Showing papers by "National Institute of Advanced Industrial Science and Technology published in 2014"

Physics of Liquid Crystals

Abstract: Over the 100 years since its discovery, liquid crystals have been the intriguing subject for both academia and industries. The textbook of de Gennes The Physics of Liquid Crystals published in 1974 is still the bible for many LC researchers, but new subjects unmentioned in the book have also risen for these years. This chapter describes the story of the recent developments and the future perspectives in physics of liquid crystals, especially focusing on the contributions by Japanese research groups for the last decade.

Metal–organic framework composites

Abstract: Metal–organic frameworks (MOFs), also known as porous coordination polymers (PCPs), synthesized by assembling metal ions with organic ligands have recently emerged as a new class of crystalline porous materials. The amenability to design as well as fine-tunable and uniform pore structures makes them promising materials for a variety of applications. Controllable integration of MOFs and functional materials is leading to the creation of new multifunctional composites/hybrids, which exhibit new properties that are superior to those of the individual components through the collective behavior of the functional units. This is a rapidly developing interdisciplinary research area. This review provides an overview of the significant advances in the development of diverse MOF composites reported till now with special emphases on the synergistic effects and applications of the composites. The most widely used and successful strategies for composite synthesis are also presented.

A promoter-level mammalian expression atlas

Abstract: Regulated transcription controls the diversity, developmental pathways and spatial organization of the hundreds of cell types that make up a mammal Using single-molecule cDNA sequencing, we mapped transcription start sites (TSSs) and their usage in human and mouse primary cells, cell lines and tissues to produce a comprehensive overview of mammalian gene expression across the human body We find that few genes are truly 'housekeeping', whereas many mammalian promoters are composite entities composed of several closely separated TSSs, with independent cell-type-specific expression profiles TSSs specific to different cell types evolve at different rates, whereas promoters of broadly expressed genes are the most conserved Promoter-based expression analysis reveals key transcription factors defining cell states and links them to binding-site motifs The functions of identified novel transcripts can be predicted by coexpression and sample ontology enrichment analyses The functional annotation of the mammalian genome 5 (FANTOM5) project provides comprehensive expression profiles and functional annotation of mammalian cell-type-specific transcriptomes with wide applications in biomedical research

Atomic mechanism of the semiconducting-to-metallic phase transition in single-layered MoS2.

Abstract: Phase transitions can be used to alter the properties of a material without adding any additional atoms and are therefore of significant technological value. In a solid, phase transitions involve collective atomic displacements, but such atomic processes have so far only been investigated using macroscopic approaches. Here, we show that in situ scanning transmission electron microscopy can be used to follow the structural transformation between semiconducting (2H) and metallic (1T) phases in single-layered MoS2, with atomic resolution. The 2H/1T phase transition involves gliding atomic planes of sulphur and/or molybdenum and requires an intermediate phase (α-phase) as a precursor. The migration of two kinds of boundaries (β- and γ-boundaries) is also found to be responsible for the growth of the second phase. Furthermore, we show that areas of the 1T phase can be controllably grown in a layer of the 2H phase using an electron beam.

