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 $\Omega_{\rm GW}(f) \propto f^3$ 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 ($k\eta_* \ll 1$), enters the horizon, for $k\eta \gtrsim 1$, 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

Designing a web-application to support home-based care of childhood CKD stages 3-5: Qualitative study of family and professional preferences

Background: There is a lack of online, evidence-based information and resources to support home-based care of childhood CKD stages 3-5. Methods. Qualitative interviews were undertaken with parents, patients and professionals to explore their views on content of the proposed online parent information and support (OPIS) web-application. Data were analysed using Framework Analysis, guided by the concept of Self-efficacy. Results: 32 parents, 26 patients and 12 professionals were interviewed. All groups wanted an application that explains, demonstrates, and enables parental clinical care-giving, with condition-specific, continously available, reliable, accessible material and a closed communication system to enable contact between families living with CKD. Professionals advocated a regularly updated application to empower parents to make informed health-care decisions. To address these requirements, key web-application components were defined as: (i) Clinical care-giving support (information on treatment regimens, video-learning tools, condition-specific cartoons/puzzles, and a question and answer area) and (ii) Psychosocial support for care-giving (social-networking, case studies, managing stress, and enhancing families' health-care experiences). Conclusions: Developing a web-application that meets parents' information and support needs will maximise its utility, thereby augmenting parents' self-efficacy for CKD caregiving, and optimising outcomes. Self-efficacy theory provides a schema for how parents' self-efficacy beliefs about management of their child's CKD could potentially be promoted by OPIS. © 2014 Swallow et al.; licensee BioMed Central Ltd

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