A versatile panel of reference gene assays for the measurement of chicken mRNA by quantitative PCR

Quantitative real-time PCR assays are widely used for the quantification of mRNA within avian experimental samples. Multiple stably-expressed reference genes, selected for the lowest variation in representative samples, can be used to control random technical variation. Reference gene assays must be reliable, have high amplification specificity and efficiency, and not produce signals from contaminating DNA. Whilst recent research papers identify specific genes that are stable in particular tissues and experimental treatments, here we describe a panel of ten avian gene primer and probe sets that can be used to identify suitable reference genes in many experimental contexts. The panel was tested with TaqMan and SYBR Green systems in two experimental scenarios: a tissue collection and virus infection of cultured fibroblasts. GeNorm and NormFinder algorithms were able to select appropriate reference gene sets in each case. We show the effects of using the selected genes on the detection of statistically significant differences in expression. The results are compared with those obtained using 28s ribosomal RNA, the present most widely accepted reference gene in chicken work, identifying circumstances where its use might provide misleading results. Methods for eliminating DNA contamination of RNA reduced, but did not completely remove, detectable DNA. We therefore attached special importance to testing each qPCR assay for absence of signal using DNA template. The assays and analyses developed here provide a useful resource for selecting reference genes for investigations of avian biology

Erratum to: 36th International Symposium on Intensive Care and Emergency Medicine

[This corrects the article DOI: 10.1186/s13054-016-1208-6.]

H.E.S.S. programme searching for VHE gamma rays associated with FRBs

Fast Radio Bursts (FRBs) are highly energetic, extremely short-lived bursts of radio flashes. Despite extensive research, the exact cause of these outbursts remains speculative. The high luminosity, short duration, and high dispersion measure of these events suggest they result from extreme, high-energy extragalactic sources, such as highly magnetized and rapidly spinning neutron stars known as magnetars. The number of detected FRBs, including repeating ones, has grown rapidly in recent years. Except for FRB 20200428D, and FRB-like radio burst that is associated to Galactic magnetar SGR 1935+2154, no multi-wavelength counterpart to any FRB has been detected yet. The High Energy Stereoscopic System (H.E.S.S.) telescope has developed a program to follow up FRBs searching for their gamma-ray counterparts, helping to uncover the nature of FRBs and FRB sources. This paper provides an overview of the searches for FRB sources conducted by H.E.S.S., including follow-up observations and simultaneous multi-wavelength campaigns with radio and X-ray observatories. Among the FRB sources observed by H.E.S.S., nine are localized with redshifts ranging between 0.11 and 0.492 from 2015 to 2022. No significant very high energy (VHE) emission was detected during these observations. We report constraints on the VHE luminosity ranging from 1044 erg s-1 and 1048 erg s-1, placing limits on the FRB's region persistent VHE emission and potential FRB afterglow emission across timescales from hours to years

The Large Array Survey Telescope -- System Overview and Performances

The Large Array Survey Telescope (LAST) is a wide-field visible-light telescope array designed to explore the variable and transient sky with a high cadence. LAST will be composed of 48, 28-cm f/2.2 telescopes (32 already installed) equipped with full-frame backside-illuminated cooled CMOS detectors. Each telescope provides a field of view (FoV) of 7.4 deg^2 with 1.25 arcsec/pix, while the system FoV is 355 deg^2 in 2.9 Gpix. The total collecting area of LAST, with 48 telescopes, is equivalent to a 1.9-m telescope. The cost-effectiveness of the system (i.e., probed volume of space per unit time per unit cost) is about an order of magnitude higher than most existing and under-construction sky surveys. The telescopes are mounted on 12 separate mounts, each carrying four telescopes. This provides significant flexibility in operating the system. The first LAST system is under construction in the Israeli Negev Desert, with 32 telescopes already deployed. We present the system overview and performances based on the system commissioning data. The Bp 5-sigma limiting magnitude of a single 28-cm telescope is about 19.6 (21.0), in 20 s (20x20 s). Astrometric two-axes precision (rms) at the bright-end is about 60 (30)\,mas in 20\,s (20x20 s), while absolute photometric calibration, relative to GAIA, provides ~10 millimag accuracy. Relative photometric precision, in a single 20 s (320 s) image, at the bright-end measured over a time scale of about 60 min is about 3 (1) millimag. We discuss the system science goals, data pipelines, and the observatory control system in companion publications.Comment: Submitted to PASP, 15p

Very-high-energy γ -Ray Emission from Young Massive Star Clusters in the Large Magellanic Cloud

The Tarantula Nebula in the Large Magellanic Cloud is known for its high star formation activity. At its center lies the young massive star cluster R136, providing a significant amount of the energy that makes the nebula shine so brightly at many wavelengths. Recently, young massive star clusters have been suggested to also efficiently produce very high-energy cosmic rays, potentially beyond PeV energies. Here, we report the detection of very-high-energy γ-ray emission from the direction of R136 with the High Energy Stereoscopic System, achieved through a multicomponent, likelihood-based modeling of the data. This supports the hypothesis that R136 is indeed a very powerful cosmic-ray accelerator. Moreover, from the same analysis, we provide an updated measurement of the γ-ray emission from 30 Dor C, the only superbubble detected at TeV energies presently. The γ-ray luminosity above 0.5 TeV of both sources is (2–3) × 1035 erg s−1. This exceeds by more than a factor of 2 the luminosity of HESS J1646−458, which is associated with the most massive young star cluster in the Milky Way, Westerlund 1. Furthermore, the γ-ray emission from each source is extended with a significance of >3σ and a Gaussian width of about 30 pc. For 30 Dor C, a connection between the γ-ray emission and the nonthermal X-ray emission appears likely. Different interpretations of the γ-ray signal from R136 are discussed

