A series of optical and one near-infrared nebular spectra covering the first year of the Type Ia supernova SN 2011fe are presented and modelled. The density profile that proved best for the early ...optical/ultraviolet spectra, "rho-11fe", was extended to lower velocities to include the regions that emit at nebular epochs. Model rho-11fe is intermediate between the fast deflagration model W7 and a low-energy delayed-detonation. Good fits to the nebular spectra are obtained if the innermost ejecta are dominated by neutron-rich, stable Fe-group species, which contribute to cooling but not to heating. The correct thermal balance can thus be reached for the strongest FeII and FeIII lines to be reproduced with the observed ratio. The 56Ni mass thus obtained is 0.47 +/- 0.05 Mo. The bulk of 56Ni has an outermost velocity of ~8500 km/s. The mass of stable iron is 0.23 +/- 0.03 Mo. Stable Ni has low abundance, ~10^{-2} Mo. This is sufficient to reproduce an observed emission line near 7400 A. A sub-Chandrasekhar explosion model with mass 1.02 Mo and no central stable Fe does not reproduce the observed line ratios. A mock model where neutron-rich Fe-group species are located above 56Ni following recent suggestions is also shown to yield spectra that are less compatible with the observations. The densities and abundances in the inner layers obtained from the nebular analysis, combined with those of the outer layers previously obtained, are used to compute a synthetic bolometric light curve, which compares favourably with the light curve of SN 2011fe.
Staphylococcus aureus is a leading cause of hospital‐acquired infections in the USA and is a major health concern as methicillin‐resistant S. aureus and other antibiotic‐resistant strains are common. ...Compounds that inhibit the S. aureus sortase (SrtA) cysteine transpeptidase may function as potent anti‐infective agents as this enzyme attaches virulence factors to the bacterial cell wall. While a variety of SrtA inhibitors have been discovered, the vast majority of these small molecules have not been optimized using structure‐based approaches. Here we have used NMR spectroscopy to determine the molecular basis through which pyridazinone‐based small molecules inhibit SrtA. These inhibitors covalently modify the active cysteine thiol and partially mimic the natural substrate of SrtA by inducing the closure of an active site loop. Computational and synthetic chemistry methods led to second‐generation analogues that are ~70‐fold more potent than the lead molecule. These optimized molecules exhibit broad‐spectrum activity against other types of class A sortases, have reduced cytotoxicity, and impair SrtA‐mediated protein display on S. aureus cell surface. Our work shows that pyridazinone analogues are attractive candidates for further development into anti‐infective agents, and highlights the utility of employing NMR spectroscopy and solubility‐optimized small molecules in structure‐based drug discovery.
NMR spectroscopy was used to determine the structure of Staphylococcus aureus sortase A transpeptidase enzyme in complex with a pyridazinone‐based small molecule, a potential anti‐infective agent. Computational and synthetic chemistry methods led to second‐generation analogs that are 70‐fold more potent than the lead molecule, less cytotoxic and effective at impairing sortase A‐mediated protein display on the surface of S. aureus. These pyridazinone analogues are attractive candidates for further development into anti‐infective agents.
We present extensive optical (\(UBVRI\), \(g'r'i'z'\), and open CCD) and near-infrared (\(ZYJH\)) photometry for the very nearby Type IIP SN ~2013ej extending from +1 to +461 days after shock ...breakout, estimated to be MJD \(56496.9\pm0.3\). Substantial time series ultraviolet and optical spectroscopy obtained from +8 to +135 days are also presented. Considering well-observed SNe IIP from the literature, we derive \(UBVRIJHK\) bolometric calibrations from \(UBVRI\) and unfiltered measurements that potentially reach 2\% precision with a \(B-V\) color-dependent correction. We observe moderately strong Si II \(\lambda6355\) as early as +8 days. The photospheric velocity (\(v_{\rm ph}\)) is determined by modeling the spectra in the vicinity of Fe II \(\lambda5169\) whenever observed, and interpolating at photometric epochs based on a semianalytic method. This gives \(v_{\rm ph} = 4500\pm500\) km s\(^{-1}\) at +50 days. We also observe spectral homogeneity of ultraviolet spectra at +10--12 days for SNe IIP, while variations are evident a week after explosion. Using the expanding photosphere method, from combined analysis of SN 2013ej and SN 2002ap, we estimate the distance to the host galaxy to be \(9.0_{-0.6}^{+0.4}\) Mpc, consistent with distance estimates from other methods. Photometric and spectroscopic analysis during the plateau phase, which we estimated to be \(94\pm7\) days long, yields an explosion energy of \(0.9\pm0.3\times10^{51}\) ergs, a final pre-explosion progenitor mass of \(15.2\pm4.2\)~M\(_\odot\) and a radius of \(250\pm70\)~R\(_\odot\). We observe a broken exponential profile beyond +120 days, with a break point at +\(183\pm16\) days. Measurements beyond this break time yield a \(^{56}\)Ni mass of \(0.013\pm0.001\)~M\(_\odot\).