Ubiquitin is phosphorylated by PINK1 to activate parkin

Abstract: Ubiquitin, known for its role in post-translational modification of other proteins, undergoes post-translational modification itself; after a decrease in mitochondrial membrane potential, the kinase enzyme PINK1 phosphorylates ubiquitin at Ser 65, and the phosphorylated ubiquitin then interacts with ubiquitin ligase (E3) enzyme parkin, which is also phosphorylated by PINK1, and this process is sufficient for full activation of parkin enzymatic activity. The small protein ubiquitin, familiar for its role in post-translational modification of other proteins by binding to them and regulating their activity or stability, is shown here to be the substrate of the kinase PINK1, which together with the ubiquitin ligase parkin is a causal gene for hereditary recessive Parkinsonism. Noriyuki Matsuda and colleagues show that following a decrease in mitochondrial membrane potential, PINK1 phosphorylates ubiquitin at serine residue 65; the phosphorylated ubiquitin then interacts with parkin, which is also phosphorylated by PINK1. This interaction allows full activation of parkin enzymatic activity, which involves tagging mitochondrial substrates with ubiquitin. PINK1 (PTEN induced putative kinase 1) and PARKIN (also known as PARK2) have been identified as the causal genes responsible for hereditary recessive early-onset Parkinsonism1,2. PINK1 is a Ser/Thr kinase that specifically accumulates on depolarized mitochondria, whereas parkin is an E3 ubiquitin ligase that catalyses ubiquitin transfer to mitochondrial substrates3,4,5. PINK1 acts as an upstream factor for parkin6,7 and is essential both for the activation of latent E3 parkin activity8 and for recruiting parkin onto depolarized mitochondria8,9,10,11,12. Recently, mechanistic insights into mitochondrial quality control mediated by PINK1 and parkin have been revealed3,4,5, and PINK1-dependent phosphorylation of parkin has been reported13,14,15. However, the requirement of PINK1 for parkin activation was not bypassed by phosphomimetic parkin mutation15, and how PINK1 accelerates the E3 activity of parkin on damaged mitochondria is still obscure. Here we report that ubiquitin is the genuine substrate of PINK1. PINK1 phosphorylated ubiquitin at Ser 65 both in vitro and in cells, and a Ser 65 phosphopeptide derived from endogenous ubiquitin was only detected in cells in the presence of PINK1 and following a decrease in mitochondrial membrane potential. Unexpectedly, phosphomimetic ubiquitin bypassed PINK1-dependent activation of a phosphomimetic parkin mutant in cells. Furthermore, phosphomimetic ubiquitin accelerates discharge of the thioester conjugate formed by UBCH7 (also known as UBE2L3) and ubiquitin (UBCH7∼ubiquitin) in the presence of parkin in vitro, indicating that it acts allosterically. The phosphorylation-dependent interaction between ubiquitin and parkin suggests that phosphorylated ubiquitin unlocks autoinhibition of the catalytic cysteine. Our results show that PINK1-dependent phosphorylation of both parkin and ubiquitin is sufficient for full activation of parkin E3 activity. These findings demonstrate that phosphorylated ubiquitin is a parkin activator.

Chemical modifications and bioconjugate reactions of nanomaterials for sensing, imaging, drug delivery and therapy.

Abstract: As prepared nanomaterials of metals, semiconductors, polymers and carbon often need surface modifications such as ligand exchange, and chemical and bioconjugate reactions for various biosensor, bioanalytical, bioimaging, drug delivery and therapeutic applications. Such surface modifications help us to control the physico-chemical, toxicological and pharmacological properties of nanomaterials. Furthermore, introduction of various reactive functional groups on the surface of nanomaterials allows us to conjugate a spectrum of contrast agents, antibodies, peptides, ligands, drugs and genes, and construct multifunctional and hybrid nanomaterials for the targeted imaging and treatment of cancers. This tutorial review is intended to provide an introduction to newcomers about how chemical and bioconjugate reactions transform the surface of nanomaterials such as silica nanoparticles, gold nanoparticles, gold quantum clusters, semiconductor quantum dots, carbon nanotubes, fullerene and graphene, and accordingly formulate them for applications such as biosensing, bioimaging, drug and gene delivery, chemotherapy, photodynamic therapy and photothermal therapy. Nonetheless, controversial reports and our growing concerns about toxicity and pharmacokinetics of nanomaterials suggest the need for not only rigorous in vivo experiments in animal models but also novel nanomaterials for practical applications in the clinical settings. Further reading of original and review articles cited herein is necessary to buildup in-depth knowledge about the chemistry, bioconjugate chemistry and biological applications of individual nanomaterials.

Functional materials derived from open framework templates/precursors: synthesis and applications

Abstract: There is a general consensus to develop renewable energy storage and conversion technologies to replace fossil fuel energy for sustainable development. Currently, the development of high performance energy storage and conversion devices is an important step on the road to alternative energy technologies. Among the newly developed materials, porous carbons and related functional materials including metal/metal oxide nanoparticles and carbon–metal/metal oxide hybrids show potential for applications in such devices. Recently, the newly emerging open framework materials, including metal–organic frameworks (MOFs) and porous organic frameworks (POFs), act as outstanding templates and/or precursors to fabricate porous carbons and related nanostructured functional materials based on their high surface areas, controllable structures and abundant metal/organic species in their scaffolds. Here, recent significant advances in the development of open frameworks for preparation of porous carbons and related nanostructured functional materials are reviewed with special emphases on the applications in the energy and environmental areas.

