Impact of breed and sex on porcine endocrine transcriptome: a bayesian biometrical analysis

Background: Transcriptome variability is due to genetic and environmental causes, much like any other complex phenotype. Ascertaining the transcriptome differences between individuals is an important step to understand how selection and genetic drift may affect gene expression. To that end, extant divergent livestock breeds offer an ideal genetic material. Results: We have analyzed with microarrays five tissues from the endocrine axis (hypothalamus, adenohypophysis, thyroid gland, gonads and fat tissue) of 16 pigs from both sexes pertaining to four extreme breeds (Duroc, Large White, Iberian and a cross with SinoEuropean hybrid line). Using a Bayesian linear model approach, we observed that the largest breed variability corresponded to the male gonads, and was larger than at the remaining tissues, including ovaries. Measurement of sex hormones in peripheral blood at slaughter did not detect any breed-related differences. Not unexpectedly, the gonads were the tissue with the largest number of sex biased genes. There was a strong correlation between sex and breed bias expression, although the most breed biased genes were not the most sex biased genes. A combined analysis of connectivity and differential expression suggested three biological processes as being primarily different between breeds: spermatogenesis, muscle differentiation and several metabolic processes. Conclusion: These results suggest that differences across breeds in gene expression of the male gonads are larger than in other endocrine tissues in the pig. Nevertheless, the strong presence of breed biased genes in the male gonads cannot be explained solely by changes in spermatogenesis nor by differences in the reproductive tract development

Nanoscale phase-engineering of thermal transport with a Josephson heat modulator

Macroscopic quantum phase coherence has one of its pivotal expressions in the Josephson effect [1], which manifests itself both in charge [2] and energy transport [3-5]. The ability to master the amount of heat transferred through two tunnel-coupled superconductors by tuning their phase difference is the core of coherent caloritronics [4-6], and is expected to be a key tool in a number of nanoscience fields, including solid state cooling [7], thermal isolation [8, 9], radiation detection [7], quantum information [10, 11] and thermal logic [12]. Here we show the realization of the first balanced Josephson heat modulator [13] designed to offer full control at the nanoscale over the phase-coherent component of thermal currents. Our device provides magnetic-flux-dependent temperature modulations up to 40 mK in amplitude with a maximum of the flux-to-temperature transfer coefficient reaching 200 mK per flux quantum at a bath temperature of 25 mK. Foremost, it demonstrates the exact correspondence in the phase-engineering of charge and heat currents, breaking ground for advanced caloritronic nanodevices such as thermal splitters [14], heat pumps [15] and time-dependent electronic engines [16-19].Comment: 6+ pages, 4 color figure

Rectification of electronic heat current by a hybrid thermal diode

We report the realization of an ultra-efficient low-temperature hybrid heat current rectifier, thermal counterpart of the well-known electric diode. Our design is based on a tunnel junction between two different elements: a normal metal and a superconducting island. Electronic heat current asymmetry in the structure arises from large mismatch between the thermal properties of these two. We demonstrate experimentally temperature differences exceeding $60$ mK between the forward and reverse thermal bias configurations. Our device offers a remarkably large heat rectification ratio up to $\sim 140$ and allows its prompt implementation in true solid-state thermal nanocircuits and general-purpose electronic applications requiring energy harvesting or thermal management and isolation at the nanoscale.Comment: 8 pages, 6 color figure

Allelic and genotypic frequencies of ASIP and MC1R genes in four West African sheep populations

