Konan University

After the Big Bang, production of heavy elements in the early Universe takes place starting from the formation of the first stars, their evolution, and explosion. The first supernova explosions have strong dynamical, thermal, and chemical feedback on the formation of subsequent stars and evolution of galaxies. However, the nature of the Universe's first stars and supernova explosions has not been well clarified. The signature of the nucleosynthesis yields of the first stars can be seen in the elemental abundance patterns observed in extremely metal-poor stars. Interestingly, those patterns show some peculiarities relative to the solar abundance pattern, which should provide important clues to understanding the nature of early generations of stars. We thus review the recent results of the nucleosynthesis yields of mainly massive stars for a wide range of stellar masses, metallicities, and explosion energies. We also provide yields tables and examine how those yields are affected by some hydrodynamical effects during supernova explosions, namely, explosion energies from those of hypernovae to faint supernovae, mixing and fallback of processed materials, asphericity, etc. Those parameters in the supernova nucleosynthesis models are constrained from observational data of supernovae and metal-poor stars. Nucleosynthesis yields are then applied to the chemical evolution model of our Galaxy and other types of galaxies to discuss how the chemical enrichment process occurred during evolution.

Abstract Hyper Suprime-Cam (HSC) is a wide-field imaging camera on the prime focus of the 8.2-m Subaru telescope on the summit of Mauna Kea in Hawaii. A team of scientists from Japan, Taiwan, and Princeton University is using HSC to carry out a 300-night multi-band imaging survey of the high-latitude sky. The survey includes three layers: the Wide layer will cover 1400 deg2 in five broad bands (grizy), with a 5 σ point-source depth of r ≈ 26. The Deep layer covers a total of 26 deg2 in four fields, going roughly a magnitude fainter, while the UltraDeep layer goes almost a magnitude fainter still in two pointings of HSC (a total of 3.5 deg2). Here we describe the instrument, the science goals of the survey, and the survey strategy and data processing. This paper serves as an introduction to a special issue of the Publications of the Astronomical Society of Japan, which includes a large number of technical and scientific papers describing results from the early phases of this survey.

Ground-based gamma-ray astronomy has had a major breakthrough with the impressive results obtained using systems of imaging atmospheric Cherenkov telescopes. Ground-based gamma-ray astronomy has a huge potential in astrophysics, particle physics and cosmology. CTA is an international initiative to build the next generation instrument, with a factor of 5-10 improvement in sensitivity in the 100 GeV-10 TeV range and the extension to energies well below 100 GeV and above 100 TeV. CTA will consist of two arrays (one in the north, one in the south) for full sky coverage and will be operated as open observatory. The design of CTA is based on currently available technology. This document reports on the status and presents the major design concepts of CTA.

Hyper Suprime-Cam (HSC) is a wide-field imaging camera on the prime focus of the 8.2-m Subaru telescope on the summit of Mauna Kea in Hawaii. A team of scientists from Japan, Taiwan, and Princeton University is using HSC to carry out a 300-night multi-band imaging survey of the high-latitude sky. The survey includes three layers: the Wide layer will cover 1400 deg2 in five broad bands (grizy), with a 5 σ point-source depth of r ≈ 26. The Deep layer covers a total of 26 deg2 in four fields, going roughly a magnitude fainter, while the UltraDeep layer goes almost a magnitude fainter still in two pointings of HSC (a total of 3.5 deg2). Here we describe the instrument, the science goals of the survey, and the survey strategy and data processing. This paper serves as an introduction to a special issue of the Publications of the Astronomical Society of Japan, which includes a large number of technical and scientific papers describing results from the early phases of this survey.

