Discovery of novel genetic networks associated with 19 economically important traits in beef cattle

Quantitative or complex traits are determined by the combined effects of many loci, and are affected by genetic networks or molecular pathways. In the present study, we genotyped a total of 138 mutations, mainly single nucleotide polymorphisms derived from 71 functional genes on a Wagyu x Limousin reference population. Two hundred forty six F₂ animals were measured for 5 carcass, 6 eating quality and 8 fatty acid composition traits. A total of 2,280 single marker-trait association runs with 120 tagged mutations selected based on the HAPLOVIEW analysis revealed 144 significant associations (P < 0.05), but 50 of them were removed from the analysis due to the small number of animals (≤ 9) in one genotype group or absence of one genotype among three genotypes. The remaining 94 single-trait associations were then placed into three groups of quantitative trait modes (QTMs) with additive, dominant and overdominant effects. All significant markers and their QTMs associated with each of these 19 traits were involved in a linear regression model analysis, which confirmed single-gene associations for 4 traits, but revealed two-gene networks for 8 traits and three-gene networks for 5 traits. Such genetic networks involving both genotypes and QTMs resulted in high correlations between predicted and actual values of performance, thus providing evidence that the classical Mendelian principles of inheritance can be applied in understanding genetic complexity of complex phenotypes. Our present study also indicated that carcass, eating quality and fatty acid composition traits rarely share genetic networks. Therefore, marker-assisted selection for improvement of one category of these traits would not interfere with improvement of another.     

HistoChoice® as an alternative to formalin fixation of undecalcified bone specimens

We compared histochemical and immunohistochemical staining as well as fluorochrome labeling in murine bone specimens that were fixed with 10% neutral buffered formalin to those fixed with HistoChoice®. We showed that sections from undecalcified tibiae fixed for 4 h in HistoChoice® resulted in enhanced toluidine blue and Von Kossa histochemical staining compared to formalin fixation. HistoChoice® produced comparable or improved staining for alkaline phosphatase. Acid phosphatase localization was better in formalin fixed specimens, but osteoclasts were visuralized more easily in HistoChoice® fixed specimens. As expected, immunohistochemical labeling was antibody dependent; some antibodies labeled better in HistoChoice® fixed specimens while others were better in formalin fixed specimens. Toluidine blue, Von Kossa, and alkaline phosphatase staining of sections fixed for 12 h produced sections that were similar to 4 h fixed sections. Fixation for 12 h preserved acid phosphatase activity better. Increasing fixation to 12 h affected immunolocalization differentially. Bone sialoprotein labeling in HistoChoice® fixed specimens was comparable to formalin fixed samples. On the other hand, after 12 h formalin fixation, osteocalcin labeling was comparable to HistoChoice®. For most histochemical applications, fixing murine bone specimens for 4 h with HistoChoice® yielded superior staining compared to formalin fixation. If immunohistochemical localization is desired, however, individual antibodies must be tested to determine which fixation process retains antigenicity better. In addition, there was no detectable difference in the intensity of fluorochrome labeling using either fixative. Finally, fixation duration did not alter the intensity of labeling.     

Dry deposition of ammonia gas drives species change faster than wet deposition of ammonium ions: evidence from a long‐term field manipulation

Although the effects of atmospheric nitrogen deposition on species composition are relatively well known, the roles of the different forms of nitrogen, in particular gaseous ammonia (NH₃), have not been tested in the field. Since 2002, we have manipulated the form of N deposition to an ombrotrophic bog, Whim, on deep peat in southern Scotland, with low ambient N (wet + dry = 8 kg N ha^?1 yr^?1) and S (4 kg S ha^?1 yr^?1) deposition. A gradient of ammonia (NH₃, dry N), from 70 kg N ha^?1 yr^?1 down to background, 3–4 kg N ha^?1 yr^?1 was generated by free air release. Wet ammonium (NH₄⁺, wet N) was provided to replicate plots in a fine rainwater spray (NH₄Cl at +8, +24, +56 kg N ha^?1 yr^?1). Automated treatments are coupled to meteorological conditions, in a globally unique, field experiment. Ammonia concentrations were converted to NH₃‐N deposition (kg N ha^?1) using a site/vegetation specific parameterization. Within 3 years, exposure to relatively modest deposition of NH₃, 20–56 kg NH₃‐N ha^?1 yr^?1 led to dramatic reductions in species cover, with almost total loss of Calluna vulgaris, Sphagnum capillifolium and Cladonia portentosa. These effects appear to result from direct foliar uptake and interaction with abiotic and biotic stresses, rather than via effects on the soil. Additional wet N by contrast, significantly increased Calluna cover after 5 years at the 56 kg N dose, but reduced cover of Sphagnum and Cladonia. Cover reductions caused by wet N were significantly different from and much smaller than those caused by equivalent dry N doses. The effects of gaseous NH₃ described here, highlight the potential for ammonia to destroy acid heathland and peat bog ecosystems. Separating the effects of gaseous ammonia and wet ammonium deposition, for a peat bog, has significant implications for regulatory bodies and conservation agencies.     