Solar cell efficiency tables (version 44)

Abstract: Consolidated tables showing an extensive listing of the highest independently confirmed efficiencies for solar cells and modules are presented. Guidelines for inclusion of results into these tables are outlined and new entries since January 2010 are reviewed. Copyright # 2010 John Wiley & Sons, Ltd.

Charge Order Driven by Fermi-Arc Instability in Bi2Sr2−xLaxCuO6+δ

Abstract: The understanding of the origin of superconductivity in cuprates has been hindered by the apparent diversity of intertwining electronic orders in these materials. We combined resonant x-ray scattering (REXS), scanning-tunneling microscopy (STM), and angle-resolved photoemission spectroscopy (ARPES) to observe a charge order that appears consistently in surface and bulk, and in momentum and real space within one cuprate family, Bi2Sr(2-x)La(x)CuO(6+δ). The observed wave vectors rule out simple antinodal nesting in the single-particle limit but match well with a phenomenological model of a many-body instability of the Fermi arcs. Combined with earlier observations of electronic order in other cuprate families, these findings suggest the existence of a generic charge-ordered state in underdoped cuprates and uncover its intimate connection to the pseudogap regime.

From Metal–Organic Framework to Nitrogen-Decorated Nanoporous Carbons: High CO2 Uptake and Efficient Catalytic Oxygen Reduction

Abstract: High-surface-area N-decorated nanoporous carbons have been successfully synthesized using the N-rich metal–organic framework ZIF-8 as a template and precursor along with furfuryl alcohol and NH4OH as the secondary carbon and nitrogen sources, respectively. These carbons exhibited remarkable CO2 adsorption capacities and CO2/N2 and CO2/CH4 selectivities. The N-decoration in these carbons resulted in excellent activity for the oxygen reduction reaction. Samples NC900 and NC1000 having moderate N contents, high surface areas, and large numbers of mesopores favored the four-electron reduction pathway, while sample NC800 having a high N content, a moderate surface area, and a large number of micropores favored the two-electron reduction process.

Core-shell-structured CNT@RuO(2) composite as a high-performance cathode catalyst for rechargeable Li-O(2) batteries.

Abstract: A RuO2 shell was uniformly coated on the surface of core CNTs by a simple sol–gel method, and the resulting composite was used as a catalyst in a rechargeable Li–O2 battery. This core–shell structure can effectively prevent direct contact between the CNT and the discharge product Li2O2, thus avoiding or reducing the formation of Li2CO3, which can induce large polarization and lead to charge failure. The battery showed a high round-trip efficiency (ca. 79 %), with discharge and charge overpotentials of 0.21 and 0.51 V, respectively, at a current of 100 mA gtotal−1. The battery also exhibited excellent rate and cycling performance.

ISRM-Suggested Method for Determining the Mode I Static Fracture Toughness Using Semi-Circular Bend Specimen

Abstract: The International Society for Rock Mechanics has so far developed two standard methods for the determination of static fracture toughness of rock. They used three different core-based specimens and tests were to be performed on a typical laboratory compression or tension load frame. Another method to determine the mode I fracture toughness of rock using semi-circular bend specimen is herein presented. The specimen is semi-circular in shape and made from typical cores taken from the rock with any relative material directions noted. The specimens are tested in three-point bending using a laboratory compression test instrument. The failure load along with its dimensions is used to determine the fracture toughness. Most sedimentary rocks which are layered in structure may exhibit fracture properties that depend on the orientation and therefore measurements in more than one material direction may be necessary. The fracture toughness measurements are expected to yield a size-independent material property if certain minimum specimen size requirements are satisfied.

MAFFT: Iterative Refinement and Additional Methods

Abstract: This chapter outlines several methods implemented in the MAFFT package. MAFFT is a popular multiple sequence alignment (MSA) program with various options for the progressive method, the iterative refinement method and other methods. We first outline basic usage of MAFFT and then describe recent practical extensions, such as dot plot and adjustment of direction in DNA alignment. We also refer to MUSCLE, another high-performance MSA program.

