0103-72.6: A New Oxygen-Rich Supernova Remnant in the Small Magellanic Cloud

0103$-$72.6, the second brightest X-ray supernova remnant (SNR) in the Small Magellanic Cloud (SMC), has been observed with the {\it Chandra X-Ray Observatory}. Our {\it Chandra} observation unambiguously resolves the X-ray emission into a nearly complete, remarkably circular shell surrounding bright clumpy emission in the center of the remnant. The observed X-ray spectrum for the central region is evidently dominated by emission from reverse shock-heated metal-rich ejecta. Elemental abundances in this ejecta material are particularly enhanced in oxygen and neon, while less prominent in the heavier elements Si, S, and Fe. We thus propose that 0103$-$72.6 is a new ``oxygen-rich'' SNR, making it only the second member of the class in the SMC. The outer shell is the limb-brightened, soft X-ray emission from the swept-up SMC interstellar medium. The presence of O-rich ejecta and the SNR's location within an H{\small II} region attest to a massive star core-collapse origin for 0103$-$72.6. The elemental abundance ratios derived from the ejecta suggest an $\sim$18 M$_{\odot}$ progenitor star.Comment: 6 pages (ApJ emulator format), including 5 figures and 2 tables. For high quality Figs.1,2, & 3, contact [email protected]. Accepted by the ApJ Letter

LMC X-1: A New Spectral Analysis of the O-star in the binary and surrounding nebula

We provide new observations of the LMC X-1 O star and its extended nebula structure using spectroscopic data from VLT/UVES as well as H$\alpha$ imaging from the Wide Field Imager on the Max Planck Gesellschaft / European Southern Observatory 2.2m telescope and ATCA imaging of the 2.1 GHz radio continuum. This nebula is one of the few known to be energized by an X-ray binary. We use a new spectrum extraction technique that is superior to other methods to obtain both radial velocities and fluxes. This provides an updated spatial velocity of $\simeq 21.0~\pm~4.8$ km s$^{-1}$ for the O star. The slit encompasses both the photo-ionized and shock-ionized regions of the nebula. The imaging shows a clear arc-like structure reminiscent of a wind bow shock in between the ionization cone and shock-ionized nebula. The observed structure can be fit well by the parabolic shape of a wind bow shock. If an interpretation of a wind bow shock system is valid, we investigate the N159-O1 star cluster as a potential parent of the system, suggesting a progenitor mass of $\sim 60$ M$_{\odot}$ for the black hole. We further note that the radio emission could be non-thermal emission from the wind bow shock, or synchrotron emission associated with the jet inflated nebula. For both wind and jet-powered origins, this would represent one of the first radio detections of such a structure.Comment: 7 Figures, 4 Table

Stretch-induced intussuceptive and sprouting angiogenesis in the chick chorioallantoic membrane

Vascular systems grow and remodel in response to not only metabolic needs, but also mechanical influences as well. Here, we investigated the influence of tissue-level mechanical forces on the patterning and structure of the chick chorioallantoic membrane (CAM) microcirculation. A dipole stretch field was applied to the CAM using custom computer-controlled servomotors. The topography of the stretch field was mapped using finite element models. After 3 days of stretch, Sholl analysis of the CAM demonstrated a 7-fold increase in conducting vessel intersections within the stretch field (p 0.05). In contrast, corrosion casting and SEM of the stretch field capillary meshwork demonstrated intense sprouting and intussusceptive angiogenesis. Both planar surface area (p < 0.05) and pillar density (p < 0.01) were significantly increased relative to control regions of the CAM. We conclude that a uniaxial stretch field stimulates the axial growth and realignment of conducting vessels as well as intussusceptive and sprouting angiogenesis within the gas exchange capillaries of the ex ovo CAM.National Institutes of Health (U.S.) (NIH grant HL95678

CaverDock: Software tool for fast screening of un/binding of ligands in protein engineering

