Quark Matter 2006: high-pT and jets

An overview of new experimental results on high-\pT{} particle production and jets in heavy ion collisions from the Quark Matter 2006 conference is presented.Comment: Presented at Quark Matter 200

Natural reassignment of CUU and CUA sense codons to alanine in Ashbya mitochondria

The discovery of diverse codon reassignment events has demonstrated that the canonical genetic code is not universal. Studying coding reassignment at the molecular level is critical for understanding genetic code evolution, and provides clues to genetic code manipulation in synthetic biology. Here we report a novel reassignment event in the mitochondria of Ashbya (Eremothecium) gossypii, a filamentous-growing plant pathogen related to yeast (Saccharomycetaceae). Bioinformatics studies of conserved positions in mitochondrial DNA-encoded proteins suggest that CUU and CUA codons correspond to alanine in A. gossypii, instead of leucine in the standard code or threonine in yeast mitochondria. Reassignment of CUA to Ala was confirmed at the protein level by mass spectrometry. We further demonstrate that a predicted is transcribed and accurately processed in vivo, and is responsible for Ala reassignment. Enzymatic studies reveal that is efficiently recognized by A. gossypii mitochondrial alanyl-tRNA synthetase (AgAlaRS). AlaRS typically recognizes the G3:U70 base pair of tRNAAla; a G3A change in Ashbya abolishes its recognition by AgAlaRS. Conversely, an A3G mutation in Saccharomyces cerevisiae confers tRNA recognition by AgAlaRS. Our work highlights the dynamic feature of natural genetic codes in mitochondria, and the relative simplicity by which tRNA identity may be switched

Evidence-Informed Guidelines for Pediatric Pandemic Planning and Response

From the executive summary: Pandemic events are unpredictable and inevitable. When they occur, the impact is both all-encompassing and asymmetrical; each pandemic targets specific, vulnerable populations, but ultimately impacts individuals, families and communities throughout the world. Regardless of origin or circumstances, the next pandemic will certainly count infants, children, and adolescents among its most vulnerable targets. As evidenced by the 2009 H1N1 influenza pandemic, children may be at higher risk than populations more typically seen as susceptible to pandemic illness (the elderly, those with weakened immune systems, etc.). Children also can function as disease vectors, spreading the virus through their ubiquitous presence in settings where they live, attend school, and play. This document is the result of a two-year international, mixed-methods study of the physical, social, and mental health effects of pandemic on children and families – particularly the impact of quarantine and hospital isolation during these events. This project also examined the psychosocial effects of pandemic disaster on professionals who care for children before, during, and after pandemic. Based on the empirical findings of this study, researchers developed a set of evidence-informed, child-focused, best practice guidelines for use by stakeholders during future pandemics across a variety of relevant fields. In addition, data gathered and analyzed for the project have been used to create a set of Kentucky-specific recommendations that respond to the state’s unique geographic and population needs

Search for positively charged strangelets and other related results with E864 at the AGS

We report on the latest results in the search for positively charged strangelets from E864's 96/97 run at the AGS with sensitivity of about $8\times 10^{-9}$ per central collision. This contribution also contains new results of a search for highly charged strangelets with $Z=+3$. Production of light nuclei, such as $^6He$ and $^6Li$, is presented as well. Measurements of yields of these rarely produced isotopes near midrapidity will help constrain the production levels of strangelets via coalescence. E864 also measures antiproton production which includes decays from antihyperons. Comparisons with antiproton yields measured by E878 as a function of centrality indicate a large antihyperon-to-antiproton ratio in central collisions.Comment: 8 pages, 4 figures; Talk at SQM'98, Padova, Italy (July 20-24th, 1998

Heavy Ion Physics at the LHC with the ATLAS Detector

The ATLAS detector at CERN will provide a high-resolution longitudinally-segmented calorimeter and precision tracking for the upcoming study of heavy ion collisions at the LHC (sqrt(s_NN)=5520 GeV). The calorimeter covers |eta|<5 with both electromagnetic and hadronic sections, while the inner detector spectrometer covers |eta|<2.5. ATLAS will study a full range of observables necessary to characterize the hot and dense matter formed at the LHC. Global measurements (particle multiplicities, collective flow) will provide access into its thermodynamic and hydrodynamic properties. Measuring complete jets out to 100's of GeV will allow detailed studies of energy loss and its effect on jets. Quarkonia will provide a handle on deconfinement mechanisms. ATLAS will also study the structure of the nucleon and nucleus using forward physics probes and ultraperipheral collisions, both enabled by segmented Zero Degree Calorimeters.Comment: 9 pages, 8 figures, submitted to the Proceedings of Quark Matter 2006, Shanghai, China, November 14-20, 200

