Splice site strength–dependent activity and genetic buffering by poly-G runs

Pre-mRNA splicing is regulated through the combinatorial activity of RNA motifs, including splice sites and splicing regulatory elements. Here we show that the activity of the G-run (polyguanine sequence) class of splicing enhancer elements is approx4-fold higher when adjacent to intermediate strength 5' splice sites (ss) than when adjacent to weak 5' ss, and approx1.3-fold higher relative to strong 5' ss. We observed this dependence on 5' ss strength in both splicing reporters and in global microarray and mRNA-Seq analyses of splicing changes following RNA interference against heterogeneous nuclear ribonucleoprotein (hnRNP) H, which cross-linked to G-runs adjacent to many regulated exons. An exon's responsiveness to changes in hnRNP H levels therefore depends in a complex way on G-run abundance and 5' ss strength. This pattern of activity enables G-runs and hnRNP H to buffer the effects of 5' ss mutations, augmenting both the frequency of 5' ss polymorphism and the evolution of new splicing patterns. Certain other splicing factors may function similarly.American Heart AssociationHuman Frontier Science Program (Strasbourg, France)National Institutes of Health (U.S.)National Science Foundation (U.S.) (equipment grant DBI-0821391

ESDA2008-59373 AN INVESTIGATION INTO EFFECT OF TRAIN CURVING ON WEAR AND CONTACT STRESSES OF WHEEL AND RAIL

ABSTRACT Some important papers concerning the studies on rail wear and wheel/rail contact stresses are reviewed. The present paper utilizes a numerical method to analyze the effect of railway vehicle curving on the wear and contact stresses of wheel/rail. The numerical method considers a combination of Kalker's non-Hertzian rolling contact theory, a material wear model and a vertical and lateral coupling dynamics model of a half vehicle and a curved track. The present analysis investigates the influence of the curving speed, the curved track super-elevation and the rail cant on the wear and the contact stresses. Through the detailed numerical analysis, it is found that the maximum contact stress depends greatly not only on the curving speed but also on the profiles of the wheel/rail. The curving speed increasing leads to increase the normal load of the wheel rolling over the high curved rail, but, decrease the normal contact stress level under the condition of the optimum match of wheel/rail profiles. The track super elevation increasing efficiently lowers the contact stresses and the wear at a constant curving speed. The rail cant has a great influence on the low rail wear of the curved track. Increasing the rail cant leads to the great growth of the low curved rail wear, the reduction in the high rail wear. The results are very useful in the maintenance of the track

Sound transmission loss of windows on high speed trains

The window is one of the main components of the high speed train car body structure through which noise can be transmitted. To study the windows’ acoustic properties, the vibration of one window of a high speed train has been measured for a running speed of 250 km/h. The corresponding interior noise and the noise in the wheel-rail area have been measured simultaneously. The experimental results show that the window vibration velocity has a similar spectral shape to the interior noise. Interior noise source identification further indicates that the window makes a contribution to the interior noise. Improvement of the window’s Sound Transmission Loss (STL) can reduce the interior noise from this transmission path. An STL model of the window is built based on wave propagation and modal superposition methods. From the theoretical results, the window’s STL property is studied and several factors affecting it are investigated, which provide indications for future low noise design of high speed train windows

Identification of wounding and topping responsive small RNAs in tobacco (Nicotiana tabacum)

<p>Abstract</p> <p>Background</p> <p>MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are two major classes of small RNAs. They play important regulatory roles in plants and animals by regulating transcription, stability and/or translation of target genes in a sequence-complementary dependent manner. Over 4,000 miRNAs and several classes of siRNAs have been identified in plants, but in tobacco only computational prediction has been performed and no tobacco-specific miRNA has been experimentally identified. Wounding is believed to induce defensive response in tobacco, but the mechanism responsible for this response is yet to be uncovered.</p> <p>Results</p> <p>To get insight into the role of small RNAs in damage-induced responses, we sequenced and analysed small RNA populations in roots and leaves from wounding or topping treated tobacco plants. In addition to confirmation of expression of 27 known miRNA families, we identified 59 novel tobacco-specific miRNA members of 38 families and a large number of loci generating phased 21- or 24-nt small RNAs (including ta-siRNAs). A number of miRNAs and phased small RNAs were found to be responsive to wounding or topping treatment. Targets of small RNAs were further surveyed by degradome sequencing.</p> <p>Conclusions</p> <p>The expression changes of miRNAs and phased small RNAs responsive to wounding or topping and identification of defense related targets for these small RNAs suggest that the inducible defense response in tobacco might be controlled by pathways involving small RNAs.</p

