Synthesis of mackinawite (FeSm) and its heterogeneous fenton-like catalytic degradation performance of rhodamine B

In this work, Mackinawite (FeSm) was synthesized by the homogeneous precipitation method, which was flower-like nanoparticles formed by the aggregation of nanosheets with a preferred orientation along the (001) plane. The heterogeneous Fenton-like degradation performance of FeSm on Rhodamine B (RhB) was investigated, results illustrated that RhB degradation was the synergistic effect of adsorption, Fenton, and the heterogeneous Fenton-like reaction. In repeated experiments, the reduction of reactivity was attributed to the oxidation of FeSm into lepidocrocite, whereas lepidocrocite has relatively low hydroxyl radicals (•OH) production reactivity. Thus, it showed excellent degradation effects in the long-time degradation of RhB. Photoluminescence (PL) technology and free radical capture experiments demonstrated that •OH produced on the surface of catalyst was the main active species to remove RhB. Meanwhile, the Fe species on the surface of FeSm was the main active center for surface-mediated reactions. The total organic carbon (TOC) test revealed that the degradation was not complete and degradation intermediates were formed. Liquid chromatography-mass spectrometry (LC-MS) technology was used to identify the degradation intermediates. On this basis, possible degradation pathways were proposed.

Genomics Analysis and Degradation Characteristics of Lignin by Streptomyces Thermocarboxydus Strain DF3-3

Background: Lignocellulose is an important raw material for biomass-to-energy conversion, and it exhibits a complex but inefficient degradation mechanism. Microbial degradation is promising due to its environmental adaptability and biochemical versatility, but the pathways used by microbes for lignin degradation have not been fully studied. Degradation intermediates and complex metabolic pathways require more study.Results: A novel actinomycete DF3-3, with the potential for lignin degradation, was screened and isolated. After morphological and molecular identification, DF3-3 was determined to be Streptomyces thermocarboxydus. The degradation of alkali lignin reached 31% within 15 days. Manganese peroxidase and laccase demonstrated their greatest activity levels, 1821.66 UL-1 and 1265.58 UL-1, respectively, on the sixth day. The highest lignin peroxidase activity was 480.33 UL-1 on the fourth day. A total of 19 lignin degradation intermediates were identified by gas chromatography-mass spectrometry (GC-MS), including 10 aromatic compounds. Genome sequencing and annotation identified 107 lignin-degrading enzyme-coding genes containing three core enzymatic systems for lignin depolymerization: laccases, peroxidases and manganese peroxidase. In total, 7 lignin metabolic pathways were predicted.Conclusions: Streptomyces thermocarboxydus strain DF3-3 has good lignin degradation ability. Degradation products and genomics analyses of DF3-3 show that it has a relatively complete lignin degradation pathway, including the β-ketoadipate pathway and peripheral reactions; gentisate pathway; anthranilate pathway; homogentisic pathway; and catabolic pathway for resorcinol. Two other pathways, the phenylacetate-CoA pathway and the 2,3-dihydroxyphenylpropionic acid pathway, are predicted based on genome data alone. This study provides the basis for future characterization of potential biotransformation enzyme systems for biomass energy conversion.

Theoretical Calculation on the Reaction Mechanisms, Kinetics and Toxicity of Acetaminophen Degradation Initiated by Hydroxyl and Sulfate Radicals in the Aqueous Phase

The •OH and SO4•− play a vital role on degrading pharmaceutical contaminants in water. In this paper, theoretical calculations have been used to discuss the degradation mechanisms, kinetics and ecotoxicity of acetaminophen (AAP) initiated by •OH and SO4•−. Two significant reaction mechanisms of radical adduct formation (RAF) and formal hydrogen atom transfer (FHAT) were investigated deeply. The results showed that the RAF takes precedence over FHAT in both •OH and SO4•− with AAP reactions. The whole and branched rate constants were calculated in a suitable temperature range of 198–338 K and 1 atm by using the KiSThelP program. At 298 K and 1 atm, the total rate constants of •OH and SO4•− with AAP were 3.23 × 109 M−1 s−1 and 4.60 × 1010 M−1 s−1, respectively, considering the diffusion-limited effect. The chronic toxicity showed that the main degradation intermediates were harmless to three aquatic organism, namely, fish, daphnia, and green algae. From point of view of the acute toxicity, some degradation intermediates were still at harmful or toxic level. These results provide theoretical guidance on the practical degradation of AAP in the water.

Degradation intermediates as an indicator of mRNA and cell metabolism

Traditional mRNA degradation rate measurements involves complex experimental design with RNA labeling or transcription blocking together with sampling at multiple timepoints. These experimental requirements limit the application of transcriptome-wide mRNA degradation rate analysis mainly in cultured cells, but rarely in in vivo samples. Therefore, a direct and simple strategy needs to be developed to study mRNA degradation rate. Here, we defined mRNA degradation intermediates as transcripts where decay is about to occur or has partially occurred in the 3′-untranslated regions after poly(A) tail deadenylation, and found that the proportion of mRNA degradation intermediates is a very simple and convenient indicator for evaluating the degradation rate of mRNA in mouse and human cell lines. In addition, we showed that a higher proportion of mRNA degradation intermediates is correlated with faster cell cycle and higher turnover rate of mouse tissues. Further, we validated that in mouse maturing oocytes where transcription is silent, the proportion of mRNA degradation intermediates is positively correlated with the mRNA degradation rate. Together, these results demonstrate that degradation intermediates can function as a good indicator of mRNA, cell, and tissue metabolism, and can be easily assayed by total RNA 3′-end sequencing from a single bulk cell sample without the need for drug treatment or multi-timepoint sampling. This finding is of great potential for studies on mRNA degradation rate at the molecular, cellular, or organic level, including samples or systems that cannot be assayed with previous methods. In addition, further application of the findings into single cells will likely greatly aid the identification and study of rare cells with unique cellular metabolism dynamics such as tissue stem cells and tumor cells.

Re-polyadenylation occurs predominantly on maternal mRNA degradation intermediates during mammalian oocyte-to-embryo transition

The nascent mRNA transcribed in the nucleus is cleaved and polyadenylated before it is transported to the cytoplasm for translation. Polyadenylation can also occur in the cytoplasm for post-transcriptional regulation, especially in neurons, oocytes and early embryos. Recently, we revealed transcriptome-wide maternal mRNA cytoplasmic re-polyadenylation during the mammalian oocyte-to-embryo transition (OET). However, the mechanism of re-polyadenylation during mammalian OET, including the sites to be re-polyadenylated and the enzymes involved, is still poorly understood. Here, by analyzing the PAIso-seq1 and PAIso-seq2 poly(A) inclusive transcriptome data during OET in mice, rats, pigs, and humans, we reveal conserved re-polyadenylation of mRNA degradation intermediates. These re-polyadenylated mRNA degradation intermediates account for over half of the polyadenylated mRNA during OET in all four species. We find that mRNA degradation intermediates for re-polyadenylation are generated through Btg4-mediated deadenylation in both mouse and human. Interestingly, the poly(A) tails on the re-polyadenylated mRNA degradation intermediates are of different lengths and contain different levels of non-A residues compared to regular polyadenylation sites, suggesting specific regulation and function of these poly(A) tails in mammalian OET. Together, our findings reveal the maternal mRNA degradation intermediates as substrates for conserved cytoplasmic dominant re-polyadenylation during mammalian OET, and uncover the mechanism of production of these mRNA degradation intermediates. These findings provide new insights into mRNA post-transcriptional regulation, and a new direction for the study of mammalian OET.