Packaging signals in single-stranded RNA viruses: nature’s alternative to a purely electrostatic assembly mechanism

The formation of a protective protein container is an essential step in the life-cycle of most viruses. In the case of single-stranded (ss)RNA viruses, this step occurs in parallel with genome packaging in a co-assembly process. Previously, it had been thought that this process can be explained entirely by electrostatics. Inspired by recent single-molecule fluorescence experiments that recapitulate the RNA packaging specificity seen in vivo for two model viruses, we present an alternative theory, which recognizes the important cooperative roles played by RNA–coat protein interactions, at sites we have termed packaging signals. The hypothesis is that multiple copies of packaging signals, repeated according to capsid symmetry, aid formation of the required capsid protein conformers at defined positions, resulting in significantly enhanced assembly efficiency. The precise mechanistic roles of packaging signal interactions may vary between viruses, as we have demonstrated for MS2 and STNV. We quantify the impact of packaging signals on capsid assembly efficiency using a dodecahedral model system, showing that heterogeneous affinity distributions of packaging signals for capsid protein out-compete those of homogeneous affinities. These insights pave the way to a new anti-viral therapy, reducing capsid assembly efficiency by targeting of the vital roles of the packaging signals, and opens up new avenues for the efficient construction of protein nanocontainers in bionanotechnology

Beam Test of a Segmented Foil SEM Grid

A prototype Secondary-electron Emission Monitor (SEM) was installed in the 8 GeV proton transport line for the MiniBooNE experiment at Fermilab. The SEM is a segmented grid made with 5 um Ti foils, intended for use in the 120 GeV NuMI beam at Fermilab. Similar to previous workers, we found that the full collection of the secondary electron signal requires a bias voltage to draw the ejected electrons cleanly off the foils, and this effect is more pronounced at larger beam intensity. The beam centroid and width resolutions of the SEM were measured at beam widths of 3, 7, and 8 mm, and compared to calculations. Extrapolating the data from this beam test, we expect a centroid and width resolutions of 20um and 25 um, respectively, in the NuMI beam which has 1 mm spot size.Comment: submitted to Nucl. Instr. Meth.

Phonological, visual, and semantic coding strategies and children's short-term picture memory span

Three experiments addressed controversies in the previous literature on the development of phonological and other forms of short-term memory coding in children, using assessments of picture memory span that ruled out potentially confounding effects of verbal input and output. Picture materials were varied in terms of phonological similarity, visual similarity, semantic similarity, and word length. Older children (6/8-year-olds), but not younger children (4/5-year-olds), demonstrated robust and consistent phonological similarity and word length effects, indicating that they were using phonological coding strategies. This confirmed findings initially reported by Conrad (1971), but subsequently questioned by other authors. However, in contrast to some previous research, little evidence was found for a distinct visual coding stage at 4 years, casting doubt on assumptions that this is a developmental stage that consistently precedes phonological coding. There was some evidence for a dual visual and phonological coding stage prior to exclusive use of phonological coding at around 5-6 years. Evidence for semantic similarity effects was limited, suggesting that semantic coding is not a key method by which young children recall lists of pictures

Future Fire Impacts on Smoke Concentrations, Visibility, and Health in the Contiguous United States

Fine particulate matter (PM2.5) from U.S. anthropogenic sources is decreasing. However, previous studies have predicted that PM2.5 emissions from wildfires will increase in the midcentury to next century, potentially offsetting improvements gained by continued reductions in anthropogenic emissions. Therefore, some regions could experience worse air quality, degraded visibility, and increases in population-level exposure. We use global climate model simulations to estimate the impacts of changing fire emissions on air quality, visibility, and premature deaths in the middle and late 21st century. We find that PM2.5 concentrations will decrease overall in the contiguous United States (CONUS) due to decreasing anthropogenic emissions (total PM2.5 decreases by 3% in Representative Concentration Pathway [RCP] 8.5 and 34% in RCP4.5 by 2100), but increasing fire-related PM2.5 (fire-related PM2.5 increases by 55% in RCP4.5 and 190% in RCP8.5 by 2100) offsets these benefits and causes increases in total PM2.5 in some regions. We predict that the average visibility will improve across the CONUS, but fire-related PM2.5 will reduce visibility on the worst days in western and southeastern U.S. regions. We estimate that the number of deaths attributable to total PM2.5 will decrease in both the RCP4.5 and RCP8.5 scenarios (from 6% to 4–5%), but the absolute number of premature deaths attributable to fire-related PM2.5 will double compared to early 21st century. We provide the first estimates of future smoke health and visibility impacts using a prognostic land-fire model. Our results suggest the importance of using realistic fire emissions in future air quality projections

