An assessment of Fe XX - Fe XXII emission lines in SDO/EVE data as diagnostics for high density solar flare plasmas using EUVE stellar observations

The Extreme Ultraviolet Variability Experiment (EVE) on the Solar Dynamics Observatory obtains extreme-ultraviolet (EUV) spectra of the full-disk Sun at a spectral resolution of ~1 A and cadence of 10 s. Such a spectral resolution would normally be considered to be too low for the reliable determination of electron density (N_e) sensitive emission line intensity ratios, due to blending. However, previous work has shown that a limited number of Fe XXI features in the 90-60 A wavelength region of EVE do provide useful N_e-diagnostics at relatively low flare densities (N_e ~ 10^11-10^12 cm^-3). Here we investigate if additional highly ionised Fe line ratios in the EVE 90-160 A range may be reliably employed as N_e-diagnostics. In particular, the potential for such diagnostics to provide density estimates for high N_e (~10^13 cm^-3) flare plasmas is assessed. Our study employs EVE spectra for X-class flares, combined with observations of highly active late-type stars from the Extreme Ultraviolet Explorer (EUVE) satellite plus experimental data for well-diagnosed tokamak plasmas, both of which are similar in wavelength coverage and spectral resolution to those from EVE. Several ratios are identified in EVE data which yield consistent values of electron density, including Fe XX 113.35/121.85 and Fe XXII 114.41/135.79, with confidence in their reliability as N_e-diagnostics provided by the EUVE and tokamak results. These ratios also allow the determination of density in solar flare plasmas up to values of ~10^13 cm^-3.Comment: 7 pages, 3 figures, 2 tables, MNRAS in pres

Fe XI emission lines in a high resolution extreme ultraviolet spectrum obtained by SERTS

New calculations of radiative rates and electron impact excitation cross sections for Fe XI are used to derive emission line intensity ratios involving 3s^23p^4 - 3s^23p^33d transitions in the 180-223 A wavelength range. These ratios are subsequently compared with observations of a solar active region, obtained during the 1995 flight Solar EUV Research Telescope and Spectrograph (SERTS). The version of SERTS flown in 1995 incorporated a multilayer grating that enhanced the instrumental sensitivity for features in the 170 - 225 A wavelength range, observed in second-order between 340 and 450 A. This enhancement led to the detection of many emission lines not seen on previous SERTS flights, which were measured with the highest spectral resolution (0.03 A) ever achieved for spatially resolved active region spectra in this wavelength range. However, even at this high spectral resolution, several of the Fe XI lines are found to be blended, although the sources of the blends are identified in the majority of cases. The most useful Fe XI electron density diagnostic line intensity ratio is I(184.80 A)/I(188.21 A). This ratio involves lines close in wavelength and free from blends, and which varies by a factor of 11.7 between N_e = 10^9 and 10^11 cm^-3, yet shows little temperature sensitivity. An unknown line in the SERTS spectrum at 189.00 A is found to be due to Fe XI, the first time (to our knowledge) this feature has been identified in the solar spectrum. Similarly, there are new identifications of the Fe XI 192.88, 198.56 and 202.42 A features, although the latter two are blended with S VIII/Fe XII and Fe XIII, respectively.Comment: 21 pages, 9 gigures, accepted for publication in the Astrophysical Journa

GPCR-OKB: the G protein coupled receptor oligomer knowledge base

Rapid expansion of available data about G Protein Coupled Receptor (GPCR) dimers/oligomers over the past few years requires an effective system to organize this information electronically. Based on an ontology derived from a community dialog involving colleagues using experimental and computational methodologies, we developed the GPCR-Oligomerization Knowledge Base (GPCR-OKB). GPCR-OKB is a system that supports browsing and searching for GPCR oligomer data. Such data were manually derived from the literature. While focused on GPCR oligomers, GPCR-OKB is seamlessly connected to GPCRDB, facilitating the correlation of information about GPCR protomers and oligomers

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

Emission lines of Fe XI in the 257--407 A wavelength region observed in solar spectra from EIS/Hinode and SERTS

Theoretical emission-line ratios involving Fe XI transitions in the 257-407 A wavelength range are derived using fully relativistic calculations of radiative rates and electron impact excitation cross sections. These are subsequently compared with both long wavelength channel Extreme-Ultraviolet Imaging Spectrometer (EIS) spectra from the Hinode satellite (covering 245-291 A), and first-order observations (235-449 A) obtained by the Solar Extreme-ultraviolet Research Telescope and Spectrograph (SERTS). The 266.39, 266.60 and 276.36 A lines of Fe XI are detected in two EIS spectra, confirming earlier identifications of these features, and 276.36 A is found to provide an electron density diagnostic when ratioed against the 257.55 A transition. Agreement between theory and observation is found to be generally good for the SERTS data sets, with discrepancies normally being due to known line blends, while the 257.55 A feature is detected for the first time in SERTS spectra. The most useful Fe XI electron density diagnostic is found to be the 308.54/352.67 intensity ratio, which varies by a factor of 8.4 between N_e = 10^8 and 10^11 cm^-3, while showing little temperature sensitivity. However, the 349.04/352.67 ratio potentially provides a superior diagnostic, as it involves lines which are closer in wavelength, and varies by a factor of 14.7 between N_e = 10^8 and 10^11 cm^-3. Unfortunately, the 349.04 A line is relatively weak, and also blended with the second-order Fe X 174.52 A feature, unless the first-order instrument response is enhanced.Comment: 9 pages, 5 figures, 13 tables; MNRAS in pres

