A survey of extended radio jets with Chandra and HST

We present the results from an X-ray and optical survey of a sample of 17 radio jets in AGN performed with Chandra and HST. The sample was selected from the radio and is unbiased toward detection at shorter wavelengths, but preferentially it includes beamed sources. We find that X-ray emission is common on kpc-scales, with over half radio jets exhibiting at least one X-ray knot on the Chandra images. The distributions of the radio-to-X-ray and radio-to-optical spectral indices for the detected jets are similar to the limits for the non-detections,suggesting all bright radio jets have X-ray counterparts which will be visible in longer observations. Comparing the radio and X-ray morphologies shows that the majority of the X-ray jets have structures that closely map the radio. Analysis of the SED of the jet knots suggest the knots in which the X-ray and radio morphologies track each other produce X-rays by IC scattering of the Cosmic Microwave Background. The remaining knots produce X-rays by the synchrotron process. Spectral changes are detected along the jets, with the ratio of the X-ray-to-radio and optical-to-radio flux densities decreasing from the inner to the outer regions. This suggests the presence of an additional contribution to the X-ray flux in the jet's inner part, either from synchrotron or IC of the stellar light. Alternatively, in a pure IC/CMB scenario, the plasma decelerates as it flows from the inner to the outer regions. Finally, the X-ray spectral indices for the brightest knots are flat, indicating that the bulk of the luminosity of the jets is emitted at GeV energies, and raising the interesting possibility of future detections with GLAST.Comment: 26 pages, 6 ps figures, 6 jpeg figures (1 replaced); accepted for publication in Ap

Quasars and the Big Blue Bump

We investigate the ultraviolet-to-optical spectral energy distributions (SEDs) of 17 active galactic nuclei (AGNs) using quasi-simultaneous spectrophotometry spanning 900-9000 Angstrom (rest frame). We employ data from the Far Ultraviolet Spectroscopic Explorer (FUSE), the Hubble Space Telescope (HST), and the 2.1-meter telescope at Kitt Peak National Observatory (KPNO). Taking advantage of the short-wavelength coverage, we are able to study the so-called "big blue bump," the region where the energy output peaks, in detail. Most objects exhibit a spectral break around 1100 Angstrom. Although this result is formally associated with large uncertainty for some objects, there is strong evidence in the data that the far-ultraviolet spectral region is below the extrapolation of the near-ultraviolet-optical slope, indicating a spectral break around 1100 Angstrom. We compare the behavior of our sample to those of non-LTE thin-disk models covering a range in black-hole mass, Eddington ratio, disk inclination, and other parameters. The distribution of ultraviolet-optical spectral indices redward of the break, and far-ultraviolet indices shortward of the break, are in rough agreement with the models. However, we do not see a correlation between the far-ultraviolet spectral index and the black hole mass, as seen in some accretion disk models. We argue that the observed spectral break is intrinsic to AGNs, although intrinsic reddening as well as Comptonization can strongly affect the far-ultraviolet spectral index. We make our data available online in digital format.Comment: 32 pages (10pt), 12 figures. Accepted for publication in Ap

Pairing of Competitive and Topologically Distinct Regulatory Modules Enhances Patterned Gene Expression

Biological networks are inherently modular, yet little is known about how modules are assembled to enable coordinated and complex functions. We used RNAi and time series, whole-genome microarray analyses to systematically perturb and characterize components of a Caenorhabditis elegans lineage-specific transcriptional regulatory network. These data are supported by selected reporter gene analyses and comprehensive yeast one-hybrid and promoter sequence analyses. Based on these results, we define and characterize two modules composed of muscle- and epidermal-specifying transcription factors that function together within a single cell lineage to robustly specify multiple cell types. The expression of these two modules, although positively regulated by a common factor, is reliably segregated among daughter cells. Our analyses indicate that these modules repress each other, and we propose that this cross-inhibition coupled with their relative time of induction function to enhance the initial asymmetry in their expression patterns, thus leading to the observed invariant gene expression patterns and cell lineage. The coupling of asynchronous and topologically distinct modules may be a general principle of module assembly that functions to potentiate genetic switches.Molecular and Cellular Biolog

A primate model of severe malarial anaemia: a comparative pathogenesis study.

