Coupled charge and valley excitations in graphene quantum Hall ferromagnets

Graphene is a two-dimensional carbon material with a honeycomb lattice and Dirac-type low-energy spectrum. In a strong magnetic field, where Coulomb interactions dominate against disorder broadening, quantum Hall ferromagnetic states realize at integer fillings. Extending the quantum Hall ferromagnetism to the fractional filling case of massless Dirac fermions, we study the elementally charge excitations which couple with the valley degrees of freedom (so-called valley skyrmions). With the use of the density matrix renomalization group (DMRG) method, the excitation gaps are calculated and extrapolated to the thermodynamic limit. These results exhibit numerical evidences and criterions of the skyrmion excitations in graphene.Comment: 5 pages, 5 figure

Robustness and the generalist niche of polyploid species: Genome shock or gradual evolution?

The prevalence of polyploidy in wild and crop species has stimulated debate over its evolutionary advantages and disadvantages. Previous studies have focused on changes occurring at the polyploidization events, including genome-wide changes termed “genome shock,” as well as ancient polyploidy. Recent bioinformatics advances and empirical studies of Arabidopsis and wheat relatives are filling a research gap: the functional evolutionary study of polyploid species using RNA-seq, DNA polymorphism, and epigenomics. Polyploid species can become generalists in natura through environmental robustness by inheriting and merging parental stress responses. Their evolvability is enhanced by mutational robustness working on inherited standing variation. The identification of key genes responsible for gradual adaptive evolution will encourage synthetic biological approaches to transfer polyploid advantages to other species

Tidal effects on magnetic gyration of a charged particle in Fermi coordinates

We examine the gyration motion of a charged particle, viewed from a reference observer falling along the Z axis into a Schwarzschild black hole. It is assumed that the magnetic field is constant and uniform along the Z axis, and that the particle has a circular orbit in the X-Y plane far from the gravitational source. When the particle as well as the reference observer approaches the black hole, its orbit is disrupted by the tidal force. The final plunging velocity increases in the non-relativistic case, but decreases if the initial circular velocity exceeds a critical value, which is approximately 0.7c. This toy model suggests that disruption of a rapidly rotating star due to a velocity-dependent tidal force may be quite different from that of a non-relativistic star. The model also suggested that collapse of the orbit after the disruption is slow in general, so that the particle subsequently escapes outside the valid Fermi coordinates.Comment: 10 pages, 12 figure

FeII/MgII Emission Line Ratios of QSOs. II. z>6 Objects

Near-infrared spectra of four QSOs located at $z>6$ are obtained with the OH-airglow suppressor mounted on the Subaru telescope. The FeII/MgII emission-line ratios of these QSOs are examined by the same fitting algorithm as in our previous study of $z<5.3$ QSOs. The fitting results show that two out of the four $z>6$ QSOs have significant FeII emission in their rest-UV spectra, while the other two have almost no FeII features. We also applied our fitting algorithm to more than 10,000 SDSS QSOs and found two trends in the distribution of FeII/MgII against redshift: (1) the upper envelope of the FeII/MgII distribution at $z>3$ shows a probable declination toward high redshift, and (2) the median distribution settles into lower ratios at $z\sim 1.5$ with small scatter compared to the other redshift. We discuss an Fe/Mg abundance evolution of QSOs with a substantial contribution from the diverse nature of the broad-line regions in high-redshift QSOs.Comment: 12 pages, 2 figures. Accepted for publication in ApJ (10 October 2004, v614

Plant sexual reproduction during climate change: gene function in natura studied by ecological and evolutionary systems biology

Background It is essential to understand and predict the effects of changing environments on plants. This review focuses on the sexual reproduction of plants, as previous studies have suggested that this trait is particularly vulnerable to climate change, and because a number of ecologically and evolutionarily relevant genes have been identified. Scope It is proposed that studying gene functions in naturally fluctuating conditions, or gene functions in natura, is important to predict responses to changing environments. First, we discuss flowering time, an extensively studied example of phenotypic plasticity. The quantitative approaches of ecological and evolutionary systems biology have been used to analyse the expression of a key flowering gene, FLC, of Arabidopsis halleri in naturally fluctuating environments. Modelling showed that FLC acts as a quantitative tracer of the temperature over the preceding 6 weeks. The predictions of this model were verified experimentally, confirming its applicability to future climate changes. Second, the evolution of self-compatibility as exemplifying an evolutionary response is discussed. Evolutionary genomic and functional analyses have indicated that A. thaliana became self-compatible via a loss-of-function mutation in the male specificity gene, SCR/SP11. Self-compatibility evolved during glacial-interglacial cycles, suggesting its association with mate limitation during migration. Although the evolution of self-compatibility may confer short-term advantages, it is predicted to increase the risk of extinction in the long term because loss-of-function mutations are virtually irreversible. Conclusions Recent studies of FLC and SCR have identified gene functions in natura that are unlikely to be found in laboratory experiments. The significance of epigenetic changes and the study of non-model species with next-generation DNA sequencers is also discusse

Discovery of H alpha absorption in the unusual broad absorption line quasar SDSS J083942.11+380526.3