Cell surface delivery and structural re-organization by pharmacological chaperones of an oligomerization-defective α1b-adrenoceptor mutant demonstrates membrane targeting of GPCR oligomers

Many G-protein-coupled receptors, including the α1b-adrenoceptor, form homo-dimers or oligomers. Mutation of hydrophobic residues in transmembrane domains I and IV alters the organization of the α1b-adrenoceptor oligomer, with transmembrane domain IV playing a critical role. These mutations also result in endoplasmic reticulum trapping of the receptor. Following stable expression of this α1b-adrenoceptor mutant, cell surface delivery, receptor function and structural organization were recovered by treatment with a range of α1b-adrenoceptor antagonists that acted at the level of the endoplasmic reticulum. This was accompanied by maturation of the mutant receptor to a terminally N-glycosylated form, and only this mature form was trafficked to the cell surface. Co-expression of the mutant receptor with an otherwise wild-type form of the α1b-adrenoceptor that is unable to bind ligands resulted in this wild-type variant also being retained in the endoplasmic reticulum. Ligand-induced cell surface delivery of the mutant α1b-adrenoceptor now allowed co-recovery to the plasma membrane of the ligand-binding-deficient mutant. These results demonstrate that interactions between α1b-adrenoceptor monomers occur at an early stage in protein synthesis, that ligands of the α1b-adrenoceptor can act as pharmacological chaperones to allow a structurally compromised form of the receptor to pass cellular quality control, that the mutated receptor is not inherently deficient in function and that an oligomeric assembly of ligand-binding-competent and -incompetent forms of the α1b-adrenoceptor can be trafficked to the cell surface by binding of a ligand to only one component of the receptor oligomer

Interaction of eukaryotic translation initiation factor 4G with the nuclear cap-binding complex provides a link between nuclear and cytoplasmic functions of the m7 guanosine cap

In eukaryotes the majority of mRNAs have an m7G cap that is added cotranscriptionally and that plays an important role in many aspects of mRNA metabolism. The nuclear cap-binding complex (CBC; consisting of CBP20 and CBP80) mediates the stimulatory functions of the cap in pre-mRNA splicing, 3' end formation, and U snRNA export. As little is known about how nuclear CBC mediates the effects of the cap in higher eukaryotes, we have characterized proteins that interact with CBC in HeLa cell nuclear extracts as potential mediators of its function. Using cross-linking and coimmunoprecipitation, we show that eukaryotic translation initiation factor 4G (eIF4G), in addition to its function in the cytoplasm, is a nuclear CBC-interacting protein. We demonstrate that eIF4G interacts with CBC in vitro and that, in addition to its cytoplasmic localization, there is a significant nuclear pool of eIF4G in mammalian cells in vivo. Immunoprecipitation experiments suggest that, in contrast to the cytoplasmic pool, much of the nuclear eIF4G is not associated with eIF4E (translation cap binding protein of eIF4F) but is associated with CBC. While eIF4G stably associates with spliceosomes in vitro and shows close association with spliceosomal snRNPs and splicing factors in vivo, depletion studies show that it does not participate directly in the splicing reaction. Taken together the data indicate that nuclear eIF4G may be recruited to pre-mRNAs via its interaction with CBC and accompanies the mRNA to the cytoplasm, facilitating the switching of CBC for eIF4F. This may provide a mechanism to couple nuclear and cytoplasmic functions of the mRNA cap structure

Minkowski distances and standardisation for clustering and classification of high dimensional data

There are many distance-based methods for classification and clustering, and for data with a high number of dimensions and a lower number of observations, processing distances is computationally advantageous compared to the raw data matrix. Euclidean distances are used as a default for continuous multivariate data, but there are alternatives. Here the so-called Minkowski distances, $L_1$ (city block)-, $L_2$ (Euclidean)-, $L_3$-, $L_4$-, and maximum distances are combined with different schemes of standardisation of the variables before aggregating them. Boxplot transformation is proposed, a new transformation method for a single variable that standardises the majority of observations but brings outliers closer to the main bulk of the data. Distances are compared in simulations for clustering by partitioning around medoids, complete and average linkage, and classification by nearest neighbours, of data with a low number of observations but high dimensionality. The $L_1$-distance and the boxplot transformation show good results.Comment: Preliminary version; final version to be published by Springer, using Springer's svmult LATEX styl