Observation and Modeling of the Solar Transition Region: II. Solutions of the Quasi-Static Loop Model

In the present work we undertake a study of the quasi-static loop model and the observational consequences of the various solutions found. We obtain the most general solutions consistent with certain initial conditions. Great care is exercised in choosing these conditions to be physically plausible (motivated by observations). We show that the assumptions of previous quasi-static loop models, such as the models of Rosner, Tucker and Vaiana (1978) and Veseckey, Antiochos and Underwood (1979), are not necessarily valid for small loops at transition region temperatures. We find three general classes of solutions for the quasi-static loop model, which we denote, radiation dominated loops, conduction dominated loops and classical loops. These solutions are then compared with observations. Departures from the classical scaling law of RTV are found for the solutions obtained. It is shown that loops of the type that we model here can make a significant contribution to lower transition region emission via thermal conduction from the upper transition region.Comment: 30 pages, 3 figures, Submitted to ApJ, Microsoft Word File 6.0/9

Extreme Ultra-Violet Spectroscopy of the Lower Solar Atmosphere During Solar Flares

The extreme ultraviolet portion of the solar spectrum contains a wealth of diagnostic tools for probing the lower solar atmosphere in response to an injection of energy, particularly during the impulsive phase of solar flares. These include temperature and density sensitive line ratios, Doppler shifted emission lines and nonthermal broadening, abundance measurements, differential emission measure profiles, and continuum temperatures and energetics, among others. In this paper I shall review some of the advances made in recent years using these techniques, focusing primarily on studies that have utilized data from Hinode/EIS and SDO/EVE, while also providing some historical background and a summary of future spectroscopic instrumentation.Comment: 34 pages, 8 figures. Submitted to Solar Physics as part of the Topical Issue on Solar and Stellar Flare

Coronal properties of the EQ Peg binary system

The activity indicators of M dwarfs are distinctly different for early and late types. The coronae of early M dwarfs display high X-ray luminosities and temperatures, a pronounced inverse FIP effect, and frequent flaring to the extent that no quiescent level can be defined in many cases. For late M dwarfs, fewer but more violent flares have been observed, and the quiescent X-ray luminosity is much lower. To probe the relationship between coronal properties with spectral type of active M dwarfs, we analyze the M3.5 and M4.5 components of the EQ Peg binary system in comparison with other active M dwarfs of spectral types M0.5 to M5.5. We investigate the timing behavior of both components of the EQ Peg system, reconstruct their differential emission measure, and investigate the coronal abundance ratios based on emission-measure independent line ratios from their Chandra HETGS spectra. Finally we test for density variations in different states of activity. The X-ray luminosity of EQ Peg A (M3.5) is by a factor of 6-10 brighter than that of EQ Peg B (M4.5). Like most other active M dwarfs, the EQ Peg system shows an inverse FIP effect. The abundances of both components are consistent within the errors; however, there seems to be a tendency toward the inverse FIP effect being less pronounced in the less active EQ Peg B when comparing the quiescent state of the two stars. This trend is supported by our comparison with other M dwarfs. As the X-ray luminosity decreases with later spectral type, so do coronal temperatures and flare rate. The amplitude of the observed abundance anomalies, i.e. the inverse FIP effect, declines; however, clear deviations from solar abundances remain.Comment: 14 pages, accepted by A&

What is the Nature of EUV Waves? First STEREO 3D Observations and Comparison with Theoretical Models

One of the major discoveries of the Extreme ultraviolet Imaging Telescope (EIT) on SOHO were intensity enhancements propagating over a large fraction of the solar surface. The physical origin(s) of the so-called `EIT' waves is still strongly debated. They are considered to be either wave (primarily fast-mode MHD waves) or non-wave (pseudo-wave) interpretations. The difficulty in understanding the nature of EUV waves lies with the limitations of the EIT observations which have been used almost exclusively for their study. Their limitations are largely overcome by the SECCHI/EUVI observations on-board the STEREO mission. The EUVI telescopes provide high cadence, simultaneous multi-temperature coverage, and two well-separated viewpoints. We present here the first detailed analysis of an EUV wave observed by the EUVI disk imagers on December 07, 2007 when the STEREO spacecraft separation was $\approx 45^\circ$. Both a small flare and a CME were associated with the wave cadence, and single temperature and viewpoint coverage. These limitations are largely overcome by the SECCHI/EUVI observations on-board the STEREO mission. The EUVI telescopes provide high cadence, simultaneous multi-temperature coverage, and two well-separated viewpoints. Our findings give significant support for a fast-mode interpretation of EUV waves and indicate that they are probably triggered by the rapid expansion of the loops associated with the CME.Comment: Solar Physics, 2009, Special STEREO Issue, in pres

On Solving the Coronal Heating Problem

This article assesses the current state of understanding of coronal heating, outlines the key elements of a comprehensive strategy for solving the problem, and warns of obstacles that must be overcome along the way.Comment: Accepted by Solar Physics; Published by Solar Physic

