Genome Sequence of Brucella abortus Vaccine Strain S19 Compared to Virulent Strains Yields Candidate Virulence Genes

The Brucella abortus strain S19, a spontaneously attenuated strain, has been used as a vaccine strain in vaccination of cattle against brucellosis for six decades. Despite many studies, the physiological and molecular mechanisms causing the attenuation are not known. We have applied pyrosequencing technology together with conventional sequencing to rapidly and comprehensively determine the complete genome sequence of the attenuated Brucella abortus vaccine strain S19. The main goal of this study is to identify candidate virulence genes by systematic comparative analysis of the attenuated strain with the published genome sequences of two virulent and closely related strains of B. abortus, 9–941 and 2308. The two S19 chromosomes are 2,122,487 and 1,161,449 bp in length. A total of 3062 genes were identified and annotated. Pairwise and reciprocal genome comparisons resulted in a total of 263 genes that were non-identical between the S19 genome and any of the two virulent strains. Amongst these, 45 genes were consistently different between the attenuated strain and the two virulent strains but were identical amongst the virulent strains, which included only two of the 236 genes that have been implicated as virulence factors in literature. The functional analyses of the differences have revealed a total of 24 genes that may be associated with the loss of virulence in S19. Of particular relevance are four genes with more than 60bp consistent difference in S19 compared to both the virulent strains, which, in the virulent strains, encode an outer membrane protein and three proteins involved in erythritol uptake or metabolism

Jet modification via π 0 -hadron correlations in Au+Au collisions at √sNN = 200 GeV

High-momentum two-particle correlations are a useful tool for studying jet-quenching effects in the quark-gluon plasma. Angular correlations between neutral-pion triggers and charged hadrons with transverse momenta in the range 4–12 GeV/c and 0.5–7 GeV/c, respectively, have been measured by the PHENIX experiment in 2014 for Au+Au collisions at √sNN = 200 GeV. Suppression is observed in the yield of high-momentum jet fragments opposite the trigger particle, which indicates jet suppression stemming from in-medium partonic energy loss, while enhancement is observed for low-momentum particles. The ratio and differences between the yield in Au+Au collisions and p+p collisions, IAA and ∆AA, as a function of the trigger-hadron azimuthal separation, ∆ϕ, are measured for the first time at the Relativistic Heavy Ion Collider. These results better quantify how the yield of low-pT associated hadrons is enhanced at wide angle, which is crucial for studying energy loss as well as medium-response effects

Systematic study of nuclear effects in p+Al, p+Au, d+Au, and 3He+Au collisions at √sNN = 200 GeV using π 0 production

The PHENIX collaboration presents a systematic study of inclusive π 0 production from p+p, p+Al, p+Au, d+Au, and 3He+Au collisions at √sNN = 200 GeV. Measurements were performed with different centrality selections as well as the total inelastic, 0%–100%, selection for all collision systems. For 0%–100% collisions, the nuclear-modification factors, RxA, are consistent with unity for pT above 8 GeV/c, but exhibit an enhancement in peripheral collisions and a suppression in central collisions. The enhancement and suppression characteristics are similar for all systems for the same centrality class. It is shown that for high-pT -π 0 production, the nucleons in the d and 3He interact mostly independently with the Au nucleus and that the counter intuitive centrality dependence is likely due to a physical correlation between multiplicity and the presence of a hard scattering process. These observations disfavor models where parton energy loss has a significant contribution to nuclear modifications in small systems. Nuclear modifications at lower pT resemble the Cronin effect – an increase followed by a peak in central or inelastic collisions and a plateau in peripheral collisions. The peak height has a characteristic ordering by system size as p+Au > d+Au > 3He+Au > p+Al. For collisions with Au ions, current calculations based on initial state cold nuclear matter effects result in the opposite order, suggesting the presence of other contributions to nuclear modifications, in particular at lower pT

AP endonuclease paralogues with distinct activities in DNA repair and bacterial pathogenesis

Oxidative stress is a principal cause of DNA damage, and mechanisms to repair this damage are among the most highly conserved of biological processes. Oxidative stress is also used by phagocytes to attack bacterial pathogens in defence of the host. We have identified and characterised two apurinic/apyrimidinic (AP) endonuclease paralogues in the human pathogen Neisseria meningitidis. The presence of multiple versions of DNA repair enzymes in a single organism is usually thought to reflect redundancy in activities that are essential for cellular viability. We demonstrate here that these two AP endonuclease paralogues have distinct activities in DNA repair: one is a typical Neisserial AP endonuclease (NApe), whereas the other is a specialised 3'-phosphodiesterase Neisserial exonuclease (NExo). The lack of AP endonuclease activity of NExo is shown to be attributable to the presence of a histidine side chain, blocking the abasic ribose-binding site. Both enzymes are necessary for survival of N. meningitidis under oxidative stress and during bloodstream infection. The novel functional pairing of NExo and NApe is widespread among bacteria and appears to have evolved independently on several occasions