Epigenomic Modifications Predict Active Promoters and Gene Structure in Toxoplasma gondii

Mechanisms of gene regulation are poorly understood in Apicomplexa, a phylum that encompasses deadly human pathogens like Plasmodium and Toxoplasma. Initial studies suggest that epigenetic phenomena, including histone modifications and chromatin remodeling, have a profound effect upon gene expression and expression of virulence traits. Using the model organism Toxoplasma gondii, we characterized the epigenetic organization and transcription patterns of a contiguous 1% of the T. gondii genome using custom oligonucleotide microarrays. We show that methylation and acetylation of histones H3 and H4 are landmarks of active promoters in T. gondii that allow us to deduce the position and directionality of gene promoters with >95% accuracy. These histone methylation and acetylation “activation” marks are strongly associated with gene expression. We also demonstrate that the pattern of histone H3 arginine methylation distinguishes certain promoters, illustrating the complexity of the histone modification machinery in Toxoplasma. By integrating epigenetic data, gene prediction analysis, and gene expression data from the tachyzoite stage, we illustrate feasibility of creating an epigenomic map of T. gondii tachyzoite gene expression. Further, we illustrate the utility of the epigenomic map to empirically and biologically annotate the genome and show that this approach enables identification of previously unknown genes. Thus, our epigenomics approach provides novel insights into regulation of gene expression in the Apicomplexa. In addition, with its compact genome, genetic tractability, and discrete life cycle stages, T. gondii provides an important new model to study the evolutionarily conserved components of the histone code

LUCI onboard Lagrange, the Next Generation of EUV Space Weather Monitoring

LUCI (Lagrange eUv Coronal Imager) is a solar imager in the Extreme UltraViolet (EUV) that is being developed as part of the Lagrange mission, a mission designed to be positioned at the L5 Lagrangian point to monitor space weather from its source on the Sun, through the heliosphere, to the Earth. LUCI will use an off-axis two mirror design equipped with an EUV enhanced active pixel sensor. This type of detector has advantages that promise to be very beneficial for monitoring the source of space weather in the EUV. LUCI will also have a novel off-axis wide field-of-view, designed to observe the solar disk, the lower corona, and the extended solar atmosphere close to the Sun-Earth line. LUCI will provide solar coronal images at a 2-3 minute cadence in a pass-band centred on 19.5 nm. Observations made through this pass-band allow for the detection and monitoring of semi-static coronal structures such as coronal holes, prominences, and active regions; as well as transient phenomena such as solar flares, limb Coronal Mass Ejections (CMEs), EUV waves, and coronal dimmings. The LUCI data will complement EUV solar observations provided by instruments located along the Sun-Earth line such as PROBA2-SWAP, SUVI-GOES and SDO-AIA, as well as provide unique observations to improve space weather forecasts. Together with a suite of other remote-sensing and in-situ instruments onboard Lagrange, LUCI will provide science quality operational observations for space weather monitoring

Spectral Imager of the Solar Atmosphere: The First Extreme-Ultraviolet Solar Integral Field Spectrograph Using Slicers

Particle acceleration, and the thermalisation of energetic particles, are fundamental processes across the universe. Whilst the Sun is an excellent object to study this phenomenon, since it is the most energetic particle accelerator in the Solar System, this phenomenon arises in many other astrophysical objects, such as active galactic nuclei, black holes, neutron stars, gamma ray bursts, solar and stellar coronae, accretion disks and planetary magnetospheres. Observations in the Extreme Ultraviolet (EUV) are essential for these studies but can only be made from space. Current spectrographs operating in the EUV use an entrance slit and cover the required field of view using a scanning mechanism. This results in a relatively slow image cadence in the order of minutes to capture inherently rapid and transient processes, and/or in the spectrograph slit ‘missing the action’. The application of image slicers for EUV integral field spectrographs is therefore revolutionary. The development of this technology will enable the observations of EUV spectra from an entire 2D field of view in seconds, over two orders of magnitude faster than what is currently possible. The Spectral Imaging of the Solar Atmosphere (SISA) instrument is the first integral field spectrograph proposed for observations at ∼180 Å combining the image slicer technology and curved diffraction gratings in a highly efficient and compact layout, while providing important spectroscopic diagnostics for the characterisation of solar coronal and flare plasmas. SISA’s characteristics, main challenges, and the on-going activities to enable the image slicer technology for EUV applications are presented in this paper

