Divergence and Shannon information in genomes

Shannon information (SI) and its special case, divergence, are defined for a DNA sequence in terms of probabilities of chemical words in the sequence and are computed for a set of complete genomes highly diverse in length and composition. We find the following: SI (but not divergence) is inversely proportional to sequence length for a random sequence but is length-independent for genomes; the genomic SI is always greater and, for shorter words and longer sequences, hundreds to thousands times greater than the SI in a random sequence whose length and composition match those of the genome; genomic SIs appear to have word-length dependent universal values. The universality is inferred to be an evolution footprint of a universal mode for genome growth.Comment: 4 pages, 3 tables, 2 figure

Regulation of shear-induced nuclear translocation of the Nrf2 transcription factor in endothelial cells

<p>Abstract</p> <p>Background</p> <p>Vascular endothelial cells (ECs) constantly experience fluid shear stresses generated by blood flow. Laminar flow is known to produce atheroprotective effects on ECs. Nrf2 is a transcription factor that is essential for the antioxidant response element (ARE)-mediated induction of genes such as heme-oxygenase 1 (HO-1). We previously showed that fluid shear stress increases intracellular reactive oxygen species (ROS) in ECs. Moreover, oxidants are known to stimulate Nrf2. We thus examined the regulation of Nrf2 in cultured human ECs by shear stress.</p> <p>Results</p> <p>Exposure of human umbilical vein endothelial cells (HUVECs) to laminar shear stress (12 dyne/cm²) induced Nrf2 nuclear translocation, which was inhibited by a phosphatidylinositol 3-kinase (PI3K) inhibitor, a protein kinase C (PKC) inhibitor, and an antioxidant agent N-acetyl cysteine (NAC), but not by other protein kinase inhibitors. Therefore, PI3K, PKC, and ROS are involved in the signaling pathway that leads to the shear-induced nuclear translocation of Nrf2. We also found that shear stress increased the ARE-binding activity of Nrf2 and the downstream expression of HO-1.</p> <p>Conclusion</p> <p>Our data suggest that the atheroprotective effect of laminar flow is partially attributed to Nrf2 activation which results in ARE-mediated gene transcriptions, such as HO-1 expression, that are beneficial to the cardiovascular system.</p

Investigation of a minor groove-binding polyamide targeted to E2F1 transcription factor in chronic myeloid leukaemia (CML) cells

No abstract available

Star Formation at 4<z<64 < z < 6 From the Spitzer Large Area Survey with Hyper-Suprime-Cam (SPLASH)

Using the first 50% of data collected for the Spitzer Large Area Survey with Hyper-Suprime-Cam (SPLASH) observations on the 1.8 deg$^2$ Cosmological Evolution Survey (COSMOS) we estimate the masses and star formation rates of 3398 $M_*>10^{10}M_\odot$ star-forming galaxies at $4 < z < 6$ with a substantial population up to $M_* \gtrsim 10^{11.5} M_\odot$. We find that the strong correlation between stellar mass and star formation rate seen at lower redshift (the "main sequence" of star-forming galaxies) extends to $z\sim6$. The observed relation and scatter is consistent with a continued increase in star formation rate at fixed mass in line with extrapolations from lower-redshift observations. It is difficult to explain this continued correlation, especially for the most massive systems, unless the most massive galaxies are forming stars near their Eddington-limited rate from their first collapse. Furthermore, we find no evidence for moderate quenching at higher masses, indicating quenching either has not occurred prior to $z \sim 6$ or else occurs rapidly, so that few galaxies are visible in transition between star-forming and quenched.Comment: ApJL, accepte

Near-Infrared Survey and Photometric Redshifts in the Extended GOODS-North field

We present deep $J$ and $H$-band images in the extended Great Observatories Origins Deep Survey-North (GOODS-N) field covering an area of 0.22 $\rm{deg}^{2}$. The observations were taken using WIRCam on the 3.6-m Canada France Hawaii Telescope (CFHT). Together with the reprocessed $K_{\rm s}$-band image, the $5\sigma$ limiting AB magnitudes (in 2" diameter apertures) are 24.7, 24.2, and 24.4 AB mag in the $J$, $H$, and $K_{\rm s}$ bands, respectively. We also release a multi-band photometry and photometric redshift catalog containing 93598 sources. For non-X-ray sources, we obtained a photometric redshift accuracy $\sigma_{\mathrm{NMAD}}=0.036$ with an outlier fraction $\eta = 7.3\%$. For X-ray sources, which are mainly active galactic nuclei (AGNs), we cross-matched our catalog with the updated 2M-CDFN X-ray catalog from Xue et al. (2016) and found that 658 out of 683 X-ray sources have counterparts. $GALEX$ UV data are included in the photometric redshift computation for the X-ray sources to give $\sigma_{\mathrm{NMAD}} = 0.040$ with $\eta=10.5\%$. Our approach yields more accurate photometric redshift estimates compared to previous works in this field. In particular, by adopting AGN-galaxy hybrid templates, our approach delivers photometric redshifts for the X-ray counterparts with fewer outliers compared to the 3D-HST catalog, which fit these sources with galaxy-only templates

