Aeromonas salmonicida, a bacterial fish pathogen, possesses a functional Type Three Secretion System (TTSS), which is essential for its virulence. The genes for this system are mainly located in a single region of the large pAsa5 plasmid. Bacteria lose the TTSS region from this plasmid through rearrangements when grown in stressful growth conditions. The A. salmonicida genome is rich in insertion sequences (ISs), which are mobile DNA elements that can cause DNA rearrangements in other bacterial species. pAsa5 possesses numerous ISs. Three IS11s from the IS256 family encircle the rearranged regions. To confirm that these IS11s are involved in pAsa5 rearrangements, 26 strains derived from strain A449 and two Canadian isolates (01-B526 and 01-B516) with a pAsa5 rearrangement were tested using a PCR approach to determine whether the rearrangements were the result of an IS11-dependent process. Nine out of the 26 strains had a positive PCR result, suggesting that the rearrangement in these strains were IS-dependent. The PCR analysis showed that all the rearrangements in the A449-derived strains were IS11-dependent process while the rearrangements in 01-B526 and 01-B516 could only be partially coupled to the action of IS11. Unidentified elements that affect IS-dependent rearrangements may be present in 01-B526 and 01-B516. Our results suggested that pAsa5 rearrangements involve IS11. This is the first study showing that ISs are involved in plasmid instability in A. salmonicida.

Aeromonas salmonicida is an important fish pathogen, mainly of salmonids. This bacterium causes a disease named furunculosis, which is particularly detrimental for the aquaculture industry. Here, we present the draft genome sequence of A. salmonicida 01-B526, a strain isolated from a brook trout that is more virulent than A. salmonicida reference strain A449, for which a genome sequence is available.

The production of e;{+}e;{-} pairs for m_{e;{+}e;{-}}<0.3 GeV/c;{2} and 1<p_{T}<5 GeV/c is measured in p+p and Au+Au collisions at sqrt[s_{NN}]=200 GeV. An enhanced yield above hadronic sources is observed. Treating the excess as photon internal conversions, the invariant yield of direct photons is deduced. In central Au+Au collisions, the excess of the direct photon yield over p+p is exponential in transverse momentum, with an inverse slope T=221+/-19;{stat}+/-19;{syst} MeV. Hydrodynamical models with initial temperatures ranging from T_{init} approximately 300-600 MeV at times of approximately 0.6-0.15 fm/c after the collision are in qualitative agreement with the data. Lattice QCD predicts a phase transition to quark gluon plasma at approximately 170 MeV.

Bose-Einstein correlations of charged kaons are used to probe Au+Au collisions at sqrt[s_{NN}]=200 GeV and are compared to charged pion probes, which have a larger hadronic scattering cross section. Three-dimensional Gaussian source radii are extracted, along with a one-dimensional kaon emission source function. The centrality dependences of the three Gaussian radii are well described by a single linear function of N_{part};{1/3} with a zero intercept. Imaging analysis shows a deviation from a Gaussian tail at r greater, similar10 fm, although the bulk emission at lower radius is well described by a Gaussian. The presence of a non-Gaussian tail in the kaon source reaffirms that the particle emission region in a heavy-ion collision is extended, and that similar measurements with pions are not solely due to the decay of long-lived resonances.

For Au+Au collisions at 200 GeV, we measure neutral pion production with good statistics for transverse momentum, p_{T}, up to 20 GeV/c. A fivefold suppression is found, which is essentially constant for 5<p_{T}<20 GeV/c. Experimental uncertainties are small enough to constrain any model-dependent parametrization for the transport coefficient of the medium, e.g., q[over ;] in the parton quenching model. The spectral shape is similar for all collision classes, and the suppression does not saturate in Au+Au collisions.

Measurements in Au+Au collisions at sqrt[s_{NN}]=200 GeV of jet correlations for a trigger hadron at intermediate transverse momentum (p_{T,trig}) with associated mesons or baryons at lower p_{T,assoc} indicate strong modification of the away-side jet. The ratio of jet-associated baryons to mesons increases with centrality and p_{T,assoc}. For the most central collisions, the ratio is similar to that for inclusive measurements. This trend is incompatible with in-vacuum fragmentation but could be due to jetlike contributions from correlated soft partons, which recombine upon hadronization.

A three-dimensional correlation function obtained from midrapidity, low p_{T}, pion pairs in central Au+Au collisions at sqrt[s_{NN}]=200 GeV is studied. The extracted model-independent source function indicates a long range tail in the directions of the pion pair transverse momentum (out) and the beam (long). A proper breakup time tau_{0} approximately 9 fm/c and a mean proper emission duration Deltatau approximately 2 fm/c, leading to sizable emission time differences (|Deltat_{LCM}| approximately 12 fm/c), are required to allow models to be successfully matched to these tails. The model comparisons also suggest an outside-in "burning" of the emission source reminiscent of many hydrodynamical models.

Differential elliptic flow (v_{2}) for varphi mesons and (anti)deuterons (d[over ])d is measured for Au+Au collisions at sqrt[s_{NN}]=200 GeV. The v_{2} for varphi mesons follows the trend of lighter pi;{+/-} and K;{+/-} mesons, suggesting that ordinary hadrons interacting with standard hadronic cross sections are not the primary driver for elliptic flow development. The v_{2} values for (d[over ])d suggest that elliptic flow is additive for composite particles. This further validation of the universal scaling of v_{2} per constituent quark for baryons and mesons suggests that partonic collectivity dominates the transverse expansion dynamics.

We present azimuthal angle correlations of intermediate transverse momentum (1-4 GeV/c) hadrons from dijets in Cu+Cu and Au+Au collisions at sqrt[s_{NN}]=62.4 and 200 GeV. The away-side dijet induced azimuthal correlation is broadened, non-Gaussian, and peaked away from Deltavarphi=pi in central and semicentral collisions in all the systems. The broadening and peak location are found to depend upon the number of participants in the collision, but not on the collision energy or beam nuclei. These results are consistent with sound or shock wave models, but pose challenges to Cherenkov gluon radiation models.

The PHENIX experiment at the BNL Relativistic Heavy Ion Collider (RHIC) has measured J/psi production for rapidities -2.2<y<2.2 in Au+Au collisions at sqrt[s_{NN}]=200 GeV. The J/psi invariant yield and nuclear modification factor R_{AA} as a function of centrality, transverse momentum, and rapidity are reported. A suppression of J/psi relative to binary collision scaling of proton-proton reaction yields is observed. Models which describe the lower energy J/psi data at the CERN Super Proton Synchrotron invoking only J/psi destruction based on the local medium density predict a significantly larger suppression at RHIC and more suppression at midrapidity than at forward rapidity. Both trends are contradicted by our data.