Cofactor specificity motifs and the induced fit mechanism in class I ketol-acid reductoisomerases

Although most sequenced members of the industrially important ketol-acid reductoisomerase (KARI) family are class I enzymes, structural studies to date have focused primarily on the class II KARIs, which arose through domain duplication. In the present study, we present five new crystal structures of class I KARIs. These include the first structure of a KARI with a six-residue β2αB (cofactor specificity determining) loop and an NADPH phosphate-binding geometry distinct from that of the seven- and 12-residue loops. We also present the first structures of naturally occurring KARIs that utilize NADH as cofactor. These results show insertions in the specificity loops that confounded previous attempts to classify them according to loop length. Lastly, we explore the conformational changes that occur in class I KARIs upon binding of cofactor and metal ions. The class I KARI structures indicate that the active sites close upon binding NAD(P)H, similar to what is observed in the class II KARIs of rice and spinach and different from the opening of the active site observed in the class II KARI of Escherichia coli. This conformational change involves a decrease in the bending of the helix that runs between the domains and a rearrangement of the nicotinamide-binding site

Gain in a quantum wire laser of high uniformity

A multi-quantum wire laser operating in the 1-D ground state has been achieved in a very high uniformity structure that shows free exciton emission with unprecedented narrow width and low lasing threshold. Under optical pumping the spontaneous emission evolves from a sharp free exciton peak to a red-shifted broad band. The lasing photon energy occurs about 5 meV below the free exciton. The observed shift excludes free excitons in lasing and our results show that Coulomb interactions in the 1-D electron-hole system shift the spontaneous emission and play significant roles in laser gain.Comment: 4 pages, 4 figures, prepared by RevTe

Indirect detection of infinite-speed MAS solid-state NMR spectra

Heavy spin-1/2 nuclides are known to possess very large chemical shift anisotropies that can challenge even the most advanced magic-angle-spinning (MAS) techniques. Wide manifolds of overlapping spinning sidebands and insufficient excitation bandwidths often obfuscate meaningful spectral information and force the use of static, low-resolution solid-state (SS)NMR methods for the characterization of materials. To address these issues, we have merged fast-magic-angle-turning (MAT) and dipolar heteronuclear multiple-quantum coherence (D-HMQC) experiments to obtain D-HMQC-MAT pulse sequences which enable the rapid acquisition of 2D SSNMR spectra that correlate isotropic 1H chemical shifts to the indirectly detected isotropic “infinite-MAS” spectra of heavy spin-1/2 nuclides. For these nuclides, the combination of fast MAS and 1H detection provides a high sensitivity, which rivals the DNP-enhanced ultra-wideline SSNMR. The new pulse sequences were used to determine the Pt coordination environments in a complex mixture of decomposition products of transplatin and in a metal-organic framework with Pt ions coordinated to the linker ligands

The Clustering of Luminous Red Galaxies in the Sloan Digital Sky Survey Imaging Data

We present the 3D real space clustering power spectrum of a sample of \~600,000 luminous red galaxies (LRGs) measured by the Sloan Digital Sky Survey (SDSS), using photometric redshifts. This sample of galaxies ranges from redshift z=0.2 to 0.6 over 3,528 deg^2 of the sky, probing a volume of 1.5 (Gpc/h)^3, making it the largest volume ever used for galaxy clustering measurements. We measure the angular clustering power spectrum in eight redshift slices and combine these into a high precision 3D real space power spectrum from k=0.005 (h/Mpc) to k=1 (h/Mpc). We detect power on gigaparsec scales, beyond the turnover in the matter power spectrum, on scales significantly larger than those accessible to current spectroscopic redshift surveys. We also find evidence for baryonic oscillations, both in the power spectrum, as well as in fits to the baryon density, at a 2.5 sigma confidence level. The statistical power of these data to constrain cosmology is ~1.7 times better than previous clustering analyses. Varying the matter density and baryon fraction, we find \Omega_M = 0.30 \pm 0.03, and \Omega_b/\Omega_M = 0.18 \pm 0.04, The detection of baryonic oscillations also allows us to measure the comoving distance to z=0.5; we find a best fit distance of 1.73 \pm 0.12 Gpc, corresponding to a 6.5% error on the distance. These results demonstrate the ability to make precise clustering measurements with photometric surveys (abridged).Comment: 23 pages, 27 figures, submitted to MNRA

