Accuracy of direct genomic breeding values for nationally evaluated traits in US Limousin and Simmental beef cattle

Background

In national evaluations, direct genomic breeding values can be considered as correlated traits to those for which phenotypes are available for traditional estimation of breeding values. For this purpose, estimates of the accuracy of direct genomic breeding values expressed as genetic correlations between traits and their respective direct genomic breeding values are required.

Methods

We derived direct genomic breeding values for 2239 registered Limousin and 2703 registered Simmental beef cattle genotyped with either the Illumina BovineSNP50 BeadChip or the Illumina BovineHD BeadChip. For the 264 Simmental animals that were genotyped with the BovineHD BeadChip, genotypes for markers present on the BovineSNP50 BeadChip were extracted. Deregressed estimated breeding values were used as observations in weighted analyses that estimated marker effects to derive direct genomic breeding values for each breed. For each breed, genotyped individuals were clustered into five groups using K-means clustering, with the aim of increasing within-group and decreasing between-group pedigree relationships. Cross-validation was performed five times for each breed, using four groups for training and the fifth group for validation. For each trait, we then applied a weighted bivariate analysis of the direct genomic breeding values of genotyped animals from all five validation sets and their corresponding deregressed estimated breeding values to estimate variance and covariance components.

Results

After minimizing relationships between training and validation groups, estimated genetic correlations between each trait and its direct genomic breeding values ranged from 0.39 to 0.76 in Limousin and from 0.29 to 0.65 in Simmental. The efficiency of selection based on direct genomic breeding values relative to selection based on parent average information ranged from 0.68 to 1.28 in genotyped Limousin and from 0.51 to 1.44 in genotyped Simmental animals. The efficiencies were higher for 323 non-genotyped young Simmental animals, born after January 2012, and ranged from 0.60 to 2.04.

Conclusions

Direct genomic breeding values show promise for routine use by Limousin and Simmental breeders to improve the accuracy of predicted genetic merit of their animals at a young age and increase response to selection. Benefits from selecting on direct genomic breeding values are greater for breeders who use natural mating sires in their herds than for those who use artificial insemination sires. Producers with unregistered commercial Limousin and Simmental cattle could also benefit from being able to identify genetically superior animals in their herds, an opportunity that has in the past been limited to seed stock animals.     

Effect of some essential oils on mycelial growth of <Emphasis Type="Italic">Penicillium digitatum</Emphasis> Sacc.

The antifungal action of four essential oils of Foeniculum vulgare (fennel), Thymus vulgaris (thyme), Eugenia caryophyllata (Clove) and Salvia officinalis (sage) was tested in vitro against Penicillium digitatum Sacc. Direct contact and vapour phase were used to test the antifungal activity of these essential oils against P. digitatum that is responsible for green mould rot of citrus fruits. The vapour phase and direct contact of clove and thyme essential oils exhibited the strongest toxicity and totally inhibited the mycelial growth of the test fungus. Thyme and clove essential oils completely inhibited P. digitatum growth either when added into the medium 600 μl l⁻¹ or by their volatiles with 24 μl per 8 cm diameter Petri dish. In in vitro mycelial growth assay showed fungistatic and fungicidal activity by clove and thyme essential oils. Sage and fennel oils did not show any inhibitory activity on this fungus. Scanning electron microscopy (SEM) was done to study the mode of action of clove oil in P. digitatum and it was observed that treatment with the oil leads to large alterations in hyphal morphology.     

Mass spectrometric quantification of the relative amounts of C6 and C3 position phosphorylated glucosyl residues in starch

The quantification of phosphate bound to the C6 and C3 positions of glucose residues in starch has received increasing interest since the importance of starch phosphorylation for plant metabolism was discovered. The method described here is based on the observation that the isobaric compounds glucose-6-phosphate (Glc6P) and glucose-3-phosphate (Glc3P) exhibit significantly different fragmentation patterns in negative ion electrospray tandem mass spectrometry (MS/MS). A simple experiment involving collision-induced dissociation (CID) MS² spectra of the sample and the two reference substances Glc3P and Glc6P permitted the quantification of the relative amounts of the two compounds in monosaccharide mixtures generated by acid hydrolysis of starch. The method was tested on well-characterized potato tuber starch. The results are consistent with those obtained by NMR analysis. In contrast to NMR, however, the presented method is fast and can be performed on less than 1 mg of starch. Starch samples of other origins exhibiting a variety of phosphorylation degrees were analyzed to assess the sensitivity and robustness of the method.     

