Constructing ecological-protecting barrier: Basic research of rainfall runoff regulation and application in the Loess Plateau of China and its implications for global arid areas

Loess Plateau is one of most eco-fragile and poverty-stricken areas in China. Drought and soil erosion are the two major obstacles to restrict economic development here. Rainfall runoff is the leading factor causing soil and water loss in this region. Rainfall runoff regulation and utilization is the inheritance, innovation and development for scientific theories of soil and water conservation in the Loess Plateau, which gives prominence to scientific gathering and detracting of rainfall runoff in terms of space and time and emphasizes on solving the drought and soil erosion by active control means and realizes the unity of regulation, preservation and utilization of rainfall runoff in space and time. The paper analyzed the progress of the applied research of rainfall runoff regulation and utilization from 4 aspects, such as the operational rules of rainfall runoff, the potential of rainfall runoff regulation and utilization, the optimal allocation of rainfall runoff and the environmental effects of rainfall runoff regulation and utilization. It also made the analysis on the current situation of rainfall runoff utilization technology. At last, the paper suggested some cases for rainfall runoff regulation and utilization in the Loess Plateau. Rainfall runoff not only brings about the integration of ecological reconstruction with economic development in the Loess Plateau, but also provides a new approach to the sustainable development as well as removing two of the biggest stumbling blocks, drought and soil erosion, in the Loess Plateau of China, which will provide more information for rainfall runoff utilization in the arid areas of the world

SFPEL-LPI: Sequence-based feature projection ensemble learning for predicting LncRNA-protein interactions.

LncRNA-protein interactions play important roles in post-transcriptional gene regulation, poly-adenylation, splicing and translation. Identification of lncRNA-protein interactions helps to understand lncRNA-related activities. Existing computational methods utilize multiple lncRNA features or multiple protein features to predict lncRNA-protein interactions, but features are not available for all lncRNAs or proteins; most of existing methods are not capable of predicting interacting proteins (or lncRNAs) for new lncRNAs (or proteins), which don't have known interactions. In this paper, we propose the sequence-based feature projection ensemble learning method, "SFPEL-LPI", to predict lncRNA-protein interactions. First, SFPEL-LPI extracts lncRNA sequence-based features and protein sequence-based features. Second, SFPEL-LPI calculates multiple lncRNA-lncRNA similarities and protein-protein similarities by using lncRNA sequences, protein sequences and known lncRNA-protein interactions. Then, SFPEL-LPI combines multiple similarities and multiple features with a feature projection ensemble learning frame. In computational experiments, SFPEL-LPI accurately predicts lncRNA-protein associations and outperforms other state-of-the-art methods. More importantly, SFPEL-LPI can be applied to new lncRNAs (or proteins). The case studies demonstrate that our method can find out novel lncRNA-protein interactions, which are confirmed by literature. Finally, we construct a user-friendly web server, available at http://www.bioinfotech.cn/SFPEL-LPI/

The Novel miRNA N-72 Regulates EGF-Induced Migration of Human Amnion Mesenchymal Stem Cells by Targeting MMP2

Human amnion mesenchymal stem cells (hAMSCs) are promising sources of stem cells in regenerative medicine. The migration stimulated by cytokines is critical for mesenchymal stem cells (MSCs)-based cytotherapy, while the regulatory mechanisms of EGF (epidermal growth factor)-induced hAMSC migration are largely unclear. Here, a novel miRNA N-72 (GenBank accession number: MH269369) has been discovered, and its function on EGF-induced migration in hAMSCs was investigated. High-purity hAMSCs were isolated and cultured in vitro, which were characterized by flow cytometry and trilineage differentiation. The N-72 located on chromosome three was conserved, and pri-N-72 owned the ability to form a stem-loop secondary structure, which was predicated by bioinformatic programs. The expression of mature N-72 was verified in several human cells including hAMSC by real-time PCR. In EGF-stimulated hAMSC, N-72 showed a significant reduction in a PI3K and p38 MAPK-dependent manner, and N-72 mimics transfection-inhibited EGF-induced migration, which was verified by scratch assay and transwell assay. Further, the predicated target gene MMP2 was proved to be a direct target of N-72 via luciferase reporter assay, real-time PCR, and Western blotting. The results that MMP2 silencing repressed hAMSC migration suggested MMP2 as a functional downstream target of N-72. In summary, we have discovered the novel N-72, and it was crucial for EGF-induced migration by targeting MMP2 in hAMSCs