Targeting nuclear transporters in cancer: Diagnostic, prognostic and therapeutic potential

The Karyopherin superfamily is a major class of soluble transport receptors consisting of both import and export proteins. The trafficking of proteins involved in transcription, cell signalling and cell cycle regulation among other functions across the nuclear membrane is essential for normal cellular functioning. However, in cancer cells, the altered expression or localization of nuclear transporters as well as the disruption of endogenous nuclear transport inhibitors are some ways in which the Karyopherin proteins are dysregulated. The value of nuclear transporters in the diagnosis, prognosis and treatment of cancer is currently being elucidated with recent studies highlighting their potential as biomarkers and therapeutic targets

Far Ultraviolet Emission in the A2597 and A2204 Brightest Cluster Galaxies

We use the Hubble Space Telescope ACS/SBC and Very Large Telescope FORS cameras to observe the Brightest Cluster Galaxies in Abell 2597 and Abell 2204 in the far-ultraviolet (FUV) F150LP and optical U, B, V, R, I Bessel filters. The FUV and U band emission is enhanced in bright, filamentary structures surrounding the BCG nuclei. These filaments can be traced out to 20 kpc from the nuclei in the FUV. Excess FUV and U band light is determined by removing emission due to the underlying old stellar population and mapped with 1 arcsec spatial resolution over the central 20 kpc regions of both galaxies. We find the FUV and U excess emission to be spatially coincident and a stellar interpretation requires the existence of a significant amount of 10000-50000 K stars. Correcting for nebular continuum emission and dust intrinsic to the BCG further increases the FUV to U band emission ratio and implies that stars alone may not suffice to explain the observations. However, lack of detailed information on the gas and dust distribution and extinction law in these systems prevents us from ruling out a purely stellar origin. Non-stellar processes, such as the central AGN, Scattering, Synchrotron and Bremsstrahlung emission are investigated and found to not be able to explain the FUV and U band measurements in A2597. Contributions from non-thermal processes not treated here should be investigated. Comparing the FUV emission to the optical H-alpha line emitting nebula shows good agreement on kpc-scales in both A2597 and A2204. In concordance with an earlier investigation by O'Dea et al. (2004) we find that O-stars can account for the ionising photons necessary to explain the observed H-alpha line emission.Comment: accepted by mnra

Acoustic scale from the angular power spectra of SDSS-III DR8 photometric luminous galaxies

We measure the acoustic scale from the angular power spectra of the Sloan Digital Sky Survey III (SDSS-III) Data Release 8 imaging catalog that includes 872,921 galaxies over ~ 10,000 deg^2 between 0.45<z<0.65. The extensive spectroscopic training set of the Baryon Oscillation Spectroscopic Survey (BOSS) luminous galaxies allows precise estimates of the true redshift distributions of galaxies in our imaging catalog. Utilizing the redshift distribution information, we build templates and fit to the power spectra of the data, which are measured in our companion paper, Ho et al. 2011, to derive the location of Baryon acoustic oscillations (BAO) while marginalizing over many free parameters to exclude nearly all of the non-BAO signal. We derive the ratio of the angular diameter distance to the sound horizon scale D_A/r_s= 9.212 + 0.416 -0.404 at z=0.54, and therefore, D_A= 1411+- 65 Mpc at z=0.54; the result is fairly independent of assumptions on the underlying cosmology. Our measurement of angular diameter distance D_A is 1.4 \sigma higher than what is expected for the concordance LCDM (Komatsu et al. 2011), in accordance to the trend of other spectroscopic BAO measurements for z >~ 0.35. We report constraints on cosmological parameters from our measurement in combination with the WMAP7 data and the previous spectroscopic BAO measurements of SDSS (Percival et al. 2010) and WiggleZ (Blake et al. 2011). We refer to our companion papers (Ho et al. 2011; de Putter et al. 2011) for investigations on information of the full power spectrum.Comment: 16 pages, 14 figures, 3 tables, submitted to Ap

