A robust linkage map of the porcine autosomes based on gene-associated SNPs

<p>Abstract</p> <p>Background</p> <p>Genetic linkage maps are necessary for mapping of mendelian traits and quantitative trait loci (QTLs). To identify the actual genes, which control these traits, a map based on gene-associated single nucleotide polymorphism (SNP) markers is highly valuable. In this study, the SNPs were genotyped in a large family material comprising more than 5,000 piglets derived from 12 Duroc boars crossed with 236 Danish Landrace/Danish Large White sows. The SNPs were identified in sequence alignments of 4,600 different amplicons obtained from the 12 boars and containing coding regions of genes derived from expressed sequence tags (ESTs) and genomic shotgun sequences.</p> <p>Results</p> <p>Linkage maps of all 18 porcine autosomes were constructed based on 456 gene-associated and six porcine EST-based SNPs. The total length of the averaged-sex whole porcine autosome was estimated to 1,711.8 cM resulting in an average SNP spacing of 3.94 cM. The female and male maps were estimated to 2,336.1 and 1,441.5 cM, respectively. The gene order was validated through comparisons to the cytogenetic and/or physical location of 203 genes, linkage to evenly spaced microsatellite markers as well as previously reported conserved synteny. A total of 330 previously unmapped genes and ESTs were mapped to the porcine autosome while ten genes were mapped to unexpected locations.</p> <p>Conclusion</p> <p>The linkage map presented here shows high accuracy in gene order. The pedigree family network as well as the large amount of meiotic events provide good reliability and make this map suitable for QTL and association studies. In addition, the linkage to the RH-map of microsatellites makes it suitable for comparison to other QTL studies.</p

Discovery of coherent pulsations from the Ultraluminous X-ray Source NGC 7793 P13

We report the detection of coherent pulsations from the ultraluminous X-ray source (ULX) NGC 7793 P13. The ≈0.42 s nearly sinusoidal pulsations were initially discovered in broadband X-ray observations using XMM-Newton and NuSTAR taken in 2016. We subsequently also found pulsations in archival XMM-Newton data taken in 2013 and 2014. The significant (≫5σ) detection of coherent pulsations demonstrates that the compact object in P13 is a neutron star, and given the observed peak luminosity of ≈10⁴⁰ erg s⁻¹ (assuming isotropy), it is well above the Eddington limit for a 1.4 M⨀ accretor. This makes P13 the second ULX known to be powered by an accreting neutron star. The pulse period varies between epochs, with a slow but persistent spin-up over the 2013–2016 period. This spin-up indicates a magnetic field of B ≈ 1.5 × 10¹² G, typical of many Galactic accreting pulsars. The most likely explanation for the extreme luminosity is a high degree of beaming; however, this is difficult to reconcile with the sinusoidal pulse profile.We would like the thank the referee for the helpful comments. M.J.M. acknowledges support from an STFC Ernest Rutherford fellowship and D.B. acknowledges financial support from the French Space Agency (CNES). This research has made use of data obtained with NuSTAR, a project led by Caltech, funded by NASA and managed by NASA/JPL, and has utilized the nustardas software package, jointly developed by the ASDC (Italy) and Caltech (USA). This research has also made use of data obtained with XMM-Newton, an ESA science mission with instruments and contributions directly funded by ESA Member States. This work made use of data supplied by the UK Swift Science Data Centre at the University of Leicester, and also made use of the XRT Data Analysis Software (XRTDAS) developed under the responsibility of the ASI Science Data Center (ASDC), Italy. This research has made use of a collection of ISIS functions (ISISscripts) provided by ECAP/Remeis observatory and MIT (http://www.sternwarte.uni-erlangen.de/isis/). Facilities: NuSTAR - The NuSTAR (Nuclear Spectroscopic Telescope Array) mission, XMM - , Swift -

Phylogeny, Diet, and Cranial Integration in Australodelphian Marsupials

Studies of morphological integration provide valuable information on the correlated evolution of traits and its relationship to long-term patterns of morphological evolution. Thus far, studies of morphological integration in mammals have focused on placentals and have demonstrated that similarity in integration is broadly correlated with phylogenetic distance and dietary similarity. Detailed studies have also demonstrated a significant correlation between developmental relationships among structures and adult morphological integration. However, these studies have not yet been applied to marsupial taxa, which differ greatly from placentals in reproductive strategy and cranial development and could provide the diversity necessary to assess the relationships among phylogeny, ecology, development, and cranial integration. This study presents analyses of morphological integration in 20 species of australodelphian marsupials, and shows that phylogeny is significantly correlated with similarity of morphological integration in most clades. Size-related correlations have a significant affect on results, particularly in Peramelia, which shows a striking decrease in similarity of integration among species when size is removed. Diet is not significantly correlated with similarity of integration in any marsupial clade. These results show that marsupials differ markedly from placental mammals in the relationships of cranial integration, phylogeny, and diet, which may be related to the accelerated development of the masticatory apparatus in marsupials

