Comparison on genomic predictions using three GBLUP methods and two single-step blending methods in the Nordic Holstein population

Background

A single-step blending approach allows genomic prediction using information of genotyped and non-genotyped animals simultaneously. However, the combined relationship matrix in a single-step method may need to be adjusted because marker-based and pedigree-based relationship matrices may not be on the same scale. The same may apply when a GBLUP model includes both genomic breeding values and residual polygenic effects. The objective of this study was to compare single-step blending methods and GBLUP methods with and without adjustment of the genomic relationship matrix for genomic prediction of 16 traits in the Nordic Holstein population.

Methods

The data consisted of de-regressed proofs (DRP) for 5 214 genotyped and 9 374 non-genotyped bulls. The bulls were divided into a training and a validation population by birth date, October 1, 2001. Five approaches for genomic prediction were used: 1) a simple GBLUP method, 2) a GBLUP method with a polygenic effect, 3) an adjusted GBLUP method with a polygenic effect, 4) a single-step blending method, and 5) an adjusted single-step blending method. In the adjusted GBLUP and single-step methods, the genomic relationship matrix was adjusted for the difference of scale between the genomic and the pedigree relationship matrices. A set of weights on the pedigree relationship matrix (ranging from 0.05 to 0.40) was used to build the combined relationship matrix in the single-step blending method and the GBLUP method with a polygenetic effect.

Results

Averaged over the 16 traits, reliabilities of genomic breeding values predicted using the GBLUP method with a polygenic effect (relative weight of 0.20) were 0.3% higher than reliabilities from the simple GBLUP method (without a polygenic effect). The adjusted single-step blending and original single-step blending methods (relative weight of 0.20) had average reliabilities that were 2.1% and 1.8% higher than the simple GBLUP method, respectively. In addition, the GBLUP method with a polygenic effect led to less bias of genomic predictions than the simple GBLUP method, and both single-step blending methods yielded less bias of predictions than all GBLUP methods.

Conclusions

The single-step blending method is an appealing approach for practical genomic prediction in dairy cattle. Genomic prediction from the single-step blending method can be improved by adjusting the scale of the genomic relationship matrix.     

Genes and Processed Paralogs Co-exist in Plant Mitochondria

RNA-mediated gene duplication has been proposed to create processed paralogs in the plant mitochondrial genome. A processed paralog may retain signatures left by the maturation process of its RNA precursor, such as intron removal and no need of RNA editing. Whereas it is well documented that an RNA intermediary is involved in the transfer of mitochondrial genes to the nucleus, no direct evidence exists for insertion of processed paralogs in the mitochondria (i.e., processed and un-processed genes have never been found simultaneously in the mitochondrial genome). In this study, we sequenced a region of the mitochondrial gene nad1, and identified a number of taxa were two different copies of the region co-occur in the mitochondria. The two nad1 paralogs differed in their (a) presence or absence of a group II intron, and (b) number of edited sites. Thus, this work provides the first evidence of co-existence of processed paralogs and their precursors within the plant mitochondrial genome. In addition, mapping the presence/absence of the paralogs provides indirect evidence of RNA-mediated gene duplication as an essential process shaping the mitochondrial genome in plants.     

Population Dynamics of Dactylella oviparasitica and Heterodera schachtii: Toward a Decision Model for Sugar Beet Planting

A series of experiments were performed to examine the population dynamics of the sugarbeet cyst nematode, Heterodera schachtii, and the nematophagus fungus Dactylella oviparasitica. After two nematode generations, the population densities of H. schachtii were measured in relation to various initial infestation densities of both D. oviparasitica and H. schachtii. In general, higher initial population densities of D. oviparasitica were associated with lower final population densities of H. schachtii. Regression models showed that the initial densities of D. oviparasitica were only significant when predicting the final densities of H. schachtii J2 and eggs as well as fungal egg parasitism, while the initial densities of J2 were significant for all final H. schachtii population density measurements. We also showed that the densities of H. schachtii-associated D. oviparasitica fluctuate greatly, with rRNA gene numbers going from zero in most field-soil-collected cysts to an average of 4.24 x 10⁸ in mature females isolated directly from root surfaces. Finally, phylogenetic analysis of rRNA genes suggested that D. oviparasitica belongs to a clade of nematophagous fungi that includes Arkansas Fungus strain L (ARF-L) and that these fungi are widely distributed. We anticipate that these findings will provide foundational data facilitating the development of more effective decision models for sugar beet planting.     

A large geometric distortion in the first photointermediate of rhodopsin, determined by double-quantum solid-state NMR

Double-quantum magic-angle-spinning NMR experiments were performed on 11,12-(13)C(2)-retinylidene-rhodopsin under illumination at low temperature, in order to characterize torsional angle changes at the C11-C12 photoisomerization site. The sample was illuminated in the NMR rotor at low temperature (~120 K) in order to trap the primary photointermediate, bathorhodopsin. The NMR data are consistent with a strong torsional twist of the HCCH moiety at the isomerization site. Although the HCCH torsional twist was determined to be at least 40°, it was not possible to quantify it more closely. The presence of a strong twist is in agreement with previous Raman observations. The energetic implications of this geometric distortion are discussed.     

