT of male db/db mice.•Thermogenesis in the BAT of male db/db mice was impaired after PM2.5 exposure.•Xanthine-derived ROS mediated the PM2.5-caused adipose tissue dysfunction in male db/db mice.
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•Key features of the Wushan skarn copper deposit are studied.•Copper mineralization involved fluid immiscibility and fluid mixing.•Magmatic and meteoric hydrothermal fluid sources are ...indicated for the deposit.
The Wushan copper skarn deposit (1.37 Mt at 1.17% Cu) is located in the Middle-Lower Yangtze River polymetallic belt. Skarn orebodies mainly occur in the Carboniferous and Permian carbonates adjacent to Early Cretaceous granodiorite porphyries (148–138 Ma). Ore deposition underwent two episodes of metallogenic events, involving hydrothermal evolution followed by skarn formation and porphyry-related mineralization. The skarn episode formed massive, disseminated, veinlet- and breccia-style mineralization at the contact zone, whereas porphyry mineralization is characterized as disseminated and veinlet-style only. Various types of fluid inclusions (daughter mineral-bearing, CO2-bearing, vapor and aqueous–vapor) are classified based on their fluid composition and phase assemblages.
The hydrothermal fluids are mainly derived from a magmatic origin, which exsolves during the melt-fluid differentiation. Primary fluid in endoskarn is interpreted as representing two immiscible phases evolving from a low-salinity initial fluid. The initial supersaturated fluid has a relative low salinity and the wide range of Th values (433–626 °C) implies heterogeneous trapping, corresponding to pressures of 371–646 bars and hydrostatic depth of 3.7–6.5 km. Primary fluid inclusions trapped in syn-ore quartz show the coexistence of S-type inclusions (~30.0 wt% NaCl equiv) with vapor-rich and liquid-rich inclusions, indicating fluid immiscibility and phase separation from heterogeneous trapping. The homogenization temperatures (347–434 °C) of primary vapor-rich inclusions represent the trapping temperatures, corresponding the trapped pressures range from 152 to 374 bars and a hydrostatic depth of 1.5–3.7 km. Copper mineralization in episode porphyry occurs on a very small scale and have a clear trend of decreasing temperatures and salinities during fluid evolution. A similar scenario occurred during the porphyry episode in which fluid immiscibility led to copper mineralization.
Significant trends of decreasing temperatures and salinities for both mineralization episodes reflect the change from a magmatic fluid-dominated system to a mixed source fluid that incorporated formation water from the country rocks and/or meteoric water. Controlled by the chemical transition of the fluid, this mixing process produced a relatively cool fluid system with lower salinities, which enhanced the precipitation of Cu–Fe sulfides. H–O–C isotope signatures further indicate that both the fluid and metal are predominantly derived from magmatic sources, and that multiple fluid pulses contributed to form skarn minerals and sulfides in the Wushan deposit.
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