A concerted systems biology analysis of phenol metabolism in Rhodococcus opacus PD630

Rhodococcus opacus PD630 metabolizes aromatic substrates and naturally produces branched-chain lipids, which are advantageous traits for lignin valorization. To provide insights into its lignocellulose hydrolysate utilization, we performed 13C-pathway tracing, 13C-pulse-tracing, transcriptional profiling, biomass composition analysis, and metabolite profiling in conjunction with 13C-metabolic flux analysis (13C-MFA) of phenol metabolism. We found that 1) phenol is metabolized mainly through the ortho–cleavage pathway; 2) phenol utilization requires a highly active TCA cycle; 3) NADPH is generated mainly via NADPH-dependent isocitrate dehydrogenase; 4) active cataplerotic fluxes increase plasticity in the TCA cycle; and 5) gluconeogenesis occurs partially through the reversed Entner–Doudoroff pathway (EDP). We also found that phenol-fed R. opacus PD630 generally has lower sugar phosphate concentrations (e.g., fructose 1,6-bisphosphatase) compared to metabolite pools in 13C-glucose-fed Escherichia coli (set as internal standards), while its TCA metabolites (e.g., malate, succinate, and α-ketoglutarate) accumulate intracellularly with measurable succinate secretion. In addition, we found that phenol utilization was inhibited by benzoate, while catabolite repressions by other tested carbon substrates (e.g., glucose and acetate) were absent in R. opacus PD630. Three adaptively-evolved strains display very different growth rates when fed with phenol as a sole carbon source, but they maintain a conserved flux network. These findings improve our understanding of R. opacus’ metabolism for future lignin valorization

Hartree-Fock Theory of Skyrmions in Quantum Hall Ferromagnets

We report on a study of the charged-skyrmion or spin-texture excitations which occur in quantum Hall ferromagnets near odd Landau level filling factors. Particle-hole symmetry is used to relate the spin-quantum numbers of charged particle and hole excitations and neutral particle-hole pair excitations. Hartree-Fock theory is used to provide quantitative estimates of the energies of these excitations and their dependence on Zeeman coupling strength, Landau level quantum numbers, and the thicknesses of the two-dimensional electron layers. For the case of $\nu$ near three we suggest the possibility of first order phase transitions with increasing Zeeman coupling strength from a many skyrmion state to one with many maximally spin-polarized quasiparticles.Comment: 26 pages, 10 figure

Structural Invariance of Sunspot Umbrae Over the Solar Cycle: 1993-2004

Measurements of maximum magnetic flux, minimum intensity, and size are presented for 12 967 sunspot umbrae detected on the NASA/NSO spectromagnetograms between 1993 and 2004 to study umbral structure and strength during the solar cycle. The umbrae are selected using an automated thresholding technique. Measured umbral intensities are first corrected for a confirming observation of umbral limb-darkening. Log-normal fits to the observed size distribution confirm that the size spectrum shape does not vary with time. The intensity-magnetic flux relationship is found to be steady over the solar cycle. The dependence of umbral size on the magnetic flux and minimum intensity are also independent of cycle phase and give linear and quadratic relations, respectively. While the large sample size does show a low amplitude oscillation in the mean minimum intensity and maximum magnetic flux correlated with the solar cycle, this can be explained in terms of variations in the mean umbral size. These size variations, however, are small and do not substantiate a meaningful change in the size spectrum of the umbrae generated by the Sun. Thus, in contrast to previous reports, the observations suggest the equilibrium structure, as testified by the invariant size-magnetic field relationship, as well as the mean size (i.e. strength) of sunspot umbrae do not significantly depend on solar cycle phase.Comment: 17 pages, 6 figures. Published in Solar Physic

Spontaneous Coherence and Collective Modes in Double-Layer Quantum Dot Systems

We study the ground state and the collective excitations of parabolically-confined double-layer quantum dot systems in a strong magnetic field. We identify parameter regimes where electrons form maximum density droplet states, quantum-dot analogs of the incompressible states of the bulk integer quantum Hall effect. In these regimes the Hartree-Fock approximation and the time-dependent Hartree-Fock approximations can be used to describe the ground state and collective excitations respectively. We comment on the relationship between edge excitations of dots and edge magneto-plasmon excitations of bulk double-layer systems.Comment: 20 pages (figures included) and also available at http://fangio.magnet.fsu.edu/~jhu/Paper/qdot_cond.ps, replaced to fix figure

Collision statistics of driven granular materials

We present an experimental investigation of the statistical properties of spherical granular particles on an inclined plane that are excited by an oscillating side-wall. The data is obtained by high-speed imaging and particle tracking techniques. We identify all particles in the system and link their positions to form trajectories over long times. Thus, we identify particle collisions to measure the effective coefficient of restitution and find a broad distribution of values for the same impact angles. We find that the energy inelasticity can take on values greater than one, which implies that the rotational degrees play an important role in energy transfer. We also measure the distance and the time between collision events in order to directly determine the distribution of path lengths and the free times. These distributions are shown to deviate from expected theoretical forms for elastic spheres, demonstrating the inherent clustering in this system. We describe the data with a two-parameter fitting function and use it to calculated the mean free path and collision time. We find that the ratio of these values is consistent with the average velocity. The velocity distribution are observed to be strongly non-Gaussian and do not demonstrate any apparent universal behavior. We report the scaling of the second moment, which corresponds to the granular temperature, and higher order moments as a function of distance from the driving wall. Additionally, we measure long time correlation functions in both space and in the velocities to probe diffusion in a dissipative gas.Comment: 12 pages, 4 figures, uses revtex

