miRseqViewer: multi-panel visualization of sequence, structure and expression for analysis of microRNA sequencing data

A Summary: Deep sequencing of small RNAs has become a routine process in recent years, but no dedicated viewer is as yet available to explore the sequence features simultaneously along with secondary structure and gene expression of microRNA (miRNA). We present a highly interactive application that visualizes the sequence alignment, secondary structure and normalized read counts in synchronous multipanel windows. This helps users to easily examine the relationships between the structure of precursor and the sequences and abundance of final products and thereby will facilitate the studies on miRNA biogenesis and regulation. The project manager handles multiple samples of multiple groups. The read alignment is imported in BAM file format. Implemented features comprise sorting, zooming, highlighting, editing, filtering, saving, exporting, etc. Currently, miRseqViewer supports 84 organisms whose annotation is available at miRBase. Availability and implementation: miRseqViewer, implemented in Java, is available at https://github.com/insoo078/mirseqviewer or at http://msv.kobic.re.kr. Contact: [email protected]

Single-Walled Carbon Nanotube-in-Binary-Polymer Nanofiber Structures and Their Use as Carbon Precursors for Electrochemical Applications

Hierarchical structuring of materials in the nanometer regime provides opportunities to achieve extraordinary characteristics of the resulting products. Here, we report unique one-dimensional hierarchical nanostructures consisting of single-walled carbon nanotubes (SWNTs), polyvinyl alcohol (PVA), and polyacrylonitrile (PAN). First, SWNT-in-binary-polymer nanofiber (SbPNF) structures were obtained through the incorporation of PVA-wrapped SWNTs into PAN, followed by the electrospinning of the SWNT/PVA/PAN solution. Importantly, the SbPNFs exhibited an aligned SWNT-in-nanofiber structure and enhanced ordering of the polymer chains. The SbPNFs were successfully converted to carbonized products [SWNT-in-carbon nanofibers (SbCNFs)] with enhanced crystallinity and tunable electrochemical properties. Compared to those of the control samples (no SWNT), the charge-transfer resistance and the surface area of the SbCNFs were two orders of magnitude lower and 11–20% higher, respectively, which resulted in better electrochemical properties. The major factors determining the properties of the SbCNFs included the SWNT content and PVA/PAN microphase behavior. Furthermore, the removal of the PVA phase from the SbPNFs provided another opportunity to control the textural properties of the carbonized products. It was found that meso- and macropores were more developed in the carbonized products (SCNFs). The specific capacitance of the SCNFs increased to a maximum of 577 F g^–1, which was 3.7 times higher than that of the SbCNFs. The SCNF with the best properties was successfully applied to electrochemical capacitors as the electrode material. It is believed that further optimization of the hierarchical nanostructures will impart attractive properties for various applications

Comprehensive analysis of alternative splicing in gastric cancer identifies epithelial-mesenchymal transition subtypes associated with survival.

Alternatively spliced RNA isoforms are a hallmark of tumors, but their nature, prevalence, and clinical implications in gastric cancer have not been comprehensively characterized. We systematically profiled the splicing landscape of 83 gastric tumors and matched normal mucosa, identifying and experimentally validating eight splicing events that can classify all gastric cancers into three subtypes: epithelial-splicing, mesenchymal-splicing, and hybrid-splicing. These subtypes were associated with distinct molecular signatures and epithelial-mesenchymal transition markers. Subtype-specific splicing events were enriched in motifs for splicing factors RBM24 and ESRP1, which were upregulated in mesenchymal-splicing and epithelial-splicing tumors, respectively. A simple classifier based only on RNA levels of RBM24 and ESRP1, which can be readily implemented in the clinic, was sufficient to distinguish gastric cancer subtypes and predict patient survival in multiple independent patient cohorts. Overall, this study provides insights into alternative splicing in gastric cancer and the potential clinical utility of splicing-based patient classification

Near-field focusing and magnification through self-assembled nanoscale spherical lenses

It is well known that a lens-based far-field optical microscope cannot resolve two objects beyond Abbe's diffraction limit. Recently, it has been demonstrated that this limit can be overcome by lensing effects driven by surface-plasmon excitation(1-3), and by fluorescence microscopy driven by molecular excitation(4). However, the resolution obtained using geometrical lens-based optics without such excitation schemes remains limited by Abbe's law even when using the immersion technique(5), which enhances the resolution by increasing the refractive indices of immersion liquids. As for submicrometre-scale or nanoscale objects, standard geometrical optics fails for visible light because the interactions of such objects with light waves are described inevitably by near-field optics(6). Here we report near-field high resolution by nanoscale spherical lenses that are self-assembled by bottom-up integration(7) of organic molecules. These nano-lenses, in contrast to geometrical optics lenses, exhibit curvilinear trajectories of light, resulting in remarkably short near-field focal lengths. This in turn results in near-field magnification that is able to resolve features beyond the diffraction limit. Such spherical nanolenses provide new pathways for lens-based near-field focusing and high-resolution optical imaging at very low intensities, which are useful for bio-imaging, near-field lithography, optical memory storage, light harvesting, spectral signal enhancing, and optical nano-sensing.close14113