An evolutionary perspective on the kinome of malaria parasites

Malaria parasites belong to an ancient lineage that diverged very early from the main branch of eukaryotes. The approximately 90-member plasmodial kinome includes a majority of eukaryotic protein kinases that clearly cluster within the AGC, CMGC, TKL, CaMK and CK1 groups found in yeast, plants and mammals, testifying to the ancient ancestry of these families. However, several hundred millions years of independent evolution, and the specific pressures brought about by first a photosynthetic and then a parasitic lifestyle, led to the emergence of unique features in the plasmodial kinome. These include taxon-restricted kinase families, and unique peculiarities of individual enzymes even when they have homologues in other eukaryotes. Here, we merge essential aspects of all three malaria-related communications that were presented at the Evolution of Protein Phosphorylation meeting, and propose an integrated discussion of the specific features of the parasite's kinome and phosphoproteome

On the nature of the deeply embedded protostar OMC-2 FIR 4

We use mid-infrared to submillimeter data from the Spitzer, Herschel, and APEX telescopes to study the bright sub-mm source OMC-2 FIR 4. We find a point source at 8, 24, and 70 $\mu$m, and a compact, but extended source at 160, 350, and 870 $\mu$m. The peak of the emission from 8 to 70 $\mu$m, attributed to the protostar associated with FIR 4, is displaced relative to the peak of the extended emission; the latter represents the large molecular core the protostar is embedded within. We determine that the protostar has a bolometric luminosity of 37 Lsun, although including more extended emission surrounding the point source raises this value to 86 Lsun. Radiative transfer models of the protostellar system fit the observed SED well and yield a total luminosity of most likely less than 100 Lsun. Our models suggest that the bolometric luminosity of the protostar could be just 12-14 Lsun, while the luminosity of the colder (~ 20 K) extended core could be around 100 Lsun, with a mass of about 27 Msun. Our derived luminosities for the protostar OMC-2 FIR 4 are in direct contradiction with previous claims of a total luminosity of 1000 Lsun (Crimier et al 2009). Furthermore, we find evidence from far-infrared molecular spectra (Kama et al. 2013, Manoj et al. 2013) and 3.6 cm emission (Reipurth et al 1999) that FIR 4 drives an outflow. The final stellar mass the protostar will ultimately achieve is uncertain due to its association with the large reservoir of mass found in the cold core.Comment: Accpeted by ApJ, 17 pages, 11 figure

Predicted Colors and Flux Densities of Protostars in the Herschel PACS and SPIRE Filters

Upcoming surveys with the Herschel Space Observatory will yield far-IR photometry of large samples of young stellar objects, which will require careful interpretation. We investigate the color and luminosity diagnostics based on Herschel broad-band filters to identify and discern the properties of low-mass protostars. We compute a grid of 2,016 protostars in various physical congurations, present the expected flux densities and flux density ratios for this grid of protostars, and compare Herschel observations of three protostars to the model results. These provide useful constraints on the range of colors and fluxes of protostar in the Herschel filters. We find that Herschel data alone is likely a useful diagnostic of the envelope properties of young starsComment: Part of HOPS KP papers to the Herschel special A&A issu

Symplectic No-core Shell-model Approach to Intermediate-mass Nuclei

We present a microscopic description of nuclei in an intermediate-mass region, including the proximity to the proton drip line, based on a no-core shell model with a schematic many-nucleon long-range interaction with no parameter adjustments. The outcome confirms the essential role played by the symplectic symmetry to inform the interaction and the winnowing of shell-model spaces. We show that it is imperative that model spaces be expanded well beyond the current limits up through fifteen major shells to accommodate particle excitations that appear critical to highly-deformed spatial structures and the convergence of associated observables.Comment: 9 pages, 8 figure

A spatial theory for emergent multiple predator-prey interactions in food webs

Predator-prey interaction is inherently spatial because animals move through landscapes to search for and consume food resources and to avoid being consumed by other species. The spatial nature of species interactions necessitates integrating spatial processes into food web theory and evaluating how predators combine to impact their prey. Here, we present a spatial modeling approach that examines emergent multiple predator effects on prey within landscapes. The modeling is inspired by the habitat domain concept derived from empirical synthesis of spatial movement and interactions studies. Because these principles are motivated by synthesis of short-term experiments, it remains uncertain whether spatial contingency principles hold in dynamical systems. We address this uncertainty by formulating dynamical systems models, guided by core habitat domain principles, to examine long-term multiple predator-prey spatial dynamics. To describe habitat domains we use classical niche concepts describing resource utilization distributions, and assume species interactions emerge from the degree of overlap between species. The analytical results generally align with those from empirical synthesis and present a theoretical framework capable of demonstrating multiple predator effects that does not depend on the small spatial or temporal scales typical of mesocosm experiments, and help bridge between empirical experiments and long-term dynamics in natural systems

Probing 5f-state configurations in URu2Si2 with U L3-edge resonant x-ray emission spectroscopy

Resonant x-ray emission spectroscopy (RXES) was employed at the U L3 absorption edge and the La1 emission line to explore the 5f occupancy, nf, and the degree of 5f orbital delocalization in the hidden order compound URu2Si2. By comparing to suitable reference materials such as UF4, UCd11, and alpha-U, we conclude that the 5f orbital in URu2Si2 is at least partially delocalized with nf = 2.87 +/- 0.08, and does not change with temperature down to 10 K within the estimated error. These results place further constraints on theoretical explanations of the hidden order, especially those requiring a localized f2 ground state.Comment: 11 pages,7 figure

Time variability in the bipolar scattered light nebula of L1527 IRS: A possible warped inner disk

Context. The bipolar outflows associated with low-mass protostars create cavities in the infalling envelope. These cavities are illuminated by the central protostar and inner disk, creating a bipolar scattered light nebula at near-infrared and mid-infrared wavelengths. The variability of the scattered light nebula in both total intensity and intensity as a function of position in the scattered light nebula can provide important insights into the structure of the inner disk that cannot be spatially resolved. Aims. We aim to determine the likelihood that a warped inner disk is the origin of the surface brightness variability in the bipolar scattered light nebula associated with L1527 IRS. Methods. We present results from near-IR imaging conducted over the course of seven years, with periods of monthly cadence monitoring. We used Monte Carlo radiative transfer models to interpret the observations. Results. We find a time varying, asymmetrical brightness in the scattered light nebulae within the outflow cavities of the protostar. Starting in 2007, the surface brightnesses of the eastern and western outflow cavities were roughly symmetric. Then, in 2009, the surface brightnesses of the cavities were found to be asymmetric, with a substantial increase in surface brightness and a larger increase in the eastern outflow cavity. More regular monitoring was conducted from 2011 to 2014, revealing a rotating pattern of surface brightness variability in addition to a slow change of the eastern and western outflow cavities toward symmetry, but still not as symmetric as observed in 2007. We find that an inner disk warp is a feasible mechanism to produce the rotating pattern of surface brightness variability.Comment: 14 pages, 7 figures. Accepted for publication in Astronomy & Astrophysic