Identifying the mechanisms underpinning recognition of structured sequences of action

© 2012 The Experimental Psychology SocietyWe present three experiments to identify the specific information sources that skilled participants use to make recognition judgements when presented with dynamic, structured stimuli. A group of less skilled participants acted as controls. In all experiments, participants were presented with filmed stimuli containing structured action sequences. In a subsequent recognition phase, participants were presented with new and previously seen stimuli and were required to make judgements as to whether or not each sequence had been presented earlier (or were edited versions of earlier sequences). In Experiment 1, skilled participants demonstrated superior sensitivity in recognition when viewing dynamic clips compared with static images and clips where the frames were presented in a nonsequential, randomized manner, implicating the importance of motion information when identifying familiar or unfamiliar sequences. In Experiment 2, we presented normal and mirror-reversed sequences in order to distort access to absolute motion information. Skilled participants demonstrated superior recognition sensitivity, but no significant differences were observed across viewing conditions, leading to the suggestion that skilled participants are more likely to extract relative rather than absolute motion when making such judgements. In Experiment 3, we manipulated relative motion information by occluding several display features for the duration of each film sequence. A significant decrement in performance was reported when centrally located features were occluded compared to those located in more peripheral positions. Findings indicate that skilled participants are particularly sensitive to relative motion information when attempting to identify familiarity in dynamic, visual displays involving interaction between numerous features

Reconceptualising adaptation to climate change as part of pathways of change and response

The need to adapt to climate change is now widely recognised as evidence of its impacts on social and natural systems grows and greenhouse gas emissions continue unabated. Yet efforts to adapt to climate change, as reported in the literature over the last decade and in selected case studies, have not led to substantial rates of implementation of adaptation actions despite substantial investments in adaptation science. Moreover, implemented actions have been mostly incremental and focused on proximate causes; there are far fewer reports of more systemic or transformative actions. We found that the nature and effectiveness of responses was strongly influenced by framing. Recent decision-oriented approaches that aim to overcome this situation are framed within a "pathways" metaphor to emphasise the need for robust decision making within adaptive processes in the face of uncertainty and inter-temporal complexity. However, to date, such "adaptation pathways" approaches have mostly focused on contexts with clearly identified decision-makers and unambiguous goals; as a result, they generally assume prevailing governance regimes are conducive for adaptation and hence constrain responses to proximate causes of vulnerability. In this paper, we explore a broader conceptualisation of "adaptation pathways" that draws on 'pathways thinking' in the sustainable development domain to consider the implications of path dependency, interactions between adaptation plans, vested interests and global change, and situations where values, interests, or institutions constrain societal responses to change. This re-conceptualisation of adaptation pathways aims to inform decision makers about integrating incremental actions on proximate causes with the transformative aspects of societal change. Case studies illustrate what this might entail. The paper ends with a call for further exploration of theory, methods and procedures to operationalise this broader conceptualisation of adaptation