The X-Ray Pulsar XTE J1858+034 Observed with NuSTAR and Fermi/GBM: Spectral and Timing Characterization plus a Cyclotron Line

Accreting X-ray pulsars (XRPs) undergo luminous X-ray outbursts during which the spectral and timing behavior of the neutron star can be studied in detail. We analyze a NuSTAR observation of the XRP XTE J1858+034 during its outburst in 2019. The spectrum is fit with a phenomenological, a semiempirical, and a physical spectral model. A candidate cyclotron line is found at 48 keV, implying a magnetic field of 5.4 × 1012 G at the site of emission. This is also supported by the physical best-fit model. We propose an orbital period of about 81 days based on the visual inspection of the X-ray outburst recurrence time. Based on Fermi/GBM data, the standard disk accretion-torque theory allowed us to infer a distance of 10.9 ± 1.0 kpc. Pulse profiles are single-peaked and show a pulsed fraction that is strongly energy-dependent at least up to 40 keV

NuSTAR and XMM-Newton observations of NGC 1365: Extreme absorption variability and a constant inner accretion disk

We present a spectral analysis of four coordinated NuSTAR+XMM-Newton observations of the Seyfert galaxy NGC 1365. These exhibit an extreme level of spectral variability, which is primarily due to variable line-of-sight absorption, revealing relatively unobscured states in this source for the first time. Despite the diverse range of absorption states, each of the observations displays the same characteristic signatures of relativistic reflection from the inner accretion disk. Through time-resolved spectroscopy we find that the strength of the relativistic iron line and the Compton reflection hump relative to the intrinsic continuum are well correlated, as expected if they are two aspects of the same broadband reflection spectrum. We apply self-consistent disk reflection models to these time-resolved spectra in order to constrain the inner disk parameters, allowing for variable, partially covering absorption to account for the vastly different absorption states observed. Each of the four observations is treated independently to test the consistency of the results obtained for the black hole spin and the disk inclination, which should not vary on observable timescales. We find both the spin and the inclination determined from the reflection spectrum to be consistent, confirming NGC 1365 hosts a rapidly rotating black hole; in all cases the dimensionless spin parameter is constrained to be a* > 0.97 (at 90% statistical confidence or better)

Body size estimation in women with anorexia nervosa and healthy controls using 3D avatars

A core feature of anorexia nervosa is an over-estimation of body size. However, quantifying this over-estimation has been problematic as existing methodologies introduce a series of artefacts and inaccuracies in the stimuli used for judgements of body size. To overcome these problems, we have: (i) taken 3D scans of 15 women who have symptoms of anorexia (referred to henceforth as anorexia spectrum disorders, ANSD) and 15 healthy control women, (ii) used a 3D modelling package to build avatars from the scans, (iii) manipulated the body shapes of these avatars to reflect biometrically accurate, continuous changes in body mass index (BMI), (iv) used these personalized avatars as stimuli to allow the women to estimate their body size. The results show that women who are currently receiving treatment for ANSD show an over-estimation of body size which rapidly increases as their own BMI increases. By contrast, the women acting as healthy controls can accurately estimate their body size irrespective of their own BMI. This study demonstrates the viability of combining 3D scanning and CGI techniques to create personalised realistic avatars of individual patients to directly assess their body image perception

A Steered Molecular Dynamics Study of Binding and Translocation Processes in the GABA Transporter

The entire substrate translocation pathway in the human GABA transporter (GAT-1) was explored for the endogenous substrate GABA and the anti-convulsive drug tiagabine. Following a steered molecular dynamics (SMD) approach, in which a harmonic restraining potential is applied to the ligand, dissociation and re-association of ligands were simulated revealing events leading to substrate (GABA) translocation and inhibitor (tiagabine) mechanism of action. We succeeded in turning the transporter from the outward facing occluded to the open-to-out conformation, and also to reorient the transporter to the open-to-in conformation. The simulations are validated by literature data and provide a substrate pathway fingerprint in terms of which, how, and in which sequence specific residues are interacted with. They reveal the essential functional roles of specific residues, e.g. the role of charged residues in the extracellular vestibule including two lysines (K76 (TM1) and K448 (TM10)) and a TM6-triad (D281, E283, and D287) in attracting and relocating substrates towards the secondary/interim substrate-binding site (S2). Likewise, E101 is highlighted as essential for the relocation of the substrate from the primary substrate-binding site (S1) towards the cytoplasm

