Non-Equilibrium Ionization States of GRB Environments

Iron spectral features are thought to be the best tracer of a progenitor of gamma-ray bursts (GRBs). The detections of spectral features such as an iron line and/or a Radiative Recombination edge and Continuum (RRC) were reported in four X-ray afterglows of GRBs. However their properties were different each other burst by burst. For example, Chandra observation of GRB 991216 reported both the strong H-like iron line together with its RRC. On the contrary, Yoshida et al. (2001) report only a detection of the strong RRC in GRB 970828 with ASCA. Since it is difficult to produce the strong RRC, we have to consider special condition for the line and/or the RRC forming region. In this paper, we point out a possibility of a ``non-equilibrium ionization state'' for the line and the RRC forming region.Comment: 10pages, 2figures. Accepted for ApJL. This is a companion paper by A.Yoshida et. a

Discovery of novel enzyme genes involved in the conversion of an arylglycerol-β-aryl ether metabolite and their use in generating a metabolic pathway for lignin valorization

Microbial conversions known as “biological funneling” have attracted attention for their ability to upgrade heterogeneous mixtures of low-molecular-weight aromatic compounds obtained by chemical lignin depolymerization. β-hydroxypropiovanillone (HPV) and its analogs can be obtained by chemoselective catalytic oxidation of lignin using 2,3-dichloro-5,6-dicyano-1,4-benzoquinone/tert-butyl nitrite/O2, followed by cleavage of arylglycerol-β-aryl ether with zinc. Sphingobium sp. strain SYK-6 can degrade HPV generated by the catabolism of arylglycerol-β-aryl ether through 2-pyrone-4,6-dicarboxylate (PDC), a promising platform chemical. Therefore, production of PDC from HPV can be achieved using the HPV catabolic pathway. However, the pathway and genes involved in the catabolism of vanilloyl acetic acid (VAA) generated during HPV catabolism have not been investigated. In the present study, we isolated SLG_24960 (vceA), which encodes an enzyme that converts VAA into a coenzyme A (CoA) derivative of vanillate (vanilloyl-CoA) from SYK-6, by shotgun cloning. The analysis of a vceA mutant indicated that this gene is not required for VAA conversion in vivo, but it encodes a major enzyme catalyzing CoA-dependent VAA conversion in vitro. We also identified SLG_12450 (vceB), whose product can convert vanilloyl-CoA to vanillate. Enzyme genes besides vceA and vceB, which are necessary for the conversions of HPV to VAA and of vanillate to PDC, were introduced and expressed in Pseudomonas putida. The resulting engineered strain completely converted 1 mM HPV into PDC after 24 h. Our results suggest that the enzyme genes that are not required for the catabolic pathway in microorganisms but can be used for the conversion of target substrates are buried in microbial genomes. These genes are, thus, useful for designing metabolic pathways to produce value-added metabolites.PostprintPeer reviewe

Discovery of Strong Radiative Recombination Continua from The Supernova Remnant IC 443 with Suzaku

We present the Suzaku spectroscopic study of the Galactic middle-aged supernova remnant (SNR) IC 443. The X-ray spectrum in the 1.75-6.0 keV band is described by an optically-thin thermal plasma with the electron temperature of 0.6 keV and several additional Lyman lines. We robustly detect, for the first time, strong radiative recombination continua (RRC) of H-like Si and S around at 2.7 and 3.5 keV. The ionization temperatures of Si and S determined from the intensity ratios of the RRC to He-like K-alpha line are 1.0 keV and 1.2 keV, respectively. We thus find firm evidence for an extremely-overionized (recombining) plasma. As the origin of the overionization, a thermal conduction scenario argued in previous work is not favored in our new results. We propose that the highly-ionized gas were made at the initial phase of the SNR evolution in dense regions around a massive progenitor, and the low electron temperature is due to a rapid cooling by an adiabatic expansion.Comment: 5 pages, 5 figures, accepted by ApJ Lette

ASCA Observations of the Supernova Remnant IC 443: Thermal Structure and Detection of Overionized Plasma

