CIPRO 2.5: Ciona intestinalis protein database, a unique integrated repository of large-scale omics data, bioinformatic analyses and curated annotation, with user rating and reviewing functionality

The Ciona intestinalis protein database (CIPRO) is an integrated protein database for the tunicate species C. intestinalis. The database is unique in two respects: first, because of its phylogenetic position, Ciona is suitable model for understanding vertebrate evolution; and second, the database includes original large-scale transcriptomic and proteomic data. Ciona intestinalis has also been a favorite of developmental biologists. Therefore, large amounts of data exist on its development and morphology, along with a recent genome sequence and gene expression data. The CIPRO database is aimed at collecting those published data as well as providing unique information from unpublished experimental data, such as 3D expression profiling, 2D-PAGE and mass spectrometry-based large-scale analyses at various developmental stages, curated annotation data and various bioinformatic data, to facilitate research in diverse areas, including developmental, comparative and evolutionary biology. For medical and evolutionary research, homologs in humans and major model organisms are intentionally included. The current database is based on a recently developed KH model containing 36 034 unique sequences, but for higher usability it covers 89 683 all known and predicted proteins from all gene models for this species. Of these sequences, more than 10 000 proteins have been manually annotated. Furthermore, to establish a community-supported protein database, these annotations are open to evaluation by users through the CIPRO website. CIPRO 2.5 is freely accessible at http://cipro.ibio.jp/2.5

CIPRO 2.5: Ciona intestinalis Protein integrated database with large-scale omics data, bioinformatic analyses and curated annotation, with ability for user rating and comments

CIPRO database is an integrated protein database for a tunicate species Ciona intestinalis that belongs to the Urochordata. Although the CIPRO database deals with proteomic and transcriptomic data of a single species, the animal is considered unique in the evolutionary tree, representing a possible origin of the vertebrates and is a good model for understanding chordate evolution, including that of humans. Furthermore, C. intestinalis has been one of the favorites of developmental biologists; there exists a huge amount of accumulated knowledge on its development and morphology, in addition to the recent genome sequence and gene expression data. The CIPRO database is aimed at not only collecting published data, but also presenting unique information, including the unpublished transcriptomic and proteomic data and human curated annotation, for the use by researchers in broad research fields of biology and bioinformatics

Anomalous Transport Phenomena in Fermi Liquids with Strong Magnetic Fluctuations

In many strongly correlated electron systems, remarkable violation of the relaxation time approximation (RTA) is observed. The most famous example would be high-Tc superconductors (HTSCs), and similar anomalous transport phenomena have been observed in metals near their antiferromagnetic (AF) quantum critical point (QCP). Here, we develop a transport theory involving resistivity and Hall coefficient on the basis of the microscopic Fermi liquid theory, by considering the current vertex correction (CVC). In nearly AF Fermi liquids, the CVC accounts for the significant enhancements in the Hall coefficient, magnetoresistance, thermoelectric power, and Nernst coefficient in nearly AF metals. According to the numerical study, aspects of anomalous transport phenomena in HTSC are explained in a unified way by considering the CVC, without introducing any fitting parameters; this strongly supports the idea that HTSCs are Fermi liquids with strong AF fluctuations. In addition, the striking \omega-dependence of the AC Hall coefficient and the remarkable effects of impurities on the transport coefficients in HTSCs appear to fit naturally into the present theory. The present theory also explains very similar anomalous transport phenomena occurring in CeCoIn5 and CeRhIn5, which is a heavy-fermion system near the AF QCP, and in the organic superconductor \kappa-(BEDT-TTF).Comment: 100 pages, Rep. Prog. Phys. 71, 026501 (2008

Fermi surfaces and orbital polarization in superconducting CeO0.5 F0.5BiS2 revealed by angle-resolved photoemission spectroscopy

We have investigated the electronic structure of BiS2-based CeO0.5F0.5BiS2 superconductor using polarization-dependent angle-resolved photoemission spectroscopy (ARPES), and succeeded in elucidating the orbital characters on the Fermi surfaces. In the rectangular Fermi pockets around the X point, the straight portion parallel to the ky direction is dominated by Bi 6px character. The orbital polarization indicates the underlying quasi-one-dimensional electronic structure of the BiS2 system. Moreover, distortions on tetragonally aligned Bi could give rise to the band Jahn-Teller effect

Hubble Space Telescope/Advanced Camera for Surveys Morphology of Lyα Emitters at Redshift 5.7 in the COSMOS Field

We present detailed morphological properties of Lyα emitters (LAEs) at z ≈ 5.7 in the COSMOS field based on Hubble Space Telescope Advanced Camera for Surveys (ACS) data. The ACS imaging in the F814W filter covered 85 LAEs of the 119 LAEs identified in the full two square degree field, and 47 LAEs of them are detected in the ACS images. Nearly half of them are spatially extended with a size larger than 0.15 arcsec (~0.88 kpc at z = 5.7) and up to 0.4 arcsec (~2.5 kpc at z = 5.7). The others are nearly unresolved compact objects. Two LAEs show double-component structures indicating interaction or merging of building components to form more massive galaxies. By stacking the ACS images of all the detected sources, we obtain a Sersic parameter of n ~ 0.7 with a half-light radius of 0.13 arcsec (0.76 kpc), suggesting that the majority of ACS detected LAEs have not spheroidal-like but disk-like or irregular light profiles. Comparing ACS F814W magnitudes (I _(814)) with Subaru/Suprime-Cam magnitudes in the NB816, i', and z' bands, we find that the ACS imaging in the F814W band mainly probes UV continuum rather than Lyα line emission. UV continuum sizes tend to be larger for LAEs with larger Lyα emission regions as traced by the NB816 imaging. The nondetection of 38 LAEs in the ACS images is likely due to the fact that their surface brightness is too low both in the UV continuum and Lyα emission. Estimating I_(814) for the ACS-undetected LAEs from the z' and NB816 magnitudes, we find that 16 of these are probably LAEs with a size larger than 0.15 arcsec in UV continuum. All these results suggest that our LAE sample contains systematically larger LAEs in UV continuum size than those previously studied at z ~ 6