Fine-mapping of a QTL influencing pork tenderness on porcine chromosome 2

<p>Abstract</p> <p>Background</p> <p>In a previous study, a quantitative trait locus (QTL) exhibiting large effects on both Instron shear force and taste panel tenderness was detected within the Illinois Meat Quality Pedigree (IMQP). This QTL mapped to the q arm of porcine chromosome 2 (SSC2q). Comparative analysis of SSC2q indicates that it is orthologous to a segment of human chromosome 5 (HSA5) containing a strong positional candidate gene, calpastatin (<it>CAST</it>). <it>CAST </it>polymorphisms have recently been shown to be associated with meat quality characteristics; however, the possible involvement of other genes and/or molecular variation in this region cannot be excluded, thus requiring fine-mapping of the QTL.</p> <p>Results</p> <p>Recent advances in porcine genome resources, including high-resolution radiation hybrid and bacterial artificial chromosome (BAC) physical maps, were utilized for development of novel informative markers. Marker density in the ~30-Mb region surrounding the most likely QTL position was increased by addition of eighteen new microsatellite markers, including nine publicly-available and nine novel markers. Two newly-developed markers were derived from a porcine BAC clone containing the <it>CAST </it>gene. Refinement of the QTL position was achieved through linkage and haplotype analyses. Within-family linkage analyses revealed at least two families segregating for a highly-significant QTL in strong positional agreement with <it>CAST </it>markers. A combined analysis of these two families yielded QTL intervals of 36 cM and 7 cM for Instron shear force and taste panel tenderness, respectively, while haplotype analyses suggested further refinement to a 1.8 cM interval containing <it>CAST </it>markers. The presence of additional tenderness QTL on SSC2q was also suggested.</p> <p>Conclusion</p> <p>These results reinforce <it>CAST </it>as a strong positional candidate. Further analysis of <it>CAST </it>molecular variation within the IMQP F₁boars should enhance understanding of the molecular basis of pork tenderness, and thus allow for genetic improvement of pork products. Furthermore, additional resources have been generated for the targeted investigation of other putative QTL on SSC2q, which may lead to further advancements in pork quality.</p

Stressed detector arrays for airborne astronomy

The development of stressed Ge:Ga detector arrays for far-infrared astronomy from the Kuiper Airborne Observatory (KAO) is discussed. Researchers successfully constructed and used a three channel detector array on five flights from the KAO, and have conducted laboratory tests of a two-dimensional, 25 elements (5x5) detector array. Each element of the three element array performs as well as the researchers' best single channel detector, as do the tested elements of the 25 channel system. Some of the exciting new science possible with far-infrared detector arrays is also discussed

LEGUS Discovery of a Light Echo Around Supernova 2012aw

We have discovered a luminous light echo around the normal Type II-Plateau Supernova (SN) 2012aw in Messier 95 (M95; NGC 3351), detected in images obtained approximately two years after explosion with the Wide Field Channel 3 on-board the Hubble Space Telescope (HST) by the Legacy ExtraGalactic Ultraviolet Survey (LEGUS). The multi-band observations span from the near-ultraviolet through the optical (F275W, F336W, F438W, F555W, and F814W). The apparent brightness of the echo at the time was ~21--22 mag in all of these bands. The echo appears circular, although less obviously as a ring, with an inhomogeneous surface brightness, in particular, a prominent enhanced brightness to the southeast. The SN itself was still detectable, particularly in the redder bands. We are able to model the light echo as the time-integrated SN light scattered off of diffuse interstellar dust in the SN environment. We have assumed that this dust is analogous to that in the Milky Way with R_V=3.1. The SN light curves that we consider also include models of the unobserved early burst of light from the SN shock breakout. Our analysis of the echo suggests that the distance from the SN to the scattering dust elements along the echo is ~45 pc. The implied visual extinction for the echo-producing dust is consistent with estimates made previously from the SN itself. Finally, our estimate of the SN brightness in F814W is fainter than that measured for the red supergiant star at the precise SN location in pre-SN images, possibly indicating that the star has vanished and confirming it as the likely SN progenitor.Comment: 10 pages, 9 figures, to appear in the Astrophysical Journa

Metabolomics analysis identifies sex-associated metabotypes of oxidative stress and the autotaxin-lysoPA axis in COPD.