The SPLASH Survey: Quiescent Galaxies Are More Strongly Clustered but Are Not Necessarily Located in High-density Environments

We use the stellar-mass-selected catalog from the Spitzer Large Area Survey with Hyper-Suprime-Cam (SPLASH) in the COSMOS field to study the environments of galaxies via galaxy density and clustering analyses up to z ~ 2.5. The clustering strength of quiescent galaxies exceeds that of star-forming galaxies, implying that quiescent galaxies are preferentially located in more massive halos. When using local density measurement, we find a clear positive quiescent fraction–density relation at z 1.5, the quiescent fraction depends little on the local density, even though clustering shows that quiescent galaxies are in more massive halos. We argue that at high redshift the typical halo size falls below 10^(13)M⊙, where intrinsically the local density measurements are so varied that they do not trace the halo mass. Our results thus suggest that in the high-redshift universe, halo mass may be the key in quenching the star formation in galaxies, rather than the conventionally measured galaxy density

The Effect of Galaxy Interactions on Molecular Gas Properties

© 2018. The American Astronomical Society. All rights reserved.Galaxy interactions are often accompanied by an enhanced star formation rate (SFR). Since molecular gas is essential for star formation, it is vital to establish whether and by how much galaxy interactions affect the molecular gas properties. We investigate the effect of interactions on global molecular gas properties by studying a sample of 58 galaxies in pairs and 154 control galaxies. Molecular gas properties are determined from observations with the JCMT, PMO, and CSO telescopes and supplemented with data from the xCOLD GASS and JINGLE surveys at 12CO(1-0) and 12CO(2-1). The SFR, gas mass (), and gas fraction (f gas) are all enhanced in galaxies in pairs by ∼2.5 times compared to the controls matched in redshift, mass, and effective radius, while the enhancement of star formation efficiency (SFE ≡SFR/) is less than a factor of 2. We also find that the enhancements in SFR, and f gas, increase with decreasing pair separation and are larger in systems with smaller stellar mass ratio. Conversely, the SFE is only enhanced in close pairs (separation <20 kpc) and equal-mass systems; therefore, most galaxies in pairs lie in the same parameter space on the SFR- plane as controls. This is the first time that the dependence of molecular gas properties on merger configurations is probed statistically with a relatively large sample and a carefully selected control sample for individual galaxies. We conclude that galaxy interactions do modify the molecular gas properties, although the strength of the effect is dependent on merger configuration.Peer reviewedFinal Accepted Versio

The ALMaQUEST Survey XII: Dense Molecular Gas as traced by HCN and HCO+^{+} in Green Valley Galaxies

We present ALMA observations of two dense gas tracers, HCN(1-0) and HCO$^{+}$(1-0), for three galaxies in the green valley and two galaxies on the star-forming main sequence with comparable molecular gas fractions as traced by the CO(1-0) emissions, selected from the ALMaQUEST survey. We investigate whether the deficit of molecular gas star formation efficiency (SFE$_{\rm mol}$) that leads to the low specific star formation rate in these green valley galaxies is due to a lack of dense gas (characterized by the dense gas fraction $f_{\rm dense}$) or the low star formation efficiency of dense gas (SFE$_{\rm dense}$). We find that SFE$_{\rm mol}$ as traced by the CO emissions, when considering both star-forming and retired spaxels together, is tightly correlated with SFE$_{\rm dense}$ and depends only weakly on $f_{\rm dense}$. The specific star formation rate (sSFR) on kpc scales is primarily driven by SFE$_{\rm mol}$ and SFE$_{\rm dense}$, followed by the dependence on $f_{\rm mol}$, and is least correlated with $f_{\rm dense}$ or the dense-to-stellar mass ratio ($R_{\rm dense}$). When compared with other works in the literature, we find that our green valley sample shows lower global SFE$_{\rm mol}$ as well as lower SFE$_{\rm dense}$ while exhibiting similar dense gas fractions when compared to star-forming and starburst galaxies. We conclude that the star formation of the 3 green valley galaxies with a normal abundance of molecular gas is suppressed mainly due to the reduced SFE$_{\rm dense}$ rather than the lack of dense gas.Comment: 20 pages, 13 figures, ApJ accepte