Effects of betaine on lipopolysaccharide-induced memory impairment in mice and the involvement of GABA transporter 2

<p>Abstract</p> <p>Background</p> <p>Betaine (glycine betaine or trimethylglycine) plays important roles as an osmolyte and a methyl donor in animals. While betaine is reported to suppress expression of proinflammatory molecules and reduce oxidative stress in aged rat kidney, the effects of betaine on the central nervous system are not well known. In this study, we investigated the effects of betaine on lipopolysaccharide (LPS)-induced memory impairment and on mRNA expression levels of proinflammatory molecules, glial markers, and GABA transporter 2 (GAT2), a betaine/GABA transporter.</p> <p>Methods</p> <p>Mice were continuously treated with betaine for 13 days starting 1 day before they were injected with LPS, or received subacute or acute administration of betaine shortly before or after LPS injection. Then, their memory function was evaluated using Y-maze and novel object recognition tests 7 and 10-12 days after LPS injection (30 μg/mouse, i.c.v.), respectively. In addition, mRNA expression levels in hippocampus were measured by real-time RT-PCR at different time points.</p> <p>Results</p> <p>Repeated administration of betaine (0.163 mmol/kg, s.c.) prevented LPS-induced memory impairment. GAT2 mRNA levels were significantly increased in hippocampus 24 hr after LPS injection, and administration of betaine blocked this increase. However, betaine did not affect LPS-induced increases in levels of mRNA related to inflammatory responses. Both subacute administration (1 hr before, and 1 and 24 hr after LPS injection) and acute administration (1 hr after LPS injection) of betaine also prevented LPS-induced memory impairment in the Y-maze test.</p> <p>Conclusions</p> <p>These data suggest that betaine has protective effects against LPS-induced memory impairment and that prevention of LPS-induced changes in GAT2 mRNA expression is crucial to this ameliorating effect.</p

Development, standardization and refinement of procedures for evaluating effects of endocrine active compounds on development and sexual differentiation of Xenopus laevis

Xenopus laevis has been introduced as a model to study effects of endocrine-active compounds (EAC) on development and sexual differentiation. However, variable and inconsistent data have raised questions about the reliability of the test methods applied. The current study was conducted in two laboratories to develop, refine, and standardize procedures and protocols. Larvae were exposed in flow-through systems to 17β-estradiol (E2), at concentrations from 0.2 to 6.0 μg E2 L−1 in Experiment 1A, and 0.015 to 2.0 μg E2 L−1 in Experiment 1B. In both studies survival (92%, 99%) and percentage of animals that completed metamorphosis (97%, 99%) indicated reproducible biological performance. Furthermore, minor variations in husbandry led to significant differences in snout-to-vent length, weight, and gonad size. In Experiment 1A, almost complete feminization occurred in all E2 treatment groups whereas a concentration response was observed in Experiment 1B resulting in an EC50 of 0.12 μg E2 L−1. The final verified protocol is suitable for determining effects of EAC on development and sexual differentiation in X. laevis

Statistical support for the hypothesis of developmental constraint in marsupial skull evolution.

Background: In contrast to placental neonates, in which all cranial bones are ossified, marsupial young have only the bones of the oral region and the exoccipital ossified at birth, in order to facilitate suckling at an early stage of development. In this study, we investigated whether this heterochronic shift in the timing of cranial ossification constrains cranial disparity in marsupials relative to placentals. Methods: We collected three-dimensional (3D) landmark data about the crania of a wide range of extant placentals and marsupials, and from six fossil metatherians (the clade including extant marsupials and their stem relatives), using a laser scanner and a 3D digitizer. Principal components analysis and delta variance tests were used to investigate the distribution and disparity of cranial morphology between different landmark sets (optimizing either number of landmarks or number of taxa) of the whole skull and of individual developmental or functional regions (neurocranium, viscerocranium, oral region) for extant placentals and marsupials. Marsupial and placental data was also compared based on shared ecological aspects including diet, habitat, and time of peak activity. Results: We found that the extant marsupial taxa investigated here occupy a much smaller area of morphospace than the placental taxa, with a significantly (P<0.01) smaller overall variance. Inclusion of fossil taxa did not significantly increase the variance of metatherian cranial shape. Fossil forms generally plotted close to or within the realm of their extant marsupial relatives. When the disparities of cranial regions were investigated separately, significant differences between placentals and marsupials were seen for the viscerocranial and oral regions, but not for the neurocranial region. Conclusion: These results support the hypothesis of developmental constraint limiting the evolution of the marsupial skull, and further suggest that the marsupial viscerocranium as a whole, rather than just the early-ossifying oral region, is developmentally constrained