Protein tunnels, channels and gates are important for enzymatic catalysis and also represent attractive targets for rational protein design and drug design [1]. Drug molecules blocking the access of natural substrate or release of products are very efficient modulators of biological activity. Here we demonstrate the application of newly in-house developed software tool CaverDock [2,3] for the analysis of the transport of ligands through tunnels in biomolecular targets. Caverdock is a new addition to the Caver Suite [4-6]. We performed virtual screening of large databases of drugs against two pharmacologically relevant targets. We have used FDA-approved drugs for both targets. Oncological drugs (133 molecules), taken from the NIH website, and anti-inflammatory (56 molecules), taken from the Drugbank website, as the libraries of ligands for the two molecular targets: (i) cytochrome P450 17A1 and (ii) leukotriene A4 hydrolase/aminopeptidase. Moreover, we will also show the unbinding of the 2,3-dichloropropan-1-ol product from a buried active site of an haloalkane dehalogenase and its variant. With this study we identified hot-spots that may be used for directed evolution or site-directed mutagenesis to create new variants for faster 2,3-dichloropropan-1-ol release [7]. Finally, we will show the difference on ligand transportation when a protein is in an open and closed conformations [8]. We will show how CaverDock tackles the problem of protein flexibility. 1. Marques, S.M., et al., 2017: Enzyme Tunnels and Gates as Relevant Targets in Drug Design. Medicinal Research Reviews 37: 1095-1139. 2. Vavra, O., et al., 2019: CaverDock 1.0: A New Tool for Analysis of Ligand Binding and Unbinding Based on Molecular Docking. Bioinformatics (under review). 3. Filipovic, J., et al, 2019: A Novel Method for Analysis of Ligand Binding and Unbinding Based on Molecular Docking. Transactions on Computational Biology and Bioinformatics (under review) 4. Chovancova, E., et al., 2012: CAVER 3.0: A Tool for Analysis of Transport Pathways in Dynamic Protein Structures. PLOS Computational Biology 8: e1002708. 5. Jurcik, A., et al., 2018: CAVER Analyst 2.0: Analysis and Visualization of Channels and Tunnels in Protein Structures and Molecular Dynamics Trajectories. Bioinformatics 34: 3586-3588. 6. Stourac, J., et al., 2019: Caver Web 1.0: Identification of Tunnels and Channels in Proteins and Analysis of Ligand Transport. Nucleic Acids Research (under review). 7. Marques, S.M., et al., 2019: Computational Study of Protein-Ligand Unbinding for Enzyme Engineering. Frontiers in Chemistry 6: 650. 8. Kokkonen, P., et al., 2018: Molecular Gating of an Engineered Enzyme Captured in Real Time. Journal of the American Chemical Society 140: 17999–18008

Plastic mulch and nitrogen fertigation in growing vegetables modify soil temperature, water and nitrate dynamics: experimental results and a modeling study

Plastic mulch in combination with drip irrigation present a common agricultural management technique practiced in commercial vegetable production. This management can result in various impacts on water and nutrient distribution and consequently affect nutrient dynamics in underlying soil. The aim of this work was to: (i) compare the effects of different mulching types (color) on soil temperature and (ii) crop growth; (iii) estimate the effect of plastic mulch cover (MULCH) on water and (iv) nitrate dynamics using HYDRUS-2D. The field experiment was designed in the Croatian coastal karst area on main plots with three levels of nitrogen fertilizer: 70, 140, and 210 kg ha−1, which were all divided in five subplots considering mulch covering with different colors types (black, brown, silver, and white) and no covering (control). Monitoring of water and nitrate dynamics was performed through lysimeters which ensured input data for HYDRUS-2D model. The experimental results showed that plastic mulch had a significant effect on soil temperature regime and crop yield. The dark color mulch (black, brown) caused higher soil temperature, which consequently enabled earlier plant development and higher yields. HYDRUS-2D simulated results showed good fitting to the field data in cumulative water and also nitrate outflow. Water flow simulations produced model efficiency of 0.84 for control (CONT) and 0.56 for MULCH systems, while nitrate simulations showed model efficiency ranging from 0.67 to 0.83 and from 0.70 to 0.93, respectively. Additional simulations exposed faster transport of nitrates below drip line in the CONT system, mostly because of the increased surface area subjected to precipitation/irrigation due to the absence of soil cover. Numerical modeling revealed large influence of plastic mulch cover on water and nutrient distribution in soil. The study suggests that under this management practice the nitrogen amounts applied via fertigation can be lowered and optimized to reduce possible negative influence on environment

CAVERDOCK: A new tool for analysis of ligand binding and unbinding based on molecular docking

