National Institute of Advanced Industrial Science and Technology

About: National Institute of Advanced Industrial Science and Technology is a government organization based out in Tsukuba, Ibaraki, Japan. It is known for research contribution in the topics: Catalysis & Thin film. The organization has 22114 authors who have published 65856 publications receiving 1669827 citations. The organization is also known as: Sangyō Gijutsu Sōgō Kenkyū-sho.

Delivering quantum dots to cells: bioconjugated quantum dots for targeted and nonspecific extracellular and intracellular imaging

Abstract: Bioconjugated nanomaterials offer endless opportunities to advance both nanobiotechnology and biomedical technology. In this regard, semiconductor nanoparticles, also called quantum dots, are of particular interest for multimodal, multifunctional and multiplexed imaging of biomolecules, cells, tissues and animals. The unique optical properties, such as size-dependent tunable absorption and emission in the visible and NIR regions, narrow emission and broad absorption bands, high photoluminescence quantum yields, large one- and multi-photon absorption cross-sections, and exceptional photostability are the advantages of quantum dots. Multimodal imaging probes are developed by interfacing the unique optical properties of quantum dots with magnetic or radioactive materials. Besides, crystalline structure of quantum dots adds scope for high-contrast X-ray and TEM imaging. Yet another unique feature of a quantum dot is its spacious and flexible surface which is promising to integrate multiple ligands and antibodies and construct multi-functional probes for bioimaging. In this critical review, we will summarize recent advancements in the preparation of biocompatible quantum dots, bioconjugation of quantum dots, and applications of quantum dots and their bioconjugates for targeted and nonspecific imaging of extracellular and intracellular proteins, organelles and functions (181 references).

Low-melting, low-viscous, hydrophobic ionic liquids: aliphatic quaternary ammonium salts with perfluoroalkyltrifluoroborates.

Abstract: A novel class of low-melting, hydrophobic ionic liquids based on relatively small aliphatic quaternary ammonium cations ([R(1)R(2)R(3)NR](+), wherein R(1), R(2), R(3) = CH(3) or C(2)H(5), R = n-C(3)H(7), n-C(4)H(9), CH(2)CH(2)OCH(3)) and perfluoroalkyltrifluoroborate anions ([R(F)BF(3)](-), R(F) = CF(3), C(2)F(5), n-C(3)F(7), n-C(4)F(9)) have been prepared and characterized. The important physicochemical and electrochemical properties of these salts, including melting point, glass transition, viscosity, density, ionic conductivity, thermal and electrochemical stability, have been determined and comparatively studied with those based on the corresponding [BF(4)](-) and [(CF(3)SO(2))(2)N](-) salts. The influence of the structure variation in the quaternary ammonium cation and perfluoroalkyltrifluoroborate ([R(F)BF(3)](-)) anion on the above physicochemical properties is discussed. Most of these salts are liquids at 25 degrees C and exhibit low viscosities (58-210 cP at 25 degrees C) and moderate conductivities (1.1-3.8 mS cm(-1)). The electrochemical windows of these salts are much larger than those of the corresponding 1,3-dialkyimidazolium salts. Additionally, a number of [R(F)BF(3)](-) salts exhibit plastic crystal behavior.

PBSIM: PacBio reads simulator--toward accurate genome assembly.

Abstract: Motivation: PacBio sequencers produce two types of characteristic reads (continuous long reads: long and high error rate and circular consensus sequencing: short and low error rate), both of which could be useful for de novo assembly of genomes. Currently, there is no available simulator that targets the specific generation of PacBio libraries. Results: Our analysis of 13 PacBio datasets showed characteristic features of PacBio reads (e.g. the read length of PacBio reads follows a log-normal distribution). We have developed a read simulator, PBSIM, that captures these features using either a model-based or sampling-based method. Using PBSIM, we conducted several hybrid error correction and assembly tests for PacBio reads, suggesting that a continuous long reads coverage depth of at least 15 in combination with a circular consensus sequencing coverage depth of at least 30 achieved extensive assembly results. Availability: PBSIM is freely available from the web under the GNU GPL v2 license (http://code.google.com/p/pbsim/). Contact: mhamada@k.u-tokyo.ac.jp Supplementary information: Supplementary data are available at Bioinformatics online.

Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information

Abstract: Motivation: Though vitally important to cell function, the mechanism of protein--DNA binding has not yet been completely understood. We therefore analysed the relationship between DNA binding and protein sequence composition, solvent accessibility and secondary structure. Using non-redundant databases of transcription factors and protein--DNA complexes, neural network models were developed to utilize the information present in this relationship to predict DNA-binding proteins and their binding residues. Results: Sequence composition was found to provide sufficient information to predict the probability of its binding to DNA with nearly 69% sensitivity at 64% accuracy for the considered proteins; sequence neighbourhood and solvent accessibility information were sufficient to make binding site predictions with 40% sensitivity at 79% accuracy. Detailed analysis of binding residues shows that some three- and five-residue segments frequently bind to DNA and that solvent accessibility plays a major role in binding. Although, binding behaviour was not associated with any particular secondary structure, there were interesting exceptions at the residue level. Over-representation of some residues in the binding sites was largely lost at the total sequence level, but a different kind of compositional preference was observed in DNA-binding proteins. Availability: Online predictions of DNA-binding proteins and binding sites are available at http://www.netasa.org/dbs-pred/