Coronal ion-cyclotron beam instabilities within the multi-fluid description

Spectroscopic observations and theoretical models suggest resonant wave-particle interactions, involving high-frequency ion-cyclotron waves, as the principal mechanism for heating and accelerating ions in the open coronal holes. However, the mechanism responsible for the generation of the ion-cyclotron waves remains unclear. One possible scenario is that ion beams originating from small-scale reconnection events can drive micro-instabilities that constitute a possible source for the excitation of ion-cyclotron waves. In order to study ion beam-driven electromagnetic instabilities, the multi-fluid model in the low-beta coronal plasma is used. While neglecting the electron inertia this model allows one to take into account ion-cyclotron wave effects that are absent from the one-fluid MHD model. Realistic models of density and temperature as well as a 2-D analytical magnetic field model are used to define the background plasma in the open-field funnel region of a polar coronal hole. Considering the WKB approximation, a Fourier plane-wave linear mode analysis is employed in order to derive the dispersion relation. Ray-tracing theory is used to compute the ray path of the unstable wave as well as the evolution of the growth rate of the wave while propagating in the coronal funnel. We demonstrate that, in typical coronal holes conditions and assuming realistic values of the beam velocity, the free energy provided by the ion beam propagating parallel the ambient field can drive micro-instabilities through resonant ion-cyclotron excitation.Comment: 8 pages, 6 figures, submitted to A&

Phase Changes in Ni-Ti Under Laser Shock Loading

Near-equiatomic Ni-Ti, known for its shape memory behavior, can decompose to martensitic phases and/or second phase compounds. This phase competition is investigated in NixTi100-x (494Ti3 but no martensite in the AQ state, consistent with resistivity and dilatometry results which showed no hysteresis indicative of first order phase changes over 1.9 K4Ti3 amounts (present in the AQ state) did change upon loading, indicating the importance of shock-induced heating. A thermodynamically complete equation of state (EOS) for NiTi in its B2 (CsCl) structure was generated by ab initio quantum mechanical calculations. This was tested by performing laser-launched flyer experiments, which showed consistency with the theoretical EOS, validating its use in the prediction of dynamic loading histories in the samples during direct drive loading

Different Transport Pathways of Individual Precursor Proteins in Mitochondria

Transport of mitochondrial precursor proteins into mitochondria of Neurospora crassa was studied in a cellfree reconstituted system. Precursors were synthesized in a reticulocyte lysate programmed with Neurospora mRNA and transported into isolated mitochondria in the absence of protein synthesis. Uptake of the following precursors was investigated: apocytochrome c, ADP/ATP carrier and subunit 9 of the oligomycin-sensitive ATPase. Addition of high concentrations of unlabelled chemically prepared apocytochrome c (1–10 μM) inhibited the appearance in the mitochondrial of labelled cytochrome c synthesized in vitro because the unlabelled protein dilutes the labelled one and because the translocation system has a limited capacity [apparent V is 1–3 pmol × min−1× (mg mitochondrial protein)−1]. Concentrations of added apocytochrome c exceeding the concentrations of precursor proteins synthesized in vitro by a factor of about 104 did not inhibit the transfer of ADP/ATP carrier or ATPase subunit 9 into mitochondria. Carbonylcyanide m-chlorophenylhydrazone, an uncoupler of oxidative phosphorylation, inhibited transfer in vitro of ADP/ATP carrier and of ATPase subunit 9, but not of cytochrome c. These findings suggest that cytochrome c and the other two proteins have different import pathways into mitochondria. It can be inferred from the data presented that different 'receptors' on the mitochondrial surface mediate the specific recognition of precursor proteins by mitochondria as a first step in the transport process

Transport of Proteins into Mitochondria

The mitochondrial ADP/ATP carrier is an integral transmembrane protein of the inner membrane. It is synthesized on cytoplasmic ribosomes. Kinetic data suggested that this protein is transferred into mitochondria in a posttranslational manner. The following results provide further evidence for such a mechanism and provide information on its details. 1. In homologous and heterologous translation systems the newly synthesized ADP/ATP carrier protein is present in the postribosomal supernatant. 2. Analysis by density gradient centrifugation and gel filtration shows, that the ADP/ATP carrier molecules in the postribosomal fraction are present as soluble complexes with apparent molecular weights of about 120000 and 500000 or larger. The carrier binds detergents such as Triton X-100 and deoxycholate forming mixed micelles with molecular weights of about 200000–400000. 3. Incubation of a postribosomal supernatant of a reticulocyte lysate containing newly synthesized ADP/ATP carrier with mitochondria isolated from Neurospora spheroplasts results in efficient transfer of the carrier into mitochondria. About 20–30% of the transferred carrier are resistant to proteinase in whole mitochondria. The authentic mature protein is also largely resistant to proteinase in whole mitochondria and sensitive after lysis of mitochondria with detergent. Integrity of mitochondria is a prerequisite for translocation into proteinase resistant position. 4. The transfer in vitro into a proteinase-resistant form is inhibited by the uncoupler carbonyl-cyanide m-chlorophenylhydrazone but not the proteinase-sensitive binding. These observations suggest that the posttranslational transfer of ADP/ATP carrier occurs via the cytosolic space through a soluble oligomeric precursor form. This precursor is taken up by intact mitochondria into an integral position in the membrane. These findings are considered to be of general importance for the intracellular transfer of insoluble membrane proteins. They support the view that such proteins can exist in a water-soluble form its precursors and upon integration into the membrane undergo a conformational change. Uptake into the membrane may involve the cleavage of an additional sequence in some proteins, but this appears not to be a prerequisite as demonstrated by the ADP/ATP carrier protein

