The majority of circular RNAs (circRNAs) spliced from coding genes contain open reading frames (ORFs) and thus, have protein coding potential. However, it remains unknown what regulates the biogenesis of these ORF-containing circRNAs, whether they are actually translated into proteins and what functions they play in specific physiological contexts. Here, we report that a large number of circRNAs are synthesized with increasing abundance when late pachytene spermatocytes develop into round and then elongating spermatids during murine spermatogenesis. For a subset of circRNAs, the back splicing appears to occur mostly at m 6 Aenriched sites, which are usually located around the start and stop codons in linear mRNAs. Consequently, approximately a half of these male germ cell circRNAs contain large ORFs with m 6 A-modified start codons in their junctions, features that have been recently shown to be associated with protein-coding potential. Hundreds of peptides encoded by the junction sequences of these circRNAs were detected using liquid chromatography coupled with mass spectrometry, suggesting that these circRNAs can indeed be translated into proteins in both developing (spermatocytes and spermatids) and mature (spermatozoa) male germ cells. The present study discovered not only a novel role of m 6 A in the biogenesis of coding circRNAs, but also a potential mechanism to ensure stable and long-lasting protein production in the absence of linear mRNAs, i.e., through production of circRNAs containing large ORFs and m 6 A-modified start codons in junction sequences.
Titanium dioxide nanoparticles (nano‐TiO2) are widely used in consumer products, raising environmental and health concerns. An overview of the toxic effects of nano‐TiO2 on human and environmental health is provided. A meta‐analysis is conducted to analyze the toxicity of nano‐TiO2 to the liver, circulatory system, and DNA in humans. To assess the environmental impacts of nano‐TiO2, aquatic environments that receive high nano‐TiO2 inputs are focused on, and the toxicity of nano‐TiO2 to aquatic organisms is discussed with regard to the present and predicted environmental concentrations. Genotoxicity, damage to membranes, inflammation and oxidative stress emerge as the main mechanisms of nano‐TiO2 toxicity. Furthermore, nano‐TiO2 can bind with free radicals and signal molecules, and interfere with the biochemical reactions on plasmalemma. At the higher organizational level, nano‐TiO2 toxicity is manifested as the negative effects on fitness‐related organismal traits including feeding, reproduction and immunity in aquatic organisms. Bibliometric analysis reveals two major research hot spots including the molecular mechanisms of toxicity of nano‐TiO2 and the combined effects of nano‐TiO2 and other environmental factors such as light and pH. The possible measures to reduce the harmful effects of nano‐TiO2 on humans and non‐target organisms has emerged as an underexplored topic requiring further investigation.
Surprisingly high rates of microbial respiration have recently been reported in hadal trench sediment, yet the potentially active microorganisms and specific microbe–microbe relationships in trench sediment are largely unknown. We investigated the bulk and active prokaryotic communities and co-occurrence interactions of different lineages in vertically sectioned sediment cores taken from the deepest points of the Mariana and Mussau Trenches. Analysis on species novelty revealed for the first time the high rate of novel lineages in the microbial communities of the hadal trenches. Using 95, 97, and 99% similarity as thresholds, averagely 22.29, 32.3, and 64.1% of total OTUs retrieved from sediments of the two trenches were identified as the potentially novel lineages, respectively. The compositions of the potentially active communities, revealed via ribosomal RNA (rRNA), were significantly different from those of bulk communities (rDNA) in all samples from both trenches. The dominant taxa in bulk communities generally accounted for low proportions in the rRNA libraries, signifying that the abundance was not necessarily related to community functions in the hadal sediments. The potentially active communities showed high diversity and composed primarily of heterotrophic lineages, supporting their potential contributions in organic carbon consumption. Network analysis revealed high modularity and non-random co-occurrence of phylogenetically unrelated taxa, indicating highly specified micro-niches and close microbial interactions in the hadal sediments tested. Combined analysis of activity potentials and network keystone scores revealed significance of phyla Chloroflexi and Gemmatimonadetes, as well as several potentially alkane-degrading taxa in maintaining microbial interactions and functions of the trench communities. Overall, our results demonstrate that the hadal trenches harbor diverse, closely interacting, and active microorganisms, despite the extreme environmental conditions.
The data collected by the wireless sensor nodes often has some spatial or temporal redundancy, and the redundant data impose unnecessary burdens on both the nodes and networks. Data prediction is helpful to improve data quality and reduce the unnecessary data transmission. However, the current data prediction methods of wireless sensor networks seldom consider how to utilize the spatial-temporal correlation among the sensory data. This paper has proposed a new data prediction method multi-node multi-feature (MNMF) based on bidirectional long short-term memory (LSTM) network. Firstly, the data quality is improved by quartile method and wavelet threshold denoising. Then, the bidirectional LSTM network is used to extract and learn the abstract features of sensory data. Finally, the abstract features are used in the data prediction by adopting the merge layer of the neural network. The experimental results show that the proposed MNMF model has better performance compared with the other methods in many evaluation indicators.
Background The full biosphere structure and functional exploration of the microbial communities of the Challenger Deep of the Mariana Trench, the deepest known hadal zone on Earth, lag far behind that of other marine realms. Results We adopt a deep metagenomics approach to investigate the microbiome in the sediment of Challenger Deep, Mariana Trench. We construct 178 metagenome-assembled genomes (MAGs) representing 26 phyla, 16 of which are reported from hadal sediment for the first time. Based on the MAGs, we find the microbial community functions are marked by enrichment and prevalence of mixotrophy and facultative anaerobic metabolism. The microeukaryotic community is found to be dominated by six fungal groups that are characterized for the first time in hadal sediment to possess the assimilatory and dissimilatory nitrate/sulfate reduction, and hydrogen sulfide oxidation pathways. By metaviromic analysis, we reveal novel hadal Caudovirales clades, distinctive virus-host interactions, and specialized auxiliary metabolic genes for modulating hosts’ nitrogen/sulfur metabolism. The hadal microbiome is further investigated by large-scale cultivation that cataloged 1070 bacterial and 19 fungal isolates from the Challenger Deep sediment, many of which are found to be new species specialized in the hadal habitat. Conclusion Our hadal MAGs and isolates increase the diversity of the Challenger Deep sediment microbial genomes and isolates present in the public. The deep metagenomics approach fills the knowledge gaps in structure and diversity of the hadal microbiome, and provides novel insight into the ecology and metabolism of eukaryotic and viral components in the deepest biosphere on earth.
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