A Quantitative, High-Throughput Reverse Genetic Screen Reveals Novel Connections between Pre–mRNA Splicing and 5′ and 3′ End Transcript Determinants

Here we present the development and implementation of a genome-wide reverse genetic screen in the budding yeast, Saccharomyces cerevisiae, that couples high-throughput strain growth, robotic RNA isolation and cDNA synthesis, and quantitative PCR to allow for a robust determination of the level of nearly any cellular RNA in the background of 5,500 different mutants. As an initial test of this approach, we sought to identify the full complement of factors that impact pre–mRNA splicing. Increasing lines of evidence suggest a relationship between pre–mRNA splicing and other cellular pathways including chromatin remodeling, transcription, and 3′ end processing, yet in many cases the specific proteins responsible for functionally connecting these pathways remain unclear. Moreover, it is unclear whether all pathways that are coupled to splicing have been identified. As expected, our approach sensitively detects pre–mRNA accumulation in the vast majority of strains containing mutations in known splicing factors. Remarkably, however, several additional candidates were found to cause increases in pre–mRNA levels similar to that seen for canonical splicing mutants, none of which had previously been implicated in the splicing pathway. Instead, several of these factors have been previously implicated to play roles in chromatin remodeling, 3′ end processing, and other novel categories. Further analysis of these factors using splicing-sensitive microarrays confirms that deletion of Bdf1, a factor that links transcription initiation and chromatin remodeling, leads to a global splicing defect, providing evidence for a novel connection between pre–mRNA splicing and this component of the SWR1 complex. By contrast, mutations in 3′ end processing factors such as Cft2 and Yth1 also result in pre–mRNA splicing defects, although only for a subset of transcripts, suggesting that spliceosome assembly in S. cerevisiae may more closely resemble mammalian models of exon-definition. More broadly, our work demonstrates the capacity of this approach to identify novel regulators of various cellular RNAs

Discovery of Cyclotron Resonance Features in the Soft Gamma Repeater SGR 1806-20

We report evidence of cyclotron resonance features from the Soft Gamma Repeater SGR 1806-20 in outburst, detected with the Rossi X-ray Timing Explorer in the spectrum of a long, complex precursor that preceded a strong burst. The features consist of a narrow 5.0 keV absorption line with modulation near its second and third harmonics (at 11.2 keV and 17.5 keV respectively). The line features are transient and are detected in the harder part of the precursor. The 5.0 keV feature is strong, with an equivalent width of ~ 500 eV and a narrow width of less than 0.4 keV. Interpreting the features as electron cyclotron lines in the context of accretion models leads to a large mass-radius ratio (M/R > 0.3 M_sun/km) that is inconsistent with neutron stars or that requires a low (5-7)x10^{11} G magnetic field that is unlikely for SGRs. The line widths are also narrow compared with those of electron cyclotron resonances observed so far in X-ray pulsars. In the magnetar picture, the features are plausibly explained as ion cyclotron resonances in an ultra-strong magnetic field that have recently been predicted from magnetar candidates. In this view, the 5.0 keV feature is consistent with a proton cyclotron fundamental whose energy and width are close to model predictions. The line energy would correspond to a surface magnetic field of 1.0x10^{15} G for SGR 1806-20, in good agreement with that inferred from the spin-down measure in the source.Comment: Published in the 2002 July 20 issue of the Astrophysical Journal Letters, 574, L5

Disease Progression and Serological Assay Performance in Heritage Breed Pigs following Brucella suis Experimental Challenge as a Model for Naturally Infected Feral Swine

Invasive feral swine (Sus scrofa) are one of the most important wildlife species for disease surveillance in the United States, serving as a reservoir for various diseases of concern for the health of humans and domestic animals. Brucella suis, the causative agent of swine brucellosis, is one such pathogen carried and transmitted by feral swine. Serology assays are the preferred field diagnostic for B. suis infection, as whole blood can be readily collected and antibodies are highly stable. However, serological assays frequently have lower sensitivity and specificity, and few studies have validated serological assays for B. suis in feral swine. We conducted an experimental infection of Ossabaw Island Hogs (a breed re-domesticated from feral animals) as a disease-free proxy for feral swine to (1) improve understanding of bacterial dissemination and antibody response following B. suis infection and (2) evaluate potential changes in the performance of serological diagnostic assays over the course of infection. Animals were inoculated with B. suis and serially euthanized across a 16-week period, with samples collected at the time of euthanasia. The 8% card agglutination test performed best, whereas the fluorescence polarization assay demonstrated no capacity to differentiate true positive from true negative animals. Froma disease surveillance perspective, using the 8%card agglutination test in parallel with either the buffered acidified plate antigen test or the Brucella abortus/suis complement fixation test provided the best performance with the highest probability of a positive assay result. Application of these combinations of diagnostic assays for B. suis surveillance among feral swine would improve understanding of spillover risks at the national level

