GenomeFingerprinter and universal genome fingerprint analysis for systematic comparative genomics

How to compare whole genome sequences at large scale has not been achieved via conventional methods based on pair-wisely base-to-base comparison; nevertheless, no attention was paid to handle in-one-sitting a number of genomes crossing genetic category (chromosome, plasmid, and phage) with farther divergences (much less or no homologous) over large size ranges (from Kbp to Mbp). We created a new method, GenomeFingerprinter, to unambiguously produce three-dimensional coordinates from a sequence, followed by one three-dimensional plot and six two-dimensional trajectory projections to illustrate whole genome fingerprints. We further developed a set of concepts and tools and thereby established a new method, universal genome fingerprint analysis. We demonstrated their applications through case studies on over a hundred of genome sequences. Particularly, we defined the total genetic component configuration (TGCC) (i.e., chromosome, plasmid, and phage) for describing a strain as a system, and the universal genome fingerprint map (UGFM) of TGCC for differentiating a strain as a universal system, as well as the systematic comparative genomics (SCG) for comparing in-one-sitting a number of genomes crossing genetic category in diverse strains. By using UGFM, UGFM-TGCC, and UGFM-TGCC-SCG, we compared a number of genome sequences with farther divergences (chromosome, plasmid, and phage; bacterium, archaeal bacterium, and virus) over large size ranges (6Kbp~5Mbp), giving new insights into critical problematic issues in microbial genomics in the post-genomic era. This paper provided a new method for rapidly computing, geometrically visualizing, and intuitively comparing genome sequences at fingerprint level, and hence established a new method of universal genome fingerprint analysis for systematic comparative genomics.Comment: 63 pages, 15 figures, 5 table

A method for the microlensed flux variance of QSOs

A fast and practical method is described for calculating the microlensed flux variance of an arbitrary source by uncorrelated stars. The required inputs are the mean convergence and shear due to the smoothed potential of the lensing galaxy, the stellar mass function, and the absolute square of the Fourier transform of the surface brightness in the source plane. The mathematical approach follows previous authors but has been generalized, streamlined, and implemented in publicly available code. Examples of its application are given for Dexter and Agol's inhomogeneous-disk models as well as the usual gaussian sources. Since the quantity calculated is a second moment of the magnification, it is only logarithmically sensitive to the sizes of very compact sources. However, for the inferred sizes of actual QSOs, it has some discriminatory power and may lend itself to simple statistical tests. At the very least, it should be useful for testing the convergence of microlensing simulations.Comment: 10 pages, 6 figure

Negative Regulators of Colonic Peripheral Regulatory T Cell Development

Peripheral Treg cells (pTreg cells) maintain immune homeostasis at mucosal interfaces, where they can develop upon activation of naïve CD4+ T cells by bacteria antigen. However, the cellular and molecular requirements that govern their differentiation in inflamed and homeostatic contexts require further elucidation. To circumvent uncertainties in existing methods of distinguishing pTreg cells from thymic Treg cells (tTreg cells), we analyzed monoclonal cell populations of CT2 and CT6 transgenic (Tg) cells that develop into pTreg cells in response to different species of endogenously presented Helicobacter antigen. In our comprehensive assessment of multiple intestinal inflammatory models, including infections and physical injury, we find that pTreg development against Helicobacter antigen is largely preserved. In one model, DSS coupled with a high-fat diet (HFD), we observed a TCR-specific defect in Treg cell development with CT6, but not CT2 Tg cells, adopting effector fates. The concurrent development of effector and pTreg cells during inflammation implicate that the cellular and molecular signals that govern pTreg cells and effector T cell development are highly sequestered, protecting the host from the aberrant generation of effector T cells against tolerogenic antigens. Transcriptional regulators regulate pTreg celll development by promoting FoxP3, antagonizing alternative effector fates, and stabilizing FoxP3 expression. Here, we capture transcriptional snapshots of activated monoclonal CT6 Tg cells pre and post FoxP3 expression to identify relevant transcriptional regulators during different stages of development. Early developing pTreg cells exhibit a burst of transcriptional activity that is not maintained in later stages. Furthermore, early developing pTreg cells transiently express Eomesodermin (Eomes) which restrains FoxP3 expression in activated, undivided cells and cells that have undergone one division. Eomes expression correlated with the expression of Nr4a family of transcription factors, which enhance FoxP3 expression. Thus, early developing pTreg cells concurrently express transcriptional regulators that promote or repress Treg cell development early in development

