2,046 research outputs found
Coordinated evolution of co-expressed gene clusters in the Drosophila transcriptome
Abstract Background Co-expression of genes that physically cluster together is a common characteristic of eukaryotic transcriptomes. This organization of transcriptomes suggests that coordinated evolution of gene expression for clustered genes may also be common. Clusters where expression evolution of each gene is not independent of their neighbors are important units for understanding transcriptome evolution. Results We used a common microarray platform to measure gene expression in seven closely related species in the Drosophila melanogaster subgroup, accounting for confounding effects of sequence divergence. To summarize the correlation structure among genes in a chromosomal region, we analyzed the fraction of variation along the first principal component of the correlation matrix. We analyzed the correlation for blocks of consecutive genes to assess patterns of correlation that may be manifest at different scales of coordinated expression. We find that expression of physically clustered genes does evolve in a coordinated manner in many locations throughout the genome. Our analysis shows that relatively few of these clusters are near heterochromatin regions and that these clusters tend to be over-dispersed relative to the rest of the genome. This suggests that these clusters are not the byproduct of local gene clustering. We also analyzed the pattern of co-expression among neighboring genes within a single Drosophila species: D. simulans. For the co-expression clusters identified within this species, we find an under-representation of genes displaying a signature of recurrent adaptive amino acid evolution consistent with previous findings. However, clusters displaying co-evolution of expression among species are enriched for adaptively evolving genes. This finding points to a tie between adaptive sequence evolution and evolution of the transcriptome. Conclusion Our results demonstrate that co-evolution of expression in gene clusters is relatively common among species in the D. melanogaster subgroup. We consider the possibility that local regulation of expression in gene clusters may drive the connection between adaptive sequence and coordinated gene expression evolution
Hubble Space Telescope NICMOS Imaging of W3 IRS 5: A Trapezium in the Making?
We present Hubble Space Telescope NICMOS imaging of W3 IRS 5, a binary
high-mass protostar. In addition to the two protostars, NICMOS images taken in
the F222M and F160W filters show three new 2.22 micron sources with very red
colors; these sources fall within a region 5600 AU in diameter, and are
coincident with a 100 solar mass dense molecular clump. Two additional point
sources are found within 0.4'' (800 AU) of one of the high-mass protostars;
these may be stellar companions or unresolved emission knots from an outflow.
We propose that these sources constitute a nascent Trapezium system in the
center of the W3 IRS 5 cluster containing as many as five proto OB stars. This
would be the first identification of a Trapezium still deeply embedded in its
natal gas.Comment: accepted to ApJ letter
Gravitational waves from self-ordering scalar fields
Gravitational waves were copiously produced in the early Universe whenever
the processes taking place were sufficiently violent. The spectra of several of
these gravitational wave backgrounds on subhorizon scales have been extensively
studied in the literature. In this paper we analyze the shape and amplitude of
the gravitational wave spectrum on scales which are superhorizon at the time of
production. Such gravitational waves are expected from the self ordering of
randomly oriented scalar fields which can be present during a thermal phase
transition or during preheating after hybrid inflation. We find that, if the
gravitational wave source acts only during a small fraction of the Hubble time,
the gravitational wave spectrum at frequencies lower than the expansion rate at
the time of production behaves as with an
amplitude much too small to be observable by gravitational wave observatories
like LIGO, LISA or BBO. On the other hand, if the source is active for a much
longer time, until a given mode which is initially superhorizon (), enters the horizon, for , we find that the gravitational
wave energy density is frequency independent, i.e. scale invariant. Moreover,
its amplitude for a GUT scale scenario turns out to be within the range and
sensitivity of BBO and marginally detectable by LIGO and LISA. This new
gravitational wave background can compete with the one generated during
inflation, and distinguishing both may require extra information.Comment: 21 pages, 2 figures, added discussion about numerical integration and
a new figure to illustrate the scale-invariance of the GW power spectrum,
conclusions unchange
The Hubble Ultra Deep Field
This paper presents the Hubble Ultra Deep Field (HUDF), a one million second
exposure of an 11 square minute-of-arc region in the southern sky with the
Hubble Space Telescope. The exposure time was divided among four filters, F435W
(B435), F606W (V606), F775W (i775), and F850LP (z850), to give approximately
uniform limiting magnitudes mAB~29 for point sources. The image contains at
least 10,000 objects presented here as a catalog. Few if any galaxies at
redshifts greater than ~4 resemble present day spiral or elliptical galaxies.