Understanding the protein-ligand interactions is crucial for engineering improved catalysts. The interaction of a protein and a ligand molecule often takes place in enzymes active site. Such functional sites may be buried inside the protein core, and therefore a transport of a ligand from outside environment to the protein inside needs to be understood. Here we present the CaverDock [1], implementing a novel method for analysis of these important transport processes. Our method is based on a modified molecular docking algorithm. It iteratively places the ligand along the tunnel in such a way that the ligand movement is contiguous and its energy is minimized. The output of the calculation is ligand trajectory and energy profile of transport process. CaverDock uses a modified version of the program AutoDock Vina [2] for molecular docking and implements a parallel heuristic algorithm to search the space of possible trajectories. Our method lies in between of geometrical approaches and molecular dynamics simulations. Contrary to geometrical methods, it provides an evaluation of chemical forces. However, it is not as computationally demanding as the methods based on molecular dynamics. The typical input of CaverDock requires setup for molecular docking and tunnel geometry obtained from Caver [3]. Typical computational time is in dozens of minutes at a single node, allowing virtual screening of a large pool of molecules. We demonstrate CaverDock usability by comparison of a ligand trajectory in different tunnels of wild type and engineered proteins; and computation of energetic profiles for a large set of substrates and inhibitors. CaverDock is available from the web site http://www.caver.cz. 1. Vavra, O., Filipovic, J., Plhak, J., Bednar, D., Marques, S., Brezovsky, J., Matyska, L., Damborsky, J., CAVERDOCK: A New Tool for Analysis of Ligand Binding and Unbinding Based on Molecular Docking. PLOS Computational Biology (submitted). 2. Trott, O., Olson, A.J., AutoDock Vina: Improving the Speed and Accuracy of Docking with a New scoring function, efficient optimization and multithreading, Journal of Computational Chemistry 31: 455-461, 2010. 3. Chovancova, E., Pavelka, A., Benes, P., Strnad, O., Brezovsky, J., Kozlikova, B., Gora, A., Sustr, V., Klvana, M., Medek, P., Biedermannova, L., Sochor, J., Damborsky, J., 2012: CAVER 3.0: A Tool for Analysis of Transport Pathways in Dynamic Protein Structures. PLOS Computational Biology 8: e1002708

Impacts of the Tropical Pacific/Indian Oceans on the Seasonal Cycle of the West African Monsoon

The current consensus is that drought has developed in the Sahel during the second half of the twentieth century as a result of remote effects of oceanic anomalies amplified by local land–atmosphere interactions. This paper focuses on the impacts of oceanic anomalies upon West African climate and specifically aims to identify those from SST anomalies in the Pacific/Indian Oceans during spring and summer seasons, when they were significant. Idealized sensitivity experiments are performed with four atmospheric general circulation models (AGCMs). The prescribed SST patterns used in the AGCMs are based on the leading mode of covariability between SST anomalies over the Pacific/Indian Oceans and summer rainfall over West Africa. The results show that such oceanic anomalies in the Pacific/Indian Ocean lead to a northward shift of an anomalous dry belt from the Gulf of Guinea to the Sahel as the season advances. In the Sahel, the magnitude of rainfall anomalies is comparable to that obtained by other authors using SST anomalies confined to the proximity of the Atlantic Ocean. The mechanism connecting the Pacific/Indian SST anomalies with West African rainfall has a strong seasonal cycle. In spring (May and June), anomalous subsidence develops over both the Maritime Continent and the equatorial Atlantic in response to the enhanced equatorial heating. Precipitation increases over continental West Africa in association with stronger zonal convergence of moisture. In addition, precipitation decreases over the Gulf of Guinea. During the monsoon peak (July and August), the SST anomalies move westward over the equatorial Pacific and the two regions where subsidence occurred earlier in the seasons merge over West Africa. The monsoon weakens and rainfall decreases over the Sahel, especially in August.Peer reviewe

Measurements of the pp → ZZ production cross section and the Z → 4ℓ branching fraction, and constraints on anomalous triple gauge couplings at √s = 13 TeV

Four-lepton production in proton-proton collisions, pp -> (Z/gamma*)(Z/gamma*) -> 4l, where l = e or mu, is studied at a center-of-mass energy of 13 TeV with the CMS detector at the LHC. The data sample corresponds to an integrated luminosity of 35.9 fb(-1). The ZZ production cross section, sigma(pp -> ZZ) = 17.2 +/- 0.5 (stat) +/- 0.7 (syst) +/- 0.4 (theo) +/- 0.4 (lumi) pb, measured using events with two opposite-sign, same-flavor lepton pairs produced in the mass region 60 4l) = 4.83(-0.22)(+0.23) (stat)(-0.29)(+0.32) (syst) +/- 0.08 (theo) +/- 0.12(lumi) x 10(-6) for events with a four-lepton invariant mass in the range 80 4GeV for all opposite-sign, same-flavor lepton pairs. The results agree with standard model predictions. The invariant mass distribution of the four-lepton system is used to set limits on anomalous ZZZ and ZZ. couplings at 95% confidence level: -0.0012 < f(4)(Z) < 0.0010, -0.0010 < f(5)(Z) < 0.0013, -0.0012 < f(4)(gamma) < 0.0013, -0.0012 < f(5)(gamma) < 0.0013

Search for massive resonances decaying in to WW,WZ or ZZ bosons in proton-proton collisions at root s=13 TeV

Peer reviewe