Public RNA-seq data-based identification and functional analyses reveal that MXRA5 retains proliferative and migratory abilities of dental pulp stem cells.

Dental pulp stem cells (DPSC) usually remain quiescent in the dental pulp tissue; however, once the dental pulp tissue is injured, DPSCs potently proliferate and migrate into the injury microenvironment and contribute to immuno-modulation and tissue repair. However, the key molecules that physiologically support the potent proliferation and migration of DPSCs have not been revealed. In this study, we searched publicly available transcriptome raw data sets, which contain comparable (i.e., equivalently cultured) DPSC and mesenchymal stem cell data. Three data sets were extracted from the Gene Expression Omnibus database and then processed and analyzed. MXRA5 was identified as the predominant DPSC-enriched gene associated with the extracellular matrix. MXRA5 is detected in human dental pulp tissues. Loss of MXRA5 drastically decreases the proliferation and migration of DSPCs, concomitantly with reduced expression of the genes associated with the cell cycle and microtubules. In addition to the known full-length isoform of MXRA5, a novel splice variant of MXRA5 was cloned in DPSCs. Recombinant MXRA5 coded by the novel splice variant potently induced the haptotaxis migration of DPSCs, which was inhibited by microtubule inhibitors. Collectively, MXRA5 is a key extracellular matrix protein in dental pulp tissue for maintaining the proliferation and migration of DPSCs.

Fermentation Supernatant of Elderly Feces with Inulin and Partially Hydrolyzed Guar Gum Maintains the Barrier of Inflammation-Induced Caco-2/HT29-MTX-E12 Co-Cultured Cells.

Intestinal barrier function declines with aging. We evaluated the effect of dietary fibers and indigestible oligosaccharides on intestinal barrier function by altering the microbiota of the elderly. The feces were anaerobically cultured with indigestible dextrin, inulin, partially hydrolyzed guar gum (PHGG), lactulose, raffinose, or alginate, and the fermented supernatant was added to inflammation-induced Caco-2/HT29-MTX-E12 co-cultured cells. Our data showed that inulin- and PHGG-derived supernatants exerted a protective effect on the intestinal barrier. The protective effect was significantly positively correlated with total short-chain fatty acids (SCFAs) and butyric acid production in the supernatant and negatively correlated with the claudin-2 (CLDN2) gene expression in the cultured cells. Furthermore, we showed that the CLDN2 levels are regulated by butyric acid. Thus, inulin and PHGG can change the intestinal environment of the elderly and maintain the intestinal barrier by accelerating the production of SCFAs and modifying the expression levels of barrier function-related genes.

Anti-inflammatory and nutritional improvement effects of dietary supplementation combined with fish oil in patients with epithelial cancer.

The present study investigated the effects of dietary supplementation combined with fish oil containing relatively low levels of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) on the inflammatory and nutritional status of patients with epithelial cancer. Fish oil capsules (498 mg EPA and 213 mg DHA) and dietary supplements (100 kcal and 5 g protein) were administered for 8 weeks to 20 patients with cancer and inflammation [C-reactive protein (CRP) ≥0.30 mg/dl]. Blood EPA levels increased significantly after 4 and 8 weeks, while no significant differences were observed in log-transformed (log) CRP levels, which were the major inflammatory indices in these patients. A declining trend was observed at 8 weeks after excluding 2 patients with suspected infection (P=0.06). A significant increase was observed from week 0 to week 8 for log interleukin-6 (IL-6) levels. After excluding the 2 patients with suspected infection, no significant difference was observed when comparing week 0 to week 8 for log IL-6. No deterioration in albumin or pre-albumin levels was observed. These results suggest that although suppression of acute inflammation associated with infection is difficult, intake of relatively low EPA and DHA supplements may be effective for mild chronic inflammation in patients with epithelial cancer without infection. Large-scale randomized clinical trials are required to make the final decision regarding efficacy. The study was registered in the University Hospital Medical Information Network Clinical Trials Registry (UMIN-CTR; 06/07/2018, UMIN000033309).