Multiwavelength Study of M8.9/3B Solar Flare from AR NOAA 10960

We present a multi-wavelength analysis of a long duration white-light solar flare (M8.9/3B) event that occurred on 4 June 2007 from NOAA AR 10960. The flare was observed by several spaceborne instruments, namely SOHO/MDI, Hinode/SOT, TRACE and STEREO/SECCHI. The flare was initiated near a small, positive-polarity, satellite sunspot at the centre of the AR, surrounded by opposite-polarity field regions. MDI images of the AR show considerable amount of changes in a small positive-polarity sunspot of delta configuration during the flare event. SOT/G-band (4305 A) images of the sunspot also suggest the rapid evolution of the positive-polarity sunspot with highly twisted penumbral filaments before the flare event, which were oriented in the counterclockwise direction. It shows the change in orientation and also remarkable disappearance of twisted penumbral filaments (~35-40%) and enhancement in umbral area (~45-50%) during the decay phase of the flare. TRACE and SECCHI observations reveal the successive activations of two helical twisted structures associated with this sunspot, and the corresponding brightening in the chromosphere as observed by the time-sequence images of SOT/Ca II H line (3968 A). The secondary-helical twisted structure is found to be associated with the M8.9 flare event. The brightening starts 6-7 min prior to the flare maximum with the appearance of secondary helical-twisted structure. The flare intensity maximizes as this structure moves away from the AR. This twisted flux-tube associated with the flare triggering, is found to be failed in eruption. The location of the flare is found to coincide with the activation site of the helical twisted structures. We conclude that the activations of successive helical twists in the magnetic flux tubes/ropes plays a crucial role in the energy build-up process and triggering of M-class solar flare without a CME.Comment: 22 pages, 12 figures, Accepted for Publication in Solar Physic

3D evolution of a filament disappearance event observed by STEREO

A filament disappearance event was observed on 22 May 2008 during our recent campaign JOP 178. The filament, situated in the southern hemisphere, showed sinistral chirality consistent with the hemispheric rule. The event was well observed by several observatories in particular by THEMIS. One day before the disappearance, H$\alpha$ observations showed up and down flows in adjacent locations along the filament, which suggest plasma motions along twisted flux rope. THEMIS and GONG observations show shearing photospheric motions leading to magnetic flux canceling around barbs. STEREO A, B spacecraft with separation angle 52.4 degrees, showed quite different views of this untwisting flux rope in He II 304 \AA\ images. Here, we reconstruct the 3D geometry of the filament during its eruption phase using STEREO EUV He II 304 \AA\ images and find that the filament was highly inclined to the solar normal. The He II 304 \AA\ movies show individual threads, which oscillate and rise to an altitude of about 120 Mm with apparent velocities of about 100 km s$^{-1}$, during the rapid evolution phase. Finally, as the flux rope expands into the corona, the filament disappears by becoming optically thin to undetectable levels. No CME was detected by STEREO, only a faint CME was recorded by LASCO at the beginning of the disappearance phase at 02:00 UT, which could be due to partial filament eruption. Further, STEREO Fe XII 195 \AA\ images showed bright loops beneath the filament prior to the disappearance phase, suggesting magnetic reconnection below the flux rope

Plasmodium falciparum heterochromatin protein 1 binds to tri-methylated histone 3 lysine 9 and is linked to mutually exclusive expression of var genes

Increasing experimental evidence shows a prominent role of histone modifications in the coordinated control of gene expression in the human malaria parasite Plasmodium falciparum. The search for the histone-mark-reading machinery that translates histone modifications into biological processes, such as formation of heterochromatin and antigenic variation is of foremost importance. In this work, we identified the first member of a histone modification specific recognition protein, an orthologue of heterochromatin protein 1 (PfHP1). Analysis of the PfHP1 amino-acid sequence revealed the presence of the two characteristic HP1 domains: a chromodomain (CD) and a chromo shadow domain (CSD). Recombinant CD binds to di- and tri-methylated lysine 9 from histone H3, but not to unmodified or methylated histone H3 in lysine 4. PfHP1 is able to interact with itself to form dimers, underlying its potential role in aggregating nucleosomes to form heterochromatin. Antibodies raised against PfHP1 detect this molecule in foci at the perinuclear region. ChIP analysis using anti-PfHP1 shows that this protein is linked to heterochromatin of subtelomeric non-coding repeat regions and monoallelic expression of the major virulence var gene family. This is the first report implicating an HP1 protein in the control of antigenic variation of a protozoan parasite