In West Africa, consumers pay a major attention on the coat colour of the sheep due to religious and cultural reasons. White coated individuals reach selling prices up to three-fold higher than black coated sheep. The aim of this study was to ascertain the genotypic and allelic frequencies of MC1R and ASIP genes in order to assess possible implementation of breeding programmes focusing on the increase of the white coated sheep frequencies. A total of 113 individuals belonging to three Burkina Faso sheep breeds (Burkina-Sahel, Djallonké and Mossi) and one Niger sheep breed (Touareg) were genotyped for the MC1R and ASIP genes. The wild allele of the ASIP gene (Awt; 54.30%) was the most frequent in the four West African sheep, particularly in Burkina-Sahel (85%) and Touareg breeds (80%). The dominant black ED allele was not identified in Burkina-Sahel and Touareg. Most of the analysed individuals were homozygous for wild MC1R allele (E+/E+) with 100, 73.5, 59 and 100% frequency in Burkina-Sahel, Djallonké, Mossi and Touareg, respectively. The Awt/Awt was the most frequent genotype on the ASIP gene in the four West African breeds (80.53%). No individuals were homozygous for the deletion (allele Adel). Although, no routine methods for detection of the genetic basis of the recessive black coat colour patterns can be easily implemented, the current results suggest the feasibility of a selection programme aiming at decreasing the frequencies of the dominant black ED allele in Burkina Faso sheep breeds.Key words: Sheep, coat colour, MC1R gene, ASIP gene, Burkina Faso, Niger

Transcriptome architecture across tissues in the pig

Background: Artificial selection has resulted in animal breeds with extreme phenotypes. As an organism is made up of many different tissues and organs, each with its own genetic programme, it is pertinent to ask: How relevant is tissue in terms of total transcriptome variability? Which are the genes most distinctly expressed between tissues? Does breed or sex equally affect the transcriptome across tissues? Results: In order to gain insight on these issues, we conducted microarray expression profiling of 16 different tissues from four animals of two extreme pig breeds, Large White and Iberian, two males and two females. Mixed model analysis and neighbor - joining trees showed that tissues with similar developmental origin clustered closer than those with different embryonic origins. Often a sound biological interpretation was possible for overrepresented gene ontology categories within differentially expressed genes between groups of tissues. For instance, an excess of nervous system or muscle development genes were found among tissues of ectoderm or mesoderm origins, respectively. Tissue accounted for ~11 times more variability than sex or breed. Nevertheless, we were able to confidently identify genes with differential expression across tissues between breeds (33 genes) and between sexes (19 genes). The genes primarily affected by sex were overall different than those affected by breed or tissue. Interaction with tissue can be important for differentially expressed genes between breeds but not so much for genes whose expression differ between sexes. Conclusion: Embryonic development leaves an enduring footprint on the transcriptome. The interaction in gene × tissue for differentially expressed genes between breeds suggests that animal breeding has targeted differentially each tissue's transcriptome

The effect of mixing entire male pigs prior to transport to slaughter on behaviour, welfare and carcass lesions

peer-reviewedData set for article is also provided.Research is needed to validate lesions recorded at meat inspection as indicators of pig welfare on farm. The aims were to determine the influence of mixing pigs on carcass lesions and to establish whether such lesions correlate with pig behaviour and lesions scored on farm. Aggressive and mounting behaviour of pigs in three single sex pens was recorded on Day −5, −2, and −1 relative to slaughter (Day 0). On Day 0 pigs were randomly allocated to 3 treatments (n = 20/group) over 5 replicates: males mixed with females (MF), males mixed with males (MM), and males unmixed (MUM). Aggressive and mounting behaviours were recorded on Day 0 at holding on farm and lairage. Skin/tail lesions were scored according to severity at the farm (Day −1), lairage, and on the carcass (Day 0). Effect of treatment and time on behaviour and lesions were analysed by mixed models. Spearman rank correlations between behaviour and lesion scores and between scores recorded at different stages were determined. In general, MM performed more aggressive behaviour (50.4 ± 10.72) than MUM (20.3 ± 9.55, P < 0.05) and more mounting (30.9 ± 9.99) than MF (11.4 ± 3.76) and MUM (9.8 ± 3.74, P < 0.05). Skin lesion scores increased between farm (Day −1) and lairage (P < 0.001), but this tended to be significant only for MF and MM (P = 0.08). There was no effect of treatment on carcass lesions and no associations were found with fighting/mounting. Mixing entire males prior to slaughter stimulated mounting and aggressive behaviour but did not influence carcass lesion scores. Carcass skin/tail lesions scores were correlated with scores recorded on farm (rskin = 0.21 and rtail = 0.18, P < 0.01) suggesting that information recorded at meat inspection could be used as indicators of pig welfare on farm.This study was part of the PIGWELFIND project funded by the Department of Agriculture, Food and the Marine (DAFM), Ireland