DMP-1 promoter-associated antisense strand non-coding RNA, panRNA-DMP-1, physically associates with EGFR to repress EGF-induced squamous cell carcinoma migration.

Accumulating evidence suggests that specific non-coding RNAs exist in many types of malignant tissues, and are involved in cancer invasion and metastasis. However, little is known about the precise roles of non-coding RNAs in squamous cell carcinoma (SQCC) invasion and migration. Recently, the dentin matrix protein-1 (DMP-1) gene locus was identified as a transcriptionally active site in squamous cell carcinoma (SQCC) tissue and cells. However, it is unclear whether RNA associated with cell migration exist at the DMP-1 gene locus in SQCC cells. We identified a novel promoter-associated non-coding RNA in the antisense strand of DMP-1 gene locus, promoter-associated non-coding RNA (panRNA)-DMP-1, by the RACE method in SQCC cells and tissues, and characterized the functions of panRNA-DMP-1 in EGF-driven SQCC cell migration. The inhibition of endogenous panRNA-DMP-1 expression by specific siRNAs and exogenous over-expression of panRNA-DMP-1 resulted in increased and suppressed cellular migration toward EGF in SQCC cells, respectively, and nuclear expression of panRNA-DMP-1 was induced by EGF stimulation. Mechanistically, suppression of panRNA-DMP-1 expression increased EGFR nuclear localization upon EGF treatment and nuclear panRNA-DMP-1 physically interacted with EGFR, which was confirmed by RNA immunoprecipitation assay using a bacteriophage-delivered PP7 RNA labeling system. Furthermore, co-immunoprecipitation assay revealed that suppression of panRNA-DMP-1 stabilized EGFR interaction with STAT3, a known co-transcription factors of EGFR, to induce migratory properties in many cancer cells. Based on these findings, panRNA-DMP-1 is an EGFR-associating RNA that inhibits the EGF-induced migratory properties of SQCC possibly by regulating EGFR nuclear localization and EGFR binding to STAT3.

Dentin phosphoprotein inhibits lipopolysaccharide-induced macrophage activation independent of its serine/aspartic acid-rich repeats.

OBJECTIVE: The objective of this study was to investigate the effects of dentin phosphoprotein (DPP) on lipopolysaccharide-induced inflammatory responses of macrophages in vitro. DESIGN: Wildtype and mutant recombinant dentin phosphoprotein (rDPP) proteins were generated using a mammalian expression system. Macrophages, phorbol 12-myristate 13-acetate-differentiated THP-1 cells, were stimulated with lipopolysaccharide in the absence or presence of rDPP proteins. After the 24-hr incubation, the inflammatory gene expression levels were examined by quantitative reverse-transcription polymerase chain reaction and the amount of secreted TNF-α protein was evaluated by enzyme-linked immunosorbent assay. Furthermore, the subcellular localization of exogenously added rDPP was examined by immunocytochemistry, and the direct binding of rDPP to lipopolysaccharide was quantified by solid-phase binding assay. RESULTS: rDPP dose-dependently reduced the expression of lipopolysaccharide-induced inflammatory genes, such as TNFα, IL-1ß, and IL-8, and TNF-α protein secretion from the macrophages. Furthermore, mutant rDPP having a shortened serine/aspartic acid-rich repeats (SDrr) was also able to inhibit lipopolysaccharide-induced inflammatory responses of macrophages. rDPP was localized adjacent to the cellular membrane rather than in the cytoplasm, and rDPP was able to bind to lipopolysaccharide. These results suggested that rDPP inhibited lipopolysaccharide-induced inflammatory responses by binding to lipopolysaccharide. CONCLUSIONS: In addition to the well-known functions of DPP for dentin mineralization that depend on the SDrr, we demonstrated that DPP possesses anti-inflammatory effects on lipopolysaccharide-stimulated macrophages that are independent of the SDrr.