We present the results of X-ray spatial and spectral studies of the ``mixed-morphology'' supernova remnant IC 443 using ASCA. IC 443 has a center-filled image in X-ray band, contrasting with the shell-like appearance in radio and optical bands. The overall X-ray emission is thermal, not from a synchrotron nebula. ASCA observed IC 443 three times, covering the whole remnant. From the image analysis, we found that the softness-ratio map reveals a shell-like structure. At the same time, its spectra require two (1.0 keV and 0.2 keV) plasma components; the emission of the 0.2 keV plasma is stronger in the region near the shell than the center. These results can be explained by a simple model that IC 443 has a hot (1.0 keV) interior surrounded by a cool (0.2 keV) outer shell. From the emission measures, we infer that the 0.2 keV plasma is denser than the 1.0 keV plasma, suggesting pressure equilibrium between the two. In addition, we found that the ionization temperature of sulfur, obtained from H-like K$\alpha$ to He-like K$\alpha$ intensity ratio, is 1.5 keV, significantly higher than the gas temperature of 1.0 keV suggested from the continuum spectrum. The same can be concluded for silicon. Neither an additional, hotter plasma component nor a multi-temperature plasma successfully accounts for this ratio, and we conclude that the 1.0 keV plasma is overionized. This is the first time that overionized gas has been detected in a SNR. For the gas to become overionized in the absence of a photoionizing flux, it must cool faster than the ions recombine. Thermal conduction from the 1.0 keV plasma to the 0.2 keV one could cause the 1.0 keV plasma to become overionized, which is plausible within an old (3$\times10^4$ yr) SNR.Comment: 11 pages, 15 figures, 2 tables, accepted for publication in The Astrophysical Journa

Enhanced abundances in three large-diameter mixed-morphology supernova remnants

We present an X-ray study of three mixed-morphology supernova remnants (SNRs), HB 21, CTB 1 and HB 3, using archival ASCA and ROSAT data. These data are complemented by archival Chandra X-ray Observatory data for CTB 1 and XMM-Newton X-ray Observatory data for HB 3. The spectra from HB 21 and HB 3 are well-described with a single-temperature thermal plasma in ionization equilibrium, while a two-temperature thermal plasma is found in CTB 1. We found enhanced abundances in all three SNRs. The elemental abundance of Mg is clearly enhanced in CTB 1, while HB 21 has enhanced abundances of Si and S. The situation is not so clear in HB 3 -- the plasma in this SNR either has significantly enhanced abundances of O, Ne and Mg, or it has marginally enhanced abundances of Mg and under-abundant Fe. We discuss the plausibility of mixed-morphology SNR models for the three SNRs and the presence of enhanced abundances. We revise a list of MM SNRs and their properties, compare the three SNRs studied here with other members of this class, and discuss the presence of enhanced elemental abundances in MM SNRs. We also report the ASCA detection of a compact source in the southern part of HB 3. The source spectrum is consistent with a power law with a photon index of ~2.7, and an unabsorbed X-ray flux of ~10^{-12} erg/cm^2/s in the 0.5--10.0 keV band. The column density towards this source differs from that towards the SNR, and it is therefore unlikely they are related.Comment: 26 pages, 15 figures, revised version (minor changes), accepted for publication in ApJ (10 Aug 2006

Non-Maxwellian electron distributions in clusters of galaxies

Thermal X-ray spectra of clusters of galaxies and other sources are commonly calculated assuming Maxwellian electron distributions. There are situations where this approximation is not valid, for instance near interfaces of hot and cold gas and near shocks. The presence of non-thermal electrons affects the X-ray spectrum. To study the role of these electrons in clusters and other environments, an efficient algorithm to calculate the X-ray spectra is needed. We approximate an arbitrary electron distribution by the sum of Maxwellian components. The decomposition is done using either a genetic algorithm or an analytical approximation. The X-ray spectrum is then evaluated using a linear combination of those Maxwellian components. Our method is fast and leads to an accurate evaluation of the spectrum. The use of Maxwellian components allows to use the standard collisional rates that are available in plasma codes such as SPEX. We give an example of a spectrum for the supra-thermal electron distribution behind a shock in a cluster of galaxies. The relative intensities of the satellite lines in such a spectrum are sensitive to the presence of the supra-thermal electrons. These lines can only be investigated with high spectral resolution. We show that the instruments on future missions like Astro-H and IXO will be able to demonstrate the presence or absence of these supra-thermal electrons.Comment: 6 pages, 4 figures, accepted for publication in Astronomy and Astrophysics, main journa