The thermodynamic parameters (delta H degree, delta S degree, and delta G degree 37) for 16 nearest-neighbor sets and one initiation factor are presented here in order to predict stability of RNA/DNA hybrid duplexes. To determine the nearest-neighbor parameters, thermodynamics for 68 different hybrid sequences (136 single-stranded oligonucleotides) with 5-13 nucleotide length including several duplexes with identical nearest-neighbors were measured by UV melting procedure. These sequences were selected to have many different combinations of nearest-neighbor pairs, and so that the number of the 16 nearest-neighbor sequences in the oligomers were as equal as possible. The structures of the hybrids were also investigated by measuring circular dichroism spectra. Comparing delta G degree 37 values of the hybrids with DNA/DNA and RNA/RNA parameters reported previously (Breslauer, K.J., Frank, R., Blöcker, H., & Marky, L.A. (1986) Proc. Natl. Acad. Sci. U.S.A. 83, 3746-3750; Freier, S.M., Kierzek, R., Jaeger, J.A., Sugimoto, N., Caruthers, M.H., Neilson, T., & Turner, D.H. (1986) Proc. Natl. Acad. Sci. U.S.A. 83, 9373-9377), RNA/RNA double helix is the most stable of the three kinds of helixes with the same nearest-neighbor sequences. Which is more stable between DNA/DNA and RNA/DNA hybrid duplexes depends on its sequence. Calculated thermodynamic values of hybrid formation with the present parameters reproduce the experimental values within reasonable errors.

Flexible porous coordination polymers change their structure in response to molecular incorporation but recover their original configuration after the guest has been removed. We demonstrated that the crystal downsizing of twofold interpenetrated frameworks of [Cu(2)(dicarboxylate)(2)(amine)](n) regulates the structural flexibility and induces a shape-memory effect in the coordination frameworks. In addition to the two structures that contribute to the sorption process (that is, a nonporous closed phase and a guest-included open phase), we isolated an unusual, metastable open dried phase when downsizing the crystals to the mesoscale, and the closed phase was recovered by thermal treatment. Crystal downsizing suppressed the structural mobility and stabilized the open dried phase. The successful isolation of two interconvertible empty phases, the closed phase and the open dried phase, provided switchable sorption properties with or without gate-opening behavior.

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTEffects of Molecular Crowding on the Structures, Interactions, and Functions of Nucleic AcidsShu-ichi Nakano*, Daisuke Miyoshi*, and Naoki Sugimoto*View Author Information Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST) and Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan*E-mail: [email protected]*E-mail: [email protected]*E-mail: [email protected]Cite this: Chem. Rev. 2014, 114, 5, 2733–2758Publication Date (Web):December 23, 2013Publication History Received22 February 2013Published online23 December 2013Published inissue 12 March 2014https://doi.org/10.1021/cr400113mCopyright © 2013 American Chemical SocietyRequest reuse permissionsArticle Views10263Altmetric-Citations404LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit Read OnlinePDF (11 MB) Get e-AlertscloseSUBJECTS:Alcohols,Genetics,Molecular structure,Molecules,Nucleic acids Get e-Alerts

A simple and straightforward method combines microwave-assisted solvothermal conditions with the coordination modulation method to achieve the size-controlled formation of the porous coordination polymer (PCP), [Cu3(btc)2] (where btc represents benzene-1,3,5-tricarboxylate) in the nano/micro regimes. The addition of a monocarboxylic acid modulator to the reaction mixture greatly influenced the morphology of the resulting sample, through competitive coordination interactions during the crystal formation process. By adjusting the concentration of dodecanoic acid additive, we could subtly control the nucleation rate of a [Cu3(btc)2] framework and, thus, the resulting crystal size. Homogeneous nanocrystals of the PCP with sizes ranging from few tenths of nanometers up to few micrometers could be successfully obtained in a controlled manner. X-ray diffractions and gas sorption measurements revealed highly crystalline particles with large pore volumes. Moreover, variations in the sorption profiles could be correlated to the size and morphology of the [Cu3(btc)2] samples, presenting affinity for gas condensation at high relative pressures or even hierarchical dual porous structures with mesoporous grain boundaries.

A spectroscopic method, which enables characterization of a single isolated quantum dot and a quantum wave function interferometry, is applied to an exciton discrete excited state in an InGaAs quantum dot. Long coherence of zero-dimensional excitonic states made possible the observation of coherent population flopping in a 0D excitonic two-level system in a time-domain interferometric measurement. Corresponding energy splitting is also manifested in an energy-domain measurement.