Identification of lipopolysaccharide binding site on high molecular weight kininogen

Plasma kallikrein kinin system (KKS) activation along with its cellular receptors expression are increased after injury and in patients with septic shock, hypotensive bacteremia and rhesus monkey infected with Salmonella typhimurium. KKS signaling cascade is activated by activated factor XII (FXIIa, Hageman factor)- and prolylcarboxypeptidase (PRCP)-dependent pathways on endothelial cells. Among the many entities that comprise the KKS, high molecular weight kininogen (HK), a bradykinin precursor, is critical in the assembly and activation of this system. HK is primarily expressed in the liver and secreted into the bloodstream. The activation of the KKS influences the permeability of the endothelium by liberating bradykinin (BK) from HK. BK is a potent inflammatory peptide which stimulates constitutive bradykinin B2 and inducible B1 receptors to release nitric oxide and prostacyclin. Regardless of the triggers, PK can only be activated on HK bound to the artificial negatively charged or to cell membrane surfaces. Since LPS has a negatively charged moiety and the ability to induce inflammatory responses in human, we determined the interaction between LPS and HK. HKH19 (HK cell binding site) and heparin inhibited LPS binding to HK with IC₅₀s of 15 nM and 20 μg/ml, respectively. C1-inhibitor and N-acetylglucosamine glycan inhibited LPS binding to HK with IC₅₀s of about 10 μg/ml and 10 mM, respectively. This novel study underscores the implication of HK in infection. We propose that HKH19, heparin, and C1-inhibitor present therapeutic potential for the treatment of sepsis and hypotensive bacteremia.     

The cytokinin 2-isopentenyladenine causes partial reversion to skotomorphogenesis and induces formation of prolamellar bodies and protochlorophyllide657 in the lip1 mutant of pea

When grown in darkness the photomorphogenic lip 1 mutant of pea ( Pisum sativum L.) has a slender stem, expanded leaves, prolamellar body (PLB) lacking plastids with the size of chloroplasts and a low level of phytochrome A. The lack of PLBs in a dark-grown material ( lip 1) created a possibility to further study the regulation of their formation in relation to plant development. Inclusion of a cytokinin, 2-isopentenyladenine (2iP), in a medium supporting growth of the pea seedlings in darkness was found to reduce epicotyl length in the wild type. In lip 1 the formation of a slender stem was inhibited and a short epicotyl developed. Furthermore, leaf expansion was inhibited, the plastid size reduced and the formation of PLBs induced. The PLB formation in lip 1 was not accompanied by an increase in the amount of protochlorophyllide (Pchlide) or Pchilde oxidoreductase (POR). In the presence of 2iP the level of phytochrome A protein was increased in lip 1 and the POR mRNA levels decreased in both lip 1 and wild-type plants. The chloroplast characteristic trans -3-hexadecenoate acyl group of phosphatidylglycerol, present in the plastids of dark-grown lip 1, was not influenced by 2iP. Thus, not all photomorphogenic processes reacted similarly in the lip 1 mutant, but leaf expansion and plastid differentiation, including PLB formation, seemed to be regulated by the same signal transduction chain. Exogenously applied brassinolide could rescue neither dark- nor light-grown defects of the lip 1 mutant. Thus, cytokinins but not brassinolides seem to be involved in the regulation of certain characteristic traits of skotomorphogenesis in pea, including plastid development and PLB formation.     

Precise two-dimensional D-bar reconstructions of human chest and phantom tank via sinc-convolution algorithm

ABSTRACT: BACKGROUND: Electrical Impedance Tomography (EIT) is used as a fast clinical imaging technique formonitoring the health of the human organs such as lungs, heart, brain and breast. Eachpractical EIT reconstruction algorithm should be efficient enough in terms of convergencerate, and accuracy. The main objective of this study is to investigate the feasibility of preciseempirical conductivity imaging using a sinc-convolution algorithm in D-bar framework. METHODS: At the first step, synthetic and experimental data were used to compute an intermediate objectnamed scattering transform. Next, this object was used in a 2-day integral equation whichwas precisely and rapidly solved via sinc-convolution algorithm to find the square root of theconductivity for each pixel of image. For the purpose of comparison, multigrid and NOSERalgorithms were implemented under a similar setting. Quality of reconstructions of syntheticmodels was tested against GREIT approved quality measures. To validate the simulationresults, reconstructions of a phantom chest and a human lung were used. RESULTS: Evaluation of synthetic reconstructions shows that the quality of sinc-convolutionreconstructions is considerably better than that of each of its competitors in terms ofamplitude response, position error, ringing, resolution and shape-deformation. In addition, theresults confirm near-exponential and linear convergence rates for sinc-convolution andmultigrid, respectively. Moreover, the least degree of relative errors and the most degree oftruth were found in sinc-convolution reconstructions from experimental phantom data.Reconstructions of clinical lung data show that the related physiological effect is wellrecovered by sinc-convolution algorithm. CONCLUSIONS: Parametric evaluation demonstrates the efficiency of sinc-convolution to reconstruct accurateconductivity images from experimental data. Excellent results in phantom and clinicalreconstructions using sinc-convolution support parametric assessment results and suggest thesinc-convolution to be used for precise clinical EIT applications.     

