Additional file 1: Figure S1. of Substance P and patterned silk biomaterial stimulate periodontal ligament stem cells to form corneal stroma in a bioengineered three-dimensional model

Substance P promotes collagen expression during induced keratocyte differentiation. (A) Immunofluorescence staining was carried out to compare the collagen expression between the control (Ctrl) and SP-treated groups (SP). The right panels are the merged picture of the left panels (collagen staining) and the middle panels (DAPI staining). (B) The integrated density of fluorescence in the different groups was quantified using ImageJ analysis software. The integrated density levels were higher in SP-treated groups. However, no significant difference was found (p ≥ 0.05). (PDF 138 kb

Vapor–Solid Nanotube Growth via Sidewall Epitaxy in an Environmental Transmission Electron Microscope

The growth of metal oxide nanotubes has been widely investigated; however, the mechanism regarding how nanotubes form remains elusive due to the lack of real time growth information. Here we report the growth of W₁₈O₄₉ nanotubes in an environmental transmission electron microscope. The real time observation of the growth dynamics indicates that the W₁₈O₄₉ nanotube is formed via the sidewall epitaxial growth on the leader W₁₈O₄₉ nanowire, which is different from the mechanism of nanowires coalescence proposed previously. Furthermore, our in situ results demonstrate that higher oxygen pressure leads to the growth of nanotubes, but low oxygen pressure results in the growth of nanowires. Such nanotube growth is presumably ascribed to the maximization of heat dissipation during fast growth. These findings may enrich our present understanding of the growth dynamics of metal oxide nanotubes and provide insight for fabricating metal oxide nanotubes

Insights into the Packing Switching of the EphA2 Transmembrane Domain by Molecular Dynamic Simulations

Receptor tyrosine kinases play an important role in mediating cell migration and adhesion associated with various biology processes. With a single-span transmembrane domain (TMD), the activities of the receptors are regulated by the definite packing configurations of the TMDs. For the EphA2 receptor, increasing studies have been conducted to investigate the packing domains that induce its switching TMD dimerization. However, the inherent transformation mechanisms including the interrelations among the involved packing domains remain unclear. Herein, we applied multiple simulation methods to explore the underlying packing mechanisms within the EphA2 TMD dimer. Our results demonstrated that the G⁵⁴⁰xxxG⁵⁴⁴ contributed to the formation of the right-handed configuration while the heptad repeat L⁵³⁵xxxG⁵³⁹xxA⁵⁴²xxxV⁵⁴⁶xxL⁵⁴⁹xxxG⁵⁵³ motif together with the FFxH⁵⁵⁹ region mediated the parallel mode. Furthermore, the FF⁵⁵⁷ residues packing mutually as rigid riveting structures were found comparable to the heptad repeat motif in maintaining the parallel configuration. In addition, the H⁵⁵⁹ residue associated definitely with the lower bilayer leaflet, which was proved to stabilize the parallel mode significantly. The simulations provide a full range of insights into the essential packing motifs or residues involved in the switching TMD dimer configurations, which can enrich our comprehension toward the EphA2 receptor

<i>De novo</i> Assembly of the Indo-Pacific Humpback Dolphin Leucocyte Transcriptome to Identify Putative Genes Involved in the Aquatic Adaptation and Immune Response

<div><p>Background</p><p>The Indo-Pacific humpback dolphin (<i>Sousa chinensis</i>), a marine mammal species inhabited in the waters of Southeast Asia, South Africa and Australia, has attracted much attention because of the dramatic decline in population size in the past decades, which raises the concern of extinction. So far, this species is poorly characterized at molecular level due to little sequence information available in public databases. Recent advances in large-scale RNA sequencing provide an efficient approach to generate abundant sequences for functional genomic analyses in the species with un-sequenced genomes.</p><p>Principal Findings</p><p>We performed a <i>de novo</i> assembly of the Indo-Pacific humpback dolphin leucocyte transcriptome by Illumina sequencing. 108,751 high quality sequences from 47,840,388 paired-end reads were generated, and 48,868 and 46,587 unigenes were functionally annotated by BLAST search against the NCBI non-redundant and Swiss-Prot protein databases (E-value<10⁻⁵), respectively. In total, 16,467 unigenes were clustered into 25 functional categories by searching against the COG database, and BLAST2GO search assigned 37,976 unigenes to 61 GO terms. In addition, 36,345 unigenes were grouped into 258 KEGG pathways. We also identified 9,906 simple sequence repeats and 3,681 putative single nucleotide polymorphisms as potential molecular markers in our assembled sequences. A large number of unigenes were predicted to be involved in immune response, and many genes were predicted to be relevant to adaptive evolution and cetacean-specific traits.</p><p>Conclusion</p><p>This study represented the first transcriptome analysis of the Indo-Pacific humpback dolphin, an endangered species. The <i>de novo</i> transcriptome analysis of the unique transcripts will provide valuable sequence information for discovery of new genes, characterization of gene expression, investigation of various pathways and adaptive evolution, as well as identification of genetic markers.</p></div

Overview of the Indo-Pacific humpback dolphin leucocytes transcriptome assembly.

<p>(A) The size distribution of the contigs obtained from <i>de novo</i> assembly of high-quality clean reads. (B) The size distribution of the unigenes produced from further assembly of contigs. (C) The size distribution of the CDS produced by searching unigene sequences against various protein databases (NR, Swiss-Prot, KEGG and COG, in order) using BLASTX (E-value<10⁻⁵). (D) Size distributions of the ESTs obtained from the ESTScan results. For unigene CDS that had no hits in the databases (NR, Swiss-Prot, KEGG and COG), the BLAST results were subjected to ESTScans and then converted into peptide sequences.</p

Summary of the unigene hits in public protein databases.

<p>Summary of the unigene hits in public protein databases.</p

GO assignment for assembled unigenes.

<p>The results are summarized in three main categories: biological process, cellular component and molecular function. In total, 37,976 unigenes were assigned to GO. Classified gene objects are depicted as absolute numbers of the total number of gene objects with GO assignments.</p

Clusters of orthologous group (COG) classification.

<p>In total, 16,467 of the 48,868 sequences with NR hits were grouped into 25 COG classifications.</p

Characterization of the assembled unigenes against NR protein databases.

<p>(<b>A</b>) E-value distribution of BLAST hits for the assembled unigenes with a cutoff of 1E-5. (<b>B</b>) Similarity distribution of the top BLAST hits for the assembled unigenes with a cutoff of 1E-5. (<b>C</b>) Species distribution of the top BLAST hits for the assembled unigenes with a cutoff of 1E-5.</p

Table3_DNA5mC Regulator-Mediated Molecular Clusters and Tumor Microenvironment Signatures in Glioblastoma.XLSX

Growing evidence links DNA methylation to tumor immunity. The impact of DNA methylation (5 mC) on the microenvironment surrounding tumors and immunotherapy remains to be clarified. Through clustering gene expression of 20 DNA methylation regulators, this study aimed at systematically analyzing DNA methylation regulator patterns and tumor microenvironment characteristics of TCGA-GBM patients. Various subtypes of glioblastoma exhibit different tumor microenvironments and DNA methylation patterns. Each DNA methylation modification was then assigned a DNA methylation score (DMS). High DMS was associated with a good prognosis. In contrast, the low DMS group had a relatively low survival rate. A correlation was also found between high DMS and enhanced immunotherapy efficacy in two immune checkpoint blocking treatment cohorts. To conclude, identifying DNA methylation regulation patterns may prove critical to understanding glioblastoma progression and differentiation, as well as future therapeutic targets.</p