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

On the mechanisms of heavy-quarkonium hadroproduction

We discuss the various mechanisms potentially at work in hadroproduction of heavy quarkonia in the light of computations of higher-order QCD corrections both in the Colour-Singlet (CS) and Colour-Octet (CO) channels and the inclusion of the contribution arising from the s-channel cut in the CS channel. We also discuss new observables meant to better discriminate between these different mechanisms.Comment: Invited review talk at 3rd International Conference On Hard And Electromagnetic Probes Of High-Energy Nuclear Collisions (HP2008), 8-14 June 2008, Illa da Toxa, Galicia, Spain. 11 pages, 21 figures, LaTeX, uses svjour.cls and svepj.clo (included

Narcissism normalisation: tourism influences and sustainability implications

The concept of narcissism normalisation suggests that individuals and societies are becoming more narcissistic due to various cultural influences. Tourism is reviewed here as one such possible influence. Exploitative, entitled and exhibitionistic tendencies associated with narcissism are wellestablished in tourism. Yet tourism is also an intimate, communal and satisfying activity which may counteract narcissism. Increases in narcissism have significant implications from a sustainable tourism perspective. Narcissism is associated with exploitative and entitled behaviours that over time cause significant harm to those people and landscapes that come into contact with. Narcissism appears to be incompatible with principles of sustainability and the challenges this poses for the industry are reviewed, while the opportunities are also explored. There are signs that narcissism, particularly those aspects relating to exhibitionism, can be co-opted to benefit sustainable development

The non-random walk of stock prices: The long-term correlation between signs and sizes

We investigate the random walk of prices by developing a simple model relating the properties of the signs and absolute values of individual price changes to the diffusion rate (volatility) of prices at longer time scales. We show that this benchmark model is unable to reproduce the diffusion properties of real prices. Specifically, we find that for one hour intervals this model consistently over-predicts the volatility of real price series by about 70%, and that this effect becomes stronger as the length of the intervals increases. By selectively shuffling some components of the data while preserving others we are able to show that this discrepancy is caused by a subtle but long-range non-contemporaneous correlation between the signs and sizes of individual returns. We conjecture that this is related to the long-memory of transaction signs and the need to enforce market efficiency.Comment: 9 pages, 5 figures, StatPhys2

An Embedding for General Relativity and its Implications for New Physics

We show that any solution of the 4D Einstein equations of general relativity in vacuum with a cosmological constant may be embedded in a solution of the 5D Ricci-flat equations with an effective 4D cosmological "constant" that is a specific function of the extra coordinate. For unified theories of the forces in higher dimensions, this has major physical implications

Heavy quarkonium: progress, puzzles, and opportunities

A golden age for heavy quarkonium physics dawned a decade ago, initiated by the confluence of exciting advances in quantum chromodynamics (QCD) and an explosion of related experimental activity. The early years of this period were chronicled in the Quarkonium Working Group (QWG) CERN Yellow Report (YR) in 2004, which presented a comprehensive review of the status of the field at that time and provided specific recommendations for further progress. However, the broad spectrum of subsequent breakthroughs, surprises, and continuing puzzles could only be partially anticipated. Since the release of the YR, the BESII program concluded only to give birth to BESIII; the $B$-factories and CLEO-c flourished; quarkonium production and polarization measurements at HERA and the Tevatron matured; and heavy-ion collisions at RHIC have opened a window on the deconfinement regime. All these experiments leave legacies of quality, precision, and unsolved mysteries for quarkonium physics, and therefore beg for continuing investigations. The plethora of newly-found quarkonium-like states unleashed a flood of theoretical investigations into new forms of matter such as quark-gluon hybrids, mesonic molecules, and tetraquarks. Measurements of the spectroscopy, decays, production, and in-medium behavior of c\bar{c}, b\bar{b}, and b\bar{c} bound states have been shown to validate some theoretical approaches to QCD and highlight lack of quantitative success for others. The intriguing details of quarkonium suppression in heavy-ion collisions that have emerged from RHIC have elevated the importance of separating hot- and cold-nuclear-matter effects in quark-gluon plasma studies. This review systematically addresses all these matters and concludes by prioritizing directions for ongoing and future efforts.Comment: 182 pages, 112 figures. Editors: N. Brambilla, S. Eidelman, B. K. Heltsley, R. Vogt. Section Coordinators: G. T. Bodwin, E. Eichten, A. D. Frawley, A. B. Meyer, R. E. Mitchell, V. Papadimitriou, P. Petreczky, A. A. Petrov, P. Robbe, A. Vair

Shrinking a large dataset to identify variables associated with increased risk of Plasmodium falciparum infection in Western Kenya