Coronal emission from the shocked circumstellar ring of SN 1987A

High resolution spectra with UVES/VLT of SN 1987A from December 2000 until November 2005 show a number of high ionization lines from gas with velocities of roughly 350 km/s, emerging from the shocked gas formed by the ejecta-ring collision. These include coronal lines from [Fe X], [Fe XI] and [Fe XIV] which have increased by a factor of about 20 during the observed period. The evolution of the lines is similar to that of the soft X-rays, indicating that they arise in the same component. The line ratios are consistent with those expected from radiative shocks with velocity 310-390 km/s, corresponding to a shock temperature of (1.6-2.5) x 10^6 K. A fraction of the coronal emission may, however, originate in higher velocity adiabatic shocks.Comment: 11 pages, 10 figures, accepted for publication in A&

Quantification of DNA-associated proteins inside eukaryotic cells using single-molecule localization microscopy

Development of single-molecule localization microscopy techniques has allowed nanometre scale localization accuracy inside cells, permitting the resolution of ultra-fine cell structure and the elucidation of crucial molecular mechanisms. Application of these methodologies to understanding processes underlying DNA replication and repair has been limited to defined in vitro biochemical analysis and prokaryotic cells. In order to expand these techniques to eukaryotic systems, we have further developed a photo-activated localization microscopy-based method to directly visualize DNA-associated proteins in unfixed eukaryotic cells. We demonstrate that motion blurring of fluorescence due to protein diffusivity can be used to selectively image the DNA-bound population of proteins. We designed and tested a simple methodology and show that it can be used to detect changes in DNA binding of a replicative helicase subunit, Mcm4, and the replication sliding clamp, PCNA, between different stages of the cell cycle and between distinct genetic backgrounds

XMM-Newton unveils the complex iron K alpha region of Mrk 279

We present the results of a ~160 ks-long XMM-Newton observation of the Seyfert 1 galaxy Mrk 279. The spectrum shows evidence of both broad and narrow emission features. The Fe K alpha line may be equally well explained by a single broad Gaussian (FWHM~10,000 km/s) or by two components: an unresolved core plus a very broad profile (FWHM~14,000 km/s). For the first time we quantified, via the "locally optimally emitting cloud" model, the contribution of the broad line region (BLR) to the absolute luminosity of the broad component of the Fe K alpha at 6.4 keV. We find that the contribution of the BLR is only ~3%. In the two-line component scenario, we also evaluated the contribution of the highly ionized gas component, which produces the FeXXVI line in the iron K region. This contribution to the narrow core of the Fe K alpha line is marginal <0.1%. Most of the luminosity of the unresolved, component of Fe K alpha may come from the obscuring torus, while the very-broad associated component may come from the accretion disk. However, models of reflection by cold gas are difficult to test because of the limited energy band. The FeXXVI line at 6.9 keV is consistent to be produced in a high column density (N_H~10^23 cm^{-2}), extremely ionized (log\xi~5.5-7) gas. This gas may be a highly ionized outer layer of the torus.Comment: 10 pages, 9 figures, accepted for publication in Astronomy and Astrophysic

Highly ionized Fe K emission lines from the LINER galaxy M 81

We present spectral and timing results from a long (130 ks) XMM-NEWTON EPIC observation of the nucleus of the Seyfert/LINER galaxy M 81. During the observation the X-ray flux varied by 20%, but there was no significant change in spectral shape. The 2-10 keV spectrum is well described by a power law continuum and three narrow Fe K emission lines at 6.4, 6.7 and 6.96 keV. The three emission lines have equivalent widths of 39, 47, and 37 eV respectively. The ratios of the three lines are thus more similar to those observed from the Galactic Centre region than to those typically observed from Seyfert galaxies. The high ionization lines most likely originate either from photoionized gas within 0.1 pc of the nucleus of M 81, or from a non-thermal distribution of cosmic-ray electrons interacting with the 0.2-0.6 keV thermal plasma which is found in the bulge of M 81.Comment: Accepted for publication in A&