POLAR -- I: linking the 21-cm signal from the epoch of reionization to galaxy formation

To self-consistently model galactic properties, reionization of the intergalactic medium, and the associated 21-cm signal, we have developed the algorithm polar by integrating the one-dimensional radiative transfer code grizzly with the semi-analytical galaxy formation code L-Galaxies 2020. Our proof-of-concept results are consistent with observations of the star formation rate history, UV luminosity function and the CMB Thomson scattering optical depth. We then investigate how different galaxy formation models affect UV luminosity functions and 21-cm power spectra, and find that while the former are most sensitive to the parameters describing the merger of halos, the latter have a stronger dependence on the supernovae feedback parameters, and both are affected by the escape fraction model.Comment: MNRAS accepte

Variation at the Calpain 3 gene is associated with meat tenderness in zebu and composite breeds of cattle

<p>Abstract</p> <p>Background</p> <p>Quantitative Trait Loci (QTL) affecting meat tenderness have been reported on Bovine chromosome 10. Here we examine variation at the Calpain 3 (<it>CAPN3</it>) gene in cattle, a gene located within the confidence interval of the QTL, and which is a positional candidate gene based on the biochemical activity of the protein.</p> <p>Results</p> <p>We identified single nucleotide polymorphisms (SNP) in the genomic sequence of the <it>CAPN3 </it>gene and tested three of these in a sample of 2189 cattle. Of the three SNP genotyped, the <it>CAPN3:c.1538+225G>T </it>had the largest significant additive effect, with an allele substitution effect in the Brahman of <it>α </it>= -0.144 kg, SE = 0.060, <it>P </it>= 0.016, and the polymorphism explained 1.7% of the residual phenotypic variance in that sample of the breed. Significant haplotype substitution effects were found for all three breeds, the Brahman, the Belmont Red, and the Santa Gertrudis. For the common haplotype, the haplotype substitution effect in the Brahman was <it>α </it>= 0.169 kg, SE = 0.056, <it>P </it>= 0.003. The effect of this gene was compared to Calpastatin in the same sample. The SNP show negligible frequencies in taurine breeds and low to moderate minor allele frequencies in zebu or composite animals.</p> <p>Conclusion</p> <p>These associations confirm the location of a QTL for meat tenderness in this region of bovine chromosome 10. SNP in or near this gene may be responsible for part of the overall difference between taurine and zebu breeds in meat tenderness, and the greater variability in meat tenderness found in zebu and composite breeds. The evidence provided so far suggests that none of these tested SNP are causative mutations.</p

Current models of the observable consequences of cosmic reionization and their detectability

A number of large current experiments aim to detect the signatures of the cosmic reionization at redshifts z &gt; 6. Their success depends crucially on understanding the character of the reionization process and its observable consequences and designing the best strategies to use. We use large-scale simulations of cosmic reionization to evaluate the reionization signatures at redshifted 21-cm and small-scale cosmic microwave background (CMB) anisotropies in the best current model for the background universe, with fundamental cosmological parameters given by Wilkinson Microwave Anisotropy Probe three-year results. We find that the optimal frequency range for observing the `global step of the 21-cm emission is 120150 MHz, while statistical studies should aim at 140160 MHz, observable by GMRT. Some strongly non-Gaussian brightness features should be detectable at frequencies up to ~190 MHz. In terms of sensitivity-signal trade-off relatively low resolutions, corresponding to beams of at least a few arcminutes, are preferable. The CMB anisotropy signal from the kinetic SunyaevZel'dovich effect from reionized patches peaks at tens of K at arcminute scales and has an rms of ~1 K, and should be observable by the Atacama Cosmology Telescope and the South Pole Telescope. We discuss the various observational issues and the uncertainties involved, mostly related to the poorly known reionization parameters and, to a lesser extend, to the uncertainties in the background cosmology

Characterisation and expression of calpain family members in relation to nutritional status, diet composition and flesh texture in gilthead sea bream (Sparus aurata).

Calpains are non-lysosomal calcium-activated neutral proteases involved in a wide range of cellular processes including muscle proteolysis linked to post-mortem flesh softening. The aims of this study were (a) to characterise several members of the calpain system in gilthead sea bream and (b) to examine their expression in relation to nutritional status and muscle tenderisation. We identified the complete open reading frame of gilthead sea bream calpains1-3, sacapn1, sacapn2, sacapn3, and two paralogs of the calpain small subunit1, sacapns1a and sacapns1b. Proteins showed 63-90% sequence identity compared with sequences from mammals and other teleost fishes, and the characteristic domain structure of vertebrate calpains. Transcripts of sacapn1, sacapn2, sacapns1a and sacapns1b had a wide tissue distribution, whereas sacapn3 was almost exclusively detected in skeletal muscle. Next, we assessed transcript expression in skeletal muscle following alteration of nutritional status by (a) fasting and re-feeding or (b) feeding four experimental diets with different carbohydrate-to-protein ratios. Fasting significantly reduced plasma glucose and increased free fatty acids and triglycerides, together with a significant increase in sacapns1b expression. Following 7 days of re-feeding, plasma parameters returned to fed values and sacapn1, sacapn2, sacapns1a and sacapns1b expression was significantly reduced. Furthermore, an increase in dietary carbohydrate content (11 to 39%) diminished growth but increased muscle texture, which showed a significant correlation with decreased sacapn1 and sacapns1a expression, whilst the other calpains remained unaffected. This study has demonstrated that calpain expression is modulated by nutritional status and diet composition in gilthead sea bream, and that the expression of several calpain members is correlated with muscle texture, indicating their potential use as molecular markers for flesh quality in aquaculture production

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

POLAR - I: linking the 21-cm signal from the epoch of reionization to galaxy formation

To self-consistently model galactic properties, reionization of the intergalactic medium, and the associated 21-cm signal, we have developed the algorithm POLAR by integrating the one-dimensional radiative transfer code GRIZZLY with the semi-analytical galaxy formation code L-GALAXIES 2020. Our proof-of-concept results are consistent with observations of the star formation rate history, UV luminosity function, and the CMB Thomson scattering optical depth. We then investigate how different galaxy formation models affect UV luminosity functions and 21-cm power spectra, and find that while the former are most sensitive to the parameters describing the merger of haloes, the latter have a stronger dependence on the supernovae feedback parameters, and both are affected by the escape fraction model.</p