Large datasets are often not amenable to analysis using traditional single-step approaches. Here, our general objective was to apply imputation techniques, principal component analysis (PCA), elastic net and generalized linear models to a large dataset in a systematic approach to extract the most meaningful predictors for a health outcome. We extracted predictors for Plasmodium falciparum infection, from a large covariate dataset while facing limited numbers of observations, using data from the People, Animals, and their Zoonoses (PAZ) project to demonstrate these techniques: data collected from 415 homesteads in western Kenya, contained over 1500 variables that describe the health, environment, and social factors of the humans, livestock, and the homesteads in which they reside. The wide, sparse dataset was simplified to 42 predictors of P. falciparum malaria infection and wealth rankings were produced for all homesteads. The 42 predictors make biological sense and are supported by previous studies. This systematic data-mining approach we used would make many large datasets more manageable and informative for decision-making processes and health policy prioritization

High-field phase-diagram of Fe arsenide superconductors

Here, we report an overview of the phase diagram of single layered and double layered Fe arsenide superconductors at high magnetic fields. Our systematic magnetotransport measurements of polycrystalline SmFeAsO$_{1-x}$F$_x$ at different doping levels confirm the upward curvature of the upper critical magnetic field $H_{c2}(T)$ as a function of temperature $T$ defining the phase boundary between the superconducting and metallic states for crystallites with the ab planes oriented nearly perpendicular to the magnetic field. We further show from measurements on single crystals that this feature, which was interpreted in terms of the existence of two superconducting gaps, is ubiquitous among both series of single and double layered compounds. In all compounds explored by us the zero temperature upper critical field $H_{c2}(0)$, estimated either through the Ginzburg-Landau or the Werthamer-Helfand-Hohenberg single gap theories, strongly surpasses the weak coupling Pauli paramagnetic limiting field. This clearly indicates the strong coupling nature of the superconducting state and the importance of magnetic correlations for these materials. Our measurements indicate that the superconducting anisotropy, as estimated through the ratio of the effective masses $\gamma = (m_c/m_{ab})^{1/2}$ for carriers moving along the c-axis and the ab planes, respectively, is relatively modest as compared to the high-$T_c$ cuprates, but it is temperature, field and even doping dependent. Finally, our preliminary estimations of the irreversibility field $H_m(T)$, separating the vortex-solid from the vortex-liquid phase in the single layered compounds, indicates that it is well described by the melting of a vortex lattice in a moderately anisotropic uniaxial superconductor.Comment: 12 pages, for Physica C, special issue on the Fe oxypnictides (revised version

Observation of Orbitally Excited B_s Mesons

We report the first observation of two narrow resonances consistent with states of orbitally excited (L=1) B_s mesons using 1 fb^{-1} of ppbar collisions at sqrt{s} = 1.96 TeV collected with the CDF II detector at the Fermilab Tevatron. We use two-body decays into K^- and B^+ mesons reconstructed as B^+ \to J/\psi K^+, J/\psi \to \mu^+ \mu^- or B^+ \to \bar{D}^0 \pi^+, \bar{D}^0 \to K^+ \pi^-. We deduce the masses of the two states to be m(B_{s1}) = 5829.4 +- 0.7 MeV/c^2 and m(B_{s2}^*) = 5839.7 +- 0.7 MeV/c^2.Comment: Version accepted and published by Phys. Rev. Let

Measurement of the Bottom-Strange Meson Mixing Phase in the Full CDF Data Set

We report a measurement of the bottom-strange meson mixing phase \beta_s using the time evolution of B0_s -> J/\psi (->\mu+\mu-) \phi (-> K+ K-) decays in which the quark-flavor content of the bottom-strange meson is identified at production. This measurement uses the full data set of proton-antiproton collisions at sqrt(s)= 1.96 TeV collected by the Collider Detector experiment at the Fermilab Tevatron, corresponding to 9.6 fb-1 of integrated luminosity. We report confidence regions in the two-dimensional space of \beta_s and the B0_s decay-width difference \Delta\Gamma_s, and measure \beta_s in [-\pi/2, -1.51] U [-0.06, 0.30] U [1.26, \pi/2] at the 68% confidence level, in agreement with the standard model expectation. Assuming the standard model value of \beta_s, we also determine \Delta\Gamma_s = 0.068 +- 0.026 (stat) +- 0.009 (syst) ps-1 and the mean B0_s lifetime, \tau_s = 1.528 +- 0.019 (stat) +- 0.009 (syst) ps, which are consistent and competitive with determinations by other experiments.Comment: 8 pages, 2 figures, Phys. Rev. Lett 109, 171802 (2012