Chronic obstructive pulmonary disease (COPD) is a heterogeneous disease and a leading cause of mortality and morbidity worldwide. The aim of this study was to investigate the sex dependency of circulating metabolic profiles in COPD.Serum from healthy never-smokers (healthy), smokers with normal lung function (smokers), and smokers with COPD (COPD; Global Initiative for Chronic Obstructive Lung Disease stages I-II/A-B) from the Karolinska COSMIC cohort (n=116) was analysed using our nontargeted liquid chromatography-high resolution mass spectrometry metabolomics platform.Pathway analyses revealed that several altered metabolites are involved in oxidative stress. Supervised multivariate modelling showed significant classification of smokers from COPD (p=2.8×10-7). Sex stratification indicated that the separation was driven by females (p=2.4×10-7) relative to males (p=4.0×10-4). Significantly altered metabolites were confirmed quantitatively using targeted metabolomics. Multivariate modelling of targeted metabolomics data confirmed enhanced metabolic dysregulation in females with COPD (p=3.0×10-3) relative to males (p=0.10). The autotaxin products lysoPA (16:0) and lysoPA (18:2) correlated with lung function (forced expiratory volume in 1 s) in males with COPD (r=0.86; p&lt;0.0001), but not females (r=0.44; p=0.15), potentially related to observed dysregulation of the miR-29 family in the lung.These findings highlight the role of oxidative stress in COPD, and suggest that sex-enhanced dysregulation in oxidative stress, and potentially the autotaxin-lysoPA axis, are associated with disease mechanisms and/or prevalence

Spin properties of dense near-surface ensembles of nitrogen-vacancy centres in diamond

We present a study of the spin properties of dense layers of near-surface nitrogen-vacancy (NV) centres in diamond created by nitrogen ion implantation. The optically detected magnetic resonance contrast and linewidth, spin coherence time, and spin relaxation time, are measured as a function of implantation energy, dose, annealing temperature and surface treatment. To track the presence of damage and surface-related spin defects, we perform in situ electron spin resonance spectroscopy through both double electron-electron resonance and cross-relaxation spectroscopy on the NV centres. We find that, for the energy ($4-30$~keV) and dose ($5\times10^{11}-10^{13}$~ions/cm$^2$) ranges considered, the NV spin properties are mainly governed by the dose via residual implantation-induced paramagnetic defects, but that the resulting magnetic sensitivity is essentially independent of both dose and energy. We then show that the magnetic sensitivity is significantly improved by high-temperature annealing at $\geq1100^\circ$C. Moreover, the spin properties are not significantly affected by oxygen annealing, apart from the spin relaxation time, which is dramatically decreased. Finally, the average NV depth is determined by nuclear magnetic resonance measurements, giving $\approx10$-17~nm at 4-6 keV implantation energy. This study sheds light on the optimal conditions to create dense layers of near-surface NV centres for high-sensitivity sensing and imaging applications.Comment: 12 pages, 7 figure

Developing sustainable small-scale fisheries livelihoods in Indonesia: Trends, enabling and constraining factors, and future opportunities

Small-scale fisheries (SSF) provide crucial contributions to livelihoods, food and nutrition security, and the well-being of coastal communities worldwide. In Indonesia, 2.5 million households are involved in SSF production, yet these households are characterised by high poverty rates and vulnerability due to declining ecosystem health and climatic change. In this study we applied the Sustainable Livelihoods Framework to analyse the characteristics and immediate and longer-term outcomes of 20 SSF livelihood-focused intervention programs implemented in coastal communities across the Indonesian Archipelago over the last two decades. Projects covered a wide range of spatial scales, funding providers and key participants. Factors supporting positive program outcomes included application of inclusive and holistic approaches to sustainable livelihoods, implemented and supported over appropriate time frames; use of participatory capacity development methodologies and locally-situated project facilitators; and collaborative engagement with local government, non-government organisations and private-sector actors. However, it was impossible to identify evidenced successes from a longer-term sustainability perspective. Short project timeframes, absence of baseline or monitoring data, pressure for satisfactory reports to donors, and limited post-project evaluation, together with invisibility of women’s work and non-commercial exchanges, affected the adequacy of assessments. Given the lack of post-project assessment among projects studied, a thorough review of longer-term project impacts is recommended, guided by the Sustainable Livelihoods Framework, to evaluate sustained improvements in livelihoods outcomes and environmental sustainability. This would support best-practice design and implementation of SSF livelihood-focused interventions, disseminated beyond academia, to influence policy and development to achieve socio-economic equity and environmental goals

Spatial mapping of band bending in semiconductor devices using in-situ quantum sensors

Band bending is a central concept in solid-state physics that arises from local variations in charge distribution especially near semiconductor interfaces and surfaces. Its precision measurement is vital in a variety of contexts from the optimisation of field effect transistors to the engineering of qubit devices with enhanced stability and coherence. Existing methods are surface sensitive and are unable to probe band bending at depth from surface or bulk charges related to crystal defects. Here we propose an in-situ method for probing band bending in a semiconductor device by imaging an array of atomic-sized quantum sensing defects to report on the local electric field. We implement the concept using the nitrogen-vacancy centre in diamond, and map the electric field at different depths under various surface terminations. We then fabricate a two-terminal device based on the conductive two-dimensional hole gas formed at a hydrogen-terminated diamond surface, and observe an unexpected spatial modulation of the electric field attributed to a complex interplay between charge injection and photo-ionisation effects. Our method opens the way to three-dimensional mapping of band bending in diamond and other semiconductors hosting suitable quantum sensors, combined with simultaneous imaging of charge transport in complex operating devices.Comment: This is a pre-print of an article published in Nature Electronics. The final authenticated version is available online at https://dx.doi.org/10.1038/s41928-018-0130-