The HOPS complex mediates autophagosome–lysosome fusion through interaction with syntaxin 17

Abstract: Membrane fusion is generally controlled by Rabs, soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs), and tethering complexes. Syntaxin 17 (STX17) was recently identified as the autophagosomal SNARE required for autophagosome-lysosome fusion in mammals and Drosophila. In this study, to better understand the mechanism of autophagosome-lysosome fusion, we searched for STX17-interacting proteins. Immunoprecipitation and mass spectrometry analysis identified vacuolar protein sorting 33A (VPS33A) and VPS16, which are components of the homotypic fusion and protein sorting (HOPS)-tethering complex. We further confirmed that all HOPS components were coprecipitated with STX17. Knockdown of VPS33A, VPS16, or VPS39 blocked autophagic flux and caused accumulation of STX17- and microtubule-associated protein light chain (LC3)-positive autophagosomes. The endocytic pathway was also affected by knockdown of VPS33A, as previously reported, but not by knockdown of STX17. By contrast, ultraviolet irradiation resistance-associated gene (UVRAG), a known HOPS-interacting protein, did not interact with the STX17-HOPS complex and may not be directly involved in autophagosome-lysosome fusion. Collectively these results suggest that, in addition to its well-established function in the endocytic pathway, HOPS promotes autophagosome-lysosome fusion through interaction with STX17.

NEAT1 long noncoding RNA regulates transcription via protein sequestration within subnuclear bodies

Abstract: Paraspeckles are subnuclear structures formed around nuclear paraspeckle assembly transcript 1 (NEAT1)/MENe/β long noncoding RNA (lncRNA). Here we show that paraspeckles become dramatically enlarged after proteasome inhibition. This enlargement is mainly caused by NEAT1 transcriptional up-regulation rather than accumulation of undegraded paraspeckle proteins. Of interest, however, using immuno-electron microscopy, we find that key paraspeckle proteins become effectively depleted from the nucleoplasm by 50% when paraspeckle assembly is enhanced, suggesting a sequestration mechanism. We also perform microarrays from NEAT1-knockdown cells and find that NEAT1 represses transcription of several genes, including the RNA-specific adenosine deaminase B2 (ADARB2) gene. In contrast, the NEAT1-binding paraspeckle protein splicing factor proline/glutamine-rich (SFPQ) is required for ADARB2 transcription. This leads us to hypothesize that ADARB2 expression is controlled by NEAT1-dependent sequestration of SFPQ. Accordingly, we find that ADARB2 expression is strongly reduced upon enhanced SFPQ sequestration by proteasome inhibition, with concomitant reduction in SFPQ binding to the ADARB2 promoter. Finally, NEAT1(-/-) fibroblasts are more sensitive to proteasome inhibition, which triggers cell death, suggesting that paraspeckles/NEAT1 attenuates the cell death pathway. These data further confirm that paraspeckles are stress-responsive nuclear bodies and provide a model in which induced NEAT1 controls target gene transcription by protein sequestration into paraspeckles.

Evolutionary origin of insect-Wolbachia nutritional mutualism.

Abstract: Obligate insect–bacterium nutritional mutualism is among the most sophisticated forms of symbiosis, wherein the host and the symbiont are integrated into a coherent biological entity and unable to survive without the partnership. Originally, however, such obligate symbiotic bacteria must have been derived from free-living bacteria. How highly specialized obligate mutualisms have arisen from less specialized associations is of interest. Here we address this evolutionary issue by focusing on an exceptional insect–Wolbachia nutritional mutualism. Although Wolbachia endosymbionts are ubiquitously found in diverse insects and generally regarded as facultative/parasitic associates for their insect hosts, a Wolbachia strain associated with the bedbug Cimex lectularius, designated as wCle, was shown to be essential for host’s growth and reproduction via provisioning of B vitamins. We determined the 1,250,060-bp genome of wCle, which was generally similar to the genomes of insect-associated facultative Wolbachia strains, except for the presence of an operon encoding the complete biotin synthetic pathway that was acquired via lateral gene transfer presumably from a coinfecting endosymbiont Cardinium or Rickettsia. Nutritional and physiological experiments, in which wCle-infected and wCle-cured bedbugs of the same genetic background were fed on B-vitamin–manipulated blood meals via an artificial feeding system, demonstrated that wCle certainly synthesizes biotin, and the wCle-provisioned biotin significantly contributes to the host fitness. These findings strongly suggest that acquisition of a single gene cluster consisting of biotin synthesis genes underlies the bedbug–Wolbachia nutritional mutualism, uncovering an evolutionary transition from facultative symbiosis to obligate mutualism facilitated by lateral gene transfer in an endosymbiont lineage.

