Clustered microRNAs' coordination in regulating protein-protein interaction network

<p>Abstract</p> <p>Background</p> <p>MicroRNAs (miRNAs), a growing class of small RNAs with crucial regulatory roles at the post-transcriptional level, are usually found to be clustered on chromosomes. However, with the exception of a few individual cases, so far little is known about the functional consequence of this conserved clustering of miRNA loci. In animal genomes such clusters often contain non-homologous miRNA genes. One hypothesis to explain this heterogeneity suggests that clustered miRNAs are functionally related by virtue of co-targeting downstream pathways.</p> <p>Results</p> <p>Integrating of miRNA cluster information with protein protein interaction (PPI) network data, our research supports the hypothesis of the functional coordination of clustered miRNAs and links it to the topological features of miRNAs' targets in PPI network. Specifically, our results demonstrate that clustered miRNAs jointly regulate proteins in close proximity of the PPI network. The possibility that two proteins yield to this coordinated regulation is negatively correlated with their distance in PPI network. Guided by the knowledge of this preference, we found several network communities enriched with target genes of miRNA clusters. In addition, our results demonstrate that the variance of this propensity can also partly be explained by protein's connectivity and miRNA's conservation.</p> <p>Conclusion</p> <p>In summary, this work supports the hypothesis of intra-cluster coordination and investigates the extent of this coordination.</p

MicroRNA-encoding long non-coding RNAs

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RNAcentral : a hub of information for non-coding RNA sequences

RNAcentral is a comprehensive database of non-coding RNA (ncRNA) sequences, collating information on ncRNA sequences of all types from a broad range of organisms. We have recently added a new genome mapping pipeline that identifies genomic locations for ncRNA sequences in 296 species. We have also added several new types of functional annotations, such as tRNA secondary structures, Gene Ontology annotations, and miRNA-target interactions. A new quality control mechanism based on Rfam family assignments identifies potential contamination, incomplete sequences, and more. The RNAcentral database has become a vital component of many workflows in the RNA community, serving as both the primary source of sequence data for academic and commercial groups, as well as a source of stable accessions for the annotation of genomic and functional features. These examples are facilitated by an improved RNAcentral web interface, which features an updated genome browser, a new sequence feature viewer, and improved text search functionality. RNAcentral is freely available at https://rnacentral.org

Effects of Matrix Modification on the Mechanical Properties of Wood–Polypropylene Composites

Polypropylene (PP) modified with two reactive monomers, divinyl benzene (DVB) and maleic anhydride (MAH), was used as the matrix to prepare wood–polypropylene composites to improve interfacial compatibility. The effects of the co-modified PP matrices with different DVB concentrations on the mechanical properties of the composites were evaluated. Compared with unmodified composites and the composites containing a coupling agent, the composites modified with MAH only, and that with both MAH and DVB, improved the tensile, flexural, and impact strengths. Interestingly, adding a small amount of DVB (0.4%) resulted in significant increase in impact strength, relative to that of the composites modified with MAH only. Dynamic mechanical analysis and fracture morphology analysis of the modified composites also suggested an improvement in interfacial adhesion owing to the matrix modification

Porous highly fluorinated polyimide/polydopamine nanocomposite films with simultaneously enhanced toughness, UV-shielding and photostability for aerospace applications

Polydopamine (PDA), also known as artificial melanin, was adopted as ultraviolet absorbent to prepare a series of porous highly fluorinated polyimide/polydopamine (FPI/PDA) films by cyclodehydration via chemical and thermal imidization. The hydrogen bond and porous structure endowed the reinforced thermal, mechanical, UV-shielding and photostability. The initial decomposition and glass transition temperatures of FPI/PDA (1 wt %) film were as high as 461.5 °C and 341.5 °C, respectively beyond pure FPI by 54.1 °C and 26.0 °C. The stress-strain curves indicated that tensile strength and fracture elongation first increased and then decreased with the increase of PDA content, and reached the maximum at 0.5 wt % PDA content, which were 1.41 and 29.47 times of FPI, respectively. UV–vis transmittance spectra, curcumin photolysis and recyclability measurement confirmed the splendid UV-shielding properties with simultaneous excellent visible light transmittance and durability of porous FPI/PDA film. FTIR and AFM manifested its superior photostability with mild variation in carbonyl absorption peaks and surface roughness after 720 h UV irradiation. The above enhancement mechanisms included synergistic UV absorption of porous FPI and PDA, photothermal conversion in a stable FPI, and PDA's free radical trapping, promoting porous FPI/PDA film as an aerospace UV shielding material

Preparation and Properties of a Novel Microcrystalline Cellulose-Filled Composites Based on Polyamide 6/High-Density Polyethylene