Sizes and Kinematics of Extended Narrow-Line Regions in Luminous Obscured AGN Selected by Broadband Images

To study the impact of active galactic nuclei (AGN) feedback on the galactic ISM, we present Magellan long-slit spectroscopy of 12 luminous nearby type 2 AGN (L_bol~10^{45.0-46.5} erg/s, z~0.1). These objects are selected from a parent sample of spectroscopically identified AGN to have high [OIII]{\lambda}5007 and WISE mid-IR luminosities and extended emission in the SDSS r-band images, suggesting the presence of extended [OIII]{\lambda}5007 emission. We find spatially resolved [OIII] emission (2-35 kpc from the nucleus) in 8 out of 12 of these objects. Combined with samples of higher luminosity type 2 AGN, we confirm that the size of the narrow-line region (R_NLR) scales with the mid-IR luminosity until the relation flattens at ~10 kpc. Nine out of 12 objects in our sample have regions with broad [OIII] linewidths (w_80>600 km/s), indicating outflows. We define these regions as the kinematically-disturbed region (KDR). The size of the KDR (R_KDR) is typically smaller than R_NLR by few kpc but also correlates strongly with the AGN mid-IR luminosity. Given the unknown density in the gas, we derive a wide range in the energy efficiency {\eta}=dot{E}/L_bol=0.01%-30%. We find no evidence for an AGN luminosity threshold below which outflows are not launched. To explain the sizes, velocity profiles, and high occurrence rates of the outflows in the most luminous AGN, we propose a scenario in which energy-conserving outflows are driven by AGN episodes with ~10^8-year durations. Within each episode the AGN flickers on shorter timescales, with a cadence of ~10^6 year active phases separated by ~10^7 years.Comment: 32 pages, 21 figures, ApJ in revie

ALMA Observations of a Candidate Molecular Outflow in an Obscured Quasar

We present Atacama Large Millimeter/Submillimeter Array (ALMA) CO (1-0) and CO (3-2) observations of SDSS J135646.10+102609.0, an obscured quasar and ultra-luminous infrared galaxy (ULIRG) with two merging nuclei and a known 20-kpc-scale ionized outflow. The total molecular gas mass is M_{mol} ~ 9^{+19}_{-6} x 10^8 Msun, mostly distributed in a compact rotating disk at the primary nucleus (M_{mol} ~ 3 x 10^8 Msun) and an extended tidal arm (M_{mol} ~ 5 x 10^8 Msun). The tidal arm is one of the most massive molecular tidal features known; we suggest that it is due to the lower chance of shock dissociation in this elliptical/disk galaxy merger. In the spatially resolved CO (3-2) data, we find a compact (r ~ 0.3 kpc) high velocity (v ~ 500 km/s) red-shifted feature in addition to the rotation at the N nucleus. We propose a molecular outflow as the most likely explanation for the high velocity gas. The outflowing mass of M_{mol} ~ 7 x 10^7 Msun and the short dynamical time of t_{dyn} ~ 0.6 Myr yield a very high outflow rate of \dot{M}_{mol} ~ 350 Msun/yr and can deplete the gas in a million years. We find a low star formation rate (< 16 Msun/yr from the molecular content and < 21 Msun/yr from the far-infrared spectral energy distribution decomposition) that is inadequate to supply the kinetic luminosity of the outflow (\dot{E} ~ 3 x 10^43 erg/s). Therefore, the active galactic nucleus, with a bolometric luminosity of 10^46 erg/s, likely powers the outflow. The momentum boost rate of the outflow (\dot{p}/(Lbol/c) ~ 3) is lower than typical molecular outflows associated with AGN, which may be related to its compactness. The molecular and ionized outflows are likely two distinct bursts induced by episodic AGN activity that varies on a time scale of 10^7 yr.Comment: 16 pages, 7 figures, ApJ accepte