3,131 research outputs found
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
- …