Substrate specificity and the effect of calcium on Trypanosomabrucei metacaspase 2

Metacaspases are cysteine peptidases found only in yeast, plants and lower eukaryotes, including the protozoa. To investigate the extended substrate specificity and effects of Ca<sup>2+</sup> on the activation of these enzymes, detailed kinetic, biochemical and structural analyses were carried out on metacaspase 2 from Trypanosoma brucei (TbMCA2). These results reveal that TbMCA2 has an unambiguous preference for basic amino acids at the P<sub>1</sub> position of peptide substrates and that this is most probably a result of hydrogen bonding from the P<sub>1</sub> residue to Asp95 and Asp211 in TbMCA2. In addition, TbMCA2 also has a preference for charged residues at the P<sub>2</sub> and P<sub>3</sub>positions and for small residues at the prime side of a peptide substrate. Studies into the effects of Ca<sup>2+</sup> on the enzyme revealed the presence of two Ca<sup>2+</sup> binding sites and a reversible structural modification of the enzyme upon Ca<sup>2+</sup> binding. In addition, the concentration of Ca<sup>2+</sup> used for activation of TbMCA2 was found to produce a differential effect on the activity of TbMCA2, but only when a series of peptides that differed in P<sub>2</sub> were examined, suggesting that Ca<sup>2+</sup>activation of TbMCA2 has a structural effect on the enzyme in the vicinity of the S2 binding pocket. Collectively, these data give new insights into the substrate specificity and Ca<sup>2+</sup> activation of TbMCA2. This provides important functional details and leads to a better understanding of metacaspases, which are known to play an important role in trypanosomes and make attractive drug targets due to their absence in humans

ALMA CO J = 6-5 observations of IRAS 16293-2422. Shocks and entrainment

Observations of higher-excited transitions of abundant molecules such as CO are important for determining where energy in the form of shocks is fed back into the parental envelope of forming stars. The nearby prototypical and protobinary low-mass hot core, IRAS 16293-2422 (I16293) is ideal for such a study. The source was targeted with ALMA for science verification purposes in band 9, which includes CO J = 6-5 (E$_{up}$/k$_B$ ~{} 116 K), at an unprecedented spatial resolution (~{}0.''2, 25 AU). I16293 itself is composed of two sources, A and B, with a projected distance of 5''. CO J = 6-5 emission is detected throughout the region, particularly in small, arcsecond-sized hotspots, where the outflow interacts with the envelope. The observations only recover a fraction of the emission in the line wings when compared to data from single-dish telescopes, with a higher fraction of emission recovered at higher velocities. The very high angular resolution of these new data reveal that a bow shock from source A coincides, in the plane of the sky, with the position of source B. Source B, on the other hand, does not show current outflow activity. In this region, outflow entrainment takes place over large spatial scales, {gsim}100 AU, and in small discrete knots. This unique dataset shows that the combination of a high-temperature tracer (e.g., CO J = 6-5) and very high angular resolution observations is crucial for interpreting the structure of the warm inner environment of low-mass protostars. Appendices are available in electronic form at http://www.aanda.orgStars and planetary system

The JCMT Gould Belt survey: Dense core clusters in Orion B

The James Clerk Maxwell Telescope Gould Belt Legacy Survey obtained SCUBA-2 observations of dense cores within three sub-regions of OrionB: LDN1622, NGC2023/2024, and NGC2068/2071, all of which contain clusters of cores. We present an analysis of the clustering properties of these cores, including the two-point correlation function and Cartwright’s Q parameter. We identify individual clusters of dense cores across all three regions using a minimal spanning tree technique, and find that in each cluster, the most massive cores tend to be centrally located. We also apply the independent M–Σ technique and find a strong correlation between core mass and the local surface density of cores. These two lines of evidence jointly suggest that some amount of mass segregation in clusters has happened already at the dense core stage