Extensive translation of circular RNAs driven by N6-methyladenosine

Extensive pre-mRNA back-splicing generates numerous circular RNAs (circRNAs) in human transcriptome. However, the biological functions of these circRNAs remain largely unclear. Here we report that N6-methyladenosine (m6A), the most abundant base modification of RNA, promotes efficient initiation of protein translation from circRNAs in human cells. We discover that consensus m6A motifs are enriched in circRNAs and a single m6A site is sufficient to drive translation initiation. This m6A-driven translation requires initiation factor eIF4G2 and m6A reader YTHDF3, and is enhanced by methyltransferase METTL3/14, inhibited by demethylase FTO, and upregulated upon heat shock. Further analyses through polysome profiling, computational prediction and mass spectrometry reveal that m6A-driven translation of circRNAs is widespread, with hundreds of endogenous circRNAs having translation potential. Our study expands the coding landscape of human transcriptome, and suggests a role of circRNA-derived proteins in cellular responses to environmental stress

Ectopic tissue engineered ligament with silk collagen scaffold for ACL regeneration: A preliminary study

Anterior cruciate ligament (ACL) reconstruction remains a formidable clinical challenge because of the lack of vascularization and adequate cell numbers in the joint cavity. In this study, we developed a novel strategy to mimic the early stage of repair in vivo, which recapitulated extra-articular inflammatory response to facilitate the early ingrowth of blood vessels and cells. A vascularized ectopic tissue engineered ligament (ETEL) with silk collagen scaffold was developed and then transferred to reconstruct the ACL in rabbits without interruption of perfusion. At 2 weeks after ACL reconstruction, more well-perfused cells and vessels were found in the regenerated ACL with ETEL, which decreased dramatically at the 4 and 12 week time points with collagen deposition and maturation. ACL treated with ETEL exhibited more mature ligament structure and enhanced ligament-bone healing post-reconstructive surgery at 4 and 12 weeks, as compared with the control group. In addition, the ETEL group was demonstrated to have higher modulus and stiffness than the control group significantly at 12 weeks post-reconstructive surgery. In conclusion, our results demonstrated that the ETEL can provide sufficient vascularity and cellularity during the early stages of healing, and subsequently promote ACL regeneration and ligament-bone healing, suggesting its clinic use as a promising therapeutic modality. Statement of Significance Early inflammatory cell infiltration, tissue and vessels ingrowth were significantly higher in the extra articular implanted scaffolds than theses in the joint cavity. By mimicking the early stages of wound repair, which provided extra-articular inflammatory stimulation to facilitate the early ingrowth of blood vessels and cells, a vascularized ectopic tissue engineered ligament (ETEL) with silk collagen scaffold was constructed by subcutaneous implantation for 2 weeks. The fully vascularized TE ligament was then transferred to rebuild ACL without blood perfusion interruption, and was demonstrated to exhibit improved ACL regeneration, bone tunnel healing and mechanical properties. (C) 2017 Published by Elsevier Ltd on behalf of Acta Materialia Inc

Intronic splicing enhancers, cognate splicing factors and context-dependent regulation rules

SummaryMost human genes produce multiple splicing isoforms with distinct functions. To systematically understand splicing regulation, we conducted an unbiased screen and identified >100 intronic splicing enhancers (ISEs) that were clustered by sequence similarity into six groups. All ISEs functioned in another cell type and heterologous introns, and their distribution and conservation patterns in different pre-mRNA regions are similar to exonic splicing silencers. Consistently all ISEs inhibited use of splice sites from exonic locations. The putative trans-factors of each ISE group were identified and validated. Five distinct ISE motifs were recognized by hnRNP H and F whose C-terminal domains were sufficient to render context-dependent activities of ISEs. The sixth group was controlled by factors that either activate or suppress splicing. This work provided a comprehensive picture of general ISE activities and provided new models of how a single element can function oppositely depending on its locations and binding factors