Dental pulp cell-derived powerful inducer of TNF-α comprises PKR containing stress granule rich microvesicles.

It is well known that dental pulp tissue can evoke some of the most severe acute inflammation observed in the human body. We found that dental pulp cells secrete a factor that induces tumor necrosis factor-α production from macrophages, and designated this factor, dental pulp cell-derived powerful inducer of TNF-α (DPIT). DPIT was induced in dental pulp cells and transported to recipient cells via microvesicles. Treatment of dental pulp cells with a PKR inhibitor markedly suppressed DPIT activity, and weak interferon signals were constitutively activated inside the cells. In recipient macrophages, stimulation with DPIT-containing supernatants from pulp cells resulted in activation of both nuclear factor-κB and MAP kinases like JNK and p38. Proteomics analyses revealed that many stress granule-related proteins were present in supernatants from dental pulp cells as well as microvesicle marker proteins like GAPDH, ß-actin, HSPA8, HSPB1, HSPE1, and HSPD1. Furthermore, giant molecule AHNAK and PKR were detected in microvesicles derived from dental pulp cells, and gene silencing of AHNAK in dental pulp cells led to reduced DPIT activity. Thus, it appeared that the core protein of DPIT was PKR, and that PKR was maintained in an active state in stress granule aggregates with AHNAK and transported via microvesicles. The activity of DPIT for TNF-α induction was far superior to that of gram-negative bacterial endotoxin. Therefore, we, report for the first time, that active PKR is transported via microvesicles as stress granule aggregates and induces powerful inflammatory signals in macrophages.

Genome-wide identification of chromatin-enriched RNA reveals that unspliced dentin matrix protein-1 mRNA regulates cell proliferation in squamous cell carcinoma.

Chromatin-enriched noncoding RNAs (ncRNAs) have emerged as key molecules in epigenetic processes by interacting with chromatin-associated proteins. Recently, protein-coding mRNA genes have been reported to be chromatin-tethered, similar with ncRNA. However, very little is known about whether chromatin-enriched mRNA is involved in the chromatin modification process. Here, we comprehensively examined chromatin-enriched RNA in squamous cell carcinoma (SQCC) cells by RNA subcellular localization analysis, which was a combination of RNA fractionation and RNA-seq. We identified 11 mRNAs as highly chromatin-enriched RNAs. Among these, we focused on the dentin matrix protein-1 (DMP-1) gene because its expression in SQCC cells has not been reported. Furthermore, we clarified that DMP-1 mRNA was retained in chromatin in its unspliced form in SQCC in vitro and in vivo. As the inhibition of the unspliced DMP-1 mRNA (unspDMP-1) expression resulted in decreased cellular proliferation in SQCC cells, we performed ChIP-qPCR to identify cell cycle-related genes whose expression was epigenetically modified by unspDMP-1, and found that the CDKN1B promoter became active in SQCC cells by inhibiting unspDMP-1 expression. This result was further validated by the increased CDKN1B gene expression in the cells treated with siRNA for unspDMP-1 and by restoration of the decreased cellular proliferation rate by simultaneously inhibiting CDKN1B expression in SQCC cells. Further, to examine whether unspDMP-1 was able to associate with the CDKN1B promoter region, SQCC cells stably expressing PP7-mCherry fusion protein were transiently transfected with the unspDMP-1 fused to 24 repeats of the PP7 RNA stem loop (unspDMP-1-24xPP7) and we found that unspDMP-1-24xPP7 was efficiently precipitated with the antibody against mCherry and was significantly enriched in the CDKN1B promoter region. Thus, unspDMP-1 is a novel chromatin-enriched RNA that epigenetically regulates cellular proliferation of SQCC.

Manipulation of single nanodiamonds to ultrathin fiber-taper nanofibers and control of NV-spin states toward fiber-integrated λ-systems.