Using the Lyman break dropout method, we find 504 B-dropouts, 204 V-dropouts,
and 54 i-dropouts. Using these samples that are at different redshifts but
derived from the same data, we find no evidence for a change in the
characteristic luminosity of galaxies but some evidence for a decrease in their
number densities between redshifts of 4 and 7. The ultraviolet luminosity
density of these samples is dominated by galaxies fainter than the
characteristic luminosity, and the HUDF reveals considerably more luminosity
than shallower surveys. The apparent ultraviolet luminosity density of galaxies
appears to decrease from redshifts of a few to redshifts greater than 6. The
highest redshift samples show that star formation was already vigorous at the
earliest epochs that galaxies have been observed, less than one billion years
after the Big Bang.Comment: 44 pages, 18 figures, to appear in the Astronomical Journal October
200
Mitigating susceptibility-induced distortions in high-resolution 3DEPI fMRI at 7T
Geometric distortion is a major limiting factor for spatial specificity in high-resolution fMRI using EPI readouts and is exacerbated at higher field strengths due to increased B0 field inhomogeneity. Prominent correction schemes are based on B0 field-mapping or acquiring reverse phase-encoded (reversed-PE) data. However, to date, comparisons of these techniques in the context of fMRI have only been performed on 2DEPI data, either at lower field or lower resolution. In this study, we investigate distortion compensation in the context of sub-millimetre 3DEPI data at 7T. B0 field-mapping and reversed-PE distortion correction techniques were applied to both partial coverage BOLD-weighted and whole brain MT-weighted 3DEPI data with matched distortion. Qualitative assessment showed overall improvement in cortical alignment for both correction techniques in both 3DEPI fMRI and whole-brain MT-3DEPI datasets. The distortion-corrected MT-3DEPI images were quantitatively evaluated by comparing cortical alignment with an anatomical reference using dice coefficient (DC) and correlation ratio (CR) measures. These showed that B0 field-mapping and reversed-PE methods both improved correspondence between the MT-3DEPI and anatomical data, with more substantial improvements consistently obtained using the reversed-PE approach. Regional analyses demonstrated that the largest benefit of distortion correction, and in particular of the reversed-PE approach, occurred in frontal and temporal regions where susceptibility-induced distortions are known to be greatest, but had not led to complete signal dropout. In conclusion, distortion correction based on reversed-PE data has shown the greater capacity for achieving faithful alignment with anatomical data in the context of high-resolution fMRI at 7T using 3DEPI
The Digital Life of Walkable Streets
Walkability has many health, environmental, and economic benefits. That is
why web and mobile services have been offering ways of computing walkability
scores of individual street segments. Those scores are generally computed from
survey data and manual counting (of even trees). However, that is costly, owing
to the high time, effort, and financial costs. To partly automate the
computation of those scores, we explore the possibility of using the social
media data of Flickr and Foursquare to automatically identify safe and walkable
streets. We find that unsafe streets tend to be photographed during the day,
while walkable streets are tagged with walkability-related keywords. These
results open up practical opportunities (for, e.g., room booking services,
urban route recommenders, and real-estate sites) and have theoretical
implications for researchers who might resort to the use social media data to
tackle previously unanswered questions in the area of walkability.Comment: 10 pages, 7 figures, Proceedings of International World Wide Web
Conference (WWW 2015
Morphologies of High Redshift, Dust Obscured Galaxies from Keck Laser Guide Star Adaptive Optics
Spitzer MIPS images in the Bootes field of the NOAO Deep Wide-Field Survey
have revealed a class of extremely dust obscured galaxy (DOG) at z~2. The DOGs
are defined by very red optical to mid-IR (observed-frame) colors, R - [24 um]
> 14 mag, i.e. f_v (24 um) / f_v (R) > 1000. They are Ultra-Luminous Infrared
Galaxies with L_8-1000 um > 10^12 -10^14 L_sun, but typically have very faint
optical (rest-frame UV) fluxes. We imaged three DOGs with the Keck Laser Guide
Star Adaptive Optics (LGSAO) system, obtaining ~0.06'' resolution in the
K'-band. One system was dominated by a point source, while the other two were
clearly resolved. Of the resolved sources, one can be modeled as a exponential
disk system. The other is consistent with a de Vaucouleurs profile typical of
elliptical galaxies. The non-parametric measures of their concentration and
asymmetry, show the DOGs to be both compact and smooth. The AO images rule out
double nuclei with separations of greater than 0.1'' (< 1 kpc at z=2), making
it unlikely that ongoing major mergers (mass ratios of 1/3 and greater) are
triggering the high IR luminosities. By contrast, high resolution images of z~2
SCUBA sources tend to show multiple components and a higher degree of
asymmetry. We compare near-IR morphologies of the DOGs with a set of z=1
luminous infrared galaxies (LIRGs; L_IR ~ 10^11 L_sun) imaged with Keck LGSAO
by the Center for Adaptive Optics Treasury Survey. The DOGs in our sample have
significantly smaller effective radii, ~1/4 the size of the z=1 LIRGs, and tend
towards higher concentrations. The small sizes and high concentrations may help
explain the globally obscured rest-frame blue-to-UV emission of the DOGs.Comment: 9 pages, 7 figures, 2 tables, accepted for publication in the
Astronomical Journa
Notes from the Field: 10 Short Lessons on One-Shot Instruction
Librarians teach. It might not be what they planned to do when they entered the profession, or it may have been a secret hope all along. Either way, librarians teach, and one teaching scenario remains quintessential: the one-shot library instruction session. In recognition of the centrality of the one-shot, this article shares several authors\u27 notes from the field. The notes provide a range of strategies for developing pedagogically sound one-shot library instruction sessions, grouped loosely into three categories: planning, delivery, and integration. The authors offer these insights in their own words in hopes that other teaching librarians may benefit from their experiences
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