The entire chloroplast genome of the monocot rice (Oryza sativa) has been sequenced and comprises 134525 bp. Predicted genes have been identified along with open reading frames (ORFs) conserved between rice and the previously sequenced chloroplast genomes, a dicot, tobacco (Nicotiana tabacum), and a liverwort (Marchantia polymorpha). The same complement of 30 tRNA and 4 rRNA genes has been conserved between rice and tobacco. Most ORFs extensively conserved between N. tabacum and M. polymorpha are also conserved intact in rice. However, several such ORFs are entirely absent in rice, or present only in severely truncated form. Structural changes are also apparent in the genome relative to tobacco. The inverted repeats, characteristic of chloroplast genome structure, have expanded outward to include several genes present only once per genome in tobacco and liverwort and the large single copy region has undergone a series of inversions which predate the divergence of the cereals. A chimeric tRNA pseudogene overlaps an apparent endpoint of the largest inversion, and a model invoking illegitimate recombination between tRNA genes is proposed which accounts simultaneously for the origin of this pseudogene, the large inversion and the creation of repeated sequences near the inversion endpoints.

The quasi-steady structure of super-critical accretion flows around a black hole is studied based on the two-dimensional radiation-hydrodynamical (2D-RHD) simulations. The super-critical flow is composed of two parts: the disk region and the outflow regions above and below the disk. Within the disk region the circular motion as well as the patchy density structure are observed, which is caused by Kelvin-Helmholtz instability and probably by convection. The mass-accretion rate decreases inward, roughly in proportion to the radius, and the remaining part of the disk material leaves the disk to form outflow because of strong radiation pressure force. We confirm that photon trapping plays an important role within the disk. Thus, matter can fall onto the black hole at a rate exceeding the Eddington rate. The emission is highly anisotropic and moderately collimated so that the apparent luminosity can exceed the Eddington luminosity by a factor of a few in the face-on view. The massaccretion rate onto the black hole increases with increase of the absorption opacity (metalicity) of the accreting matter. This implies that the black hole tends to grow up faster in the metal rich regions as in starburst galaxies or star-forming regions.

We present diffuse Lyα halos (LAHs) identified in the composite Subaru narrowband images of 100 − 3600 Lyα emitters (LAEs) at z = 2.2, 3.1, 3.7, 5.7, and 6.6. First, we carefully examine potential artifacts mimicking LAHs that include a large-scale point-spread function (PSF) made by instrumental and atmospheric effects. Based on our critical test with composite images of non-LAE samples whose narrowbandmagnitude and source-size distributions are the same as our LAE samples, we confirm that no artifacts can produce a diffuse extended feature similar to our LAHs. After this test, we measure the scale lengths of exponential profile for the LAHs estimated from our z = 2.2 − 6.6 LAE samples of L Lyα 2 × 10 42 erg s −1 . We obtain the scale lengths of ≃ 5 − 10 kpc at z = 2.2 − 5.7, and find no evolution of scale lengths in this redshift range beyond our measurement uncertainties. Combining this result and the previously-known UV-continuum size evolution, we infer that the ratio of LAH to UVcontinuum sizes is nearly constant at z = 2.2 − 5.7. The scale length of our z = 6.6 LAH is larger than 5 − 10 kpc just beyond the error bar, which is a hint that the scale lengths of LAHs would increase from z = 5.7 to 6.6. If this increase is confirmed by future large surveys with significant improvements of statistical and systematical errors, this scale length change at z 6 would be a signature of increasing fraction of neutral hydrogen scattering Lyα photons, due to cosmic reionization.

We present a statistical study of velocities of Lyα, interstellar (IS) absorption, and nebular lines and gas covering fraction for Lyα emitters (LAEs) at z ≃ 2. We make a sample of 22 LAEs with a large Lyα equivalent width (EW) of 50Å based on our deep Keck/LRIS observations, in conjunction with spectroscopic data from the Subaru/FMOS program and the literature. We estimate the average velocity offset of Lyα from a systemic redshift determined with nebular lines to be ∆v Lyα = 234 ± 9 km s −1 . Using a Kolmogorv-Smirnov test, we confirm the previous claim of Hashimoto et al. (2013) that the average ∆v Lyα of LAEs is smaller than that of LBGs. Our LRIS data successfully identify blue-shifted multiple IS absorption lines in the UV continua of four LAEs on an individual basis. The average velocity offset of IS absorption lines from a systemic redshift is ∆v IS = 204 ± 27 km s −1 , indicating LAE's gas outflow with a velocity comparable to typical LBGs. Thus, the ratio, R Lyα IS ≡ ∆v Lyα /∆v IS of LAEs, is around unity, suggestive of low impacts on Lyα transmission by resonant scattering of neutral hydrogen in the IS medium. We find an anti-correlation between Lyα EW and the covering fraction, f c , estimated from the depth of absorption lines, where f c is an indicator of average neutral hydrogen column density, N HI . The results of our study support the idea that N HI is a key quantity determining Lyα emissivity.