Accuracies of genomic breeding values in American Angus beef cattle using K-means clustering for cross-validation

Background

Genomic selection is a recently developed technology that is beginning to revolutionize animal breeding. The objective of this study was to estimate marker effects to derive prediction equations for direct genomic values for 16 routinely recorded traits of American Angus beef cattle and quantify corresponding accuracies of prediction.

Methods

Deregressed estimated breeding values were used as observations in a weighted analysis to derive direct genomic values for 3570 sires genotyped using the Illumina BovineSNP50 BeadChip. These bulls were clustered into five groups using K-means clustering on pedigree estimates of additive genetic relationships between animals, with the aim of increasing within-group and decreasing between-group relationships. All five combinations of four groups were used for model training, with cross-validation performed in the group not used in training. Bivariate animal models were used for each trait to estimate the genetic correlation between deregressed estimated breeding values and direct genomic values.

Results

Accuracies of direct genomic values ranged from 0.22 to 0.69 for the studied traits, with an average of 0.44. Predictions were more accurate when animals within the validation group were more closely related to animals in the training set. When training and validation sets were formed by random allocation, the accuracies of direct genomic values ranged from 0.38 to 0.85, with an average of 0.65, reflecting the greater relationship between animals in training and validation. The accuracies of direct genomic values obtained from training on older animals and validating in younger animals were intermediate to the accuracies obtained from K-means clustering and random clustering for most traits. The genetic correlation between deregressed estimated breeding values and direct genomic values ranged from 0.15 to 0.80 for the traits studied.

Conclusions

These results suggest that genomic estimates of genetic merit can be produced in beef cattle at a young age but the recurrent inclusion of genotyped sires in retraining analyses will be necessary to routinely produce for the industry the direct genomic values with the highest accuracy.     

Total cost estimation for implementing genome-enabled selection in a multi-level swine production system

Background

Determining an animal’s genetic merit using genomic information can improve estimated breeding value (EBV) accuracy; however, the magnitude of the accuracy improvement must be large enough to recover the costs associated with implementing genome-enabled selection. One way to reduce costs is to genotype nucleus herd selection candidates using a low-density chip and to use high-density chip genotyping for animals that are used as parents in the nucleus breeding herd. The objective of this study was to develop a tool to estimate the cost structure associated with incorporating genome-enabled selection into multi-level commercial breeding programs.

Results

For the purpose of this deterministic study, it was assumed that a commercial pig is created from a terminal line sire and a dam that is a cross between two maternal lines. It was also assumed that all male and female selection candidates from the 1000 sow maternal line nucleus herds were genotyped at low density and all animals used for breeding at high density. With the assumptions used in this analysis, it was estimated that genome-enabled selection costs for a maternal line would be approximately US$0.082 per weaned pig in the commercial production system. A total of US$0.164 per weaned pig is needed to incorporate genome-enabled selection into the two maternal lines. Similarly, for a 600 sow terminal line nucleus herd and genotyping only male selection candidates with the low-density panel, the cost per weaned pig in the commercial herd was estimated to be US$0.044. This means that US$0.21 per weaned pig produced at the commercial level and sired by boars obtained from the nucleus herd breeding program needs to be added to the genetic merit value in order to break even on the additional cost required when genome-enabled selection is used in both maternal lines and the terminal line.

Conclusions

By modifying the input values, such as herd size and genotyping strategy, a flexible spreadsheet tool developed from this work can be used to estimate the additional costs associated with genome-enabled selection. This tool will aid breeders in estimating the economic viability of incorporating genome-enabled selection into their specific breeding program.     

Multidisciplinary transmural rehabilitation for older persons with a stroke: the design of a randomised controlled trial

Background

Stroke is one of the major causes of loss of independence, decreased quality of life and mortality among elderly people. About half of the elderly stroke patients discharged after rehabilitation in a nursing home still experience serious impairments in daily functioning one year post stroke, which can lead to difficulties in picking up and managing their social life. The aim of this study is to evaluate the effectiveness and feasibility of a new multidisciplinary transmural rehabilitation programme for older stroke patients.

Methods

A two group multicentre randomised controlled trial is used to evaluate the effects of the rehabilitation programme. The programme consists of three care modules: 1) neurorehabilitation treatment for elderly stroke patients; 2) empowerment training for patient and informal caregiver; and 3) stroke education for patient and informal caregiver. The total programme has a duration of between two and six months, depending on the individual problems of the patient and informal caregiver. The control group receives usual care in the nursing home and after discharge.Patients aged 65 years and over are eligible for study participation when they are admitted to a geriatric rehabilitation unit in a nursing home due to a recent stroke and are expected to be able to return to their original home environment after discharge. Data are gathered by face-to-face interviews, self-administered questionnaires, focus groups and registration forms. Primary outcomes for patients are activity level after stroke, functional dependence, perceived quality of life and social participation. Outcomes for informal caregivers are perceived care burden, objective care burden, quality of life and perceived health. Outcome measures of the process evaluation are implementation fidelity, programme deliverance and the opinion of the stroke professionals, patients and informal caregivers about the programme. Outcome measures of the economic evaluation are the healthcare utilisation and associated costs. Data are collected at baseline, and after six and 12 months. The first results of the study will be expected in 2014.