CHIMPS: the 13CO/C18O (J = 3 to 2) Heterodyne Inner Milky Way Plane Survey

We present the 13CO/C18O (J = 3 → 2) Heterodyne Inner Milky Way Plane Survey (CHIMPS) which has been carried out using the Heterodyne Array Receiver Program on the 15 m James Clerk Maxwell Telescope (JCMT) in Hawaii. The high-resolution spectral survey currently covers |b| ≤ 0.5° and 28° ≲ l ≲ 46°, with an angular resolution of 15 arcsec in 0.5 km s-1 velocity channels. The spectra have a median rms of ˜0.6 K at this resolution, and for optically thin gas at an excitation temperature of 10 K, this sensitivity corresponds to column densities of NH2 ˜ 3 × 1020 cm-2 and NH2 ˜ 4 × 1021 cm-2 for 13CO and C18O, respectively. The molecular gas that CHIMPS traces is at higher column densities and is also more optically thin than in other publicly available CO surveys due to its rarer isotopologues, and thus more representative of the three-dimensional structure of the clouds. The critical density of the J = 3 → 2 transition of CO is ≳104 cm-3 at temperatures of ≤20 K, and so the higher density gas associated with star formation is well traced. These data complement other existing Galactic plane surveys, especially the JCMT Galactic Plane Survey which has similar spatial resolution and column density sensitivity, and the Herschel infrared Galactic Plane Survey. In this paper, we discuss the observations, data reduction and characteristics of the survey, presenting integrated-emission maps for the region covered. Position-velocity diagrams allow comparison with Galactic structure models of the Milky Way, and while we find good agreement with a particular four-arm model, there are some significant deviations.Peer reviewedFinal Accepted Versio

Feedback in W49A diagnosed with radio recombination lines and models

We present images of radio recombination lines (RRLs) at wavelengths around 17 cm from the star-forming region W49A to determine the kinematics of ionized gas in the THOR survey (The H I/OH/Recombination line survey of the inner Milky Way) at an angular resolution of 16.′′8 x 13.′′8. The distribution of ionized gas appears to be affected by feedback processes from the star clusters in W49A. The velocity structure of the RRLs shows a complex behavior with respect to the molecular gas. We find a shell-like distribution of ionized gas as traced by RRL emission surrounding the central cluster of OB stars in W49A. We describe the evolution of the shell with the recent feedback model code WARPFIELD that includes the important physical processes and has previously been applied to the 30 Doradus region in the Large Magellanic Cloud. The cloud structure and dynamics of W49A are in agreement with a feedback-driven shell that is re-collapsing. The shell may have triggered star formation in other parts of W49A. We suggest that W49A is a potential candidate for star formation regulated by feedback-driven and re-collapsing shells.We would like to thank the referee for the detailed, helpful, and insightful comments, which considerably improved the paper. M.R.R. is a fellow of the International Max Planck Research School for Astronomy and Cosmic Physics (IMPRS) at the University of Heidelberg. H.B., M.R.R., Y.W., J.S. and J.C.M. acknowledge support from the European Research Council under the Horizon 2020 Framework Program via the ERC Consolidator Grant CSF-648505. M.R.R., D.R., H.B., E.W.P., S.C.O.G. and R.S.K. acknowledge support from the Deutsche Forschungsgemeinschaft (DFG) via Sonderforschungsbereich (SFB) 881 “The Milky Way System” (sub-projects B1, B2 and B8). S.C.O.G., E.W.P. and R.S.K. further acknowledge support from the DFG via Priority Program SPP 1573 “Physics of the Interstellar Medium” (grant numbers KL1358/18.1, KL 1358/19.2, and GL 668/2–1) and from the European Research Council via the ERC Advanced Grant STARLIGHT (project number 339177). The research was carried out in part at the Jet Propulsion Laboratory, which is operated forNASA by the California Institute of Technology. R.J.S. acknowledges support from an STFC Ernest Rutherford fellowship. S.E.R. acknowledges support from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement # 706390. F.B. acknowledges funding from the European Union’s Horizon 2020 research and innovation programme (grant agreement No 726384 – EMPIRE)