We report on the coupling of single nitrogen vacancy (NV) centers to ultrathin fiber-taper nanofibers by the manipulation of single diamond nanocrystals on the nanofibers under real-time observation of nanodiamond fluorescence. Spin-dependent fluorescence of the single NV centers is efficiently detected through the nanofiber. We show control of the spin sub-level structure of the electronic ground state using an external magnetic field and clearly observe a frequency fine tuning of [Formula: see text]. This observation demonstrates a possibility of realizing fiber-integrated quantum λ-systems, which can be used for various quantum information devices including push-pull quantum memory and quantum gates.

Dentin sialophosphoprotein is a potentially latent bioactive protein in dentin.

BACKGROUND: Dentin sialophosphoprotein (DSPP) belongs to the family of small integrin-binding ligand N-linked glycoproteins (SIBLINGs), which share common biochemical features such as an arginine-glycine-aspartic acid (RGD) integrin-binding site. However, amino acid sequence analyses suggest that DSPP has lost some common features, but acquired other unique features, such as repeat sequences of serine-serine-aspartic acid (SDrr) that are not observed in other SIBLINGs proteins. HIGHLIGHT: We review the biochemical features of DSPP using genetically modified mice and proteomic analyses. DSPP of some species lack the RGD sites unlike other SIBLING proteins such as dentin matrix protein-1 (DMP-1) and bone sialoprotein (BSP). We previously identified that mouse and human RGD domains in DSPP required the cleavage of an Ala-Ser peptide bond, next to the RGD domains, to become active. Other species such as bovine, sheep, and bears, possess a Thr-Ser bond next to the RGD domain, which is intrinsically unable to sequester the ability of the RGD domain. To predict the functional importance of certain proteins/domains based on evolutionary conservation rates, the RGD domain of DSPP did not appear to have pivotal roles compared to other SIBLINGs. However, upon investigating the peptide bond next to the RGD domains of DSPP in 37 species, we found most catarrhini, in which humans are classified, possess the Ala-Ser bond. CONCLUSION: The functions of DSPP for integrin-mediated signaling possibly arize from the proteolytic cleavage of the peptide bonds close to the RGD domain and induce reactionary dentinogenesis in vivo.

Dense arrays of highly aligned graphene nanoribbons produced by substrate-controlled metal-assisted etching of graphene.

Dense arrays of aligned graphene nanoribbons (GNRs) are fabricated by substrate-controlled etching of large-area single-layer graphene. An adequate choice of etching substrate and catalyst deposition method allows densities up to 25 nanoribbons µm(-1) to be obtained with average widths of 19 nm. The efficacy of the method is evidenced by the high on/off ratios of back-gated transistors made with these GNRs, which can go up to 5000.

Near-Infrared photoluminescence in the femtosecond time region in monolayer graphene on SiO2.

We investigate the dynamical properties of photoexcited carriers in a single monolayer of graphene at room temperature in air using femtosecond time-resolved luminescence spectroscopy. The luminescence kinetics are observed in the near-infrared region of 0.7-1.4 eV and analyzed based on the two-temperature model describing the cooling of thermalized carriers via the carrier-optical phonon interaction. The observed luminescence in the range 0.7-0.9 eV is well reproduced by the model. In the range 1.0-1.4 eV, however, the luminescence, which decays in ∼300 fs, cannot be reproduced by this model. These results indicate that the carrier system is not completely thermalized in ∼300 fs. We also show the importance of the carrier-doping effect induced by the substrate and surrounding environment in the carrier cooling dynamics and the predominance of optical phonons over acoustic phonons in the carrier-phonon interactions even at a temperature of ∼400 K.

Instrumentation of a PLC-regulated temperature cycler with a PID control unit and its use for miniaturized PCR systems with reduced volumes of aqueous sample droplets isolated in oil phase in a microwell.