A polarimetrically oriented X-ray stare at the accreting pulsar EXO 2030+375

Accreting X-ray pulsars (XRPs) are presumably ideal targets for polarization measurements, as their high magnetic field strength is expected to polarize the emission up to a polarization degree of ~80%. However, such expectations are being challenged by recent observations of XRPs with the Imaging X-ray Polarimeter Explorer (IXPE). Here we report on the results of yet another XRP, EXO 2030+375, observed with IXPE and contemporarily monitored with Insight-HXMT and SRG/ART-XC. In line with recent results obtained with IXPE for similar sources, analysis of the EXO 2030+375 data returns a low polarization degree of 0%-3% in the phase-averaged study and variation in the range 2%-7% in the phase-resolved study. Using the rotating vector model we constrain the geometry of the system and obtain a value for the magnetic obliquity of ~$60^{\circ}$. Considering also the estimated pulsar inclination of ~$130^{\circ}$, this indicates that the magnetic axis swings close to the observer line of sight. Our joint polarimetric, spectral and timing analysis hint to a complex accreting geometry where magnetic multipoles with asymmetric topology and gravitational light bending significantly affect the observed source behavior.Comment: A&A accepted. Proofs versio

X-ray polarimetry of the accreting pulsar GX 301-2

The phase- and energy-resolved polarization measurements of accreting X-ray pulsars (XRPs) allow us to test different theoretical models of their emission, as well as to provide an avenue to determine the emission region geometry. We present the results of the observations of the XRP GX 301-2 performed with the Imaging X-ray Polarimetry Explorer (IXPE). GX 301-2 is a persistent XRP with one of the longest known spin periods of ~680 s. A massive hyper-giant companion star Wray 977 supplies mass to the neutron star via powerful stellar winds. We do not detect significant polarization in the phase-averaged data using spectro-polarimetric analysis, with the upper limit on the polarization degree (PD) of 2.3% (99% confidence level). Using the phase-resolved spectro-polarimetric analysis we get a significant detection of polarization (above 99% c.l.) in two out of nine phase bins and marginal detection in three bins, with a PD ranging between ~3% and ~10%, and a polarization angle varying in a very wide range from ~0 deg to ~160 deg. Using the rotating vector model we obtain constraints on the pulsar geometry using both phase-binned and unbinned analysis getting excellent agreement. Finally, we discuss possible reasons for a low observed polarization in GX 301-2.Comment: 10 pages, 10 figures, submitted to A&

IXPE Observations of the Quintessential Wind-accreting X-Ray Pulsar Vela X-1

The radiation from accreting X-ray pulsars was expected to be highly polarized, with some estimates for the polarization degree of up to 80%. However, phase-resolved and energy-resolved polarimetry of X-ray pulsars is required in order to test different models and to shed light on the emission processes and the geometry of the emission region. Here we present the first results of the observations of the accreting X-ray pulsar Vela X-1 performed with the Imaging X-ray Polarimetry Explorer. Vela X-1 is considered to be the archetypal example of a wind-accreting, high-mass X-ray binary system, consisting of a highly magnetized neutron star accreting matter from its supergiant stellar companion. The spectropolarimetric analysis of the phase-averaged data for Vela X-1 reveals a polarization degree (PD) of 2.3% ± 0.4% at the polarization angle (PA) of −47.°3 ± 5.°4. A low PD is consistent with the results obtained for other X-ray pulsars and is likely related to the inverse temperature structure of the neutron star atmosphere. The energy-resolved analysis shows the PD above 5 keV reaching 6%–10% and a ∼90° difference in the PA compared to the data in the 2–3 keV range. The phase-resolved spectropolarimetric analysis finds a PD in the range 0%–9% with the PA varying between −80° and 40°

