Defined mutations in the 5' nontranslated sequence of Sindbis virus RNA

We have constructed 24 deletion mutants which contain deletions of from 1 to 15 nucleotides in the 5' nontranslated region of Sindbis virus RNA and tested the effect of these mutations on virus replication. The results showed that the first 44 nucleotides, which are capable of forming a hairpin structure, are important for virus replication, as all deletions tested in this region were either lethal or resulted in virus that grew poorly in comparison to the parental virus. Many of these deletions had different effects in mosquito cells than in chicken cells, suggesting that cellular factors, presumably proteins, bind to this region. This domain may function in at least two processes in viral replication. It seems likely that in the minus strand, this sequence element is bound by the viral replicase and promotes RNA replication. In the plus strand, this element may modulate initiation of translation of the nonstructural proteins. The results suggest that the hairpin structure itself is important. All deletions within it had deleterious effects on virus replication, and in particular, deletion of one of the G residues at nucleotide 7 or 8 or of one of the C residues at nucleotide 36 or 37 which are theoretically base-paired with these G's resulted in temperature-sensitive viruses that behaved very similarly. In contrast, large deletions between the 44-nucleotide hairpin and the translation start site at nucleotides 60 to 62 resulted in virus that grew as well as or better than the parental virus in both chicken and mosquito cells. The A residue at position 5 of the HRSP strain used was examined in more detail. Deletion of this A was lethal, whereas substitution by G resulted in a virus that grew poorly, despite the fact that G is present at position 5 in the AR339 parent of HRSP. U at position 5 resulted in a virus that grew less well than the A5 strain but better than the G5 mutant

Mutagenesis of the conserved 51-nucleotide region of Sindbis virus

We have constructed 25 site-specific mutations in a domain of 51 nucleotides in Sindbis virus that is highly conserved among all alphaviruses sequenced to date. These 51 nucleotides are capable of forming two hairpin structures and are found from nucleotides 155 to 205 in Sindbis virus within the region encoding nsP1. Of the mutations, 21 were silent and did not lead to a change in the amino acid sequence encoded. These silent mutations changed not only the linear sequence but also the stability of the hairpins in most cases. Two double mutants that were constructed led to the replacement of one base pair by another so that the linear sequence was altered but the nature of the hairpins was not. All of the mutants with silent mutations were viable, but 19 of the 21 mutants were severely impaired for growth in both chicken and mosquito cells. Compared with the parental virus, they grew slowly and produced virus at rates of 10(-1) to 10(-4) times the parental rate. Surprisingly, however, the plaques produced by these mutants were indistinguishable from those produced by the parental virus. Two of the silent mutations, found within the first hairpin structure, produced virus at a faster rate than the parental virus. It is clear that the exact sequence of this region is important for some aspect of virus replication. We suggest that one or more proteins, either virus encoded or cellular, bind to the hairpin structures in a sequence-specific fashion in a step that promotes replication of the viral RNA. Of the mutations that resulted in a change of coding, only one of four was viable, suggesting that the amino acid sequence encoded in this domain is essential for virus replication

Rational invariants of even ternary forms under the orthogonal group

In this article we determine a generating set of rational invariants of minimal cardinality for the action of the orthogonal group $\mathrm{O}_3$ on the space $\mathbb{R}[x,y,z]_{2d}$ of ternary forms of even degree $2d$. The construction relies on two key ingredients: On one hand, the Slice Lemma allows us to reduce the problem to dermining the invariants for the action on a subspace of the finite subgroup $\mathrm{B}_3$ of signed permutations. On the other hand, our construction relies in a fundamental way on specific bases of harmonic polynomials. These bases provide maps with prescribed $\mathrm{B}_3$-equivariance properties. Our explicit construction of these bases should be relevant well beyond the scope of this paper. The expression of the $\mathrm{B}_3$-invariants can then be given in a compact form as the composition of two equivariant maps. Instead of providing (cumbersome) explicit expressions for the $\mathrm{O}_3$-invariants, we provide efficient algorithms for their evaluation and rewriting. We also use the constructed $\mathrm{B}_3$-invariants to determine the $\mathrm{O}_3$-orbit locus and provide an algorithm for the inverse problem of finding an element in $\mathbb{R}[x,y,z]_{2d}$ with prescribed values for its invariants. These are the computational issues relevant in brain imaging.Comment: v3 Changes: Reworked presentation of Neuroimaging application, refinement of Definition 3.1. To appear in "Foundations of Computational Mathematics