Trial registration

International Standard Randomised Controlled Trial Register Number ISRCTN62286281, The Dutch Trial Register NTR2412

     

Free fatty acid production in Escherichia coli under phosphate-limited conditions

Microbially synthesized fatty acids are an attractive platform for producing renewable alternatives to petrochemically derived transportation fuels and oleochemicals. Free fatty acids (FFA) are a direct precursor to many high-value compounds that can be made via biochemical and ex vivo catalytic pathways. To be competitive with current petrochemicals, flux through these pathways must be optimized to approach theoretical yields. Using a plasmid-free, FFA-producing strain of Escherichia coli, a set of chemostat experiments were conducted to gather data for FFA production under phosphate limitation. A prior study focused on carbon-limited conditions strongly implicated non-carbon limitations as a preferred media formulation for maximizing FFA yield. Here, additional data were collected to expand an established kinetic model of FFA production and identify targets for further metabolic engineering. The updated model was able to successfully predict the strain’s behavior and FFA production in a batch culture. The highest yield observed under phosphate-limiting conditions (0.1 g FFA/g glucose) was obtained at a dilution rate of 0.1 h^?1, and the highest biomass-specific productivity (0.068 g FFA/gDCW/h) was observed at a dilution rate of 0.25 h^?1. Phosphate limitation increased yield (～45 %) and biomass-specific productivity (～300 %) relative to carbon-limited cultivations using the same strain. FFA production under phosphate limitation also led to a cellular maintenance energy ～400 % higher (0.28 g/gDCW/h) than that seen under carbon limitation.     

Metastasis of bronchogenic carcinoma to the thumb

Bone metastasis in the hand is rare. The etiology is quite different from that of metastasis to other bones; bronchogenic carcinoma is by far the most frequent case. Distal phalanges are mainly involved with irregular osteolysis and cortical destruction. Differential diagnosis of phalangeal metastasis includes osteomyelitis, rheumatoid arthritis and gout. The prognosis is always that of metastatic bronchial cancer with an average survival of three months. Treatment may involve distal digital amputation or antalgic radiotherapy. A case of bronchogenic carcinoma with metastasis to the thumb is presented. The metastasis was located in the distal phalanx of the left thumb. The primary tumor was located in the lung. Treatment consisted of amputation. The overall survival was five months.     

The multiple sex chromosomes of platypus and echidna are not completely identical and several share homology with the avian Z

Background

Sex-determining systems have evolved independently in vertebrates. Placental mammals and marsupials have an XY system, birds have a ZW system. Reptiles and amphibians have different systems, including temperature-dependent sex determination, and XY and ZW systems that differ in origin from birds and placental mammals. Monotremes diverged early in mammalian evolution, just after the mammalian clade diverged from the sauropsid clade. Our previous studies showed that male platypus has five X and five Y chromosomes, no SRY, and DMRT1 on an X chromosome. In order to investigate monotreme sex chromosome evolution, we performed a comparative study of platypus and echidna by chromosome painting and comparative gene mapping.

Results

Chromosome painting reveals a meiotic chain of nine sex chromosomes in the male echidna and establishes their order in the chain. Two of those differ from those in the platypus, three of the platypus sex chromosomes differ from those of the echidna and the order of several chromosomes is rearranged. Comparative gene mapping shows that, in addition to bird autosome regions, regions of bird Z chromosomes are homologous to regions in four platypus X chromosomes, that is, X₁, X₂, X₃, X₅, and in chromosome Y₁.

Conclusion

Monotreme sex chromosomes are easiest to explain on the hypothesis that autosomes were added sequentially to the translocation chain, with the final additions after platypus and echidna divergence. Genome sequencing and contig anchoring show no homology yet between platypus and therian Xs; thus, monotremes have a unique XY sex chromosome system that shares some homology with the avian Z.     

Genomic selection of purebred animals for crossbred performance in the presence of dominant gene action

Background

Genomic selection is an appealing method to select purebreds for crossbred performance. In the case of crossbred records, single nucleotide polymorphism (SNP) effects can be estimated using an additive model or a breed-specific allele model. In most studies, additive gene action is assumed. However, dominance is the likely genetic basis of heterosis. Advantages of incorporating dominance in genomic selection were investigated in a two-way crossbreeding program for a trait with different magnitudes of dominance. Training was carried out only once in the simulation.

