Integrated Four Comparative-Omics Reveals the Mechanism of the Terpenoid Biosynthesis in Two Different Overwintering Cryptomeria fortunei Phenotypes

Chinese cedar (Cryptomeria fortunei) is a tree species with important ornamental, medicinal, and economic value. Terpenoids extracted from the essential oil of C. fortunei needles have been considered valuable ingredients in the pharmaceutical and cosmetic industries. However, the possible gene regulation mechanisms that limit terpenoid biosynthesis in this genus are poorly understood. Here, we adopted integrated metabolome analysis, transcriptome, small-RNA (sRNA), and degradome sequencing to analyze the differences in terpenoid regulatory mechanisms in two different overwintering C. fortunei phenotypes (wild-type and an evergreen mutant). A total of 1447/6219 differentially synthesized metabolites (DSMs)/unigenes (DEGs) were detected through metabolome/transcriptome analyses, and these DSMs/DEGs were significantly enriched in flavonoid and diterpenoid biosynthesis pathways. In C. fortunei needles, 587 microRNAs (miRNAs), including 67 differentially expressed miRNAs (DERs), were detected. Among them, 8346 targets of 571 miRNAs were predicted using degradome data, and a 72-miRNA-target regulatory network involved in the metabolism of terpenoids and polyketides was constructed. Forty-one targets were further confirmed to be involved in terpenoid backbone and diterpenoid biosynthesis, and target analyses revealed that two miRNAs (i.e., aly-miR168a-5p and aof-miR396a) may be related to the different phenotypes and to differential regulation of diterpenoid biosynthesis. Overall, these results reveal that C. fortunei plants with the evergreen mutation maintain high terpenoid levels in winter through miRNA-target regulation, which provides a valuable resource for essential oil-related bioengineering research.

miR-188-3p-targeted Regulation of ATG7 Affects Cell Autophagy in Patients With Non-obstructive Azoospermia

Background: Studies have found that ATG7 knockout mice have defects in acrosome development, and the sperm formed by them are similar to human round-headed sperm. miR-188-3p expression is alleviated in the testis tissues of NOA samples. It is unclear whether ATG7 gene is related to non-obstructive azoospermia and whether miR-188-3p and ATG7 have direct target regulation relationship to affect spermatogenesis.Methods: The testicular tissues of 14 non-obstructive azoospermia (NOA) patients and 13 healthy patients were collected for basic scientific research from October 2017 to June 2018. High-throughput sequencing, qRT-PCR, Western blot, immunohistochemical staining, immunofluorescence, electron microscope, and luciferase experiment were performed to confirm the correlation between miR-188-3p and ATG7 in non-obstructive azoospermia.Results: ATG7 was highly expressed in NOA group. ATG7 protein was localized in the cytoplasm of spermatogenic cells at various levels, and the expression in NOA group was dramatically higher than that of normal individuals. After overexpression of miR-188-3p, the ATG7 3'UTR-WT luciferase activity was impeded; while the ATG7 3'UTR-MUT luciferase activity had no significant difference. LC3 and Beclin-1 gene and protein expression in the NOA samples were elevated in comparison with the normal samples; LC3 was mainly located in the cytoplasm of spermatogenic cells at all levels. LC3 and Beclin-1 genes expression after miR-188-3p overexpression were prominently in comparison with the normal samples; after miR-188-3p was inhibited, LC3 and Beclin-1 expressions were dramatically higher. The degree of LC3 punctate aggregation in the miR-188-3p mimic NC samples was greater, and that in the miR-188-3p inhibitor group was greater. The number of autophagosomes of the miR-188-3p mimic samples was less compared with the mimic NC group.Conclusion: We demonstrated here that the ATG7 gene was located in all levels of spermatogenic cells and was highly expressed in the NOA group. The expression of ATG7 gene was negatively correlated with miR-188-3p that may regulate the target gene ATG7 to participate in autophagy and affect the occurrence of NOA.