Neutron monitors and muon detectors for solar modulation studies: Interstellar flux, yield function, and assessment of critical parameters in count rate calculations

Particles count rates at given Earth location and altitude result from the convolution of (i) the interstellar (IS) cosmic-ray fluxes outside the solar cavity, (ii) the time-dependent modulation of IS into Top-of-Atmosphere (TOA) fluxes, (iii) the rigidity cut-off (or geomagnetic transmission function) and grammage at the counter location, (iv) the atmosphere response to incoming TOA cosmic rays (shower development), and (v) the counter response to the various particles/energies in the shower. Count rates from neutron monitors or muon counters are therefore a proxy to solar activity. In this paper, we review all ingredients, discuss how their uncertainties impact count rate calculations, and how they translate into variation/uncertainties on the level of solar modulation $\varphi$ (in the simple Force-Field approximation). The main uncertainty for neutron monitors is related to the yield function. However, many other effects have a significant impact, at the 5-10\% level on $\varphi$ values. We find no clear ranking of the dominant effects, as some depend on the station position and/or the weather and/or the season. An abacus to translate any variation of count rates (for neutron and $\mu$ detectors) to a variation of the solar modulation $\varphi$ is provided.Comment: 28 pages, 16 figures, 9 tables, match accepted version in AdSR (minor corrections, Dorman (1974,2004,2009) reference textbooks added

Dynamic hysteresis from zigzag domain walls

We investigate dynamic hysteresis in ferromagnetic thin films with zigzag domain walls. We introduce a discrete model describing the motion of a wall in a disordered ferromagnet with in-plane magnetization, driven by an external magnetic field, considering the effects of dipolar interactions and anisotropy. We analyze the effects of external field frequency and temperature on the coercive field by Monte Carlo simulations, and find a good agreement with the experimental data reported in literature for Fe/GaAs films. This implies that dynamic hysteresis in this case can be explained by a single propagating domain wall model without invoking domain nucleation.Comment: 10 pages, 13 figures; minor modifications and two figures adde

BIOFUELS, AGRICULTURE AND CLIMATE CHANGE

In the context of ever-increasing petroleum prices combined with concerns about climate change, timing of adoption and rate of diffusion of land-based fuels and backstop technologies for transportation use are examined in this paper. A global model of land allocation joined with a Hotelling model has been developed. Using this framework, effects of climate and energy policies on world agricultural and energy markets have been explored. Further, their regional impacts are also analyzed. Whereas mandatory blending bio-fuels have substantial effects on world food prices and do not succeed in curbing down carbon emissions fluxes, carbon targets are expected to speed up date of adoption of backstop technologies. Then, sensitivity scenarios with regards to technological parameters reveal that higher is the rate of technological change, earlier backstop technologies are adopted and lower is the stock of carbon accumulated into the atmosphere. Finally, interplay between land-based fuels and deforestation has been studied. Results show that land-based fuels production speeds up world deforestation and causes substantial carbon emissions due to conversion of forests into agricultural lands.Ricardian rents, land use, biofuels, Resource /Energy Economics and Policy,

