Temporal evolution of solar energetic particle spectra

During solar flares and coronal mass ejections, solar energetic par- ticles (SEPs) may be released into the interplanetary medium and near-Earth locations. The energy spectra of SEP events at 1 AU are typically averaged over the entire event or studied in a few snapshots. In this paper we analyze the time evolution of the energy spectra of four large selected SEP events using a large number of snapshots. We use a multi-spacecraft and multi-instrument approach for the observations, obtained over a wide SEP energy range. We find large differences in the spectra at the beginning of the events as measured by different instruments. We show that over time, a wave-like structure is observed traveling through the spectra from the highest energies to the lowest energies, creating an “arch” shape which then straightens into a power law later in the event, after times of the order of 10 hours. We discuss the processes that determine SEP intensities and their role in shaping the spectral time evolution

The Structure of a Rigorously Conserved RNA Element within the SARS Virus Genome

We have solved the three-dimensional crystal structure of the stem-loop II motif (s2m) RNA element of the SARS virus genome to 2.7-Å resolution. SARS and related coronaviruses and astroviruses all possess a motif at the 3′ end of their RNA genomes, called the s2m, whose pathogenic importance is inferred from its rigorous sequence conservation in an otherwise rapidly mutable RNA genome. We find that this extreme conservation is clearly explained by the requirement to form a highly structured RNA whose unique tertiary structure includes a sharp 90° kink of the helix axis and several novel longer-range tertiary interactions. The tertiary base interactions create a tunnel that runs perpendicular to the main helical axis whose interior is negatively charged and binds two magnesium ions. These unusual features likely form interaction surfaces with conserved host cell components or other reactive sites required for virus function. Based on its conservation in viral pathogen genomes and its absence in the human genome, we suggest that these unusual structural features in the s2m RNA element are attractive targets for the design of anti-viral therapeutic agents. Structural genomics has sought to deduce protein function based on three-dimensional homology. Here we have extended this approach to RNA by proposing potential functions for a rigorously conserved set of RNA tertiary structural interactions that occur within the SARS RNA genome itself. Based on tertiary structural comparisons, we propose the s2m RNA binds one or more proteins possessing an oligomer-binding-like fold, and we suggest a possible mechanism for SARS viral RNA hijacking of host protein synthesis, both based upon observed s2m RNA macromolecular mimicry of a relevant ribosomal RNA fold

Energetic particle influence on the Earth's atmosphere

This manuscript gives an up-to-date and comprehensive overview of the effects of energetic particle precipitation (EPP) onto the whole atmosphere, from the lower thermosphere/mesosphere through the stratosphere and troposphere, to the surface. The paper summarizes the different sources and energies of particles, principally galactic cosmic rays (GCRs), solar energetic particles (SEPs) and energetic electron precipitation (EEP). All the proposed mechanisms by which EPP can affect the atmosphere are discussed, including chemical changes in the upper atmosphere and lower thermosphere, chemistry-dynamics feedbacks, the global electric circuit and cloud formation. The role of energetic particles in Earth’s atmosphere is a multi-disciplinary problem that requires expertise from a range of scientific backgrounds. To assist with this synergy, summary tables are provided, which are intended to evaluate the level of current knowledge of the effects of energetic particles on processes in the entire atmosphere

An Observational Overview of Solar Flares

We present an overview of solar flares and associated phenomena, drawing upon a wide range of observational data primarily from the RHESSI era. Following an introductory discussion and overview of the status of observational capabilities, the article is split into topical sections which deal with different areas of flare phenomena (footpoints and ribbons, coronal sources, relationship to coronal mass ejections) and their interconnections. We also discuss flare soft X-ray spectroscopy and the energetics of the process. The emphasis is to describe the observations from multiple points of view, while bearing in mind the models that link them to each other and to theory. The present theoretical and observational understanding of solar flares is far from complete, so we conclude with a brief discussion of models, and a list of missing but important observations.Comment: This is an article for a monograph on the physics of solar flares, inspired by RHESSI observations. The individual articles are to appear in Space Science Reviews (2011

On the mechanisms governing gas penetration into a tokamak plasma during a massive gas injection

A new 1D radial fluid code, IMAGINE, is used to simulate the penetration of gas into a tokamak plasma during a massive gas injection (MGI). The main result is that the gas is in general strongly braked as it reaches the plasma, due to mechanisms related to charge exchange and (to a smaller extent) recombination. As a result, only a fraction of the gas penetrates into the plasma. Also, a shock wave is created in the gas which propagates away from the plasma, braking and compressing the incoming gas. Simulation results are quantitatively consistent, at least in terms of orders of magnitude, with experimental data for a D 2 MGI into a JET Ohmic plasma. Simulations of MGI into the background plasma surrounding a runaway electron beam show that if the background electron density is too high, the gas may not penetrate, suggesting a possible explanation for the recent results of Reux et al in JET (2015 Nucl. Fusion 55 093013)