In the present study, lithium chloride (LiCl) was utilized as a modifier to reduce the melting point of polyamide 6 (PA6), and then 15 wt % microcrystalline cellulose (MCC) was compounded with low melting point PA6/high-density polyethylene (HDPE) by hot pressing. Crystallization analysis revealed that as little as 3 wt % LiCl transformed the crystallographic forms of PA6 from semi-crystalline to an amorphous state (melting point: 220 °C to none), which sharply reduced the processing temperature of the composites. LiCl improved the mechanical properties of the composites, as evidenced by the fact that the impact strength of the composites was increased by 90%. HDPE increased the impact strength of PA6/MCC composites. In addition, morphological analysis revealed that incorporation of LiCl and maleic anhydride grafted high-density polyethylene (MAPE) improved the interfacial adhesion. LiCl increased the glass transition temperature of the composites (the maximum is 72.6 °C)

Eco-Environmental Geological Features of Mangrove in Dongchong, Shenzhen City

Mangroves are halophytic forest plant communities located on saline marshes in estuaries of tropical and subtropical bays. They are one of the most vulnerable ecosystems in the world and are severely threatened by urban development, environmental pollution, aquaculture, and other problems. The Dongchong mangrove forest is a relatively well-preserved mangrove forest in China, with a large area and a typical Excoecaria agallocha landscape, which has significant ornamental and ecological conservation value. The aim of this study is to provide basic support not only for mangrove ecological conservation and restoration, but also to construct and manage nature's reserves. The eco-environmental geological characteristics of mangroves were investigated using geology, geomorphology, pedology, ecology, and other methods, and a typical eco-environmental geological profile of the mangrove in Dongchong was drawn. The results show that the strata in the study area are mainly Quaternary sediments and rhyolites of the Nanshancun Formation of the Early Cretaceous. Faults are developed in the west of Dongchong Mangrove Wetland Park. The main environmental geological problems are uneven ground settlement, ground subsidence, and ground cracks. The concentration of F- in the surface water are high, and the water quality is slightly lower than that of the Class III water standard; however, the groundwater is freshwater with low salinity and hardness. Cd and Tl are locally significant in the surface soil of the study area. N, P, CaCO3, Org, and B are deficient in the soil, whereas the K content is mainly medium. A part of the soil is polluted by heavy metals, particularly As, followed by Cd. However, the mangrove leaves are rich in nutrients, indicating that the lack of soil nutrient elements and heavy-metal pollution are not the major factors limiting the growth of mangroves in this region. Improving the growth environment of mangroves should include expanding the landscape area and reinforcing reserve management. In the rock-soil-plant ecosystem, As, Pb, Cd, and B are significantly rich in the soil, indicating that their contents have a slight correlation with their parent rocks. Ni, Cu, Zn, and K are limited by the parent rock contents, and some elements including P, Mo, and Cr show enrichment capacity in the soil. The BCF >2 of mangroves of the mangrove forests in Dongchong are P and B, indicating that the mangrove trees have a higher absorption capacity for P and B. In contrast, the BCF values of As, Pb, and Cd are relatively low, which, in addition to the weak absorption capacity of the mangrove trees for these elements and combined with the geochemical characteristics of the soils in the study area, are also affected by the high Cd and As contents of the soil. All the data presented in this paper are from the project, "Ecological and Environmental Geological Survey of Shenzhen Nature Reserves," for which we express our sincere gratitude

Lisinopril Protects Against the Adriamycin Nephropathy and Reverses the Renalase Reduction: Potential Role of Renalase in Adriamycin Nephropathy

Aims: To investigate the potential role of renalase in adriamycin nephropathy and the effect of lisinopril on the regulation of renalase. Methods: Adriamycin nephropathy was induced in male Wistar rats (n=12) by a single injection of adriamycin at 2 mg/kg body weight. Rats were then randomly assigned to a model group or a treatment group, to which were administered distilled water or the angiotensin converting enzyme inhibitor lisinopril, respectively, for 12 weeks. Six normal rats served as controls. At the end of study, physiological parameters and systolic blood pressure were measured. Glomerulosclerosis and tubulointerstitial injury were assessed by histopathology Renalase protein expression in kidney was quantified by immunohistochemistry and immunoblotting. The serum concentration and urinary excretion of renalase were determined by enzyme-linked immunosorbent assay. Results: In model group rats, proteinuria and systolic blood pressure were elevated. Increased serum renalase concentration was observed; however, renalase protein expression in the kidney was significantly decreased. Compared with the model group, decreased proteinuria, lower systolic blood pressure, and fewer morphologic lesions were detected in the treatment group. Although levels of serum renalase were similar, accumulation of renalase in urine and kidney tissue increased notably in the treatment group compared with the model group. Conclusions: This study suggests that renalase may be involved in the process of adriamycin-induced renal injuries. Lisinopril may attenuate adriamycin-induced kidney injury by controlling blood pressure, which may be partially attributed to the renalase expression and secretion