Study of the Structure of Hyperbranched Polyglycerol Coatings and Their Antibiofouling and Antithrombotic Applications

While blood‐contacting materials are widely deployed in medicine in vascular stents, catheters, and cannulas, devices fail in situ because of thrombosis and restenosis. Furthermore, microbial attachment and biofilm formation is not an uncommon problem for medical devices. Even incremental improvements in hemocompatible materials can provide significant benefits for patients in terms of safety and patency as well as substantial cost savings. Herein, a novel but simple strategy is described for coating a range of medical materials, that can be applied to objects of complex geometry, involving plasma‐grafting of an ultrathin hyperbranched polyglycerol coating (HPG). Plasma activation creates highly reactive surface oxygen moieties that readily react with glycidol. Irrespective of the substrate, coatings are uniform and pinhole free, comprising O─C─O repeats, with HPG chains packing in a fashion that holds reversibly binding proteins at the coating surface. In vitro assays with planar test samples show that HPG prevents platelet adhesion and activation, as well as reducing (>3 log) bacterial attachment and preventing biofilm formation. Ex vivo and preclinical studies show that HPG‐coated nitinol stents do not elicit thrombosis or restenosis, nor complement or neutrophil activation. Subcutaneous implantation of HPG coated disks under the skin of mice shows no evidence of toxicity nor inflammation

TrawlerWeb: an online de novo motif discovery tool for next-generation sequencing datasets

Abstract Background A strong focus of the post-genomic era is mining of the non-coding regulatory genome in order to unravel the function of regulatory elements that coordinate gene expression (Nat 489:57–74, 2012; Nat 507:462–70, 2014; Nat 507:455–61, 2014; Nat 518:317–30, 2015). Whole-genome approaches based on next-generation sequencing (NGS) have provided insight into the genomic location of regulatory elements throughout different cell types, organs and organisms. These technologies are now widespread and commonly used in laboratories from various fields of research. This highlights the need for fast and user-friendly software tools dedicated to extracting cis-regulatory information contained in these regulatory regions; for instance transcription factor binding site (TFBS) composition. Ideally, such tools should not require prior programming knowledge to ensure they are accessible for all users. Results We present TrawlerWeb, a web-based version of the Trawler_standalone tool (Nat Methods 4:563–5, 2007; Nat Protoc 5:323–34, 2010), to allow for the identification of enriched motifs in DNA sequences obtained from next-generation sequencing experiments in order to predict their TFBS composition. TrawlerWeb is designed for online queries with standard options common to web-based motif discovery tools. In addition, TrawlerWeb provides three unique new features: 1) TrawlerWeb allows the input of BED files directly generated from NGS experiments, 2) it automatically generates an input-matched biologically relevant background, and 3) it displays resulting conservation scores for each instance of the motif found in the input sequences, which assists the researcher in prioritising the motifs to validate experimentally. Finally, to date, this web-based version of Trawler_standalone remains the fastest online de novo motif discovery tool compared to other popular web-based software, while generating predictions with high accuracy. Conclusions TrawlerWeb provides users with a fast, simple and easy-to-use web interface for de novo motif discovery. This will assist in rapidly analysing NGS datasets that are now being routinely generated. TrawlerWeb is freely available and accessible at: http://trawler.erc.monash.edu.au

Additional file 1: of TrawlerWeb: an online de novo motif discovery tool for next-generation sequencing datasets

Table S1. Details of the assessment of TrawlerWeb. Detailed table of Fig. 1b showing, for each ChIP experiment, the ability of individual programs to uncover the correct binding site in yeast. For each individual ChIP experiment, the success or failure of 8 different algorithms including TrawlerWeb is shown. The results from the 6 algorithms (Coverage, AlignACE, Kellis, mdscan, MEME, and MEME-c) were extracted from Harbison et al. 2004 [38]. The matching motifs found by TrawlerWeb are identical to that found by Trawler_standalone (detailed previously in Ettwiller et al. 2007 [5]). The results from RSAT were performed by this study, where the matching motifs found by RSAT were described in the last column. (XLSX 190 kb

Additional file 2: of TrawlerWeb: an online de novo motif discovery tool for next-generation sequencing datasets

Table S2. Details of motif occurrence comparison between web-based motif discovery software. The highest scoring motifs discovered in DREME, MEME, RSAT peak-motifs, and TrawlerWeb and their corresponding occurrences are illustrated here. For the highest scoring motif, the number of motif occurrences were expressed as a percentage of the total number of input sequences. *MEME-ChIP pre-processes submitted sequences longer than 100 by trimming them evenly from both ends to get the centered 100 bp sequence and discards trimmed sequences containing only Ns from repeat masking. **MEME motif discovery automatically limits the run to a randomly sampled 600 sequences to reduce run time. (XLSX 576 kb