X-ray pulsar GRO J1008−-57 as an orthogonal rotator

X-ray polarimetry is a unique way to probe geometrical configuration of highly-magnetized accreting neutron stars (X-ray pulsars). GRO J1008$-$57 is the first transient X-ray pulsar observed at two different flux levels by the Imaging X-ray Polarimetry Explorer (IXPE) during its outburst in November 2022. The polarization properties were found to be independent of the source luminosity, with the polarization degree varying between non-detection to about 15% over the pulse phase. Fitting the phase-resolved spectro-polarimetric data with the rotating vector model allowed us to estimate the pulsar inclination (130 deg, which is in good agreement with the orbital inclination), the position angle (75 deg) of the pulsar spin axis, and the magnetic obliquity (74 deg). This makes GRO J1008$-$57 the first confidently identified X-ray pulsar as a nearly orthogonal rotator. The results are discussed in the context of the neutron star atmosphere models and theories of pulsars' axis alignment.Comment: 11 pages, 7 figures, submitted to A&A. arXiv admin note: text overlap with arXiv:2209.0244

X-ray polarimetry reveals the magnetic field topology on sub-parsec scales in Tycho's supernova remnant

Supernova remnants are commonly considered to produce most of the Galactic cosmic rays via diffusive shock acceleration. However, many questions about the physical conditions at shock fronts, such as the magnetic-field morphology close to the particle acceleration sites, remain open. Here we report the detection of a localized polarization signal from some synchrotron X-ray emitting regions of Tycho's supernova remnant made by the Imaging X-ray Polarimetry Explorer. The derived polarization degree of the X-ray synchrotron emission is 9+/-2% averaged over the whole remnant, and 12+/-2% at the rim, higher than the 7-8% polarization value observed in the radio band. In the west region the polarization degree is 23+/-4%. The X-ray polarization degree in Tycho is higher than for Cassiopeia A, suggesting a more ordered magnetic-field or a larger maximum turbulence scale. The measured tangential polarization direction corresponds to a radial magnetic field, and is consistent with that observed in the radio band. These results are compatible with the expectation of turbulence produced by an anisotropic cascade of a radial magnetic-field near the shock, where we derive a magnetic-field amplification factor of 3.4+/-0.3. The fact that this value is significantly smaller than those expected from acceleration models is indicative of highly anisotropic magnetic-field turbulence, or that the emitting electrons either favor regions of lower turbulence, or accumulate close to where the magnetic-field orientation is preferentially radially oriented due to hydrodynamical instabilities.Comment: 31 pages, 7 figures, 3 tables. Accepted for publication in ApJ. Revised versio

The IXPE View of GRB 221009A

We present the IXPE observation of GRB 221009A, which includes upper limits on the linear polarization degree of both prompt and afterglow emission in the soft X-ray energy band. GRB 221009A is an exceptionally bright gamma-ray burst (GRB) that reached Earth on 2022 October 9 after traveling through the dust of the Milky Way. The Imaging X-ray Polarimetry Explorer (IXPE) pointed at GRB 221009A on October 11 to observe, for the first time, the 2–8 keV X-ray polarization of a GRB afterglow. We set an upper limit to the polarization degree of the afterglow emission of 13.8% at a 99% confidence level. This result provides constraints on the jet opening angle and the viewing angle of the GRB, or alternatively, other properties of the emission region. Additionally, IXPE captured halo-rings of dust-scattered photons that are echoes of the GRB prompt emission. The 99% confidence level upper limit to the prompt polarization degree depends on the background model assumption, and it ranges between ∼55% and ∼82%. This single IXPE pointing provides both the first assessment of X-ray polarization of a GRB afterglow and the first GRB study with polarization observations of both the prompt and afterglow phases

The first X-ray polarimetric observation of the black hole binary LMC X-1

We report on an X-ray polarimetric observation of the high-mass X-ray binary LMC X-1 in the high/soft state, obtained by the Imaging X-ray Polarimetry Explorer (IXPE) in October 2022. The measured polarization is below the minimum detectable polarization of 1.1 per cent (at the 99 per cent confidence level). Simultaneously, the source was observed with the NICER, NuSTAR and SRG/ART-XC instruments, which enabled spectral decomposition into a dominant thermal component and a Comptonized one. The low 2-8 keV polarization of the source did not allow for strong constraints on the black-hole spin and inclination of the accretion disc. However, if the orbital inclination of about 36 degrees is assumed, then the upper limit is consistent with predictions for pure thermal emission from geometrically thin and optically thick discs. Assuming the polarization degree of the Comptonization component to be 0, 4, or 10 per cent, and oriented perpendicular to the polarization of the disc emission (in turn assumed to be perpendicular to the large scale ionization cone orientation detected in the optical band), an upper limit to the polarization of the disc emission of 1.0, 0.9 or 0.9 per cent, respectively, is found (at the 99 per cent confidence level).Comment: 12 pages, 9 figures, 4 tables. Accepted for publication in MNRA