A monoclonal antibody raised against bacterially expressed MPV17 sequences shows peroxisomal, endosomal and lysosomal localisation in U2OS cells

Recessive mutations in the MPV17 gene cause mitochondrial DNA depletion syndrome, a fatal infantile genetic liver disease in humans. Loss of function in mice leads to glomerulosclerosis and sensineural deafness accompanied with mitochondrial DNA depletion. Mutations in the yeast homolog Sym1, and in the zebra fish homolog tra cause interesting, but not obviously related phenotypes, although the human gene can complement the yeast Sym1 mutation. The MPV17 protein is a hydrophobic membrane protein of 176 amino acids and unknown function. Initially localised in murine peroxisomes, it was later reported to be a mitochondrial inner membrane protein in humans and in yeast. To resolve this contradiction we tested two new mouse monoclonal antibodies directed against the human MPV17 protein in Western blots and immunohistochemistry on human U2OS cells. One of these monoclonal antibodies showed specific reactivity to a protein of 20 kD absent in MPV17 negative mouse cells. Immunofluorescence studies revealed colocalisation with peroxisomal, endosomal and lysosomal markers, but not with mitochondria. This data reveal a novel connection between a possible peroxisomal/endosomal/lysosomal function and mitochondrial DNA depletion

Comparative Analysis of Human Protein-Coding and Noncoding RNAs between Brain and 10 Mixed Cell Lines by RNA-Seq

In their expression process, different genes can generate diverse functional products, including various protein-coding or noncoding RNAs. Here, we investigated the protein-coding capacities and the expression levels of their isoforms for human known genes, the conservation and disease association of long noncoding RNAs (ncRNAs) with two transcriptome sequencing datasets from human brain tissues and 10 mixed cell lines. Comparative analysis revealed that about two-thirds of the genes expressed between brain and cell lines are the same, but less than one-third of their isoforms are identical. Besides those genes specially expressed in brain and cell lines, about 66% of genes expressed in common encoded different isoforms. Moreover, most genes dominantly expressed one isoform and some genes only generated protein-coding (or noncoding) RNAs in one sample but not in another. We found 282 human genes could encode both protein-coding and noncoding RNAs through alternative splicing in the two samples. We also identified more than 1,000 long ncRNAs, and most of those long ncRNAs contain conserved elements across either 46 vertebrates or 33 placental mammals or 10 primates. Further analysis showed that some long ncRNAs differentially expressed in human breast cancer or lung cancer, several of those differentially expressed long ncRNAs were validated by RT-PCR. In addition, those validated differentially expressed long ncRNAs were found significantly correlated with certain breast cancer or lung cancer related genes, indicating the important biological relevance between long ncRNAs and human cancers. Our findings reveal that the differences of gene expression profile between samples mainly result from the expressed gene isoforms, and highlight the importance of studying genes at the isoform level for completely illustrating the intricate transcriptome

Exploring the functional role of the CHRM2 gene in human cognition: results from a dense genotyping and brain expression study

<p>Abstract</p> <p>Background</p> <p>The <it>CHRM2 </it>gene, located on the long arm of chromosome 7 (7q31-35), is involved in neuronal excitability, synaptic plasticity and feedback regulation of acetylcholine release, and has been implicated in higher cognitive processing. The aim of this study is the identification of functional (non)coding variants underlying cognitive phenotypic variation.</p> <p>Methods</p> <p>We previously reported an association between polymorphisms in the 5'UTR regions of the <it>CHRM2 </it>gene and intelligence.. However, no functional variants within this area have currently been identified. In order to identify the relevant functional variant(s), we conducted a denser coverage of SNPs, using two independent Dutch cohorts, consisting of a children's sample (N = 371 ss; mean age 12.4) and an adult sample (N= 391 ss; mean age 37.6). For all individuals standardized intelligence measures were available. Subsequently, we investigated genotype-dependent <it>CHRM2 </it>gene expression levels in the brain, to explore putative enhancer/inhibition activity exerted by variants within the muscarinic acetylcholinergic receptor.</p> <p>Results</p> <p>Using a test of within-family association two of the previously reported variants – rs2061174, and rs324650 – were again strongly associated with intelligence (<it>P </it>< 0.01). A new SNP (rs2350780) showed a trend towards significance. SNP rs324650, is located within a short interspersed repeat (SINE). Although the function of short interspersed repeats remains contentious, recent research revealed potential functionality of SINE repeats in a gene-regulatory context. Gene-expression levels in post-mortem brain material, however were not dependent on rs324650 genotype.</p> <p>Conclusion</p> <p>Using a denser coverage of SNPs in the <it>CHRM2 </it>gene, we confirmed the 5'UTR regions to be most interesting in the context of intelligence, and ruled out other regions of this gene. Although no correlation between genomic variants and gene expression was found, it would be interesting to examine allele-specific effects on CHRM2 transcripts expression in much more detail, for example in relation to transcripts specific halve-life and their relation to LTP and memory.</p