Non-monotonic variation with salt concentration of the second virial coefficient in protein solutions

The osmotic virial coefficient $B_2$ of globular protein solutions is calculated as a function of added salt concentration at fixed pH by computer simulations of the ``primitive model''. The salt and counter-ions as well as a discrete charge pattern on the protein surface are explicitly incorporated. For parameters roughly corresponding to lysozyme, we find that $B_2$ first decreases with added salt concentration up to a threshold concentration, then increases to a maximum, and then decreases again upon further raising the ionic strength. Our studies demonstrate that the existence of a discrete charge pattern on the protein surface profoundly influences the effective interactions and that non-linear Poisson Boltzmann and Derjaguin-Landau-Verwey-Overbeek (DLVO) theory fail for large ionic strength. The observed non-monotonicity of $B_2$ is compared to experiments. Implications for protein crystallization are discussed.Comment: 43 pages, including 17 figure

Dual stem cell therapy synergistically improves cardiac function and vascular regeneration following myocardial infarction

Since both myocardium and vasculature in the heart are excessively damaged following myocardial infarction (MI), therapeutic strategies for treating MI hearts should concurrently target both so as to achieve true cardiac repair. Here we demonstrate a concomitant method that exploits the advantages of cardiomyocytes derived from human induced pluripotent stem cells (hiPSC-CMs) and human mesenchymal stem cell-loaded patch (hMSC-PA) to amplify cardiac repair in a rat MI model. Epicardially implanted hMSC-PA provide a complimentary microenvironment which enhances vascular regeneration through prolonged secretion of paracrine factors, but more importantly it significantly improves the retention and engraftment of intramyocardially injected hiPSC-CMs which ultimately restore the cardiac function. Notably, the majority of injected hiPSC-CMs display adult CMs like morphology suggesting that the secretomic milieu of hMSC-PA constitutes pleiotropic effects in vivo. We provide compelling evidence that this dual approach can be a promising means to enhance cardiac repair on MI hearts.11Ysciescopu

Six Years of Chandra Observations of Supernova Remnants

We present a review of the first six years of Chandra X-ray Observatory observations of supernova remnants. From the official "first-light" observation of Cassiopeia A that revealed for the first time the compact remnant of the explosion, to the recent million-second spectrally-resolved observation that revealed new details of the stellar composition and dynamics of the original explosion, Chandra observations have provided new insights into the supernova phenomenon. We present an admittedly biased overview of six years of these observations, highlighting new discoveries made possible by Chandra's unique capabilities.Comment: 82 pages, 28 figures, for the book Astrophysics Update

Modeling the Subsurface Structure of Sunspots

While sunspots are easily observed at the solar surface, determining their subsurface structure is not trivial. There are two main hypotheses for the subsurface structure of sunspots: the monolithic model and the cluster model. Local helioseismology is the only means by which we can investigate subphotospheric structure. However, as current linear inversion techniques do not yet allow helioseismology to probe the internal structure with sufficient confidence to distinguish between the monolith and cluster models, the development of physically realistic sunspot models are a priority for helioseismologists. This is because they are not only important indicators of the variety of physical effects that may influence helioseismic inferences in active regions, but they also enable detailed assessments of the validity of helioseismic interpretations through numerical forward modeling. In this paper, we provide a critical review of the existing sunspot models and an overview of numerical methods employed to model wave propagation through model sunspots. We then carry out an helioseismic analysis of the sunspot in Active Region 9787 and address the serious inconsistencies uncovered by \citeauthor{gizonetal2009}~(\citeyear{gizonetal2009,gizonetal2009a}). We find that this sunspot is most probably associated with a shallow, positive wave-speed perturbation (unlike the traditional two-layer model) and that travel-time measurements are consistent with a horizontal outflow in the surrounding moat.Comment: 73 pages, 19 figures, accepted by Solar Physic

Anisotropic flow of charged hadrons, pions and (anti-)protons measured at high transverse momentum in Pb-Pb collisions at sNN=2.76\sqrt{s_{\rm NN}}=2.76 TeV

The elliptic, $v_2$, triangular, $v_3$, and quadrangular, $v_4$, azimuthal anisotropic flow coefficients are measured for unidentified charged particles, pions and (anti-)protons in Pb-Pb collisions at $\sqrt{s_{\rm NN}} = 2.76$ TeV with the ALICE detector at the Large Hadron Collider. Results obtained with the event plane and four-particle cumulant methods are reported for the pseudo-rapidity range $|\eta|<0.8$ at different collision centralities and as a function of transverse momentum, $p_{\rm T}$, out to $p_{\rm T}=20$ GeV/$c$. The observed non-zero elliptic and triangular flow depends only weakly on transverse momentum for $p_{\rm T}>8$ GeV/$c$. The small $p_{\rm T}$ dependence of the difference between elliptic flow results obtained from the event plane and four-particle cumulant methods suggests a common origin of flow fluctuations up to $p_{\rm T}=8$ GeV/$c$. The magnitude of the (anti-)proton elliptic and triangular flow is larger than that of pions out to at least $p_{\rm T}=8$ GeV/$c$ indicating that the particle type dependence persists out to high $p_{\rm T}$.Comment: 16 pages, 5 captioned figures, authors from page 11, published version, figures at http://aliceinfo.cern.ch/ArtSubmission/node/186