Characterization of heterotic quantitative trait loci in maize by evaluation of near-isogenic lines and their crosses at two competition levels

In a previous study on a maize (Zea mays L.) population of recombinant inbreds derived from B73 7 H99, we identified several quantitative trait loci (QTL) for agronomic traits with high dominance-additive ratio. Then, for four of these QTL, we developed families of near-isogenic lines (NILs) homozygous either for the QTL allele from B73 (BB) or from H99 (HH); for two of these QTL, the NILs' families were produced in two different genetic backgrounds. The present study was conducted to: (1) characterize these QTL for agronomic traits and (2) verify whether their effects were influenced by the genetic background, inbreeding level and plant density (PD). The six NILs' families were tested across 3 years and in three experiments at different inbreeding levels as NILs per se and their reciprocal crosses (Experiment 1), NILs crossed to related inbreds B73 and H99 (Experiment 2) and NILs crossed to four unrelated inbreds (Experiment 3). Experiment 2 was conducted at two PDs (4.5 and 9.0 plants m -2). Results of Experiments 1 and 2 confirmed previous findings as to QTL effects, with dominance-additive ratio superior to 1 for several traits; as a tendency, dominance effects were more pronounced in Experiment 1. The QTL effects were also confirmed in Experiment 3. The interactions involving QTL effects, families and PD were generally negligible, suggesting a certain stability of the QTL. Results emphasize the importance of dominance effects for these QTL, suggesting that they might deserve further studies, using the NILs' families and their crosses as base materials

Mapping genetic factors affecting heterosis in maize

Mapping genetics fators affecting heterosis in maize Elisabetta Frascaroli*, Maria Angela Can\ue8*, Pierangelo Landi*, Giorgio Pea\u2020, Michele Morgante\u2021, Mario Enrico P\ue8\u2020 * Dipartimento di Scienze e Tecnologie Agroambientali, Universit\ue0 di Bologna, Bologna, Italy \u2020 Dipartimento di Scienze Biomolecolari e Biotecnologie, Universit\ue0 di Milano, Milano, Italy \u2021 Dipartimento di Scienze Agrarie ed Ambientali, Universit\ue0 di Udine, and Istituto di Genomica Applicata Parco Scientifico e Tecnologico di Udine "Luigi Danieli", Udine, Italy Abstract The term heterosis describes the superiority of heterozygous genotypes for one or more characteristics in comparison with the corresponding parental homozygotes. The higher productivity of the heterozygotes is exploited through the development of hybrid varieties in several crop species, and historically it represented one of the most outstanding advancement in plant improvement. Despite the long history of successes, especially in maize (Zea mays L.), the genetic bases of heterosis are not well understood yet. The application of molecular markers for the dissection of the genetic basis of many quantitative traits prompted the development of different approaches for the evaluation of heterosis. Our research was conducted on the genetic material developed from the single cross between maize inbred lines H99 and B73 in order to: (i) study the level of heterosis for traits of agronomic importance; (ii) identify the genomic regions (QTL quantitative trait loci) most involved in heterosis; (iii) investigate the relationships between the level of molecular marker heterozygosity and the phenotypic performance; (iv) estimate the genetic effects involved (i.e., allelic and non-allelic interactions). Materials were the basic generations, the derived 142 recombinant inbred lines (RILs) and the three testcross populations obtained by crossing the 142 RILs to each parent and their F1. RIL population was genotyped with a total of 158 marker loci arranged in a genetic linkage map. All genotypes were field-tested in three locations. The field layout was a randomized complete block design for basic generations, and a modified split-plot design for the four populations. Least square means over locations were used for subsequent analyses. Classical genetic analises were conducted following the North Caroline Model III (NCIII) and Triple Test Cross (TTC) designs. Moreover, Composite Interval Mapping was performed to search for QTL by combining plant\u2019s phenotypic and marker\u2019s genotypic data. QTL analysis was conducted on testcross populations\u2019 means and on derived datasets concerning additive and dominance effects only. Thresholds for declaring putative QTL were defined by permutations. A mixed linear model was then used to map digenic epistatic QTL. Among the examined traits, seedling weight (SW), number of kernels per plant (NK) and grain yield (GY) showed heterosis greater than 100% and dominance degree higher than one. Several QTL were identified prevailingly in the additive-dominance range, for traits with low heterosis, and prevailingly in the dominance-overdominance range for plant height (PH), SW, NK and GY. Only a few QTL with digenic epistasis were identified. Some chromosome regions presented overlaps of overdominant QTL for SW, PH, NK and GY, suggesting pleiotropic effects on the overall plant vigor