Kepler-22b: A 2.4 Earth-radius Planet in the Habitable Zone of a Sun-like Star

A search of the time-series photometry from NASA's Kepler spacecraft reveals a transiting planet candidate orbiting the 11th magnitude G5 dwarf KIC 10593626 with a period of 290 days. The characteristics of the host star are well constrained by high-resolution spectroscopy combined with an asteroseismic analysis of the Kepler photometry, leading to an estimated mass and radius of 0.970 +/- 0.060 MSun and 0.979 +/- 0.020 RSun. The depth of 492 +/- 10ppm for the three observed transits yields a radius of 2.38 +/- 0.13 REarth for the planet. The system passes a battery of tests for false positives, including reconnaissance spectroscopy, high-resolution imaging, and centroid motion. A full BLENDER analysis provides further validation of the planet interpretation by showing that contamination of the target by an eclipsing system would rarely mimic the observed shape of the transits. The final validation of the planet is provided by 16 radial velocities obtained with HIRES on Keck 1 over a one year span. Although the velocities do not lead to a reliable orbit and mass determination, they are able to constrain the mass to a 3{\sigma} upper limit of 124 MEarth, safely in the regime of planetary masses, thus earning the designation Kepler-22b. The radiative equilibrium temperature is 262K for a planet in Kepler-22b's orbit. Although there is no evidence that Kepler-22b is a rocky planet, it is the first confirmed planet with a measured radius to orbit in the Habitable Zone of any star other than the Sun.Comment: Accepted to Ap

Production and Decay of D_1(2420)^0 and D_2^*(2460)^0

We have investigated $D^{+}\pi^{-}$ and $D^{*+}\pi^{-}$ final states and observed the two established $L=1$ charmed mesons, the $D_1(2420)^0$ with mass $2421^{+1+2}_{-2-2}$ MeV/c$^{2}$ and width $20^{+6+3}_{-5-3}$ MeV/c$^{2}$ and the $D_2^*(2460)^0$ with mass $2465 \pm 3 \pm 3$ MeV/c$^{2}$ and width $28^{+8+6}_{-7-6}$ MeV/c$^{2}$. Properties of these final states, including their decay angular distributions and spin-parity assignments, have been studied. We identify these two mesons as the $j_{light}=3/2$ doublet predicted by HQET. We also obtain constraints on {\footnotesize $\Gamma_S/(\Gamma_S + \Gamma_D)$} as a function of the cosine of the relative phase of the two amplitudes in the $D_1(2420)^0$ decay.Comment: 15 pages in REVTEX format. hardcopies with figures can be obtained by sending mail to: [email protected]

Measurement of the branching fraction for Υ(1S)→τ+τ−\Upsilon (1S) \to \tau^+ \tau^-

We have studied the leptonic decay of the $\Upsilon (1S)$ resonance into tau pairs using the CLEO II detector. A clean sample of tau pair events is identified via events containing two charged particles where exactly one of the particles is an identified electron. We find $B(\Upsilon(1S) \to \tau^+ \tau^-) = (2.61~\pm~0.12~{+0.09\atop{-0.13}})$. The result is consistent with expectations from lepton universality.Comment: 9 pages, RevTeX, two Postscript figures available upon request, CLNS 94/1297, CLEO 94-20 (submitted to Physics Letters B

Study of the B^0 Semileptonic Decay Spectrum at the Upsilon(4S) Resonance

We have made a first measurement of the lepton momentum spectrum in a sample of events enriched in neutral B's through a partial reconstruction of B0 --> D*- l+ nu. This spectrum, measured with 2.38 fb**-1 of data collected at the Upsilon(4S) resonance by the CLEO II detector, is compared directly to the inclusive lepton spectrum from all Upsilon(4S) events in the same data set. These two spectra are consistent with having the same shape above 1.5 GeV/c. From the two spectra and two other CLEO measurements, we obtain the B0 and B+ semileptonic branching fractions, b0 and b+, their ratio, and the production ratio f+-/f00 of B+ and B0 pairs at the Upsilon(4S). We report b+/b0=0.950 (+0.117-0.080) +- 0.091, b0 = (10.78 +- 0.60 +- 0.69)%, and b+ = (10.25 +- 0.57 +- 0.65)%. b+/b0 is equivalent to the ratio of charged to neutral B lifetimes, tau+/tau0.Comment: 14 page, postscript file also available at http://w4.lns.cornell.edu/public/CLN