Conservation and turnover of miRNAs and their highly complementary targets in early branching animals

MicroRNAs (miRNAs) are crucial post-transcriptional regulators that have been extensively studied in Bilateria, a group comprising the majority of extant animals, where more than 30 conserved miRNA families have been identified. By contrast, bilaterian miRNA targets are largely not conserved. Cnidaria is the sister group to Bilateria and thus provides a unique opportunity for comparative studies. Strikingly, like their plant counterparts, cnidarian miRNAs have been shown to predominantly have highly complementary targets leading to transcript cleavage by Argonaute proteins. Here, we assess the conservation of miRNAs and their targets by small RNA sequencing followed by miRNA target prediction in eight species of Anthozoa (sea anemones and corals), the earliest-branching cnidarian class. We uncover dozens of novel miRNAs but only a few conserved ones. Further, given their high complementarity, we were able to computationally identify miRNA targets in each species. Besides evidence for conservation of specific miRNA target sites, which are maintained between sea anemones and stony corals across 500 Myr of evolution, we also find indications for convergent evolution of target regulation by different miRNAs. Our data indicate that cnidarians have only few conserved miRNAs and corresponding targets, despite their high complementarity, suggesting a high evolutionary turnover.

Research progress of natural plant products inducing apoptosis of tumor stem cells

Compared to general cancer cells, cancer stem cells are stronger and more difficult to be killed by drugs. Therefore, traditional treatment methods have low efficacy according to cancer stem cells. In essence, one of the main causes of cancer survival, proliferation, transfer, and recurrence is the presence of cancer stem cells. In recent years, a large number of studies have demonstrated that natural plant products have powerful in killing cancer cells and have various structures, which possess low toxicity, multi-target regulation advantages in inducing cancer stem cells to apoptosis. Therefore, this provides new ideas for developing anti-cancer drugs by inducing cancer stem cell apoptosis by natural plant products. In this article, we will introduce the apoptotic mechanism of tumor stem cells, the importance of eliminating tumor stem cells, and the benefits of natural plant products in cancer treatment. In addition, this paper reviewed nine categories of chemicals in natural plant products that induce apoptosis of tumor stem cells and their mechanisms of action. We also summarized the mechanism of natural plant products inducing apoptosis of tumor stem cells. This review provides an important reference for the personalized treatment of cancer.

sRNATargetDigger: A bioinformatics software for bidirectional identification of sRNA-target pairs with co-regulatory sRNAs information

Identification of the target genes of microRNAs (miRNAs), trans-acting small interfering RNAs (ta-siRNAs), and small interfering RNAs (siRNAs) is an important step for understanding their regulatory roles in plants. In recent years, many bioinformatics software packages based on small RNA (sRNA) high-throughput sequencing (HTS) and degradome sequencing data analysis have provided strong technical support for large-scale mining of sRNA-target pairs. However, sRNA-target regulation is achieved using a complex network of interactions since one transcript might be co-regulated by multiple sRNAs and one sRNA may also affect multiple targets. Currently used mining software can realize the mining of multiple unknown targets using known sRNA, but it cannot rule out the possibility of co-regulation of the same target by other unknown sRNAs. Hence, the obtained regulatory network may be incomplete. We have developed a new mining software, sRNATargetDigger, that includes two function modules, “Forward Digger” and “Reverse Digger”, which can identify regulatory sRNA-target pairs bidirectionally. Moreover, it has the ability to identify unknown sRNAs co-regulating the same target, in order to obtain a more authentic and reliable sRNA-target regulatory network. Upon re-examination of the published sRNA-target pairs in Arabidopsis thaliana, sRNATargetDigger found 170 novel co-regulatory sRNA-target pairs. This software can be downloaded from http://www.bioinfolab.cn/sRNATD.html.

Unravelling the developmental and functional significance of an ancient Argonaute duplication

MicroRNAs (miRNAs) base-pair to messenger RNA targets and guide Argonaute proteins to mediate their silencing. This target regulation is considered crucial for animal physiology and development. However, this notion is based exclusively on studies in bilaterians, which comprise almost all lab model animals. To fill this phylogenetic gap, we characterize the functions of two Argonaute paralogs in the sea anemone Nematostella vectensis of the phylum Cnidaria, which is separated from bilaterians by ~600 million years. Using genetic manipulations, Argonaute-immunoprecipitations and high-throughput sequencing, we provide experimental evidence for the developmental importance of miRNAs in a non-bilaterian animal. Additionally, we uncover unexpected differential distribution of distinct miRNAs between the two Argonautes and the ability of one of them to load additional types of small RNAs. This enables us to postulate a novel model for evolution of miRNA precursors in sea anemones and their relatives, revealing alternative trajectories for metazoan miRNA evolution.