Ancient DNA connects large-scale migration with the spread of Slavs

The second half of the first millennium CE in Central and Eastern Europe was accompanied by fundamental cultural and political transformations. This period of change is commonly associated with the appearance of the Slavs, which is supported by textual evidence1,2 and coincides with the emergence of similar archaeological horizons3,4,5,6. However, so far there has been no consensus on whether this archaeological horizon spread by migration, Slavicisation or a combination of both. Genetic data remain sparse, especially owing to the widespread practice of cremation in the early phase of the Slavic settlement. Here we present genome-wide data from 555 ancient individuals, including 359 samples from Slavic contexts from as early as the seventh century CE. Our data demonstrate large-scale population movement from Eastern Europe during the sixth to eighth centuries, replacing more than 80% of the local gene pool in Eastern Germany, Poland and Croatia. Yet, we also show substantial regional heterogeneity as well as a lack of sex-biased admixture, indicating varying degrees of cultural assimilation of the autochthonous populations. Comparing archaeological and genetic evidence, we find that the change in ancestry in Eastern Germany coincided with a change in social organization, characterized by an intensification of inter- and intra-site genetic relatedness and patrilocality. On the European scale, it appears plausible that the changes in material culture and language between the sixth and eighth centuries were connected to these large-scale population movements

The Vanishing of the Primary Emission Region in PKS 1510-089

In 2021 July, PKS 1510-089 exhibited a significant flux drop in the high-energy γ-ray (by a factor 10) and optical (by a factor 5) bands and remained in this low state throughout 2022. Similarly, the optical polarization in the source vanished, resulting in the optical spectrum being fully explained through the steady flux of the accretion disk and the broad-line region. Unlike the aforementioned bands, the very-high-energy γ-ray and X-ray fluxes did not exhibit a significant flux drop from year to year. This suggests that the steady-state very-high-energy γ-ray and X-ray fluxes originate from a different emission region than the vanished parts of the high-energy γ-ray and optical jet fluxes. The latter component has disappeared through either a swing of the jet away from the line of sight or a significant drop in the photon production efficiency of the jet close to the black hole. Either change could become visible in high-resolution radio images

COMAP Early Science: IV. Power Spectrum Methodology and Results

We present the power spectrum methodology used for the first-season COMAP analysis, and assess the quality of the current data set. The main results are derived through the Feed-feed Pseudo-Cross-Spectrum (FPXS) method, which is a robust estimator with respect to both noise modeling errors and experimental systematics. We use effective transfer functions to take into account the effects of instrumental beam smoothing and various filter operations applied during the low-level data processing. The power spectra estimated in this way have allowed us to identify a systematic error associated with one of our two scanning strategies, believed to be due to residual ground or atmospheric contamination. We omit these data from our analysis and no longer use this scanning technique for observations. We present the power spectra from our first season of observing and demonstrate that the uncertainties are integrating as expected for uncorrelated noise, with any residual systematics suppressed to a level below the noise. Using the FPXS method, and combining data on scales $k=0.051-0.62 \,\mathrm{Mpc}^{-1}$ we estimate $P_\mathrm{CO}(k) = -2.7 \pm 1.7 \times 10^4\mu\textrm{K}^2\mathrm{Mpc}^3$, the first direct 3D constraint on the clustering component of the CO(1-0) power spectrum in the literature.Comment: Paper 4 of 7 in series. 18 pages, 11 figures, as accepted in Ap

COMAP Early Science: III. CO Data Processing

We describe the first season COMAP analysis pipeline that converts raw detector readouts to calibrated sky maps. This pipeline implements four main steps: gain calibration, filtering, data selection, and map-making. Absolute gain calibration relies on a combination of instrumental and astrophysical sources, while relative gain calibration exploits real-time total-power variations. High efficiency filtering is achieved through spectroscopic common-mode rejection within and across receivers, resulting in nearly uncorrelated white noise within single-frequency channels. Consequently, near-optimal but biased maps are produced by binning the filtered time stream into pixelized maps; the corresponding signal bias transfer function is estimated through simulations. Data selection is performed automatically through a series of goodness-of-fit statistics, including $\chi^2$ and multi-scale correlation tests. Applying this pipeline to the first-season COMAP data, we produce a dataset with very low levels of correlated noise. We find that one of our two scanning strategies (the Lissajous type) is sensitive to residual instrumental systematics. As a result, we no longer use this type of scan and exclude data taken this way from our Season 1 power spectrum estimates. We perform a careful analysis of our data processing and observing efficiencies and take account of planned improvements to estimate our future performance. Power spectrum results derived from the first-season COMAP maps are presented and discussed in companion papers.Comment: Paper 3 of 7 in series. 26 pages, 23 figures, submitted to Ap