Cell-Free Synthesis of the Mitochondrial ADP/ATP Carrier Protein of Neurospora crassa

ADP/ATP carrier protein was synthesized in heterologous cell-free systems programmed with Neurospora poly(A)-containing RNA and homologous cell-free systems from Neurospora. The apparent molecular weight of the product obtained in vitro was the same as that of the authentic mitochondrial protein. The primary translation product obtained in reticulocyte lysates starts with formylmethionine when formylated initiator methionyl-tRNA (fMet-tRNAfMet) was present. The product synthesized in vitro was released from the ribosomes into the postribosomal supernatant. The evidence presented indicates that the ADP/ATP carrier is synthesized as a polypeptide with the same molecular weight as the mature monomeric protein and does not carry an additional sequence

Sagittal jaw position in relation to body posture in adult humans – a rasterstereographic study

BACKGROUND: The correlations between the sagittal jaw position and the cranio – cervical inclination are described in literature. Only few studies focus on the sagittal jaw position and the body posture using valid and objective orthopaedic examination methods. The aim of this study was to test the hypothesis that patients with malocclusions reveal significant differences in body posture compared to those without (upper thoracic inclination, kyphotic angle, lordotic angle and lower lumbar inclination). METHODS: Eighty-four healthy adult patients (with a mean age = 25.6 years and ranging from 16.1 to 55.8 years) were examined with informed consent. The orthodontic examination horizontal overjet (distance between upper and lower incisors) was determined by using an orthodontic digital sliding calliper. The subjects were subdivided in respect of the overjet with the following results: 18 revealed a normal overjet (Class I), 38 had an increased overjet (Class II) and 28 had an reversed overjet (Class III). Rasterstereography was used to carry out a three – dimensional back shape analysis. This method is based on photogrammetry. A three-dimensional shape was produced by analysing the distortion of parallel horizontal white light lines projected on the patient's back, followed by mathematical modelling. On the basis of the sagittal profile the upper thoracic inclination, the thoracic angle, the lordotic angle and the pelvic inclination were determined with a reported accuracy of 2.8° and the correlations to the sagittal jaw position were calculated by means of ANOVA, Scheffé and Kruskal-Wallis procedures. RESULTS: Between the different overjet groups, no statistically significant differences or correlations regarding the analysed back shape parameters could be obtained. However, comparing males and females there were statistically significant differences in view of the parameters 'lordotic angle' and 'pelvic inclination'. CONCLUSION: No correlations between overjet and variables of the thoracic, lordotic or the pelvic inclination could be observed

Fabrication of Beryllium Capsules with Copper-Doped Layers for NIF Targets: A Progress Report

The sputtering of beryllium (Be) has been used at LLNL for nearly 30 years in the fabrication of laser targets. Several years ago the prospect of using sputtering to fabricate spherical Be capsules for National Ignition Facility (NIF) targets began to be explored and a basic strategy was developed that involved sputtering down onto plastic mandrels bouncing in a pan. While this appears to be very straightforward in principle, in practice sputtering has been used almost exclusively to make thin films (< 1 micron) on flat substrates. Thick films pose a significant challenge for sputtering while materials on spherical substrates are essentially unexplored. More recently, based on computational results, the point design for the first NIF ignition target capsule was specified as a Be capsule with Cu-doped layers of specific thickness, each layer with a different concentration of copper. While the work described here was motivated by the need to make the layered capsules, the primary progress on Be capsules has been the development of a more complete metallurgical understanding of the materials that are fabricated and the beginning of the exploration of the relationship between the sputter processing and microstructure of these spherical samples. At least two barriers to growth to full thickness (i.e. 170 microns) have been identified and efforts to overcome these barriers are underway

Enrichment analysis of Alu elements with different spatial chromatin proximity in the human genome