Abstract
Several thousand core-collapse supernovae (CCSNe) of different flavors have been discovered so far. However, identifying their progenitors has remained an outstanding open question in ...astrophysics. Studies of SN host galaxies have proven to be powerful in providing constraints on the progenitor populations. In this paper, we present all CCSNe detected between 2009 and 2017 by the Palomar Transient Factory. This sample includes 888 SNe of 12 distinct classes out to redshift
z
≈ 1. We present the photometric properties of their host galaxies from the far-ultraviolet to the mid-infrared and model the host-galaxy spectral energy distributions to derive physical properties. The galaxy mass function of Type Ic, Ib, IIb, II, and IIn SNe ranges from 10
5
to 10
11.5
M
⊙
, probing the entire mass range of star-forming galaxies down to the least-massive star-forming galaxies known. Moreover, the galaxy mass distributions are consistent with models of star-formation-weighted mass functions. Regular CCSNe are hence direct tracers of star formation. Small but notable differences exist between some of the SN classes. Type Ib/c SNe prefer galaxies with slightly higher masses (i.e., higher metallicities) and star formation rates than Type IIb and II SNe. These differences are less pronounced than previously thought. H-poor superluminous supernovae (SLSNe) and SNe Ic-BL are scarce in galaxies above 10
10
M
⊙
. Their progenitors require environments with metallicities of < 0.4 and < 1 solar, respectively. In addition, the hosts of H-poor SLSNe are dominated by a younger stellar population than all other classes of CCSNe. Our findings corroborate the notion that low metallicity and young age play an important role in the formation of SLSN progenitors.
Site-specifically modified protein bioconjugates have important applications in biology, chemistry, and medicine. Functionalizing specific protein side chains with enzymes using mild reaction ...conditions is of significant interest, but remains challenging. Recently, the lysine-isopeptide bond forming activity of the sortase enzyme that builds surface pili in
(
SrtA) has been reconstituted
. A mutationally activated form of
SrtA was shown to be a promising bioconjugating enzyme that can attach Leu-Pro-Leu-Thr-Gly peptide fluorophores to a specific lysine residue within the N-terminal domain of the SpaA protein (
SpaA), enabling the labeling of target proteins that are fused to
SpaA. Here we present a detailed analysis of the
SrtA catalyzed protein labeling reaction. We show that the first step in catalysis is rate limiting, which is the formation of the
SrtA-peptide thioacyl intermediate that subsequently reacts with a lysine ε-amine in
SpaA. This intermediate is surprisingly stable, limiting spurious proteolysis of the peptide substrate. We report the discovery of a new enzyme variant (
SrtA
) that has significantly improved transpeptidation activity, because it completely lacks an inhibitory polypeptide appendage ("lid") that normally masks the active site. We show that the presence of the lid primarily impairs formation of the thioacyl intermediate and not the recognition of the
SpaA substrate. Quantitative measurements reveal that
SrtA
generates its cross-linked product with a catalytic turnover number of 1.4 ± 0.004 h
and that it has apparent
values of 0.16 ± 0.04 and 1.6 ± 0.3 mM for its
SpaA and peptide substrates, respectively.
SrtA
is 7-fold more active than previously studied variants, labeling >90% of
SpaA with peptide within 6 h. The results of this study further improve the utility of
SrtA as a protein labeling tool and provide insight into the enzyme catalyzed reaction that underpins protein labeling and pilus biogenesis.