To improve the previous DNA/DNA nearest-neighbor parameters, thermodynamic parameters (deltaH degrees, deltaS degrees and deltaG degrees) of 50 DNA/DNA duplexes were measured. Enthalpy change of a helix initiation factor is also considered though the parameters reported recently did not contain the factor. A helix initiation factor for DNA/DNA duplex determined here was the same as that of RNA/RNA duplex (deltaG degrees(37) = 3.4 kcal/mol). The improved nearest-neighbor parameters reproduced not only these 50 experimental values used here but also 15 other experimental values obtained in different studies. Comparing deltaG degrees(37) values of DNA/DNA nearest-neighbor parameters obtained here with those of RNA/RNA and RNA/DNA, RNA/RNA duplex was generally the most stable of the three kinds of duplexes with the same nearest-neighbor sequences. Which is more stable between DNA/DNA and RNA/DNA duplexes is sequence dependent.

The design of crystal morphology, or exposed crystal facets, has enabled the development (e.g., catalytic activities, material attributes, and oriented film formation) of porous coordination polymers (PCPs) without changing material compositions. However, because crystal growth mechanisms are not fully understood, control of crystal morphology still remains challenging. Herein, we report the morphology design of [Cu(3)(btc)(2)](n) (btc = benzene-1,3,5-tricarboxylate) by the coordination modulation method (modulator = n-dodecanoic acid or lauric acid). A morphological transition (octahedron-cuboctahedron-cube) in the [Cu(3)(btc)(2)](n) crystal was observed with an increase in concentration of the modulator. By suitably defining a coarse-grained standard unit of [Cu(3)(btc)(2)](n) as its cuboctahedron main pore and determining its attachment energy on crystal surfaces, Monte Carlo coarse-grain modeling revealed the population and orientation of carboxylates and elucidated an important role of the modulator in determining the <100>- and <111>-growth throughout the crystal growth process. This comprehension, in fact, successfully led to designed crystal morphologies with oriented growth on bare substrates. Because selective crystal orientations on the bare substrates were governed by crystal morphology, this contribution also casts a new light on the unexplored issue of the significance of morphology design of PCPs.

Steroid-resistant nephrotic syndrome (SRNS) is a frequent cause of end-stage renal failure. Identification of single-gene causes of SRNS has generated some insights into its pathogenesis; however, additional genes and disease mechanisms remain obscure, and SRNS continues to be treatment refractory. Here we have identified 6 different mutations in coenzyme Q10 biosynthesis monooxygenase 6 (COQ6) in 13 individuals from 7 families by homozygosity mapping. Each mutation was linked to early-onset SRNS with sensorineural deafness. The deleterious effects of these human COQ6 mutations were validated by their lack of complementation in coq6-deficient yeast. Furthermore, knockdown of Coq6 in podocyte cell lines and coq6 in zebrafish embryos caused apoptosis that was partially reversed by coenzyme Q10 treatment. In rats, COQ6 was located within cell processes and the Golgi apparatus of renal glomerular podocytes and in stria vascularis cells of the inner ear, consistent with an oto-renal disease phenotype. These data suggest that coenzyme Q10-related forms of SRNS and hearing loss can be molecularly identified and potentially treated.

We present the first measurement of planet frequency beyond the "snow line" for planet/star mass-ratios[-4.5200) microlensing events during 2005-8. The sample host stars have typical mass M_host 0.5 Msun, and detection is sensitive to planets over a range of projected separations (R_E/s_max,R_E*s_max), where R_E 3.5 AU sqrt(M_host/Msun) is the Einstein radius and s_max (q/5e-5)^{2/3}, corresponding to deprojected separations ~3 times the "snow line". Though frenetic, the observations constitute a "controlled experiment", which permits measurement of absolute planet frequency. High-mag events are rare, but the high-mag channel is efficient: half of high-mag events were successfully monitored and half of these yielded planet detections. The planet frequency derived from microlensing is a factor 7 larger than from RV studies at factor ~25 smaller separations [2