We discovered an H alpha absorption in a broad H alpha emission line of an unusual broad absorption line quasar, SDSS J083942.11+380526.3 at z=2.318, by near-infrared spectroscopy with the Cooled Infrared Spectrograph and Camera for OHS (CISCO) on the Subaru telescope. The Presence of non-stellar H alpha absorption is known only in the Seyfert galaxy NGC 4151 to date, thus our discovery is the first case for quasars. The H alpha absorption line is blueshifted by 520 km/s relative to the H alpha emission line, and its redshift almost coincides with those of UV low-ionization metal absorption lines. The width of the H alpha absorption (~ 340 km/s) is similar to those of the UV low-ionization absorption lines. These facts suggest that the H alpha and the low-ionization metal absorption lines are produced by the same low-ionization gas which has a substantial amount of neutral gas. The column density of the neutral hydrogen is estimated to be ~ 10^18 cm^-2 by assuming a gas temperature of 10,000 K from the analysis of the curve of growth. The continuum spectrum is reproduced by a reddened (E(B-V) ~ 0.15 mag for the SMC-like reddening law) composite quasar spectrum. Furthermore, the UV spectrum of SDSS J083942.11+380526.3 shows a remarkable similarity to that of NGC 4151 in its low state, suggesting the physical condition of the absorber in SDSS J083942.11+380526.3 is similar to that of NGC 4151 in the low state. As proposed for NGC 4151, SDSS J083942.11+380526.3 may be also seen through the close direction of the surface of the obscuring torus.Comment: Accepted for publication in Ap

Massive galaxies in cosmological simulations: UV-selected sample at redshift z=2

We study the properties of galaxies at z=2 in a Lambda CDM universe, using two different types of hydrodynamic simulation methods (Eulerian TVD and SPH) and a spectrophotometric analysis in the Un, G, R filter set. The simulated galaxies at z=2 satisfy the color-selection criteria proposed by Adelberger et al. (2004) when we assume Calzetti extinction with E(B-V)=0.15. We find that the number density of simulated galaxies brighter than R<25.5 at z=2 is about 2e-2 h^3/Mpc^3, roughly one order of magnitude larger than that of Lyman break galaxies at z=3. The most massive galaxies at z=2 have stellar masses >~1e11 Msun, and their observed-frame G-R colors lie in the range 0.0<G-R<1.0. They typically have been continuously forming stars with a rate exceeding 30 Msun/yr over a few Gyrs from z=10 to z=2, although the TVD simulation indicates a more sporadic star formation history than the SPH simulations. Of order half of their stellar mass was already assembled by z~4. The reddest massive galaxies at z=2 with G-R >= 1.0 and Mstar>1e10 Msun/h finished the build-up of their stellar mass by z~3. Interestingly, our study suggests that the majority of the most massive galaxies at z=2 should be detectable at rest-frame UV wavelengths, contrary to some recent claims made on the basis of near-IR studies of galaxies at the same epoch, provided the median extinction is less than E(B-V)<0.3. However, our results also suggest that the fraction of stellar mass contained in galaxies that pass the color-selection criteria could be as low as 50% of the total stellar mass in the Universe at z=2. Our simulations suggest that the missing stellar mass is contained in fainter (R>25.5) and intrinsically redder galaxies. Our results do not suggest that hierarchical galaxy formation fails to account for the massive galaxies at z>=1. (abridged)Comment: 35 pages, 11 figures. Submitted to ApJ. Error in AB magnitude calculation corrected. Higher resolution version available at http://cfa-www.harvard.edu/~knagamine/redgal.ps.g

MAA3 (MAGATAMA3) Helicase Gene is Required for Female Gametophyte Development and Pollen Tube Guidance in Arabidopsis thaliana

The female gametophyte plays a central role in the sexual reproduction of angiosperms. We previously isolated the maa3 (magatama3) mutant of Arabidopsis thaliana, defective in development of the female gametophyte, micropylar pollen tube guidance, and preventing the attraction of multiple pollen tubes. We here observed that the nucleolus of polar nuclei is small, and that the fusion of polar nuclei often did not occur at the time of pollination. The MAA3 gene encodes a homolog of yeast Sen1 helicase, required for RNA metabolism. It is suggested that MAA3 may regulate RNA molecules responsible for nucleolar organization and pollen tube guidanc

Polyploidy before and after domestication of crop species

Recent advances in the genomics of polyploid species answer some of the long-standing questions about the role of polyploidy in crop species. Here, we summarize the current literature to reexamine scenarios in which polyploidy played a role both before and after domestication. The prevalence of polyploidy can help to explain environmental robustness in agroecosystems. This review also clarifies the molecular basis of some agriculturally advantageous traits of polyploid crops, including yield increments in polyploid cotton via subfunctionalization, modification of a separated sexuality to selfing in polyploid persimmon via neofunctionalization, and transition to a selfing system via nonfunctionalization combined with epistatic interaction between duplicated S-loci. The rapid progress in genomics and genetics is discussed along with how this will facilitate functional studies of understudied polyploid crop species

Genome-wide quantification of homeolog expression ratio revealed nonstochastic gene regulation in synthetic allopolyploid Arabidopsis

Genome duplication with hybridization, or allopolyploidization, occurs commonly in plants, and is considered to be a strong force for generating new species. However, genome-wide quantification of homeolog expression ratios was technically hindered because of the high homology between homeologous gene pairs. To quantify the homeolog expression ratio using RNA-seq obtained from polyploids, a new method named HomeoRoq was developed, in which the genomic origin of sequencing reads was estimated using mismatches between the read and each parental genome. To verify this method, we first assembled the two diploid parental genomes of Arabidopsis halleri subsp. gemmifera and Arabidopsis lyrata subsp. petraea (Arabidopsis petraea subsp. umbrosa), then generated a synthetic allotetraploid, mimicking the natural allopolyploid Arabidopsis kamchatica. The quantified ratios corresponded well to those obtained by Pyrosequencing. We found that the ratios of homeologs before and after cold stress treatment were highly correlated (r = 0.870). This highlights the presence of nonstochastic polyploid gene regulation despite previous research identifying stochastic variation in expression. Moreover, our new statistical test incorporating overdispersion identified 226 homeologs (1.11% of 20 369 expressed homeologs) with significant ratio changes, many of which were related to stress responses. HomeoRoq would contribute to the study of the genes responsible for polyploid-specific environmental response