The clustering of galaxies in the SDSS-III Baryon Oscillation Spectroscopic Survey: cosmological implications of the large-scale two-point correlation function

We obtain constraints on cosmological parameters from the spherically averaged redshift-space correlation function of the CMASS Data Release 9 (DR9) sample of the Baryonic Oscillation Spectroscopic Survey (BOSS). We combine this information with additional data from recent CMB, SN and BAO measurements. Our results show no significant evidence of deviations from the standard flat-Lambda CDM model, whose basic parameters can be specified by Omega_m = 0.285 +- 0.009, 100 Omega_b = 4.59 +- 0.09, n_s = 0.96 +- 0.009, H_0 = 69.4 +- 0.8 km/s/Mpc and sigma_8 = 0.80 +- 0.02. The CMB+CMASS combination sets tight constraints on the curvature of the Universe, with Omega_k = -0.0043 +- 0.0049, and the tensor-to-scalar amplitude ratio, for which we find r < 0.16 at the 95 per cent confidence level (CL). These data show a clear signature of a deviation from scale-invariance also in the presence of tensor modes, with n_s <1 at the 99.7 per cent CL. We derive constraints on the fraction of massive neutrinos of f_nu < 0.049 (95 per cent CL), implying a limit of sum m_nu < 0.51 eV. We find no signature of a deviation from a cosmological constant from the combination of all datasets, with a constraint of w_DE = -1.033 +- 0.073 when this parameter is assumed time-independent, and no evidence of a departure from this value when it is allowed to evolve as w_DE(a) = w_0 + w_a (1 - a). The achieved accuracy on our cosmological constraints is a clear demonstration of the constraining power of current cosmological observations.Comment: 26 pages, 15 figures. Minor changes to match version accepted by MNRA

Evolution of the Most Massive Galaxies to z=0.6: I. A New Method for Physical Parameter Estimation

We use principal component analysis (PCA) to estimate stellar masses, mean stellar ages, star formation histories (SFHs), dust extinctions and stellar velocity dispersions for ~290,000 galaxies with stellar masses greater than $10^{11}Msun and redshifts in the range 0.4<z<0.7 from the Baryon Oscillation Spectroscopic Survey (BOSS). We find the fraction of galaxies with active star formation first declines with increasing stellar mass, but then flattens above a stellar mass of 10^{11.5}Msun at z~0.6. This is in striking contrast to z~0.1, where the fraction of galaxies with active star formation declines monotonically with stellar mass. At stellar masses of 10^{12}Msun, therefore, the evolution in the fraction of star-forming galaxies from z~0.6 to the present-day reaches a factor of ~10. When we stack the spectra of the most massive, star-forming galaxies at z~0.6, we find that half of their [OIII] emission is produced by AGNs. The black holes in these galaxies are accreting on average at ~0.01 the Eddington rate. To obtain these results, we use the stellar population synthesis models of Bruzual & Charlot (2003) to generate a library of model spectra with a broad range of SFHs, metallicities, dust extinctions and stellar velocity dispersions. The PCA is run on this library to identify its principal components over the rest-frame wavelength range 3700-5500A. We demonstrate that linear combinations of these components can recover information equivalent to traditional spectral indices such as the 4000A break strength and HdA, with greatly improved S/N. This method is able to recover physical parameters such as stellar mass-to-light ratio, mean stellar age, velocity dispersion and dust extinction from the relatively low S/N BOSS spectra. We examine the sensitivity of our stellar mass estimates to the input parameters in our model library and the different stellar population synthesis models.Comment: 20 pages, 18 Figures, submitted to MNRA