Root aeration via aerenchymatous phellem: three-dimensional micro-imaging and radial O2 profiles in Melilotus siculus

? Internal root aeration enables waterlogging-tolerant species to grow in anoxic soil. Secondary aerenchyma, in the form of aerenchymatous phellem, is of importance to root aeration in some dicotyledonous species. Little is known about this type of aerenchyma in comparison with primary aerenchyma. ? Micro-computed tomography was employed to visualize, in three dimensions, the microstructure of the aerenchymatous phellem in roots of Melilotus siculus. Tissue porosity and respiration were also measured for phellem and stelar tissues. A multiscale, three-dimensional, diffusion-respiration model compared the predicted O(2) profiles in roots with those measured using O(2) microelectrodes. ? Micro-computed tomography confirmed the measured high porosity of aerenchymatous phellem (44-54%) and the low porosity of stele (2-5%) A network of connected gas spaces existed in the phellem, but not within the stele. O(2) partial pressures were high in the phellem, but fell below the detection limit in the thicker upper part of the stele, consistent with the poorly connected low porosity and high respiratory demand. ? The presented model integrates and validates micro-computed tomography with measured radial O(2) profiles for roots with aerenchymatous phellem, confirming the existence of near-anoxic conditions at the centre of the stele in the basal parts of the root, coupled with only hypoxic conditions towards the apex.     

Direct and indirect climatic drivers of biotic interactions: ice-cover and carbon runoff shaping Arctic char Salvelinus alpinus and brown trout Salmo trutta competitive asymmetries

One of the major challenges in ecological climate change impact science is to untangle the climatic effects on biological interactions and indirect cascading effects through different ecosystems. Here, we test for direct and indirect climatic drivers on competitive impact of Arctic char (Salvelinus alpinus L.) on brown trout (Salmo trutta L.) along a climate gradient in central Scandinavia, spanning from coastal to high-alpine environments. As a measure of competitive impact, trout food consumption was measured using ¹³⁷Cs tracer methodology both during the ice-covered and ice-free periods, and contrasted between lakes with or without char coexistence along the climate gradient. Variation in food consumption between lakes was best described by a linear mixed effect model including a three-way interaction between the presence/absence of Arctic char, season and Secchi depth. The latter is proxy for terrestrial dissolved organic carbon run-off, strongly governed by climatic properties of the catchment. The presence of Arctic char had a negative impact on trout food consumption. However, this effect was stronger during ice-cover and in lakes receiving high carbon load from the catchment, whereas no effect of water temperature was evident. In conclusion, the length of the ice-covered period and the export of allochthonous material from the catchment are likely major, but contrasting, climatic drivers of the competitive interaction between two freshwater lake top predators. While future climatic scenarios predict shorter ice-cover duration, they also predict increased carbon run-off. The present study therefore emphasizes the complexity of cascading ecosystem effects in future effects of climate change on freshwater ecosystems.     

The use of PET/CT scanning technique for 3D visualization and quantification of real-time soil/plant interactions

Aims

Conventional methodology using destructive sampling, which is laborious and has poor spatial and temporal resolution, has limited our understanding of soil-plant interactions. New non-invasive tomographic techniques have the potential to significantly improve our knowledge. In this study we demonstrated the simultaneous use of PET (positron emission tomography) and CT (X-ray computed tomography) to (a) non-destructively image a whole plant growing in sand, and (b) to link the observed morphology with recently assimilated C. The PET scanner was used to detect and visualize the location of the short-lived radioisotope ¹¹C (with a half-life of 20.4?min) taken up by the plant through ¹¹C-labelled CO₂. This provided information on carbon translocation and the metabolism of photo-assimilates in the plant as well as root structure. The CT scanners yielded data on soil and root structure.

Methods

A medical PET/CT scanner was used to scan a fodder radish plant growing in a pot with test soil composed of homogenous sand. We constructed an air-plant-soil controller system (APS) to control the environmental conditions, such as CO₂, temperature and light during the experiment. The plant was allowed to assimilate ¹¹CO₂ for 90?min before PET scanning was initiated. We carried out PET scanning for 60?min. Subsequently, the aerial parts of the plant was cut off and the pot was rescanned using a micro-CT scanner to obtain more detailed information on structure of the root system and the growth medium structure.

Results

The acquired PET and CT images gave images clearly visualizing the architecture and morphology of root and soil. Using a CT scanner, we were able to detect the main taproot located at 0 to 30?mm depth. With the PET scanner, we were able to measure a signal down to 82?mm below the surface of the sand. We found the highest concentration of ¹¹C at the position of the main root. The PET images, at different time intervals, showed the translocation and metabolisation of photo-assimilates from top to root. Using the micro-CT scanner (voxel size of 90?μm), we were able to detect roots down to 100?mm depth. These findings correlated the PET signals measured down to 82?mm depth.

