Design and evaluation of 16S rRNA sequence based oligonucleotide probes for the detection and quantification of Comamonas testosteroni in mixed microbial communities

Background The β-proteobacterial species Comamonas testosteroni is capable of biotransformation and also biodegradation of a range of chemical compounds and thus potentially useful in chemical manufacturing and bioremediation. The ability to detect and quantify members of this species in mixed microbial communities thus may be desirable. Results We have designed an oligonucleotide probe for use in fluorescent in situ hybridization (FISH) and two pairs of PCR primers targeting a C. testosteroni subgroup. The FISH probe and one of the PCR primer pairs are suitable for quantification of C. testosteroni in mixed microbial communities using FISH followed by quantitative image analysis or real-time quantitative PCR, respectively. This has been shown by analysis of samples from an enrichment of activated sludge on testosterone resulting in an increase in abundance and finally isolation of C. testosteroni. Additionally, we have successfully used quantitative PCR to follow the C. testosteroni abundance during a laboratory scale wastewater bioaugmentation experiment. Conclusion The oligonucleotides presented here provide a useful tool to study C. testosteroni population dynamics in mixed microbial communities

Centrality dependence of high energy jets in p+Pb collisions at the LHC

The recently measured centrality dependence of high energy jets in proton-lead collisions at the LHC is investigated. We hypothesize that events with jets of very high energy (a few hundred GeV) are characterized by a suppressed number of soft particles, thus shifting these events into more peripheral bins. This naturally results in the suppression (enhancement) of the nuclear modification factor, $R_{pA}$, in central (peripheral) collisions. Our calculations suggest that a moderate suppression of the order of $20\%$, for $10^{3}$ GeV jets, can quantitatively reproduce the experimental data. We further extract the suppression factor as a function of jet energy and test our conjecture using available $R_{pA}$ data for various centralities.Comment: 5 pages, 4 figures; extended discussion, comparison with data adde

Geometrically nonlinear analysis of thin-walled composite box beams

A general geometrically nonlinear model for thin-walled composite space beams with arbitrary lay-ups under various types of loadings has been presented by using variational formulation based on the classical lamination theory. The nonlinear governing equations are derived and solved by means of an incremental Newton–Raphson method. A displacement-based one-dimensional finite element model that accounts for the geometric nonlinearity in the von Kármán sense is developed. Numerical results are obtained for thin-walled composite box beam under vertical load to investigate the effect of geometric nonlinearity and address the effects of the fiber orientation, laminate stacking sequence, load parameter on axial–flexural–torsional response

Direct Photon Production in Au+Au Collisions at RHIC-PHENIX Experiment

Direct photons have been measured with the PHENIX experiment in Au+Au collisions at $\sqrt{s_\mathrm{NN}}$ = 200 GeV. The direct photon result obtained with PHENIX-EMCal up to 18 GeV/$c$ is consistent with the NLO pQCD calculation scaled by the nuclear overlap function. The measurement using internal conversion of photons into $e^+e^-$ shows the enhancement of the yield comparing with NLO pQCD calculation.Comment: 4 pages, 5 figures. Contributed parallel talk at Hard Probes 2006, Asilomar CA USA, Jun. 9-16, 200

Direct photons measured by the PHENIX experiment at RHIC

Results from the PHENIX experiment at RHIC on direct photon production in p+p, d+Au, and Au+Au collisions at sqrt(s_NN) = 200 GeV are presented. In p+p collisions, direct photon production at high p_T behaves as expected from perturbative QCD calculations. The p+p measurement serves as a baseline for direct photon production in Au+Au collisions. In d+Au collisions, no effects of cold nuclear matter are found within the large uncertainty of the measurement. In Au+Au collisions, the production of high p_T direct photons scales as expected for particle production in hard scatterings. This supports jet quenching models, which attribute the suppression of high p_T hadrons to the energy loss of fast partons in the medium produced in the collision. Low p_T direct photons, measured via e+e- pairs with small invariant mass, are possibly related to the production of thermal direct photons.Comment: 5 pages, 5 figures, Proceedings of the Hot Quarks 2006 Workshop for young scientists on the physics of ultra-relativistic nucleus-nucleus collisions, Villasimius, Sardinia, Italy, May 15--20, 200

Conformational Dynamics of Supramolecular Protein Assemblies in the EMDB

The Electron Microscopy Data Bank (EMDB) is a rapidly growing repository for the dissemination of structural data from single-particle reconstructions of supramolecular protein assemblies including motors, chaperones, cytoskeletal assemblies, and viral capsids. While the static structure of these assemblies provides essential insight into their biological function, their conformational dynamics and mechanics provide additional important information regarding the mechanism of their biological function. Here, we present an unsupervised computational framework to analyze and store for public access the conformational dynamics of supramolecular protein assemblies deposited in the EMDB. Conformational dynamics are analyzed using normal mode analysis in the finite element framework, which is used to compute equilibrium thermal fluctuations, cross-correlations in molecular motions, and strain energy distributions for 452 of the 681 entries stored in the EMDB at present. Results for the viral capsid of hepatitis B, ribosome-bound termination factor RF2, and GroEL are presented in detail and validated with all-atom based models. The conformational dynamics of protein assemblies in the EMDB may be useful in the interpretation of their biological function, as well as in the classification and refinement of EM-based structures.Comment: Associated online data bank available at: http://lcbb.mit.edu/~em-nmdb