A first-generation porcine whole-genome radiation hybrid map

A whole-genome radiation hybrid (WG-RH) panel was used to generate a first-generation radiation map of the porcine (Sus scrofa) genome. Over 900 Type I and II markers were used to amplify the INRA-University of Minnesota porcine Radiation Hybrid panel (IMpRH) comprised of 118 hybrid clones. Average marker retention frequency of 29.3% was calculated with 757 scorable markers. The RHMAP program established 128 linkage groups covering each chromosome (n = 19) at a lod ≥ 4.8. Fewer than 10% of the markers (59) could not be placed within any linkage group at a lod score ≥4.8. Linkage group order for each chromosome was determined by incorporating linkage data from the swine genetic map as well as physical assignments. The current map has an estimated ratio of ∼70 kb/cR and a maximum theoretical resolution of 145 kb. This initial map forms a template for establishing accurate YAC and BAC contigs and eventual positional cloning of genes associated with complex traits. Received: 8 January 1999 / Accepted: 13 April 1999     

Using minimal supplements of trace minerals as a method of reducing trace mineral content of poultry manure

Experiments were conducted with broilers and layers with the aim of reducing manure content of zinc, copper and manganese by using lower supplemented levels of mineral proteinates. Broilers were fed maize-soy diets containing conventional levels of trace minerals provided by inorganic salts. Other treatments involved use of mineral proteinates fed at from 70–20% of the control diet levels. Diet generally had no effect (P>0.05) on body weight or feed efficiency to 42 d. A total collection procedure showed that at the lowest level of mineral proteinate supplementation excretion of zinc, manganese and copper was reduced by 38%, 52% and 21%, respectively. In a second study, layers were fed either conventional sources and levels of trace minerals, no trace minerals, or 20% of regular levels as mineral proteinates. Diet had no effect on egg numbers from 38–70 weeks. Egg size was always reduced in birds fed diets devoid of supplemental trace minerals. Using the lower levels of diet minerals, there was a 66% reduction in excretion of zinc and 78% reduction in excretion of manganese. It seems as though we are overfeeding trace minerals, and that with judicious use of mineral proteinates, it is possible to maintain performance while concomitantly reducing mineral content of manure.     

Inhibition of the cGAS‐STING pathway ameliorates the premature senescence hallmarks of Ataxia‐Telangiectasia brain organoids

Ataxia‐telangiectasia (A‐T) is a genetic disorder caused by the lack of functional ATM kinase. A‐T is characterized by chronic inflammation, neurodegeneration and premature ageing features that are associated with increased genome instability, nuclear shape alterations, micronuclei accumulation, neuronal defects and premature entry into cellular senescence. The causal relationship between the detrimental inflammatory signature and the neurological deficiencies of A‐T remains elusive. Here, we utilize human pluripotent stem cell‐derived cortical brain organoids to study A‐T neuropathology. Mechanistically, we show that the cGAS‐STING pathway is required for the recognition of micronuclei and induction of a senescence‐associated secretory phenotype (SASP) in A‐T olfactory neurosphere‐derived cells and brain organoids. We further demonstrate that cGAS and STING inhibition effectively suppresses self‐DNA‐triggered SASP expression in A‐T brain organoids, inhibits astrocyte senescence and neurodegeneration, and ameliorates A‐T brain organoid neuropathology. Our study thus reveals that increased cGAS and STING activity is an important contributor to chronic inflammation and premature senescence in the central nervous system of A‐T and constitutes a novel therapeutic target for treating neuropathology in A‐T patients.     

TAP score: torsion angle propensity normalization applied to local protein structure evaluation

Background  

Experimentally determined protein structures may contain errors and require validation. Conformational criteria based on the Ramachandran plot are mainly used to distinguish bet ween distorted and adequately refined models. While the readily available criteria are sufficient to detect totally wrong structures, establishing the more subtle differences between plausible structures remains more challenging.     

Influence of steam pelleting on the feeding value of Tower and Candle rapeseed products for broiler chickens

Male broiler chickens were offered diets containing up to 30% Tower rapeseed meal, with these diets being prepared in mash or steam pelleted (crumble) form. In 4 experiments, birds receiving a maize and soya bean meal control diet showed a significant improvement in weight gain when crumbles, rather than mash diets, were used. With isocaloric, isonitrogenous diets containing rapeseed meal, no such improvement in growth rate was observed. Steam pelleting exerted no consistent effect on feed conversion. There was no significant difference in the growth rate of birds receiving mash diets irrespective of composition, while for crumbled diets, birds consuming the maize and soya bean control diet were heavier than comparable rapeseed-fed birds, with this difference being significant in 2 experiments. By adding fat, necessary to maintain rapeseed diets isocaloric, after the pelleting process, it was shown that fat per se was not responsible for failure to elicit a growth response with pelleted rapeseed meal diets. The response to pelleting was similar with diets prepared in an experimental pelleting machine at the university or by a commercial feed mill. Reduction in amino acid availability, in particular of arginine, is tentatively discussed in relation to the non-improved growth rate observed with pelleted diets containing rapeseed meal. Improvement in growth rate with pelleted vs. mash diets containing whole, raw rapeseeds is interpreted as a response to the heat treatment involved with the pelleting process.