Analysis of the Pseudoalteromonas tunicata genome reveals properties of a surface-associated life style in the marine environment

Background: Colonisation of sessile eukaryotic host surfaces (e.g. invertebrates and seaweeds) by bacteria is common in the marine environment and is expected to create significant inter-species competition and other interactions. The bacterium Pseudoalteromonas tunicata is a successful competitor on marine surfaces owing primarily to its ability to produce a number of inhibitory molecules. As such P. tunicata has become a model organism for the studies into processes of surface colonisation and eukaryotic host-bacteria interactions. Methodology/Principal Findings: To gain a broader understanding into the adaptation to a surface-associated life-style, we have sequenced and analysed the genome of P. tunicata and compared it to the genomes of closely related strains. We found that the P. tunicata genome contains several genes and gene clusters that are involved in the production of inhibitory compounds against surface competitors and secondary colonisers. Features of P. tunicata's oxidative stress response, iron scavenging and nutrient acquisition show that the organism is well adapted to high-density communities on surfaces. Variation of the P. tunicata genome is suggested by several landmarks of genetic rearrangements and mobile genetic elements (e.g. transposons, CRISPRs, phage). Surface attachment is likely to be mediated by curli, novel pili, a number of extracellular polymers and potentially other unexpected cell surface proteins. The P. tunicata genome also shows a utilisation pattern of extracellular polymers that would avoid a degradation of its recognised hosts, while potentially causing detrimental effects on other host types. In addition, the prevalence of recognised virulence genes suggests that P. tunicata has the potential for pathogenic interactions. Conclusions/Significance: The genome analysis has revealed several physiological features that would provide P. tunciata with competitive advantage against other members of the surface-associated community. We have also identified properties that could mediate interactions with surfaces other than its currently recognised hosts. This together with the detection of known virulence genes leads to the hypothesis that P. tunicata maintains a carefully regulated balance between beneficial and detrimental interactions with a range of host surfaces. © 2008 Thomas et al

Radiatively inefficient MHD accretion-ejection structures

We present magnetohydrodynamic simulations of a resistive accretion disk continuously launching transmagnetosonic, collimated jets. We time-evolve the full set of magnetohydrodynamic equations, but neglect radiative losses in the energetics (radiatively inefficient). Our calculations demonstrate that a jet is self-consistently produced by the interaction of an accretion disk with an open, initially bent large-scale magnetic field. A constant fraction of heated disk material is launched in the inner equipartition disk regions, leading to the formation of a hot corona and a bright collimated, super-fastmagnetosonic jet. We illustrate the complete dynamics of the ``hot'' near steady-state outflow (where thermal pressure $\simeq$ magnetic pressure) by showing force balance, energy budget and current circuits. The evolution to this near stationary state is analyzed in terms of the temporal variation of energy fluxes controlling the energetics of the accretion disk. We find that unlike advection-dominated accretion flow, the energy released by accretion is mainly sent into the jet rather than transformed into disk enthalpy. These magnetized, radiatively inefficient accretion-ejection structures can account for under-luminous thin disks supporting bright fast collimated jets as seen in many systems displaying jets (for instance M87).Comment: Astrophysical Journal (in press). Figures are missing due to file size restrictions. To have the complete paper just click on http://www-laog.obs.ujf-grenoble.fr/~fcasse/MS56638.pd

Whole Exome Sequencing to Estimate Alloreactivity Potential Between Donors and Recipients in Stem Cell Transplantation

Whole exome sequencing was performed on HLA-matched stem cell donors and transplant recipients to measure sequence variation contributing to minor histocompatibility antigen differences between the two. A large number of nonsynonymous single nucleotide polymorphisms were identified in each of the nine unique donor-recipient pairs tested. This variation was greater in magnitude in unrelated donors as compared with matched related donors. Knowledge of the magnitude of exome variation between stem cell transplant recipients and donors may allow more accurate titration of immunosuppressive therapy following stem cell transplantation.Comment: 12 pages- main article, 29 pages total, 5 figures, 1 supplementary figur

The PHENIX Experiment at RHIC

The physics emphases of the PHENIX collaboration and the design and current status of the PHENIX detector are discussed. The plan of the collaboration for making the most effective use of the available luminosity in the first years of RHIC operation is also presented.Comment: 5 pages, 1 figure. Further details of the PHENIX physics program available at http://www.rhic.bnl.gov/phenix

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes

To extend understanding of the genetic architecture and molecular basis of type 2 diabetes (T2D), we conducted a meta-analysis of genetic variants on the Metabochip involving 34,840 cases and 114,981 controls, overwhelmingly of European descent. We identified ten previously unreported T2D susceptibility loci, including two demonstrating sex-differentiated association. Genome-wide analyses of these data are consistent with a long tail of further common variant loci explaining much of the variation in susceptibility to T2D. Exploration of the enlarged set of susceptibility loci implicates several processes, including CREBBP-related transcription, adipocytokine signalling and cell cycle regulation, in diabetes pathogenesis

The gunshot-related injuries in trauma (GRIT) study: a profile of patients affected by gunshot related orthopaedic injuries across South Africa

Background: South Africa has one of the highest gun related mortality in the world - 20 people per day. The available data however do not reflect the substantial number of patients suffering non-lethal firearm injuries. Gunshot related injury has been recognised as a highly costly healthcare problem by individual treating centres in South Africa and other countries, however no &#x2018;national picture&#x2019; has been examined in detail. Objectives: This study sought to explore the burden of gunshot related orthopaedic injuries across South Africa. Method: A multicentre research network was established across South Africa and 37 orthopaedic units across nine provinces participated. A prospective, observational cohort study was performed during a two-week period in 2019. Cases were screened, enrolled and reported by the local orthopaedic teams. Patients were included if they had at least one acute gunshot related orthopaedic fracture referred to the orthopaedic service. Patients were asked additional questions around baseline health-related quality of life (HRQOL) and personal circumstances. Follow up was at 8 weeks following the injury. Results: Thirty-seven centres enrolled 135 patients over the two-week study period. The Western Cape had the highest number of reported cases 52 (39%), followed by Gauteng (35, 26%) and KwaZulu-Natal (29, 21%). The median age of patients was 30.5 years and the majority were male (89%). Forty three percent of patients had been either shot or stabbed previously, prior to this injury. Fifty-two percent of all cases required fracture fixation surgery and 11% of cases required wound debridement without fracture fixation. HRQOL data were collected successfully at baseline, but fewer than 25% of cases had follow up data. Conclusion: Gunshot-related orthopaedic injuries represent a significant burden of disease in the South African healthcare environment. This study highlights several areas for further research in both the management of the injuries and associated outcomes.</p