Cardioprotective role of extracellular vesicles: A highlight on exosome beneficial effects in cardiovascular diseases

Extracellular vesicles (EVs) are nano-sized vesicles, released from many cell types including cardiac cells, have recently emerged as intercellular communication tools in cell dynamics. EVs are an important mediator of signaling within cells that influencing the functional behavior of the target cells. In heart complex, cardiac cells can easily use EVs to transport bioactive molecules such as proteins, lipids, and RNAs to the regulation of neighboring cell function. Cross-talk between intracardiac cells plays pivotal roles in the heart homeostasis and in adaptive responses of the heart to stress. EVs were released by cardiomyocytes under baseline conditions, but stress condition such as hypoxia intensifies secretome capacity. EVs secreted by cardiac progenitor cells and cardiosphere-derived cells could be pinpointed as important mediators of cardioprotection and cardiogenesis. Furthermore, EVs from many different types of stem cells could potentially exert a therapeutic effect on the damaged heart. Recent evidence shows that cardiac-derived EVs are rich in microRNAs, suggesting a key role in the controlling of cellular processes. EVs harboring exosomes may be clinically useful in cell-free therapy approaches and potentially act as prognosis and diagnosis biomarkers of cardiovascular diseases.     

Steroidogenic characteristics of the adrenal cortex of the mare studied by electron microscopy

The three concentric zones of the horse adrenal cortex (zonae glomerulosa, fasciculata and reticularis) showed marked interpenetration and exhibited a different relative development according to their position in the gland. Whereas the three cortical zones each had a specific histological structure, the ultrastructure of their cells showed a certain qualitative homogeneity. The differences corresponded essentially to the relative abundance of the constituents which are generally considered typical of steroidogeneous cells: mitochondria with vesicular cristae, smooth endoplasmic reticulum and lipid droplets. Their importance increased progressively from the zona glomerulosa to the zona reticularis. In this zone, the presence of gap and septate-like cell junctions, and mitochondria with vesicular cristae in close proximity to a smooth endoplasmic reticulum with numerous dilated tubules, suggested that steroidogenesis may be the most active. Ultrastructural findings were indicative of only quantitative differences between the steroidogenic capacities of the three zones of the mare adrenal cortex.     

Improvement in infected wound healing in type 1 diabetic rat by the synergistic effect of photobiomodulation therapy and conditioned medium

We investigated the effects of photobiomodulation therapy (PBMT) and conditioned medium (CM) of human bone marrow mesenchymal stem cells (hBM-MSC) individually and/or in combination on the stereological parameters and the expression of basic fibroblast growth factor (bFGF), hypoxia-inducible factor (HIF-1α), and stromal cell–derived factor-1α (SDF-1α) in a wound model infected with methicillin-resistant Staphylococcus aureus (MRSA) in diabetic rats. CM was provided by culturing hBM-MSCs. Type 1 diabetes mellitus (T1DM) was induced in 72 rats, divided into four groups, harboring 18 rats each: group 1 served as a control group, group 2 received PBMT, group 3 received CM, and group 4 received CM + PBMT. On days 4, 7, and 15, six animals from each group were euthanized and the skin samples were separated for stereology examination and gene expression analysis by real-time polymerase chain reaction. In the CM + PBMT, CM, and PBMT groups, significant decreases were induced in the number of neutrophils (1460 ± 93, 1854 ± 138, 1719 ± 248) and macrophages (539 ± 69, 804 ± 63, 912 ± 41), and significant increases in the number of fibroblasts (1073 ± 116, 836 ± 75, 912 ± 41) and angiogenesis (15 230 ± 516, 13 318 ± 1116, 14 041 ± 867), compared with those of the control group (2690 ± 371, 1139 ± 145, 566 ± 90, 12 585 ± 1219). Interestingly, the findings of the stereological examination in the CM + PBMT group were statistically more significant than those in the other groups. In the PBMT group, in most cases, the expression of bFGF, HIF-1α, and SDF-1α, on day 4 (27.7 ± 0.14, 28.8 ± 0.52, 27.5 ± 0.54) and day 7 (26.8 ± 1.4, 29.6 ± 1.4, 28.3 ± 1.2) were more significant than those in the control (day 4, 19.3 ± 0.42, 25.5 ± 0.08, 22.6 ± 0.04; day 7, 22.3 ± 0.22, 28.3 ± 0.59, 24.3 ± 0.19) and other treatment groups. The application of PBMT + CM induced anti-inflammatory and angiogenic activities, and hastened wound healing process in a T1 DM model of MRSA infected wound.