Beyond the disk: EUV coronagraphic observations of the Extreme Ultraviolet Imager on board Solar Orbiter

Most observations of the solar corona beyond 2 Rs consist of broadband visible light imagery from coronagraphs. The associated diagnostics mainly consist of kinematics and derivations of the electron number density. While the measurement of the properties of emission lines can provide crucial additional diagnostics of the coronal plasma (temperatures, velocities, abundances, etc.), these observations are comparatively rare. In visible wavelengths, observations at these heights are limited to total eclipses. In the VUV range, very few additional observations have been achieved since the pioneering results of UVCS. One of the objectives of the Full Sun Imager (FSI) channel of the EUI telescope on board the Solar Orbiter mission has been to provide very wide field-of-view EUV diagnostics of the morphology and dynamics of the solar atmosphere in temperature regimes that are typical of the lower transition region and of the corona. FSI carries out observations in two narrowbands of the EUV spectrum centered on 17.4 nm and 30.4 nm that are dominated, respectively, by lines of Fe IX/X (formed in the corona around 1 MK) and by the resonance line of He II (formed around 80 kK in the lower transition region). Unlike previous EUV imagers, FSI includes a moveable occulting disk that can be inserted in the optical path to reduce the amount of instrumental stray light to a minimum. FSI detects signals at 17.4 nm up to the edge of its FOV (7~Rs), which is about twice further than was previously possible. Comparisons with observations by the LASCO and Metis coronagraphs confirm the presence of morphological similarities and differences between the broadband visible light and EUV emissions, as documented on the basis of prior eclipse and space-based observations. The very-wide-field observations of FSI are paving the way for future dedicated instruments

Beyond the disk: EUV coronagraphic observations of the Extreme Ultraviolet Imager on board Solar Orbiter

Context. Most observations of the solar corona beyond 2 R consist of broadband visible light imagery carried out with coronagraphs. The associated diagnostics mainly consist of kinematics and derivations of the electron number density. While the measurement of the properties of emission lines can provide crucial additional diagnostics of the coronal plasma (temperatures, velocities, abundances, etc.), these types of observations are comparatively rare. In visible wavelengths, observations at these heights are limited to total eclipses. In the ultraviolet (UV) to extreme UV (EUV) range, very few additional observations have been achieved since the pioneering results of the Ultraviolet Coronagraph Spectrometer (UVCS). Aims. One of the objectives of the Full Sun Imager (FSI) channel of the Extreme Ultraviolet Imager (EUI) on board the Solar Orbiter mission has been to provide very wide field-of-view EUV diagnostics of the morphology and dynamics of the solar atmosphere in temperature regimes that are typical of the lower transition region and of the corona. Methods. FSI carries out observations in two narrowbands of the EUV spectrum centered on 17.4 nm and 30.4 nm that are dominated, respectively, by lines of FeIX/X (formed in the corona around 1 MK) and by the resonance line of HeII (formed around 80 kK in the lower transition region). Unlike previous EUV imagers, FSI includes a moveable occulting disk that can be inserted in the optical path to reduce the amount of instrumental stray light to a minimum. Results. FSI detects signals at 17.4 nm up to the edge of its field of view (7 R), which is about twice further than was previously possible. Operation at 30.4 nm are for the moment compromised by an as-yet unidentified source of stray light. Comparisons with observations by the LASCO and Metis coronagraphs confirm the presence of morphological similarities and differences between the broadband visible light and EUV emissions, as documented on the basis of prior eclipse and space-based observations. Conclusions. The very-wide-field observations of FSI out to about 3 and 7 R, without and with the occulting disk, respectively, are paving the way for future dedicated instruments