Human Novel MicroRNA Seq-915_x4024 in Keratinocytes Contributes to Skin Regeneration by Suppressing Scar Formation

Early in gestation, wounds in fetal skin heal by regeneration, in which microRNAs play key roles. Seq-915_x4024 is a novel microRNA candidate confirmed by deep sequencing and mirTools 2.0. It is highly expressed in fetal keratinocytes during early gestation. Using an in vitro wound-healing assay, Transwell cell migration assay, and MTS proliferation assay, we demonstrated that keratinocytes overexpressing seq-915_x4024 exhibited higher proliferative activity and the ability to promote fibroblast migration and fibroblast proliferation. These characteristics of keratinocytes are the same biological behaviors as those of fetal keratinocytes, which contribute to skin regeneration. In addition, seq-915_x4024 suppressed the expression of the pro-inflammatory markers TNF-α, IL-6, and IL-8 and the pro-inflammatory chemokines CXCL1 and CXCL5. We also demonstrated that seq-915_x4024 regulates TGF-β isoforms and the extracellular matrix. Moreover, using an in vivo wound-healing model, we demonstrated that overexpression of seq-915_x4024 in keratinocytes suppresses inflammatory cell infiltration and scar formation. Using bioinformatics analyses, luciferase reporter assays, and western blotting, we further demonstrated that Sar1A, Smad2, TNF-α, and IL-8 are direct targets of seq-915_x4024. Furthermore, the expression of phosphorylated Smad2 and Smad3 was reduced by seq-915_x4024. Seq-915_x4024 could be used as an anti-fibrotic factor for the treatment of wound healing. Keywords: microRNA, skin regeneration, keratinocytes, wound healing, scar formatio

Dynamic Expression of Novel MiRNA Candidates and MiRNA-34 Family Members in Early- to Mid-Gestational Fetal Keratinocytes Contributes to Scarless Wound Healing by Targeting the TGF-β Pathway - Fig 2

<p>(a) Comparison of qRT-PCR data with NGS data for the six novel miRNA candidates {shown in (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0126087#pone.0126087.g001" target="_blank">Fig 1b</a>)} and four known miRNAs (hsa-miR-99b-3p, hsa-miR-190a, hsa-miR-3614-5p and hsa-miR-99a-3p). (b) Correlation analysis of the miRNA expression levels detected by NGS and qRT-PCR. The data were transformed to log2 values of the relative expression levels in late-gestational fetal KCs. The qRT-PCR results were normalized to the U6 snRNA expression levels. (c) Genomic locations of differentially expressed miRNAs and novel miRNA candidates found within 10 kb of each other. (d) Expression changes of statistically significant miRNAs in late-gestational fetal KCs detected by NGS. The data were transformed to log2 values of the relative expression levels in late-gestational fetal KCs.</p

Significantly differentially expressed miRNAs between mid- and late-gestational fetal KCs.

<p>(a) Eighty-eight known miRNAs that exhibited a change in expression of more than 2.0-fold in late-gestational fetal KCs. Fifteen of these were statistically up-regulated, and the others were statistically down-regulated. The read number of the miRNAs was normalized to the total number of high-quality reads that matched the human genome from each sample (12591141/12266070/12065253/12074661/13021411/12659579). MG represents mid-gestational, and LG represents late-gestational. The ratio represents the relative expression of miRNAs in late-gestational KCs. (b) Twenty-two novel miRNA candidates that exhibited a change in expression of more than 2.0-fold in late-gestational fetal KCs. Two of them were statistically up-regulated, and the others were statistically down-regulated. The read number of miRNAs was normalized to the total number of high-quality reads that matched the human genome from each sample (12591141/12266070/12065253/12074661/13021411/12659579). MG represents mid-gestational, and LG represents late-gestational. The ratio represents the relative expression of miRNAs in late-gestational KCs.</p