We have developed a temperature cycler for polymerase chain reaction (PCR) in a microwell fabricated on a polymer/glass chip. The entire system consisted of three subsystems, which included (1) a thermal conditioner, (2) a proportional-integral-derivative (PID) control signal conditioner and (3) a data acquisition subsystem. The subsystems were regulated coordinately by a ladder logic program written for the programmable logic control (PLC) so that an actual sample temperature could be timed, changed and maintained according to the programmed temperature cycles. The present temperature control system showed high accuracy, stability and minimum overshoot with reduced heating and cooling transition rates. Applicability of the temperature controller to the miniaturized PCR system with reduced volumes of aqueous sample droplets isolated in an oil phase was confirmed by successful amplifications of a target DNA sequence in the microwell.

Direct detection of mutant DNA in a mixed population of higher copy number wild-type DNA based on ligase detection reaction in conjunction with fluorescence resonance energy transfer.

We have developed an analytical system capable of detecting point mutations in a higher copy number of wild-type DNA based on an allele-specific ligase detection reaction (LDR) in conjunction with fluorescence resonance energy transfer (FRET). Streptavidin-functionalized quantum dots (QDs) used as FRET donors effectively captured biotinylated LDR products (target DNA strands) labeled with fluorophores as a FRET acceptor, enabling the formation of a sensitive energy transfer pair and direct detection of the targets without any post-LDR separation process, which is generally required for the LDR-based mutation analysis. Our experiments indicated that the present system had an ability to detect one mutant sequence in 10 normal sequences at a signal-to-background ratio of ca. 3.9.

Epitaxial chemical vapor deposition growth of single-layer graphene over cobalt film crystallized on sapphire.

Epitaxial chemical vapor deposition (CVD) growth of uniform single-layer graphene is demonstrated over Co film crystallized on c-plane sapphire. The single crystalline Co film is realized on the sapphire substrate by optimized high-temperature sputtering and successive H(2) annealing. This crystalline Co film enables the formation of uniform single-layer graphene, while a polycrystalline Co film deposited on a SiO(2)/Si substrate gives a number of graphene flakes with various thicknesses. Moreover, an epitaxial relationship between the as-grown graphene and Co lattice is observed when synthesis occurs at 1000 °C; the direction of the hexagonal lattice of the single-layer graphene completely matches with that of the underneath Co/sapphire substrate. The orientation of graphene depends on the growth temperature and, at 900 °C, the graphene lattice is rotated at 22 ± 8° with respect to the Co lattice direction. Our work expands a possibility of synthesizing single-layer graphene over various metal catalysts. Moreover, our CVD growth gives a graphene film with predefined orientation, and thus can be applied to graphene engineering, such as cutting along a specific crystallographic direction, for future electronics applications.

Thioglucose-stabilized gold nanoparticles as a novel platform for colorimetric bioassay based on nanoparticle aggregation.

Gold nanoparticles stabilized with thioglucose (TGlu-AuNPs), which have carboxyl groups on the particle surface as anchoring sites for covalent immobilization of biomolecules, were prepared by the chemical reduction of HAuCl4 using 1-thio-ß-D-glucose as a reducing and stabilizing agent, and their application to colorimetric bioassay was demonstrated using the carbohydrate-lectin system. p-Aminophenyl α-D-mannose (Man-NH2) was covalently attached by a conventional method to the activated carboxyl groups on the TGlu-AuNPs. On addition of Con A to the Man-AuNPs, multiple binding events occurred between Con A and the mannoses immobilized on the particle surface. This Con A-induced aggregation resulted in a significant red shift in local surface plasmon resonance. The binding isotherm showed a sigmoidal curve, indicating cooperativity in the binding of Con A and the Man-AuNPs. In addition, Hill plots showed two nonequivalent binding modes, with the Kd values for high- and low-affinity binding of 11.3 and 66.5 pM, respectively, which was significantly lower than that for methyl-α-D-mannose binding to Con A. The enhanced binding affinity between Man-AuNPs and Con A involves the cluster effect of the carbohydrate groups on the AuNPs. A linear correlation curve was obtained in the range 10-100 nM (R2=0.983). The limit of detection (LOD) for Con A was 9.0 nM in aqueous buffer, which is comparable to that of other conventional methods such as ELISA.