The effect of molecular crowding on the structure and stability of biomolecules has become a subject of increasing interest because it can clarify how biomolecules behave under cell-mimicking conditions. Here, we quantitatively analyzed the effects of molecular crowding on the thermodynamics of antiparallel G-quadruplex formation via Hoogsteen base pairs and of antiparallel hairpin-looped duplex (HP duplex) formation via Watson-Crick base pairs. The free energy change at 25 degrees C for G-quadruplex formation decreased from -3.5 to -5.5 kcal mol(-1) when the concentration of poly(ethylene glycol) 200 was increased from 0 to 40 wt %, whereas that of duplex formation increased from -9.8 to -6.9 kcal mol(-1). These results showed that the antiparallel G-quadruplex is stabilized under molecular crowding conditions, but that the HP duplex is destabilized. Moreover, plots of stability (ln K(obs)) of the DNA structures versus water activity (ln a(w)) demonstrated that the ln K(obs) for G-quadruplex formation decreased linearly as the ln a(w) increased, whereas that for duplex formation increased linearly with the increase in ln a(w), suggesting that the slope approximately equals the number of water molecules released or taken up during the formation of these structures. Thus, molecular crowding affects the thermodynamics of DNA structure formation by altering the hydration of the DNA. The stabilization of the DNA structures with Hoogsteen base pairs and destabilization of DNA structures with Watson-Crick base pairs under molecular crowding conditions lead to structural polymorphism of DNA sequences regulated by the state of hydration.

Abstract Recent detection of gravitational waves from a neutron star (NS) merger event GW170817 and identification of an electromagnetic counterpart provide a unique opportunity to study the physical processes in NS mergers. To derive properties of ejected material from the NS merger, we perform radiative transfer simulations of kilonova, optical and near-infrared emissions powered by radioactive decays of r-process nuclei synthesized in the merger. We find that the observed near-infrared emission lasting for &amp;gt;10 d is explained by 0.03 M⊙ of ejecta containing lanthanide elements. However, the blue optical component observed at the initial phases requires an ejecta component with a relatively high electron fraction (Ye). We show that both optical and near-infrared emissions are simultaneously reproduced by the ejecta with a medium Ye of ∼0.25. We suggest that a dominant component powering the emission is post-merger ejecta, which exhibits that the mass ejection after the first dynamical ejection is quite efficient. Our results indicate that NS mergers synthesize a wide range of r-process elements and strengthen the hypothesis that NS mergers are the origin of r-process elements in the Universe.

We compare four different methods for analyzing time-varying signals, the frequency and amplitude of which are both varying (small BT signals, where B is the bandwidth and T the duration). All four methods give results which depend on the frequency bandwidth of the analyzing filter. But the modified moving window method (MMWM) (Kodera et al. [10]) is the one which gives the most significant result whatever the value of the filtering bandwidth. This is demonstrated both by a mathematical treatment and by a numerical simulation. In general, there are two characteristic curves in the frequency-time plane: one which gives the instantaneous frequency as a function of time and the other which gives the group delay time as a function of frequency. For signals with small BT values, these two curves are distinct and the different analyzing methods approach one or the other curve, or neither of them, depending on the bandwidth of the filtering window. The ability of each method to resolve multicomponent signals is discussed. The influence of the scaling factors used for the visualization of the signal in a two-dimensional plane is also studied.

We perform cosmological hydrodynamics simulations with non-equilibrium primordial chemistry to obtain 59 minihalos that host first stars. The obtained minihalos are used as initial conditions of local three dimensional radiation hydrodynamics simulations to investigate the formation of the first stars. We find two-thirds of the minihalos host multiple stars, while the rest of them have single stars. The mass of the stars found in our simulations are in the range of 1 Msun \la M \la 300 Msun, peaking at several x 10 Msun. Most of the very massive stars of \ga 140 Msun are born as single stars, although not all of the single stars are very massive. We also find a few stars of \la 1 Msun that are kicked by the gravitational three body interactions to the position distant from the center of mass. The frequency that a star forming minihalo contains a binary system is \sim 50%. We also investigate the abundance pattern of the stellar remnants by summing up the contributions from the first stars in the simulations. Consequently, the pattern is compatible with that of the low metallicity Damped Lyman-alpha systems or the Extremely Metal Poor (EMP) stars, if the mass spectrum obtained in our experiment is shifted to the low mass side by 0.2 dex. If we consider the case that an EMP star is born in the remnant of the individual minihalo without mixing with others, the chemical signature of the pair instability supernova is more prominent, because most of them are born as single stars.