ABSTRACT
We present BVRI and unfiltered light curves of 93 Type Ia supernovae (SNe Ia) from the Lick Observatory Supernova Search (LOSS) follow-up program conducted between 2005 and 2018. Our sample ...consists of 78 spectroscopically normal SNe Ia, with the remainder divided between distinct subclasses (3 SN 1991bg-like, 3 SN 1991T-like, 4 SNe Iax, 2 peculiar, and 3 super-Chandrasekhar events), and has a median redshift of 0.0192. The SNe in our sample have a median coverage of 16 photometric epochs at a cadence of 5.4 d, and the median first observed epoch is ∼4.6 d before maximum B-band light. We describe how the SNe in our sample are discovered, observed, and processed, and we compare the results from our newly developed automated photometry pipeline to those from the previous processing pipeline used by LOSS. After investigating potential biases, we derive a final systematic uncertainty of 0.03 mag in BVRI for our data set. We perform an analysis of our light curves with particular focus on using template fitting to measure the parameters that are useful in standardizing SNe Ia as distance indicators. All of the data are available to the community, and we encourage future studies to incorporate our light curves in their analyses.
During the first few days after explosion, Type II supernovae (SNe) are dominated by relatively simple physics. Theoretical predictions regarding early-time SN light curves in the ultraviolet (UV) ...and optical bands are thus quite robust. We present, for the first time, a sample of \(57\) \(R\)-band Type II SN light curves that are well monitored during their rise, having \(>5\) detections during the first 10 days after discovery, and a well-constrained time of explosion to within \(1-3\) days. We show that the energy per unit mass (\(E/M\)) can be deduced to roughly a factor of five by comparing early-time optical data to the model of Rabinak & Waxman (2011), while the progenitor radius cannot be determined based on \(R\)-band data alone. We find that Type II SN explosion energies span a range of \(E/M=(0.2-20)\times 10^{51} \; \rm{erg/(10 M}_\odot\)), and have a mean energy per unit mass of \(\left\langle E/M \right\rangle = 0.85\times 10^{51} \; \rm{erg/(10 M}_\odot\)), corrected for Malmquist bias. Assuming a small spread in progenitor masses, this indicates a large intrinsic diversity in explosion energy. Moreover, \(E/M\) is positively correlated with the amount of \(^{56}\rm{Ni}\) produced in the explosion, as predicted by some recent models of core-collapse SNe. We further present several empirical correlations. The peak magnitude is correlated with the decline rate (\(\Delta m_{15}\)), the decline rate is weakly correlated with the rise time, and the rise time is not significantly correlated with the peak magnitude. Faster declining SNe are more luminous and have longer rise times. This limits the possible power sources for such events.
SN 2013dy is a Type Ia supernova for which we have compiled an extraordinary dataset spanning from 0.1 to ~ 500 days after explosion. We present 10 epochs of ultraviolet (UV) through near-infrared ...(NIR) spectra with HST/STIS, 47 epochs of optical spectra (15 of them having high resolution), and more than 500 photometric observations in the BVrRiIZYJH bands. SN 2013dy has a broad and slowly declining light curve (delta m(B) = 0.92 mag), shallow Si II 6355 absorption, and a low velocity gradient. We detect strong C II in our earliest spectra, probing unburned progenitor material in the outermost layers of the SN ejecta, but this feature fades within a few days. The UV continuum of SN 2013dy, which is strongly affected by the metal abundance of the progenitor star, suggests that SN 2013dy had a relatively high-metallicity progenitor. Examining one of the largest single set of high-resolution spectra for a SN Ia, we find no evidence of variable absorption from circumstellar material. Combining our UV spectra, NIR photometry, and high-cadence optical photometry, we construct a bolometric light curve, showing that SN 2013dy had a maximum luminosity of 10.0^{+4.8}_{-3.8} * 10^{42} erg/s. We compare the synthetic light curves and spectra of several models to SN 2013dy, finding that SN 2013dy is in good agreement with a solar-metallicity W7 model.
Cercospora leaf blight (CLB), caused by
,
, and
, is a significant soybean
(L.) Merr. disease in regions with hot and humid conditions causing yield loss in the United States and Canada. There is ...limited information regarding resistant soybean cultivars, and there have been marginal efforts to identify the genomic regions underlying resistance to CLB. A Genome-Wide Association Study was conducted using a diverse panel of 460 soybean accessions from maturity groups III to VII to identify the genomic regions associated to the CLB disease. These accessions were evaluated for CLB in different regions of the southeastern United States over 3 years. In total, the study identified 99 Single Nucleotide Polymorphism (SNPs) associated with the disease severity and 85 SNPs associated with disease incidence. Across multiple environments, 47 disease severity SNPs and 23 incidence SNPs were common. Candidate genes within 10 kb of these SNPs were involved in biotic and abiotic stress pathways. This information will contribute to the development of resistant soybean germplasm. Further research is warranted to study the effect of pyramiding desirable genomic regions and investigate the role of identified genes in soybean CLB resistance.
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