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.     

Excited state intramolecular hydrogen atom transfer of phenylethynyl-substituted 2′-hydroxychalcones

(E)-1-[2-Hydroxy-4-(phenylethynyl)phenyl]-3-[4-(phenylethynyl)phenyl]prop-2-en-1-one (1), (E)-1-[2-hydroxy-4-(phenylethynyl)phenyl]-3-phenylprop-2-en-1-one (2), and (E)-1-(2-hydroxyphenyl)-3-[4-(phenylethynyl)phenyl]prop-2-en-1-one (3), which belong to a new class of 2′-hydroxychalcones with phenylethynyl group(s) at the para position of the phenyl ring, were synthesized, and their photochemical properties were investigated. The lowest energy absorption band of 1 peaks at a longer wavelength (383 nm) with a much larger molar extinction coefficient (5.0 × 10⁴ M ^?1 cm^?1) than that of the parent 2′-hydroxychalcone (2′HC) (2.0 × 10⁴ M ^?1 cm^?1 at 318 nm). Upon photoexcitation, all three compounds underwent excited-state intramolecular hydrogen atom transfer (ESIHT) to produce an excited tautomer that emitted fluorescence with a large Stokes shift in the longer wavelength region at 600–700 nm. The quantum yield of the tautomer fluorescence of 1 was not high at 298 K (Φ _f = 9.1 × 10^?5), but was highest among 2′HC and its analogues. The Φ _f values of 1–3 increased 10–30 fold upon reducing the temperature from 298 to 77 K.     

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.     

One-dimensional migration of interstitial clusters in SUS316L and its model alloys at elevated temperatures

For self-interstitial atom (SIA) clusters in various concentrated alloys, one-dimensional (1D) migration is induced by electron irradiation around 300 K. But at elevated temperatures, the 1D migration frequency decreases to less than one-tenth of that around 300 K in iron-based bcc alloys. In this study, we examined mechanisms of 1D migration at elevated temperatures using in situ observation of SUS316L and its model alloys with high-voltage electron microscopy. First, for elevated temperatures, we examined the effects of annealing and short-term electron irradiation of SIA clusters on their subsequent 1D migration. In annealed SUS316L, 1D migration was suppressed and then recovered by prolonged irradiation at 300 K. In high-purity model alloy Fe-18Cr-13Ni, annealing or irradiation had no effect. Addition of carbon or oxygen to the model alloy suppressed 1D migration after annealing. Manganese and silicon did not suppress 1D migration after annealing but after short-term electron irradiation. The suppression was attributable to the pinning of SIA clusters by segregated solute elements, and the recovery was to the dissolution of the segregation by interatomic mixing under electron irradiation. Next, we examined 1D migration of SIA clusters in SUS316L under continuous electron irradiation at elevated temperatures. The 1D migration frequency at 673 K was proportional to the irradiation intensity. It was as high as half of that at 300 K. We proposed that 1D migration is controlled by the competition of two effects: induction of 1D migration by interatomic mixing and suppression by solute segregation.     

Rational Design and Identification of a Non‐Peptidic Aggregation Inhibitor of Amyloid‐β Based on a Pharmacophore Motif Obtained from cyclo[‐Lys‐Leu‐Val‐Phe‐Phe‐]

Inhibition of pathogenic protein aggregation may be an important and straightforward therapeutic strategy for curing amyloid diseases. Small‐molecule aggregation inhibitors of Alzheimer’s amyloid‐β (Aβ) are extremely scarce, however, and are mainly restricted to dye‐ and polyphenol‐type compounds that lack drug‐likeness. Based on the structure‐activity relationship of cyclic Aβ16–20 (cyclo‐[KLVFF]), we identified unique pharmacophore motifs comprising side‐chains of Leu², Val³, Phe⁴, and Phe⁵ residues without involvement of the backbone amide bonds to inhibit Aβ aggregation. This finding allowed us to design non‐peptidic, small‐molecule aggregation inhibitors that possess potent activity. These molecules are the first successful non‐peptidic, small‐molecule aggregation inhibitors of amyloids based on rational molecular design.