Water in star-forming regions with Herschel (WISH): VI. Constraints on UV and X-ray irradiation from a survey of hydrides in low- to high-mass young stellar objects

[Context] Hydrides are simple compounds containing one or a few hydrogen atoms bonded to a heavier atom. They are fundamental precursor molecules in cosmic chemistry and many hydride ions have become observable in high quality for the first time thanks to the Herschel Space Observatory. Ionized hydrides such as CH+ and OH+ (and also HCO+), which affect the chemistry of molecules such as water, provide complementary information on irradiation by far-UV (FUV) or X-rays and gas temperature.[Aims] We explore hydrides of the most abundant heavier elements in an observational survey covering young stellar objects (YSOs) with different mass and evolutionary state. The focus is on hydrides associated with the dense protostellar envelope and outflows, contrary to previous work that focused on hydrides in diffuse foreground clouds.[Methods] Twelve YSOs were observed with HIFI on Herschel in six spectral settings providing fully velocity-resolved line profiles as part of the Water in star-forming regions with Herschel (WISH) program. The YSOs include objects of low (Class 0 and I), intermediate, and high mass, with luminosities ranging from 4 L⊙ to 2 × 105 L⊙.[Results] The targeted lines of CH+, OH+, H2O+, C+, and CH are detected mostly in blue-shifted absorption. H3O+ and SH+ are detected in emission and only toward some high-mass objects. The observed line parameters and correlations suggest two different origins related to gas entrained by the outflows and to the circumstellar envelope. The derived column densities correlate with bolometric luminosity and envelope mass for all molecules, best for CH, CH+, and HCO+. The column density ratios of CH+/OH+ are estimated from chemical slab models, assuming that the H2 density is given by the specific density model of each object at the beam radius. For the low-mass YSOs the observed ratio can be reproduced for an FUV flux of 2–400 times the interstellar radiation field (ISRF) at the location of the molecules. In two high-mass objects, the UV flux is 20–200 times the ISRF derived from absorption lines, and 300–600 ISRF using emission lines. Upper limits for the X-ray luminosity can be derived from H3O+ observations for some low-mass objects.[Conclusions] If the FUV flux required for low-mass objects originates at the central protostar, a substantial FUV luminosity, up to 1.5 L⊙, is required. There is no molecular evidence for X-ray induced chemistry in the low-mass objects on the observed scales of a few 1000 AU. For high-mass regions, the FUV flux required to produce the observed molecular ratios is smaller than the unattenuated flux expected from the central object(s) at the Herschel beam radius. This is consistent with an FUV flux reduced by circumstellar extinction or by bloating of the protostar.The work on star formation at ETH Zurich was partially funded by the Swiss National Science Foundation (grant No. 200020-113556). Astrochemistry in Leiden is supported by the Netherlands Research School for Astronomy (NOVA), by a Royal Netherlands Academy of Arts and Sciences (KNAW) professor prize, and by the European Union A-ERC grant 291141 CHEMPLAN. Support for this work was also provided by NASA (Herschel OT funding) through an award issued by JPL/ Caltech

The composition of the protosolar disk and the formation conditions for comets

Conditions in the protosolar nebula have left their mark in the composition of cometary volatiles, thought to be some of the most pristine material in the solar system. Cometary compositions represent the end point of processing that began in the parent molecular cloud core and continued through the collapse of that core to form the protosun and the solar nebula, and finally during the evolution of the solar nebula itself as the cometary bodies were accreting. Disentangling the effects of the various epochs on the final composition of a comet is complicated. But comets are not the only source of information about the solar nebula. Protostellar disks around young stars similar to the protosun provide a way of investigating the evolution of disks similar to the solar nebula while they are in the process of evolving to form their own solar systems. In this way we can learn about the physical and chemical conditions under which comets formed, and about the types of dynamical processing that shaped the solar system we see today. This paper summarizes some recent contributions to our understanding of both cometary volatiles and the composition, structure and evolution of protostellar disks.Comment: To appear in Space Science Reviews. The final publication is available at Springer via http://dx.doi.org/10.1007/s11214-015-0167-