Identification of putative domain linkers by a neural network – application to a large sequence database

BACKGROUND: The reliable dissection of large proteins into structural domains represents an important issue for structural genomics/proteomics projects. To provide a practical approach to this issue, we tested the ability of neural network to identify domain linkers from the SWISSPROT database (101602 sequences). RESULTS: Our search detected 3009 putative domain linkers adjacent to or overlapping with domains, as defined by sequence similarity to either Protein Data Bank (PDB) or Conserved Domain Database (CDD) sequences. Among these putative linkers, 75% were "correctly" located within 20 residues of a domain terminus, and the remaining 25% were found in the middle of a domain, and probably represented failed predictions. Moreover, our neural network predicted 5124 putative domain linkers in structurally un-annotated regions without sequence similarity to PDB or CDD sequences, which suggest to the possible existence of novel structural domains. As a comparison, we performed the same analysis by identifying low-complexity regions (LCR), which are known to encode unstructured polypeptide segments, and observed that the fraction of LCRs that correlate with domain termini is similar to that of domain linkers. However, domain linkers and LCRs appeared to identify different types of domain boundary regions, as only 32% of the putative domain linkers overlapped with LCRs. CONCLUSION: Overall, our study indicates that the two methods detect independent and complementary regions, and that the combination of these methods can substantially improve the sensitivity of the domain boundary prediction. This finding should enable the identification of novel structural domains, yielding new targets for large scale protein analyses

Individual Stellar Halos of Massive Galaxies Measured to 100 kpc at 0.3<z<0.50.3<z<0.5 using Hyper Suprime-Cam

Massive galaxies display extended light profiles that can reach several hundreds of kilo parsecs. These stellar halos provide a fossil record of galaxy assembly histories. Using data that is both wide (~100 square degree) and deep (i>28.5 mag/arcsec^2 in i-band), we present a systematic study of the stellar halos of a sample of more than 3000 galaxies at 0.3 < z < 0.5 with $\log M_{\star}/M_{\odot} > 11.4$. Our study is based on high-quality (0.6 arcsec seeing) imaging data from the Hyper Suprime-Cam (HSC) Subaru Strategic Program (SSP), which enables us to individually estimate surface mass density profiles to 100 kpc without stacking. As in previous work, we find that more massive galaxies exhibit more extended outer profiles. When this extended light is not properly accounted for as a result of shallow imaging or inadequate profile modeling, the derived stellar mass function can be significantly underestimated at the highest masses. Across our sample, the ellipticity of outer light profiles increases substantially as we probe larger radii. We show for the first time that these ellipticity gradients steepen dramatically as a function of galaxy mass, but we detect no mass-dependence in outer color gradients. Our results support the two-phase formation scenario for massive galaxies in which outer envelopes are built up at late times from a series of merging events. We provide surface mass surface mass density profiles in a convenient tabulated format to facilitate comparisons with predictions from numerical simulations of galaxy formation.Comment: Submitted to MNRAS; 23 pages, 8 figures, 2 appendix; Data will be made available here: http://massivegalaxies.com/ once the paper is publishe

Effects of Imipramine and Lithium on the Suppression of Cell Proliferation in the Dentate Gyrus of the Hippocampus in Adrenocorticotropic Hormone-treated Rats

We examined the influence of chronic adrenocorticotropic hormone (ACTH) treatment on the number of Ki-67-positive cells in the dentate gyrus of the hippocampus in rats. ACTH treatment for 14 days decreased the number of such cells. The administration of imipramine or lithium alone for 14 days had no effect in saline-treated rats. The effect of ACTH was blocked by the administration of imipramine. Furthermore, the coadministration of imipramine and lithium for 14 days significantly increased the number of Ki-67-positive cells in both the saline and ACTH-treated rats. The coadministration of imipramine and lithium normalized the cell proliferation in the dentate gyrus of the hippocampus in rats treated with ACTH

Subaru Deep Survey V. A Census of Lyman Break Galaxies at z=4 and 5 in the Subaru Deep Fields: Photometric Properties

(abridged) We investigate photometric properties of Lyman Break Galaxies (LBGs) at z=3.5-5.2 based on large samples of 2,600 LBGs detected in deep (i'~27) and wide-field (1,200 arcmin^2) images taken in the Subaru Deep Field (SDF) and the Subaru/XMM Deep Field (SXDF). The selection criteria for the LBG samples are examined with 85 spectroscopically identified objects and by Monte Carlo simulations. We find in the luminosity functions of LBGs (i) that the number density of bright galaxies (M_{1700}<-22; corresponding to SFR_{corr}>100 Msolar yr^{-1}) decreases significantly from z=4 to 5 and (ii) that the faint-end slope of the luminosity function may become steeper towards higher redshifts. We estimate dust extinction of z=4 LBGs with M<M^* from UV slopes, and obtain E(B-V)=0.15+/-0.03 as the mean value. The dust extinction remains constant with apparent luminosity, but increases with intrinsic luminosity. We find no evolution in dust extinction between LBGs at z=3 and 4. We investigate the evolution of UV-luminosity density at 1700A, rho, and find that rho does not significantly change from z=3 to z=5, i.e., rho(z=4)/rho(z=3)=1.0+/-0.2 and rho(z=5)/rho(z=3)=0.8+/-0.4, thus the cosmic star-formation rate (SFR) density remains constant. We find that the stellar mass density estimated from the cosmic SFR is consistent with those derived directly from the stellar mass function at z=0-1, but exceeds those at z~3 by a factor of 3. We find that the ratio of the UV-luminosity density of Ly-a emitters (LAEs) to that of LBGs is ~60% at z=5, and thus about a half of the star formation at z=5 probably occurs in LAEs. We obtain a constraint on the escape fraction of UV-ionizing photons produced by LBGs, f_{esc}>~0.13.Comment: 41 pages, 22 figures, ApJ in press. Paper with high resolution figures is available at http://hikari.astron.s.u-tokyo.ac.jp/~ouchi/work/astroph/SDS_V_VI/SDS_V.pdf (PDF

Gnarled-Trunk Evolutionary Model of Influenza A Virus Hemagglutinin

Human influenza A viruses undergo antigenic changes with gradual accumulation of amino acid substitutions on the hemagglutinin (HA) molecule. A strong antigenic mismatch between vaccine and epidemic strains often requires the replacement of influenza vaccines worldwide. To establish a practical model enabling us to predict the future direction of the influenza virus evolution, relative distances of amino acid sequences among past epidemic strains were analyzed by multidimensional scaling (MDS). We found that human influenza viruses have evolved along a gnarled evolutionary pathway with an approximately constant curvature in the MDS-constructed 3D space. The gnarled pathway indicated that evolution on the trunk favored multiple substitutions at the same amino acid positions on HA. The constant curvature was reasonably explained by assuming that the rate of amino acid substitutions varied from one position to another according to a gamma distribution. Furthermore, we utilized the estimated parameters of the gamma distribution to predict the amino acid substitutions on HA in subsequent years. Retrospective prediction tests for 12 years from 1997 to 2009 showed that 70% of actual amino acid substitutions were correctly predicted, and that 45% of predicted amino acid substitutions have been actually observed. Although it remains unsolved how to predict the exact timing of antigenic changes, the present results suggest that our model may have the potential to recognize emerging epidemic strains