A new approach to develop the Raman carbonaceous material geothermometer for low-grade metamorphism using peak width

Abstract: The Raman spectra of carbonaceous material (CM) from 19 metasediment samples collected from six widely separated areas of Southwest Japan and metamorphosed at temperatures from 165 to 655°C show systematic changes with metamorphic temperature that can be classified into four types: low-grade CM (c. 150–280°C), medium-grade CM (c. 280–400°C), high-grade CM (c. 400–650°C), and well-crystallized graphite (> c. 650°C). The Raman spectra of low-grade CM exhibit features typical of amorphous carbon, in which several disordered bands (D-band) appear in the first-order region. In the Raman spectra of medium-grade CM, the graphite band (G-band) can be recognized and several abrupt changes occur in the trends for several band parameters. The observed changes indicate that CM starts to transform from amorphous carbon to crystallized graphite at around 280°C, and this transformation continues until 400°C. The G-band becomes the most prominent peak at high-grade CM suggesting that the CM structure is close to that of well-crystallized graphite. In the highest temperature sample of 655°C, the Raman spectra of CM show a strong G-band with almost no recognizable D-band, implying the CM grain is well-crystallized graphite. In the Raman spectra of low- to medium-grade CM, comparisons of several band parameters with the known metamorphic temperature show inverse correlations between metamorphic temperature and the full width at half maximum (FWHM) of the D1- and D2-bands. These correlations are calibrated as new Raman CM geothermometers, applicable in the range of c. 150–400°C. Details of the methodology for peak decomposition of Raman spectra from the low to medium temperature range are also discussed with the aim of establishing a robust and user-friendly geothermometer.

Properties of Individual Dopant Atoms in Single‐Layer MoS2: Atomic Structure, Migration, and Enhanced Reactivity

Abstract: Single-layered MoS2 doped with Re (n-type) and Au (p-type) are investigated by in situ scanning transmission electron microscopy. Re atoms substituting Mo sites enhance the local chemical affinity, evidenced by agglomeration of other dopant/impurity atoms. Au atoms exist as adatoms and show larger mobility under the electron beam. These behaviors are consistent with density functional theory calculations.

MiR-133 promotes cardiac reprogramming by directly repressing Snai1 and silencing fibroblast signatures

Abstract: Fibroblasts can be directly reprogrammed into cardiomyocyte-like cells (iCMs) by overexpression of cardiac transcription factors or microRNAs. However, induction of functional cardiomyocytes is inefficient, and molecular mechanisms of direct reprogramming remain undefined. Here, we demonstrate that addition of miR-133a (miR-133) to Gata4, Mef2c, and Tbx5 (GMT) or GMT plus Mesp1 and Myocd improved cardiac reprogramming from mouse or human fibroblasts by directly repressing Snai1, a master regulator of epithelial-to-mesenchymal transition. MiR-133 overexpression with GMT generated sevenfold more beating iCMs from mouse embryonic fibroblasts and shortened the duration to induce beating cells from 30 to 10 days, compared to GMT alone. Snai1 knockdown suppressed fibroblast genes, upregulated cardiac gene expression, and induced more contracting iCMs with GMT transduction, recapitulating the effects of miR-133 overexpression. In contrast, overexpression of Snai1 in GMT/miR-133-transduced cells maintained fibroblast signatures and inhibited generation of beating iCMs. MiR-133-mediated Snai1 repression was also critical for cardiac reprogramming in adult mouse and human cardiac fibroblasts. Thus, silencing fibroblast signatures, mediated by miR-133/Snai1, is a key molecular roadblock during cardiac reprogramming.

