Azimuthal jet flavor tomography with CUJET2.0 of nuclear collisions at RHIC and LHC

A perturbative QCD based jet tomographic Monte Carlo model, CUJET2.0, is presented to predict jet quenching observables in relativistic heavy ion collisions at RHIC/BNL and LHC/CERN energies. This model generalizes the DGLV theory of flavor dependent radiative energy loss by including multi-scale running strong coupling effects. It generalizes CUJET1.0 by computing jet path integrations though more realistic 2+1D transverse and longitudinally expanding viscous hydrodynamical fields contrained by fits to low $p_T$ flow data. The CUJET2.0 output depends on three control parameters, $(\alpha_{max},f_E,f_M)$, corresponding to an assumed upper bound on the vacuum running coupling in the infrared and two chromo-electric and magnetic QGP screening mass scales $(f_E \mu(T), f_M \mu(T))$ where $\mu(T)$ is the 1-loop Debye mass. We compare numerical results as a function of $\alpha_{max}$ for pure and deformed HTL dynamically enhanced scattering cases corresponding to $(f_E=1,2, f_M=0)$ to data of the nuclear modification factor, $R^f_{AA}(p_T,\phi; \sqrt{s}, b)$ for jet fragment flavors $f=\pi,D, B, e$ at $\sqrt{s}=0.2-2.76$ ATeV c.m. energies per nucleon pair and with impact parameter $b=2.4, 7.5$ fm. A $\chi^2$ analysis is presented and shows that $R^\pi_{AA}$ data from RHIC and LHC are consistent with CUJET2.0 at the $\chi^2/d.o.f< 2$ level for $\alpha_{max}=0.23-0.30$. The corresponding $\hat{q}(E_{jet}, T)/T^3$ effective jet transport coefficient field of this model is computed to facilitate comparison to other jet tomographic models in the literature. The predicted elliptic asymmetry, $v_2(p_T;\sqrt{s},b)$ is, however, found to significantly underestimated relative to RHIC and LHC data. We find the $\chi^2_{v_2}$ analysis shows that $v_2$ is very sensitive to allowing even as little as 10\% variations of the path averaged $\alpha_{max}$ along in and out of reaction plane paths.Comment: 87 pages, 32 figures; v3: typos corrected, new references and discussions included; accepted by JHE

Analysis of Thisbe and Pyramus functional domains reveals evidence for cleavage of Drosophila FGFs

Background: As important regulators of developmental and adult processes in metazoans, Fibroblast Growth Factor (FGF) proteins are potent signaling molecules whose activities must be tightly regulated. FGFs are known to play diverse roles in many processes, including mesoderm induction, branching morphogenesis, organ formation, wound healing and malignant transformation; yet much more remains to be learned about the mechanisms of regulation used to control FGF activity. Results: In this work, we conducted an analysis of the functional domains of two Drosophila proteins, Thisbe (Ths) and Pyramus (Pyr), which share homology with the FGF8 subfamily of ligands in vertebrates. Ths and Pyr proteins are secreted from Drosophila Schneider cells (S2) as smaller N-terminal fragments presumably as a result of intracellular proteolytic cleavage. Cleaved forms of Ths and Pyr can be detected in embryonic extracts as well. The FGF-domain is contained within the secreted ligand portion, and this domain alone is capable of functioning in the embryo when ectopically expressed. Through targeted ectopic expression experiments in which we assay the ability of full-length, truncated, and chimeric proteins to support cell differentiation, we find evidence that (1) the C-terminal domain of Pyr is retained inside the cell and does not seem to be required for receptor activation and (2) the C-terminal domain of Ths is secreted and, while also not required for receptor activation, this domain does plays a role in limiting the activity of Ths when present. Conclusions: We propose that differential protein processing may account for the previously observed inequalities in signaling capabilities between Ths and Pyr. While the regulatory mechanisms are likely complex, studies such as ours conducted in a tractable model system may be able to provide insights into how ligand processing regulates growth factor activity

Enhanced heterogeneity of rpoB in Mycobacterium tuberculosis found at low pH.

OBJECTIVES: The aim of this study was to gain an insight into the molecular mechanisms of the evolution of rifampicin resistance in response to controlled changes in the environment. METHODS: We determined the proportion of rpoB mutants in the chemostat culture and characterized the sequence of mutations found in the rifampicin resistance-determining region of rpoB in a steady-state chemostat at pH 7.0 and 6.2. RESULTS: The overall proportion of rpoB mutants of strain H37Rv remained constant for 37 days at pH 7.0, ranging between 3.6 x 10(-8) and 8.9 x 10(-8); however, the spectrum of mutations varied. The most commonly detected mutation, serine to leucine mutation at codon 531 (S531L), increased from 40% to 89%, while other mutations (S531W, H526Y, H526D, H526R, S522L and D516V) decreased over the 37 day sampling period. Changing the pH from 7.0 to 6.2 did not significantly alter the overall proportion of mutants, but resulted in a decrease in the percentage of strains harbouring S531L (from 89% to 50%) accompanied by an increase in the range of different mutations from 4 to 12. CONCLUSIONS: The data confirm that the fitness of strains with the S531L mutation is greater than that of strains containing other mutations. We also conclude that at low pH the environment is permissive for a wider spectrum of mutations, which may provide opportunities for a successful mutant to survive