Experimental detection of proteolytic activity in a signal peptide peptidase of Arabidopsis thaliana

Background

The ubiquitin ligase COP1, COnstitutively Photomorphogenic 1, functions in many biological responses in mammalian cells, but its downstream pathway remains unclear.

Results

Here, we identified FIP200, a key regulator of mammalian autophagy, as a novel COP1-interacting protein by yeast two-hybrid screening. The interaction was confirmed by a GST-pulldown assay. Split-GFP analysis revealed that interaction between COP1 and FIP200 predominantly occurred in the cytoplasm and was enhanced in cells treated with UV irradiation. Different forms of FIP200 protein were expressed in cultured mammalian cells, and ectopic expression of COP1 reduced one of such forms.

Conclusions

These data suggest that COP1 modulates FIP200-associated activities, which may contribute to a variety of cellular functions that COP1 is involved in.     

Convenient Method for Dehalogenation of Aryl Halides

Reductive dehalogenation of aryl halides was achieved using hydrogen and a palladium catalyst. By using deuterium gas, the deuterated arenes were readily prepared.     

Universal fluorescent labeling of amplification products using locked nucleic acids

Amplification/hybridization‐based genetic analyses using primers containing locked nucleic acids (LNAs) present many benefits. Here, we developed a novel design for universal fluorescent PCR using LNAs. Universal fluorescent PCR generates intermediate nonlabeled fragments and final fluorescent fragments in a two‐step amplification process that uses locus‐specific primers with universal tails and universal fluorescent primers. In this study, a few standard nucleotides were replaced with LNAs only in the fluorescent universal primers. The sequence of the fluorescent universal primer significantly affected the amplification efficiency. For primers with three LNAs, the fluorescent primers with stable M13(‐47) sequences provided the most efficient signal (approximately tenfold higher than the primers with M13(‐21) sequences at lower Tm values). Moreover, AT‐rich LNA substitutions in the fluorescent primers produced much lower amplification efficiencies than GC‐rich substitutions. GC‐rich LNAs produced greater differences in Tm values among primers, and resulted in the preferential production of fluorescently labeled amplicons. The specificity and sensitivity of LNA‐containing fluorescent primers were assessed by genotyping eight STRs in Japanese individuals, and full STR profiles could be generated using as little as 0.25 ng of genomic DNA. The method permitted clear discrimination of alleles and represents sensitive STR genotyping at a reduced cost.     

Templated nucleation of hybrid iron oxide nanoparticles on polysaccharide nanogels

Novel organic–inorganic hybrid nanoparticles consisting of polymer–hydrogel nanoparticles (nanogels) and iron oxide were developed for potential biomedical applications. Hybrid nanoparticles were prepared by a simple procedure using polysaccharide nanogels as a reactive site for iron oxide formation. The hybrid nanoparticles have a narrow size distribution with a diameter of approximately 30 nm and show high colloidal stability. These nanohybrid particles could be used as a contrast medium for magnetic resonance imaging or for magnetic hyperthermia therapy.     

Effects of post-deposition annealing on chemical composition of SiNx film in SiO2/SiNx/SiO2/Si stacked structure

To systematically evaluate the quality of SiN_x films in multi-stacked structures, we investigated the effects of post-deposition annealing (PDA) on the film properties of SiN_x within the SiO₂/SiN_x/SiO₂/Si stacked structure by performing X-ray photoelectron spectroscopy (XPS), X-ray reflectivity (XRR), Fourier transform infrared (FT-IR) spectroscopy, and scanning transmission electron microscope–electron energy loss spectroscopy (STEM-EELS) analyses. The XPS results showed that PDA induces the oxidation of the SiN_x layer. In particular, new finding is that Si-rich SiN_x in the SiN_x layer is preferentially oxidized by PDA even in multi-stacked structure. The XRR results showed that the SiN_x layer becomes thinner, whereas the interface layer between the SiN_x layer and Si becomes thicker. It is concluded by STEM-EELS and XPS that this interface layer is SiON layer. The density of N–H and Si–H bonding within the stacked structure strongly depends on the PDA temperature. Our study helps elucidate the properties of SiN_x films in stacked structures from various perspectives.     

Dispersion of Carbon Nanotubes with “Green” Detergents

Solubilization of carbon nanotubes (CNTs) is a fundamental technique for the use of CNTs and their conjugates as nanodevices and nanobiodevices. In this work, we demonstrate the preparation of CNT suspensions with “green” detergents made from coconuts and bamboo as fundamental research in CNT nanotechnology. Single-walled CNTs (SWNTs) with a few carboxylic acid groups (3–5%) and pristine multi-walled CNTs (MWNTs) were mixed in each detergent solution and sonicated with a bath-type sonicator. The prepared suspensions were characterized using absorbance spectroscopy, scanning electron microscopy, and Raman spectroscopy. Among the eight combinations of CNTs and detergents (two types of CNTs and four detergents, including sodium dodecyl sulfate (SDS) as the standard), SWNTs/MWNTs were well dispersed in all combinations except the combination of the MWNTs and the bamboo detergent. The stability of the suspensions prepared with coconut detergents was better than that prepared with SDS. Because the efficiency of the bamboo detergents against the MWNTs differed significantly from that against the SWNTs, the natural detergent might be useful for separating CNTs. Our results revealed that the use of the “green” detergents had the advantage of dispersing CNTs as well as SDS.     

Induced long-range attractive potentials of human serum albumin by ligand binding

Small-angle x-ray scattering and dielectric spectroscopy investigation on the solutions of recombinant human serum albumin and its heme hybrid revealed that heme incorporation induces a specific long-range attractive potential between protein molecules. This is evidenced by the enhanced forward intensity upon heme binding, despite no hindrance to rotatory Brownian motion, unbiased colloid osmotic pressure, and discontiguous nearest-neighbor distance, confirming monodispersity of the proteins. The heme-induced potential may play a trigger role in recognition of the ligand-filled human serum albumins in the circulatory system.     

Thermal or Mechanical Stimuli‐Induced Photoluminescence Color Change of a Molecular Assembly Composed of an Amphiphilic Anthracene Derivative in Water

Molecular assemblies that change photoluminescence color in response to thermal or mechanical stimulation without dissociation into the monomeric states in water are described herein. A dumbbell‐shaped amphiphilic compound forms micellar molecular assemblies in water and exhibits yellow photoluminescence derived from excimer formation of the luminescent core, which contains a 2,6‐diethynylanthracene moiety. Annealing of the aqueous solution induces a photoluminescence color change from yellow to green (λ_{em, max}=558→525 nm). The same photoluminescence color change is also achieved by rubbing the yellow‐photoluminescence‐emitting molecular assemblies adsorbed on glass substrates with cotton wool in water. The observed green photoluminescence is ascribed to micelles that are distinct from the yellow‐photoluminescence‐emitting micelles, on the basis of transmission electron microscopy observations, atomic force microscopy observations, and dynamic light scattering measurements. We examined the relationship between the structure of the molecular assemblies and the photophysical properties of the anthracene derivative in water before and after thermal or mechanical stimulation and concluded that thermal or mechanical stimuli‐induced slight changes of the molecular‐assembled structures in the micelles result in the change in the photoluminescence color from yellow to green in water.