Genome sequence of the tsetse fly (Glossina morsitans ): Vector of African trypanosomiasis

Abstract: Tsetse flies are the sole vectors of human African trypanosomiasis throughout sub-Saharan Africa. Both sexes of adult tsetse feed exclusively on blood and contribute to disease transmission. Notable differences between tsetse and other disease vectors include obligate microbial symbioses, viviparous reproduction, and lactation. Here, we describe the sequence and annotation of the 366-megabase Glossina morsitans morsitans genome. Analysis of the genome and the 12,308 predicted protein–encoding genes led to multiple discoveries, including chromosomal integrations of bacterial (Wolbachia) genome sequences, a family of lactation-specific proteins, reduced complement of host pathogen recognition proteins, and reduced olfaction/chemosensory associated genes. These genome data provide a foundation for research into trypanosomiasis prevention and yield important insights with broad implications for multiple aspects of tsetse biology.

Machine learning with systematic density-functional theory calculations: Application to melting temperatures of single- and binary-component solids

Abstract: A combination of systematic density-functional theory (DFT) calculations and machine learning techniques has a wide range of potential applications. This study presents an application of the combination of systematic DFT calculations and regression techniques to the prediction of the melting temperature for single and binary compounds. Here we adopt the ordinary least-squares regression, partial least-squares regression, support vector regression, and Gaussian process regression. Among the four kinds of regression techniques, SVR provides the best prediction. The inclusion of physical properties computed by the DFT calculation to a set of predictor variables makes the prediction better. In addition, limitation of the predictive power is shown when extrapolation from the training dataset is required. Finally, a simulation to find the highest melting temperature toward the efficient materials design using kriging is demonstrated. The kriging design finds the compound with the highest melting temperature much faster than random designs. This result may stimulate the application of kriging to efficient materials design for a broad range of applications.

An expanded genomic representation of the phylum cyanobacteria.

Abstract: Molecular surveys of aphotic habitats have indicated the presence of major uncultured lineages phylogenetically classified as members of the Cyanobacteria. One of these lineages has recently been proposed as a nonphotosynthetic sister phylum to the Cyanobacteria, the Melainabacteria, based on recovery of population genomes from human gut and groundwater samples. Here, we expand the phylogenomic representation of the Melainabacteria through sequencing of six diverse population genomes from gut and bioreactor samples supporting the inference that this lineage is nonphotosynthetic, but not the assertion that they are strictly fermentative. We propose that the Melainabacteria is a class within the phylogenetically defined Cyanobacteria based on robust monophyly and shared ancestral traits with photosynthetic representatives. Our findings are consistent with theories that photosynthesis occurred late in the Cyanobacteria and involved extensive lateral gene transfer and extends the recognized functionality of members of this phylum.

A quinone-based oligomeric lithium salt for superior Li–organic batteries

Abstract: Organic electrode materials are promising alternatives to transition-metal based intercalation compounds for the next generation of high-performance and sustainable batteries. Herein, a novel quinone-based organic, lithium salt of poly(2,5-dihydroxy-p-benzoquinonyl sulfide) (Li2PDHBQS), was successfully synthesized through a simple one-step polycondensation reaction, and applied as a cathode for Li–organic batteries. As an oligomeric lithium salt with average polymerization degree of 7, Li2PDHBQS combines the advantages of the O⋯Li⋯O coordination bond and increased molecular weight, thus solves absolutely the dissolution problem of active material in non-aqueous electrolytes, which has seriously hindered development of organic electrode materials. Benefiting from the high theoretical capacity, intrinsic insolubility, fast reaction kinetics of the quinone group, accelerated Li-ion transport and uniform blending with conductive carbon, as well as the stable amorphous structure, Li2PDHBQS shows superior comprehensive electrochemical performance including high reversible capacity (268 mA h g−1), high cycling stability (1500 cycles, 90%), high rate capability (5000 mA g−1, 83%) and high Coulombic efficiency (99.9–100.1%). Investigation of the structure–property relationship of Li2PDHBQS and its analogues also gives new insights into developing novel quinone-based organic electrode materials, for building better Li–organic or Na–organic batteries beyond traditional Li-ion batteries.