Severe malarial anaemia (SMA) is the most common life-threatening complication of Plasmodium falciparum infection in African children. SMA is characterised by haemolysis and inadequate erythropoiesis, and is associated with dysregulated inflammatory responses and reduced complement regulatory protein levels (including CD35). However, a deeper mechanistic understanding of the pathogenesis requires improved animal models. In this comparative study of two closely related macaque species, we interrogated potential causal factors for their differential and temporal relationships to onset of SMA. We found that rhesus macaques inoculated with blood-stage Plasmodium coatneyi developed SMA within 2 weeks, with no other severe outcomes, whereas infected cynomolgus macaques experienced only mild/ moderate anaemia. The abrupt drop in haematocrit in rhesus was accompanied by consumption of haptoglobin (haemolysis) and poor reticulocyte production. Rhesus developed a greater inflammatory response than cynomolgus macaques, and had lower baseline levels of CD35 on red blood cells (RBCs) leading to a significant reduction in the proportion of CD35+ RBCs during infection. Overall, severe anaemia in rhesus macaques infected with P. coatneyi has similar features to SMA in children. Our comparisons are consistent with an association of low baseline CD35 levels on RBCs and of early inflammatory responses with the pathogenesis of SMA

Genetic diversity in the modern horse illustrated from genome-wide SNP data

Horses were domesticated from the Eurasian steppes 5,000-6,000 years ago. Since then, the use of horses for transportation, warfare, and agriculture, as well as selection for desired traits and fitness, has resulted in diverse populations distributed across the world, many of which have become or are in the process of becoming formally organized into closed, breeding populations (breeds). This report describes the use of a genome-wide set of autosomal SNPs and 814 horses from 36 breeds to provide the first detailed description of equine breed diversity. F(ST) calculations, parsimony, and distance analysis demonstrated relationships among the breeds that largely reflect geographic origins and known breed histories. Low levels of population divergence were observed between breeds that are relatively early on in the process of breed development, and between those with high levels of within-breed diversity, whether due to large population size, ongoing outcrossing, or large within-breed phenotypic diversity. Populations with low within-breed diversity included those which have experienced population bottlenecks, have been under intense selective pressure, or are closed populations with long breed histories. These results provide new insights into the relationships among and the diversity within breeds of horses. In addition these results will facilitate future genome-wide association studies and investigations into genomic targets of selection

Genetic Diversity in the Modern Horse Illustrated from Genome-Wide SNP Data

Horses were domesticated from the Eurasian steppes 5,000–6,000 years ago. Since then, the use of horses for transportation, warfare, and agriculture, as well as selection for desired traits and fitness, has resulted in diverse populations distributed across the world, many of which have become or are in the process of becoming formally organized into closed, breeding populations (breeds). This report describes the use of a genome-wide set of autosomal SNPs and 814 horses from 36 breeds to provide the first detailed description of equine breed diversity. FST calculations, parsimony, and distance analysis demonstrated relationships among the breeds that largely reflect geographic origins and known breed histories. Low levels of population divergence were observed between breeds that are relatively early on in the process of breed development, and between those with high levels of within-breed diversity, whether due to large population size, ongoing outcrossing, or large within-breed phenotypic diversity. Populations with low within-breed diversity included those which have experienced population bottlenecks, have been under intense selective pressure, or are closed populations with long breed histories. These results provide new insights into the relationships among and the diversity within breeds of horses. In addition these results will facilitate future genome-wide association studies and investigations into genomic targets of selection

Standardised Data on Initiatives – STARDIT: Beta Version

There is currently no standardised way to share information across disciplines about initiatives, including felds such as health, environment, basic science, manufacturing, media and international development. All problems, including complex global problems such as air pollution and pandemics require reliable data sharing between disciplines in order to respond efectively. Current reporting methods also lack information about the ways in which diferent people and organisations are involved in initiatives, making it difcult to collate and appraise data about the most efective ways to involve diferent people. The objective of STARDIT (Standardised Data on Initiatives) is to address current limitations and inconsistencies in sharing data about initiatives. The STARDIT system features standardised data reporting about initiatives, including who has been involved, what tasks they did, and any impacts observed. STARDIT was created to help everyone in the world fnd and understand information about collective human actions, which are referred to as ‘initiatives’. STARDIT enables multiple categories of data to be reported in a standardised way across disciplines, facilitating appraisal of initiatives and aiding synthesis of evidence for the most effective ways for people to be involved in initiatives

Genome evolution in the allotetraploid frog Xenopus laevis

To explore the origins and consequences of tetraploidy in the African clawed frog, we sequenced the Xenopus laevis genome and compared it to the related diploid X. tropicalis genome. We characterize the allotetraploid origin of X. laevis by partitioning its genome into two homoeologous subgenomes, marked by distinct families of ???fossil??? transposable elements. On the basis of the activity of these elements and the age of hundreds of unitary pseudogenes, we estimate that the two diploid progenitor species diverged around 34 million years ago (Ma) and combined to form an allotetraploid around 17-18 Ma. More than 56% of all genes were retained in two homoeologous copies. Protein function, gene expression, and the amount of conserved flanking sequence all correlate with retention rates. The subgenomes have evolved asymmetrically, with one chromosome set more often preserving the ancestral state and the other experiencing more gene loss, deletion, rearrangement, and reduced gene expression.ope