Ion Diffusion Velocity Measurements in a Multi-Ion-Species Plasma Shock

Collisional plasma shocks generated from supersonic flows are an important feature in many astrophysical and laboratory high-energy-density plasmas. Compared to single-ion-species plasma shocks, plasma shock fronts with multiple ion species contain additional structure, including interspecies ion separation driven by gradients in species concentration, temperature, pressure, and electric potential. We present time-resolved density and temperature measurements of two ion species in collisional plasma shocks produced by head-on merging of supersonic plasma jets, allowing determination of the diffusion velocity of the ion species. Our results demonstrate that the lighter ion species diffuse faster than the heavier species within a shock front, consistent with predictions from the inter-ion-species transport theory. Results from the experiment approach quantitative agreement with theoretical prediction and 1D ion-Fokker-Planck kinetic simulation

The Mid-Infrared Instrument for the James Webb Space Telescope, V: Predicted Performance of the MIRI Coronagraphs

The imaging channel on the Mid-Infrared Instrument (MIRI) is equipped with four coronagraphs that provide high contrast imaging capabilities for studying faint point sources and extended emission that would otherwise be overwhelmed by a bright point-source in its vicinity. Such bright sources might include stars that are orbited by exoplanets and circumstellar material, mass-loss envelopes around post-main-sequence stars, the near-nuclear environments in active galaxies, and the host galaxies of distant quasars. This paper describes the coronagraphic observing modes of MIRI, as well as performance estimates based on measurements of the MIRI flight model during cryo-vacuum testing. A brief outline of coronagraphic operations is also provided. Finally, simulated MIRI coronagraphic observations of a few astronomical targets are presented for illustration

Rational optimization of tolC as a powerful dual selectable marker for genome engineering

Selection has been invaluable for genetic manipulation, although counter-selection has historically exhibited limited robustness and convenience. TolC, an outer membrane pore involved in transmembrane transport in E. coli, has been implemented as a selectable/counter-selectable marker, but counter-selection escape frequency using colicin E1 precludes using tolC for inefficient genetic manipulations and/or with large libraries. Here, we leveraged unbiased deep sequencing of 96 independent lineages exhibiting counter-selection escape to identify loss-of-function mutations, which offered mechanistic insight and guided strain engineering to reduce counter-selection escape frequency by ∼40-fold. We fundamentally improved the tolC counter-selection by supplementing a second agent, vancomycin, which reduces counter-selection escape by 425-fold, compared colicin E1 alone. Combining these improvements in a mismatch repair proficient strain reduced counter-selection escape frequency by 1.3E6-fold in total, making tolC counter-selection as effective as most selectable markers, and adding a valuable tool to the genome editing toolbox. These improvements permitted us to perform stable and continuous rounds of selection/counter-selection using tolC, enabling replacement of 10 alleles without requiring genotypic screening for the first time. Finally, we combined these advances to create an optimized E. coli strain for genome engineering that is ∼10-fold more efficient at achieving allelic diversity than previous best practices

De novo design of bioactive protein switches.

Allosteric regulation of protein function is widespread in biology, but is challenging for de novo protein design as it requires the explicit design of multiple states with comparable free energies. Here we explore the possibility of designing switchable protein systems de novo, through the modulation of competing inter- and intramolecular interactions. We design a static, five-helix 'cage' with a single interface that can interact either intramolecularly with a terminal 'latch' helix or intermolecularly with a peptide 'key'. Encoded on the latch are functional motifs for binding, degradation or nuclear export that function only when the key displaces the latch from the cage. We describe orthogonal cage-key systems that function in vitro, in yeast and in mammalian cells with up to 40-fold activation of function by key. The ability to design switchable protein functions that are controlled by induced conformational change is a milestone for de novo protein design, and opens up new avenues for synthetic biology and cell engineering