Transposable elements (TEs) have no longer been totally considered as “junk DNA” for quite a time since the continual discoveries of their multifunctional roles in eukaryote genomes. As one of the most important and abundant TEs that still active in human genome, Alu, a SINE family, has demonstrated its indispensable regulatory functions at sequence level, but its spatial roles are still unclear. Technologies based on 3C(chromosomeconformation capture) have revealed the mysterious three-dimensional structure of chromatin, and make it possible to study the distal chromatin interaction in the genome. To find the role TE playing in distal regulation in human genome, we compiled the new released Hi-C data, TE annotation, histone marker annotations, and the genome-wide methylation data to operate correlation analysis, and found that the density of Alu elements showed a strong positive correlation with the level of chromatin interactions (hESC: r=0.9, P<2.2×1016; IMR90 fibroblasts: r = 0.94, P < 2.2 × 1016) and also have a significant positive correlation withsomeremote functional DNA elements like enhancers and promoters (Enhancer: hESC: r=0.997, P=2.3×10−4; IMR90: r=0.934, P=2×10−2; Promoter: hESC: r = 0.995, P = 3.8 × 10−4; IMR90: r = 0.996, P = 3.2 × 10−4). Further investigation involving GC content and methylation status showed the GC content of Alu covered sequences shared a similar pattern with that of the overall sequence, suggesting that Alu elements also function as the GC nucleotide and CpG site provider. In all, our results suggest that the Alu elements may act as an alternative parameter to evaluate the Hi-C data, which is confirmed by the correlation analysis of Alu elements and histone markers. Moreover, the GC-rich Alu sequence can bring high GC content and methylation flexibility to the regions with more distal chromatin contact, regulating the transcription of tissue-specific genes

MethylExtract: High-Quality methylation maps and SNV calling from whole genome bisulfite sequencing data

[v2; ref status: indexed, http://f1000r.es/301]Whole genome methylation profiling at a single cytosine resolution is now feasible due to the advent of high-throughput sequencing techniques together with bisulfite treatment of the DNA. To obtain the methylation value of each individual cytosine, the bisulfite-treated sequence reads are first aligned to a reference genome, and then the profiling of the methylation levels is done from the alignments. A huge effort has been made to quickly and correctly align the reads and many different algorithms and programs to do this have been created. However, the second step is just as crucial and non-trivial, but much less attention has been paid to the final inference of the methylation states. Important error sources do exist, such as sequencing errors, bisulfite failure, clonal reads, and single nucleotide variants. We developed MethylExtract, a user friendly tool to: i) generate high quality, whole genome methylation maps and ii) detect sequence variation within the same sample preparation. The program is implemented into a single script and takes into account all major error sources. MethylExtract detects variation (SNVs – Single Nucleotide Variants) in a similar way to VarScan, a very sensitive method extensively used in SNV and genotype calling based on non-bisulfite-treated reads. The usefulness of MethylExtract is shown by means of extensive benchmarking based on artificial bisulfite-treated reads and a comparison to a recently published method, called Bis-SNP. MethylExtract is able to detect SNVs within High-Throughput Sequencing experiments of bisulfite treated DNA at the same time as it generates high quality methylation maps. This simultaneous detection of DNA methylation and sequence variation is crucial for many downstream analyses, for example when deciphering the impact of SNVs on differential methylation. An exclusive feature of MethylExtract, in comparison with existing software, is the possibility to assess the bisulfite failure in a statistical way. The source code, tutorial and artificial bisulfite datasets are available at http://bioinfo2.ugr.es/MethylExtract/ and http://sourceforge.net/projects/methylextract/, and also permanently accessible from 10.5281/zenodo.7144.This work was supported by the Spanish Government [BIO2008-01353 to JLO and BIO2010-20219 to MH], and Basque country 'AE' grant (GB)

Identification and QTL mapping of resistance to Turnip yellows virus (TuYV) in oilseed rape, Brassica napus

Key message Partially dominant resistance to Turnip yellows virus associated with one major QTL was identified in the natural allotetraploid oilseed rape cultivar Yudal. Abstract Turnip yellows virus (TuYV) is transmitted by the peach-potato aphid (Myzus persicae) and causes severe yield losses in commercial oilseed rape crops (Brassica napus). There is currently only one genetic resource for resistance to TuYV available in brassica, which was identified in the re-synthesised B. napus line ‘R54’. In our study, 27 mostly homozygous B. napus accessions, either doubled-haploid (DH) or inbred lines, representing a diverse subset of the B. napus genepool, were screened for TuYV resistance/susceptibility. Partial resistance to TuYV was identified in the Korean spring oilseed rape, B. napus variety Yudal, whilst the dwarf French winter oilseed rape line Darmor-bzh was susceptible. QTL mapping using the established Darmor-bzh × Yudal DH mapping population (DYDH) revealed one major QTL explaining 36% and 18% of the phenotypic variation in two independent experiments. A DYDH line was crossed to Yudal, and reciprocal backcross (BC1) populations from the F1 with either the susceptible or resistant parent revealed the dominant inheritance of the TuYV resistance. The QTL on ChrA04 was verified in the segregating BC1 population. A second minor QTL on ChrC05 was identified in one of the two DYDH experiments, and it was not observed in the BC1 population. The TuYV resistance QTL in ‘R54’ is within the QTL interval on Chr A04 of Yudal; however, the markers co-segregating with the ‘R54’ resistance are not conserved in Yudal, suggesting an independent origin of the TuYV resistances. This is the first report of the QTL mapping of TuYV resistance in natural B. napus