Network Pharmacological Analysis of Huanglian Jiedu Decoction for Anti- Atherosclerosis

Objective: We aimed to predict the possible active components,key targets and pathways of Huanglian Jiedu Decoction(HLJDD) for anti-atherosclerosis. Methods: The TCMSP database was searched to obtain the active components and targets of HLJDD, the GeneCards and OMIM databases were searched to obtain related targets of atherosclerosis, and we obtain the intersection targets of them, which are the potential targets of HLJDD for anti-atherosclerosis.Application of Cytoscape 3.6.0 software to build a herbal-active ingredient-potential target regulation network.We perform protein-protein interaction(PPI) network analysis of potential targets through STRING 11.0 database and obtain the key targets,and the results of PPI network of key targets were visualized by Cytoscape3.6.0 software. Gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of the key targets were performed using STRING11.0 database, and we finally constructed the possible pharmacological network of HLJDD for anti-atherosclerosis .Results: We finally obtained 14 key active ingredients of HLJDD, 65 key targets of anti-atherosclerosis, and 14 key active ingredients corresponded to 52 of these targets. These targets are mainly involved in biological processes such as reaction to organic substance, reaction to chemical stimulation,etc.They mainly involved in biological signaling pathways such as pathways in cancer,IL-17 signaling pathway,etc. Conclusion: HLJDD may act on 52 key targets such as PTGS2, HSP90AA1 and RELA through 14 key active ingredients, and influence the signaling pathways including fluid shear stress and atherosclerosis,PI3K-Akt signaling pathway,IL-17 signaling pathway,AGE-RAGE signaling pathway in diabetic complications,TNF signaling pathway,etc.Thus, it may play an anti-atherosclerosis role by inhibiting inflammatory reaction, oxidative stress and improving hemodynamics,etc.

ConnecTF: A platform to build gene networks by integrating transcription factor-target gene interactions

Deciphering gene regulatory networks (GRNs) is both a promise and challenge of systems biology. The promise is identifying key transcription factors (TFs) that enable an organism to react to changes in its environment. The challenge is constructing GRNs that involve hundreds of TFs and hundreds of thousands of interactions with their genome-wide target genes validated by high-throughput sequencing. To address this challenge, we developed ConnecTF, a species-independent web-based platform for constructing validated GRNs and to refine inferred GRNs via combined analysis of genome-wide studies of TF-target gene binding, TF-target regulation and other TF-centric omic data. We demonstrate the functionality of ConnecTF in three case studies, showing how integration within and across TF-target datasets uncovers biological insights. Case study 1 uses integration of TF-target gene regulation and binding datasets to uncover mode-of-action and identify potential TF partners for 14 TFs in abscisic acid signaling. Case study 2 demonstrates how genome-wide TF-target data and automated functions in ConnecTF are used to conduct precision/recall analysis and pruning of an inferred GRN for nitrogen signaling. In case study 3, we use ConnecTF to chart a network path from NLP7, a master TF in nitrogen signaling, to direct secondary TF2s, to its indirect targets, in an approach called Network Walking. The public version of ConnecTF (https://ConnecTF.org) contains 3,738,278 TF-target interactions for 423 TFs in Arabidopsis, and 839,210 TF-target interactions for 139 TFs in maize. The database and tools in ConnecTF should advance the exploration of GRNs in plant systems biology applications for models and crops.

Physico-mechanical and technological characteristics of composite materials based on mixtures of secondary thermoplastics

The physico-mechanical and technological characteristics of mixed waste of thermoplastic polymers, including that from the recyclable electronic and electrical equipment based on ABS plastic, were investigated. Target modifying additives were introduced into the composite system to improve the compatibility of polymer components of mixtures and the stable rheological properties of composition during processing. It is established that the secondary polymers behavior in their mixtures is caused by combination of their rheological characteristics and other parameters of mutual compatibility, that has significant impact on phase composition and microphases mutual order. Dispersed additives make a significant contribution to these processes, affecting the structuring of the associated polymer microvolumes. Target regulation of the rheological properties of components will ensure the achievement of acceptable and reproducible physico-mechanical characteristics and technological parameters of process, which will create prerequisites for the production of competitive products with a high guaranteed service life without use of scarce raw materials. Composite materials have been developed that are adapted to stable processing by extrusion, injection molding, and formation molding into technical products with acceptable performance characteristics.