Emergent Properties of Tumor Microenvironment in a Real-life Model of Multicell Tumor Spheroids

Multicellular tumor spheroids are an important {\it in vitro} model of the pre-vascular phase of solid tumors, for sizes well below the diagnostic limit: therefore a biophysical model of spheroids has the ability to shed light on the internal workings and organization of tumors at a critical phase of their development. To this end, we have developed a computer program that integrates the behavior of individual cells and their interactions with other cells and the surrounding environment. It is based on a quantitative description of metabolism, growth, proliferation and death of single tumor cells, and on equations that model biochemical and mechanical cell-cell and cell-environment interactions. The program reproduces existing experimental data on spheroids, and yields unique views of their microenvironment. Simulations show complex internal flows and motions of nutrients, metabolites and cells, that are otherwise unobservable with current experimental techniques, and give novel clues on tumor development and strong hints for future therapies.Comment: 20 pages, 10 figures. Accepted for publication in PLOS One. The published version contains links to a supplementary text and three video file

Flavour Physics in the Soft Wall Model

We extend the description of flavour that exists in the Randall-Sundrum (RS) model to the soft wall (SW) model in which the IR brane is removed and the Higgs is free to propagate in the bulk. It is demonstrated that, like the RS model, one can generate the hierarchy of fermion masses by localising the fermions at different locations throughout the space. However, there are two significant differences. Firstly the possible fermion masses scale down, from the electroweak scale, less steeply than in the RS model and secondly there now exists a minimum fermion mass for fermions sitting towards the UV brane. With a quadratic Higgs VEV, this minimum mass is about fifteen orders of magnitude lower than the electroweak scale. We derive the gauge propagator and despite the KK masses scaling as $m_n^2\sim n$, it is demonstrated that the coefficients of four fermion operators are not divergent at tree level. FCNC's amongst kaons and leptons are considered and compared to calculations in the RS model, with a brane localised Higgs and equivalent levels of tuning. It is found that since the gauge fermion couplings are slightly more universal and the SM fermions typically sit slightly further towards the UV brane, the contributions to observables such as $\epsilon_K$ and $\Delta m_K$, from the exchange of KK gauge fields, are significantly reduced.Comment: 33 pages, 15 figures, 5 tables; v2: references added; v3: modifications to figures 4,5 and 6. version to appear in JHE

SU(7) Unification of SU(3)_C*SU(4)_W* U(1)_{B-L}

We propose the SUSY SU(7) unification of the SU(3)_C* SU(4)_W* U(1)_{B-L} model. Such unification scenario has rich symmetry breaking chains in a five-dimensional orbifold. We study in detail the SUSY SU(7) symmetry breaking into SU(3)_C* SU(4)_W* U(1)_{B-L} by boundary conditions in a Randall-Sundrum background and its AdS/CFT interpretation. We find that successful gauge coupling unification can be achieved in our scenario. Gauge unification favors low left-right and unification scales with tree-level \sin^2\theta_W=0.15. We use the AdS/CFT dual of the conformal supersymmetry breaking scenario to break the remaining N=1 supersymmetry. We employ AdS/CFT to reproduce the NSVZ formula and obtain the structure of the Seiberg duality in the strong coupling region for 3/2N_c<N_F<3N_C. We show that supersymmetry is indeed broken in the conformal supersymmetry breaking scenario with a vanishing singlet vacuum expectation value.Comment: 25 pages, 1 figure