Conclusions

We conclude that the simultaneous use of PET and CT technologies was successfully applied for soil-plant studies. The combined PET/CT technology has potential to provide new fundamental insight into soil-plant interactions and especially into the effect of abiotic stresses in spite of the limitation due to spatial resolution.     

<Emphasis Type="Italic">NetMHCcons</Emphasis>: a consensus method for the major histocompatibility complex class I predictions

A key role in cell-mediated immunity is dedicated to the major histocompatibility complex (MHC) molecules that bind peptides for presentation on the cell surface. Several in silico methods capable of predicting peptide binding to MHC class I have been developed. The accuracy of these methods depends on the data available characterizing the binding specificity of the MHC molecules. It has, moreover, been demonstrated that consensus methods defined as combinations of two or more different methods led to improved prediction accuracy. This plethora of methods makes it very difficult for the non-expert user to choose the most suitable method for predicting binding to a given MHC molecule. In this study, we have therefore made an in-depth analysis of combinations of three state-of-the-art MHC–peptide binding prediction methods (NetMHC, NetMHCpan and PickPocket). We demonstrate that a simple combination of NetMHC and NetMHCpan gives the highest performance when the allele in question is included in the training and is characterized by at least 50 data points with at least ten binders. Otherwise, NetMHCpan is the best predictor. When an allele has not been characterized, the performance depends on the distance to the training data. NetMHCpan has the highest performance when close neighbours are present in the training set, while the combination of NetMHCpan and PickPocket outperforms either of the two methods for alleles with more remote neighbours. The final method, NetMHCcons, is publicly available at , and allows the user in an automatic manner to obtain the most accurate predictions for any given MHC molecule.     

Microarray expression analysis in delayed cardioprotection: the effect of exercise, AICAR, or metformin and the possible role of AMP-activated protein kinase (AMPK)

AMP-activated protein kinase (AMPK) is an enzyme which may be involved in cardioprotective mechanisms in the ischemic heart. Exercise, AICAR, and metformin, all known activators of AMPK, induce delayed cardioprotection which protects the heart against ischemia-reperfusion injury. The objective was to determine the effect of exercise, AICAR, and metformin on gene expression profile and to demonstrate possible interactions in different genes and functions. Rats were divided into either an exercise, AICAR, metformin, or control group. 3, 12, and 24 h after either a single bout of exercise training, a single injection of AICAR or a single dose of metformin, hearts were removed and gene expression profiles were analyzed in tissue from the left ventricle using Affymetrix gene chip probe arrays. Ingenuity Pathway Analysis (IPA) tool was used to analyze the regulated genes for relevant functions and diseases. Each gene chip identified up to 30,000 different probesets of which Ingenuity identified approximately up to 12,000 genes. A total of 147, 304, and 114 different genes in the left ventricle whose expressions were altered >2.0-fold were identified in the exercise, AICAR, and metformin group, respectively. Seventy eight different genes were overlapping the exercise and AICAR group at 24 h. Ingenuity identified six overlapping genes between the exercise, AICAR, and metformin groups including NR4A3, TNFRSF12A, HBB, PENK, PAP, and MAP4K4. IPA software revealed an overabundance of focus molecules in all three intervention groups involving functions related to cell death, cellular growth and proliferation, gene expression and cancer. Exercise, AICAR, and metformin regulate several genes in the rat myocardium with the majority of overlapping genes observed in the exercise and AICAR group. Changes in gene programming mainly involved inflammatory and opioid systems recognized as cardioprotective pathways. Some of these genes may represent possible candidate genes involved in the molecular mechanisms of AMPK-induced delayed PC.     

Lipids, curvature stress, and the action of lipid prodrugs: free fatty acids and lysolipid enhancement of drug transport across liposomal membranes

Molecular shape and its impact on bilayer curvature stress are powerful concepts for describing the effects of lipids and fatty acids on fundamental membrane properties, such as passive permeability and derived properties like drug transport across liposomal membranes. We illustrate these relationships by studying the effects of fatty acids and lysolipids on the permeation of a potent anti-cancer drug, doxorubicin, across the bilayer of a liposome in which the drug is encapsulated. Using a simple fluorescence assay, we have systematically studied the passive permeation of doxorubicin across liposomal membranes in different lipid phases: the solid-ordered phase (DPPC bilayers), the liquid-disordered phase (POPC lipid bilayers), and the liquid-ordered phase induced by high levels of cholesterol (DOPC + cholesterol lipid bilayers). The effect of different free fatty acids (FA) and lysolipids (LL), separately and in combination, on permeability was assessed to elucidate the possible mechanism of phospholipase A₂-triggered release in cancer tissue of liposomal doxorubicin formulations. In all cases, FAs applied separately lead to significant enhancement of permeability, most pronounced in liquid-disordered bilayers and less pronounced in solid and solid-ordered bilayers. LLs applied separately had only a marginal effect on permeability. FA and LL applied in combination lead to a synergistic enhancement of permeability in solid bilayers, whereas in liquid-disordered bilayers, the combined effect suppressed the otherwise strong permeability enhancement due to the FAs.