MTar: a computational microRNA target prediction architecture for human transcriptome

<p>Abstract</p> <p>Background</p> <p>MicroRNAs (miRNAs) play an essential task in gene regulatory networks by inhibiting the expression of target mRNAs. As their mRNA targets are genes involved in important cell functions, there is a growing interest in identifying the relationship between miRNAs and their target mRNAs. So, there is now a imperative need to develop a computational method by which we can identify the target mRNAs of existing miRNAs. Here, we proposed an efficient machine learning model to unravel the relationship between miRNAs and their target mRNAs.</p> <p>Results</p> <p>We present a novel computational architecture MTar for miRNA target prediction which reports 94.5% sensitivity and 90.5% specificity. We identified 16 positional, thermodynamic and structural parameters from the wet lab proven miRNA:mRNA pairs and MTar makes use of these parameters for miRNA target identification. It incorporates an Artificial Neural Network (ANN) verifier which is trained by wet lab proven microRNA targets. A number of hitherto unknown targets of many miRNA families were located using MTar. The method identifies all three potential miRNA targets (5' seed-only, 5' dominant, and 3' canonical) whereas the existing solutions focus on 5' complementarities alone.</p> <p>Conclusion</p> <p>MTar, an ANN based architecture for identifying functional regulatory miRNA-mRNA interaction using predicted miRNA targets. The area of target prediction has received a new momentum with the function of a thermodynamic model incorporating target accessibility. This model incorporates sixteen structural, thermodynamic and positional features of residues in miRNA: mRNA pairs were employed to select target candidates. So our novel machine learning architecture, MTar is found to be more comprehensive than the existing methods in predicting miRNA targets, especially human transcritome.</p

An integrated expression atlas of miRNAs and their promoters in human and mouse

MicroRNAs (miRNAs) are short non-coding RNAs with key roles in cellular regulation. As part of the fifth edition of the Functional Annotation of Mammalian Genome (FANTOM5) project, we created an integrated expression atlas of miRNAs and their promoters by deep-sequencing 492 short RNA (sRNA) libraries, with matching Cap Analysis Gene Expression (CAGE) data, from 396 human and 47 mouse RNA samples. Promoters were identified for 1,357 human and 804 mouse miRNAs and showed strong sequence conservation between species. We also found that primary and mature miRNA expression levels were correlated, allowing us to use the primary miRNA measurements as a proxy for mature miRNA levels in a total of 1,829 human and 1,029 mouse CAGE libraries. We thus provide a broad atlas of miRNA expression and promoters in primary mammalian cells, establishing a foundation for detailed analysis of miRNA expression patterns and transcriptional control regions

The swelling behaviour of lignosulfonate-treated expansive soil

This paper presents results regarding the potential of lignosulfonate (LS) to control the swelling of expansive soil. One-dimensional swell tests were performed on untreated and LS-treated remoulded samples of Australian expansive soil from the state of Queensland. The test results indicated that LS has significant influence on the swelling behaviour of this expansive soil. The results were compared with those of identical cement-treated soil samples, and it was found that LS could be a economical and environmentally friendly alternative to traditional alkaline additives. In addition, the behaviour of LS-treated specimens during repeated freezing and thawing cycles was measured. The results indicated significant improvement in the percentage mass loss in LS-treated specimens compared with cementtreated specimens. The microstructural analysis of the untreated and the LS-treated samples showed soil surface area reduction in the treated specimens, which in turn reduced the affinity of the specimens towards moisture uptake, resulting in a reduction in the swell potential of the otherwise expansive soil. The use of LS as a novel non-traditional stabiliser for expansive soil appears to be a viable solution in view of the sustainable use of waste by-products and green construction

Mechanisms of stabilization of expansive soil with lignosulfonate admixture

This study investigated and identified the mechanisms by which a remoulded expansive soil was modified or altered by a non-traditional admixture, lignosulfonate (LS). To achieve this objective, untreated and LS treated samples of expansive soil were examined microscopically using X-ray Diffraction (XRD), a Scanning Electron Microscope coupled with Energy Dispersive Spectroscopy (SEM/EDS), Fourier Transform Infrared (FTIR), Computed Tomography (CT-Scan), Nuclear Magnetic Resonance (NMR), Cation Exchange Capacity (CEC), and the role of Specific Surface Area (SSA). The interest was to identify and compare any physical and chemical changes between the untreated and treated samples and then propose the most likely reaction modes between the admixture and the soil minerals. The results indicated that the percent swell is intimately related to the amount of water that is adsorbed by the expansive clay minerals. Furthermore, the amount of moisture in an expansive soil is influenced by a small addition of organic (cationic) compound such as LS. The adsorption of LS on the mineral surfaces provided waterproofing effect on soil due to the hydrophobic nature of LS, which in turn contributed to a decrease in the extent of swelling of the otherwise expansive soil. The basal and peripheral adsorption of LS led to smearing and subsequent agglomeration of soil particles restricting water ingress into the soil body. In addition, the cationic exchange between the admixture and the soil particle surfaces (i.e. replacing the negative surfaces on clay lattices) prompted flocculation, which further decreased the soil's affinity to water

Potential use of lignosulfonate for expansive soil stabilisation

This study involved the laboratory evaluation of the effectiveness of lignosulfonate (LS) admixture in improving engineering properties (i.e. swell potential, unconfined compressive strength, durability, compaction characteristics, permeability, consolidation characteristics and shrinkage behaviour) of a remoulded expansive soil. Standard geotechnical laboratory tests performed on untreated and LS-treated soil specimens compacted at optimum moisture content and maximum dry unit weight showed significant and consistent improvements in the engineering properties of the soil. The swell potential of the soil decreased by 23% while maintaining its ductility and pH value. The improved soil resistance to repeated freeze-thaw/wet-dry cycles was also observed in the LS-treated specimens. Likewise, the compressive strength, consolidation characteristics and shrinkage limit improved appreciably. However, the compaction characteristics and permeability of the treated soil remained relatively unchanged. With over 50 Mt of global annual production of LS, the successful use of LS as an alternative admixture for expansive soil stabilisation provides viable solutions to the sustainable use of the lignin by-products from paper manufacturing industry

Bacterial biofilm colonization and succession in tropical marine waters are similar across different types of stone materials used in seawall construction.

Seawalls are important in protecting coastlines from currents, erosion, sea-level rise, and flooding. They are, however, associated with reduced biodiversity, due to their steep orientation, lack of microhabitats, and the materials used in their construction. Hence, there is considerable interest in modifying seawalls to enhance the settlement and diversity of marine organisms, as microbial biofilms play a critical role facilitating algal and invertebrate colonization. We assessed how different stone materials, ranging from aluminosilicates to limestone and concrete, affect biofilm formation. Metagenomic assessment of marine microbial communities indicated no significant impact of material on microbial diversity, irrespective of the diverse surface chemistry and topography. Based on KEGG pathway analysis, surface properties appeared to influence the community composition and function during the initial stages of biofilm development, but this effect disappeared by Day 31. We conclude that marine biofilms converged over time to a generic marine biofilm, rather than the underlying stone substrata type playing a significant role in driving community composition