Soil hydraulic properties of a Nitisol in Kabete, Kenya

Water relations are among the most important physical phenomena that affect the use of soils for agricultural, ecological, environmental, and engineering purposes. To formulate soil-water relationships, soil hydraulic properties are required as essential inputs. The most important hydraulic properties are the soil-water retention curve and the hydraulic conductivity. The objective of this study was to determine the soil hydraulic properties of a Nitisol, at Kabete Campus Field Station. Use of an internal drainage procedure to characterize the hydraulic properties and soil and water retention curves allowed for the establishment of the moisture and matric potential at field capacity and permanent wilting point. The Bt2 (84 -115) and Bt3 (115 - 143 cm) had the highest clay contents of 619 compared to Ap, AB and Bt1 horizons. The PWP was attained at soil moisture contents of 0.223, 0.284, 0277, 0.307 and 0.314 m3m-3 in the Ap, AB, Bt1, Bt2, and Bt3 horizons, respectively. Horizontal saturated hydraulic conductivity (Ksat) was high at 6.0 cm hr-1 in Ap horizon and decreased to 0.4 cm hr-1 in the subsurface horizon (Bt3). Ksat in the vertical direction was higher than horizontal and ranged from 8.3 cm hr-1 in surface layer to 0.6 cm hr-1 in Bt3 horizon, with exception of Bt1 and Bt2 where horizontal Ksat was greater than vertical. The Ap horizon also had the highest crop extractable water. Though the AB and Bt1 had the same water content at low matric suction, the variation was very wide as the SWRC approached saturation point. Bt1 and Bt2 also had similar water contents at suction range of – 7kPa after which Bt1, tended towards Bt3. Bt3 had the narrowest range of crop extractable water and thus was attributed to texture. The Bt3 retained the most amount of water at 0.314 m3m-3concluding that θPWP increased with depth. The total available water capacity between FC and PWP in the profile was 79.2 mm m-1. The study observed that the field capacity, crop available water contents and hydraulic conductivities were influenced positively by soil organic matter. The Van Genuchten parameters of air entry value (α) and pore size distribution (n) indicated that pore size distribution was not even in the AP and AB horizons. The field capacity was attained at higher matric potential at -5kPa for Bt1 while Bt2 and AP, AB, Bt2 and Bt3 was at -10kPa.The functional relationship, K(θ) = aθb that deals with water redistribution as a result of soil hydraulic properties and evaporative demand of the atmosphere was highly correlated to soil moisture content and texture with R2 values > 0.85

Neutron monitors and muon detectors for solar modulation studies: 2. ϕ\phi time series

The level of solar modulation at different times (related to the solar activity) is a central question of solar and galactic cosmic-ray physics. In the first paper of this series, we have established a correspondence between the uncertainties on ground-based detectors count rates and the parameter $\phi$ (modulation level in the force-field approximation) reconstructed from these count rates. In this second paper, we detail a procedure to obtain a reference $\phi$ time series from neutron monitor data. We show that we can have an unbiased and accurate $\phi$ reconstruction ($\Delta\phi/\phi\simeq 10\%$). We also discuss the potential of Bonner spheres spectrometers and muon detectors to provide $\phi$ time series. Two by-products of this calculation are updated $\phi$ values for the cosmic-ray database and a web interface to retrieve and plot $\phi$ from the 50's to today (\url{http://lpsc.in2p3.fr/crdb}).Comment: 15 pages, 5 figures, 2 tables. AdSR, in press. Web interface to get modulation parameter phi(t): new tab in http://lpsc.in2p3.fr/crd

Topological defects in flat nanomagnets: the magnetostatic limit

We discuss elementary topological defects in soft magnetic nanoparticles in the thin-film geometry. In the limit dominated by magnetostatic forces the low-energy defects are vortices (winding number n = +1), cross ties (n = -1), and edge defects with n = -1/2. We obtain topological constraints on the possible composition of domain walls. The simplest domain wall in this regime is composed of two -1/2 edge defects and a vortex, in accordance with observations and numerics.Comment: 3 pages, eps figures. Proceedings of MMM 0