Molecularly imprinted polymer gel with embedded gold nanoparticle was prepared on a gold substrate of a chip for a surface plasmon resonance (SPR) sensor for fabricating an SPR sensor sensitive to a low molecular weight analyte. The sensing is based on swelling of the imprinted polymer gel that is triggered by an analyte binding event within the polymer gel. The swelling causes greater distance between the gold nanoparticles and substrate, shifting a dip of an SPR curve to a higher SPR angle. The polymer synthesis was conducted by radical polymerization of a mixture of acrylic acid, N-isopropylacrylamide, N,N'-methylenebisacrylamide, and gold nanoparticles in the presence of dopamine as model template species on a sensor chip coated with allyl mercaptan. The modified sensor chip showed an increasing SPR angle in response to dopamine concentration, which agrees with the expected sensing mechanism. Furthermore, the gold nanoparticles were shown to be effective for enhancing the signal intensity (the change of SPR angle) by comparison with a sensor chip immobilizing no gold nanoparticles. The analyte binding process and the consequent swelling appeared to be reversible, allowing one the repeated use of the presented sensor chip.

The effects of counter ion on a nucleic acid duplex stability were investigated. Since a linear free energy relationship for the thermostability of oligonucleotide duplexes between those in 1 M and in 100 mM NaCl-phosphate buffer were observed regardless of whether they are DNA-DNA, RNA-RNA or RNA-DNA duplexes, simple prediction systems for [Delta] G degrees 37as well as T mvalues in 100 mM NaCl-phosphate buffer were established. These predictions were successful with an average error of only 2.4 degrees C for T mand 5. 7% for G degrees 37values. The number of Na+newly bound to a duplex when the duplex forms (-[Delta] n) was significantly influenced by the base composition, and -[Delta] n for d(GCCAGTTAA)/d(TTAACTGGC) was different for MgCl2, CaCl2, BaCl2and MnCl2(from 0.70 to 0.76 with the same order of the duplex stability). Almost no additive effects on the duplex stability was observed for NaCl and MgCl2, suggesting a competitive binding for these cations. The sequence-dependent manner of [Delta] n suggests the presence of preferential base pairs or nearest-neighbor base pairs for the cation binding, which would affect nearest-neighbor parameters.

We report the detection of an extrasolar planet of mass ratio q ~ 2 × 10−4 in microlensing event MOA-2007-BLG-192. The best-fit microlensing model shows both the microlensing parallax and finite source effects, and these can be combined to obtain the lens masses of M = 0.060+ 0.028−0.021 M☉ for the primary and m = 3.3+ 4.9−1.6 M⊕ for the planet. However, the observational coverage of the planetary deviation is sparse and incomplete, and the radius of the source was estimated without the benefit of a source star color measurement. As a result, the 2 σ limits on the mass ratio and finite source measurements are weak. Nevertheless, the microlensing parallax signal clearly favors a substellar mass planetary host, and the measurement of finite source effects in the light curve supports this conclusion. Adaptive optics images taken with the Very Large Telescope (VLT) NACO instrument are consistent with a lens star that is either a brown dwarf or a star at the bottom of the main sequence. Follow-up VLT and/or Hubble Space Telescope (HST) observations will either confirm that the primary is a brown dwarf or detect the low-mass lens star and enable a precise determination of its mass. In either case, the lens star, MOA-2007-BLG-192L, is the lowest mass primary known to have a companion with a planetary mass ratio, and the planet, MOA-2007-BLG-192Lb, is probably the lowest mass exoplanet found to date, aside from the lowest mass pulsar planet.