SUMMARY Long intergenic noncoding RNAs (lincRNA) are important regulators of gene expression. Although lincRNAs are expressed in immune cells, their functions in immunity are largely unexplored. Here we identify an immunoregulatory lincRNA, lincRNA-EPS, that is precisely regulated in macrophages to control the expression of immune response genes (IRGs). Transcriptome analysis of macrophages from lincRNA-EPS-deficient mice, combined with gain-of-function and rescue experiments, revealed a specific role for this lincRNA in restraining IRG expression. Consistently, lincRNA-EPS-deficient mice manifest enhanced inflammation and lethality following endotoxin challenge in vivo. lincRNA-EPS associates with chromatin at regulatory regions of IRGs to control nucleosome positioning and repress transcription. Further, lincRNA-EPS mediates these effects by interacting with heterogeneous nuclear ribonucleoprotein L via a CANACA motif located in its 3′ end. Together, these findings identify lincRNA-EPS as a repressor of inflammatory responses highlighting the importance of lincRNAs in the immune system.

We demonstrate, for the first time, the application of ordered mesoporous carbons with large pore sizes prepared from the surfactant-templating approach in efficient disposal of wastewater containing bulky dye molecules. The adsorption amount for the bulky dye (methylthionine chloride, fuchsin basic, rhodamine B, brilliant yellow, methyl orange, or Sudan G) is almost twice that of the activated carbon in which mesopores contribute almost 100% to the total surface area and volume. The ordered mesoporous carbon adsorbent has a high adsorption rate (>99.9%) for low-concentration dyes, good performance in decoloration regardless of the dye nature, including basic, acidic, or azo dyes, and high stability after dye elution. To establish the relationship between the pore texture and adsorption properties, three kinds of ordered mesoporous carbons with different pore sizes, surface areas, and pore volumes have been synthesized by using phenolic resins as carbon sources and triblock copolymer as a structure-directing agent. The XRD, TEM, and N 2 sorption measurements reveal that all mesoporous carbonaceous materials have the highly ordered 2D hexagonal mesostructure, high surface areas (398-2580 m 2 /g), large pore volumes (0.51-2.16 cm 3 /g), and uniform pore sizes ranging from 4.5 to 6.4 nm. The adsorption capacities are compared and the pore occupation is estimated to understand the adsorption behaviors in the ordered mesopores with different diameters and models. The spatial effect of dye molecules is the determinative factor for the adsorption in ordered mesoporous carbons with various pore textural properties. The mesoporous carbon with an extremely high surface area (2580 m 2 /g), a large pore volume (2.16 cm 3 /g), and bimodal pores (6.4 and 1.7 nm) prepared from the silica-carbon composite shows the highest adsorption capacities for bulky basic dyes among the three ordered mesoporous carbons.

BackgroundRecent innovations in sequencing technologies have provided researchers with the ability to rapidly characterize the microbial content of an environmental or clinical sample with unprecedented resolution. These approaches are producing a wealth of information that is providing novel insights into the microbial ecology of the environment and human health. However, these sequencing-based approaches produce large and complex datasets that require efficient and sensitive computational analysis workflows. Many recent tools for analyzing metagenomic-sequencing data have emerged, however, these approaches often suffer from issues of specificity, efficiency, and typically do not include a complete metagenomic analysis framework.ResultsWe present PathoScope 2.0, a complete bioinformatics framework for rapidly and accurately quantifying the proportions of reads from individual microbial strains present in metagenomic sequencing data from environmental or clinical samples. The pipeline performs all necessary computational analysis steps; including reference genome library extraction and indexing, read quality control and alignment, strain identification, and summarization and annotation of results. We rigorously evaluated PathoScope 2.0 using simulated data and data from the 2011 outbreak of Shiga-toxigenic Escherichia coli O104:H4.ConclusionsThe results show that PathoScope 2.0 is a complete, highly sensitive, and efficient approach for metagenomic analysis that outperforms alternative approaches in scope, speed, and accuracy. The PathoScope 2.0 pipeline software is freely available for download at: http://sourceforge.net/projects/pathoscope/.

The complexity of transcriptome-wide protein—RNA interaction networks is incompletely understood. While emerging studies are greatly expanding the known universe of RNA-binding proteins, methods for the discovery and characterization of protein—RNA interactions remain resource intensive and technically challenging. Here we introduce a UV-C crosslinking and immunoprecipitation platform, irCLIP, which provides an ultraefficient, fast, and nonisotopic method for the detection of protein—RNA interactions using far less material than standard protocols.