Transcriptomic landscape of lncRNAs in inflammatory bowel disease

BACKGROUND: Inflammatory bowel disease (IBD) is a complex multi-factorial inflammatory disease with Crohn’s disease (CD) and ulcerative colitis (UC) being the two most common forms. A number of transcriptional profiling studies have provided compelling evidence that describe the role of protein-coding genes and microRNAs in modulating the immune responses in IBD. METHODS: In the present study, we performed a genome-wide transcriptome profiling of lncRNAs and protein-coding genes in 96 colon pinch biopsies (inflamed and non-inflamed) extracted from multiple colonic locations from 45 patients (CD = 13, UC = 20, controls = 12) using an expression microarray platform. RESULTS: In our study, we identified widespread dysregulation of lncRNAs and protein-coding genes in both inflamed and non-inflamed CD and UC compared to the healthy controls. In cases of inflamed CD and UC, we identified 438 and 745 differentially expressed lncRNAs, respectively, while in cases of the non-inflamed CD and UC, we identified 12 and 19 differentially expressed lncRNAs, respectively. We also observed significant enrichment (P-value <0.001, Pearson’s Chi-squared test) for 96 differentially expressed lncRNAs and 154 protein-coding genes within the IBD susceptibility loci. Furthermore, we found strong positive expression correlations for the intersecting and cis-neighboring differentially expressed IBD loci-associated lncRNA-protein-coding gene pairs. The functional annotation analysis of differentially expressed genes revealed their involvement in the immune response, pro-inflammatory cytokine activity and MHC protein complex. CONCLUSIONS: The lncRNA expression profiling in both inflamed and non-inflamed CD and UC successfully stratified IBD patients from the healthy controls. Taken together, the identified lncRNA transcriptional signature along with clinically relevant parameters suggest their potential as biomarkers in IBD. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13073-015-0162-2) contains supplementary material, which is available to authorized users

The identification and functional annotation of RNA structures conserved in vertebrates

Structured elements of RNA molecules are essential in, e.g., RNA stabilization, localization, and protein interaction, and their conservation across species suggests a common functional role. We computationally screened vertebrate genomes for conserved RNA structures (CRSs), leveraging structure-based, rather than sequence-based, alignments. After careful correction for sequence identity and GC content, we predict ∼516,000 human genomic regions containing CRSs. We find that a substantial fraction of human–mouse CRS regions (1) colocalize consistently with binding sites of the same RNA binding proteins (RBPs) or (2) are transcribed in corresponding tissues. Additionally, a CaptureSeq experiment revealed expression of many of our CRS regions in human fetal brain, including 662 novel ones. For selected human and mouse candidate pairs, qRT-PCR and in vitro RNA structure probing supported both shared expression and shared structure despite low abundance and low sequence identity. About 30,000 CRS regions are located near coding or long noncoding RNA genes or within enhancers. Structured (CRS overlapping) enhancer RNAs and extended 3′ ends have significantly increased expression levels over their nonstructured counterparts. Our findings of transcribed uncharacterized regulatory regions that contain CRSs support their RNA-mediated functionality.</jats:p

A Comparison of Protein Kinases Inhibitor Screening Methods Using Both Enzymatic Activity and Binding Affinity Determination

<div><p>Binding assays are increasingly used as a screening method for protein kinase inhibitors; however, as yet only a weak correlation with enzymatic activity-based assays has been demonstrated. We show that the correlation between the two types of assays can be improved using more precise screening conditions. Furthermore a marked improvement in the correlation was found by using kinase constructs containing the catalytic domain in presence of additional domains or subunits.</p></div

Binding and activity-based screening data comparison based on kinase-inhibitor pairs.

<p>Scatter plot comparison of our IC₅₀ and T_m shift data divided into proteins with only the catalytic domains (<b>A</b>) and proteins with additional domains/subunits only (<b>B</b>). The dashed horizontal line corresponds to an IC₅₀ of 0.5 µM. The dashed vertical line in the plots of 4°C Tm shift corresponds to a binding affinity <1 µM. A significant correlation of binding and inhibition is observed (P<0.001).</p

Protein kinase constructs and properties.

<p>Protein kinase constructs and properties. Overview of the constructsused in this study, indicating protein name and Uniprot-ID (U-ID), protein domain contents and the corresponding amino acids of the relative Uniprot sequences (FL: full length; CD: catalytic domain). Also indicated is K_m for ATP that we determined for each construct, the concentration of ATP present in the assay for each kinase, the amount of enzyme used and the assay substrate peptide sequence (5F: 5-FAM or 5- Fluorescein AMidite tag).</p

Binding and activity-based screening data comparison based on kinase-inhibitor pairs.

<p><b>A</b>, Recreation of a scatter plot from Anastassiadis <i>et al</i>. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0098800#pone.0098800-Anastassiadis1" target="_blank">[2]</a> with comparison of their data, % activity of control (Ctrl) at 0.5 µM compound with T_m shift data obtained from Fedorov <i>et al. </i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0098800#pone.0098800-Fedorov1" target="_blank">[5]</a>. (<b>B</b>) Scatter plot comparison of our IC₅₀ and T_m shift data. The dashed horizontal line corresponds in <b>A</b> to 50% activity at 0.5 µM compound and in <b>B</b> to an IC₅₀ of 0.5 µM. The dashed vertical line in the plots of 4°C Tm shift corresponds to a binding affinity <1 µM. A significant correlation of binding and inhibition is observed for both analyses (P<0.001).</p

1^st DeepWind 5 MW Baseline design

AbstractThe first 5MW baseline design of the DeepWind concept is presented for a Darrieus type floating wind turbine system for water depths of more than 150 m. This design will be used as design reference to test the next technological improvements of sub-component level, being based as much as possible on existing technology.The iterative design process involves all sub-components and the potential constraints, and the most important dependencies are highlighted and the selected design presented. The blades are designed with constraints to minimize the gravitational loads and to be produced in a controlled pultrusion process. The floating platform is a slender cylindrical structure (i.e. spar buoy) rotating along with the rotor. The stability of the platform is achieved by adding counter weight at the bottom of the structure. During operations, the rotor is tilted and acts as a gyro, describing an elliptical trajectory on the water plane. The generator is placed at the bottom of the platform and uses 5MW direct drive technology.The conceptual design is evaluated with numerical simulations in the time domain using the aero-elastic code HAWC2. In order to investigate the concept, a double-disc blade element momentum (BEM) code for VAWTs has been included in the numerical solver through a dll.The analysis of the design is carried out in two different steps:1) to estimate natural frequencies of the platform in order to avoid major resonance problems, 2)to evaluate the baseline concept for certain load cases. A site has been chosen for the floating turbine off Norway as representative for external conditions. The structure is verified according to an ultimate strength analysis, including loads from wind, waves and currents. The stability of the platform is investigated, considering the displacements of the spar buoy and the maximum inclination angle, which is kept lower than 15 degrees