Results

When the dominance variance and heterosis were large and overdominance was present, a dominance model including both additive and dominance SNP effects gave substantially greater cumulative response to selection than the additive model. Extra response was the result of an increase in heterosis but at a cost of reduced purebred performance. When the dominance variance and heterosis were realistic but with overdominance, the advantage of the dominance model decreased but was still significant. When overdominance was absent, the dominance model was slightly favored over the additive model, but the difference in response between the models increased as the number of quantitative trait loci increased. This reveals the importance of exploiting dominance even in the absence of overdominance. When there was no dominance, response to selection for the dominance model was as high as for the additive model, indicating robustness of the dominance model. The breed-specific allele model was inferior to the dominance model in all cases and to the additive model except when the dominance variance and heterosis were large and with overdominance. However, the advantage of the dominance model over the breed-specific allele model may decrease as differences in linkage disequilibrium between the breeds increase. Retraining is expected to reduce the advantage of the dominance model over the alternatives, because in general, the advantage becomes important only after five or six generations post-training.

Conclusion

Under dominance and without retraining, genomic selection based on the dominance model is superior to the additive model and the breed-specific allele model to maximize crossbred performance through purebred selection.     

Structure of human high density lipoprotein reassembled in vitro. Radioimmunoassay studies.

Immunologic approaches to studying lipoprotein structure have been limited because the methods have not been quantitative enough. Recently we reported (Schonfeld, G., and Pfleger, B. (1974) J. Clin. Invest. 54, 236-246) a radioimmunoassay for human apoprotein A-1 (ApoA-I). Only 8% of the ApoA-I of high density lipoprotein (HDL) reacted in the radioimmunoassay system consisting of rabbit anti-human ApoA-I, 125I-ApoA-I, and unlabeled ApoA-I. We suggested that the ApoA-I in HDL were poorly reactive in the radioimmunoassay because they were "masked" by lipid- or protein-protein interactions. To test this, "lipoproteins" were reconstituted from lipids and apoproteins and assayed for their reactivity in the radioimmunoassay. Apo-HDL, ApoA-I alone, or ApoA-I + ApoA-II were sonified with lecithin or with lipids extracted from HDL. Sonicates were fractionated by ultracentrifugation or by Sepharose 4B chromatography. HDLs were also made by incubating dispersed lecithin or lecithin + cholesterol with Apo-HDL, ApoA-I, or ApoA-II. The lipoproteins were analyzed for lipids and protein chemically. Apoprotein compositions were determined by polyacrylamide disc gel electrophoresis. ApoA-I content by radioimmunoassay then was compared with the ApoA-I content obtained by disc gel electrophoresis. Most reconstituted "lipoproteins" had less than the expected ApoA-I contents. Discrepancies between ApoA-I contents were greatest for lipoproteins prepared from Apo-HDL and HDL-lipids (20 to 30% of expected contents). Discrepancies were smaller for particles prepared with lecithin, with ApoA-I alone or with ApoA-I + ApoA-II (40 to 85% of expected). HDLs made by incubation were less reactive than those prepared by sonication. Thus, the reactivity of ApoA-I in the radioimmunoassay could be diminished by causing it to interact with lipids or their apoproteins, or both, suggesting that antigenic sites became masked. From this one can extrapolate that the poor reactivity of the ApoA-I in HDL isolated from plasma also may have been due to the masking of some of its antigenic determinants. The identification of the determinants involved awaits the development of radioimmunoassays for specific regions of ApoA-I.     

Can Nep1-like proteins form oligomers?

Nep1-like proteins (NLPs) are a novel family of microbial elicitors of plant necrosis that induce a hypersensitive-like response in dicot plants. The spatial structure and role of these proteins are yet unknown. In a paper published in BMC Plant Biology (2008; 8:50) we have proposed that the core region of Nep1-like proteins (NLPs) belong to the Cupin superfamily. Based on what is known about the Cupin superfamily, in this addendum to the paper we discuss how NLPs could form oligomers.Key words: quaternary structure, necrosis and ethylene inducing proteins, NLPs, MpNEP1, MpNEP2, NPP1, Moniliophthora perniciosa, Phytophthora parasiticaCupins may be organized as monomers, dimers, hexamers and octamers of β-barrel domains.¹ To the best of our knowledge trimers have not been detected yet. The interaction of two monomers building up a dimeric structure is basically performed by three types of interactions: hydrophobic interactions between β-strands in different subunits, salt bridges and hydrogen bonds between β-strands. In cupin dimers, the hydrophobic interactions occur between two βI strands in different subunits (Fig. 1A and B). This strand represents the central axis of rotation of the dimer as one residue in βI interacts with the corresponding residue in the other subunit (Fig. 1B). Therefore, all residues in βI must be hydrophobic, as one residue interacts with the other subunit and the next one in the sequence interacts with the interior of the protein. Charged residues in βI would disrupt such interactions. Most cupin dimers have strong hydrophobic residues such as tryptophan (W), phenylalanine (F) and methionine (M) pointing towards the own subunit (↓), while small hydrophobic residues such as leucine (L), isoleucine (I), and valine (V) point to the other subunit (↑). A particular case is leucine that interacts with other subunits, for instance, βI = liaW (positions 217–220 in Fig. 1B) and βI = LVsw of type I and II NLP consensuses, respectively. Therefore, the pattern of hydropathicity suggests that the side chain orientation is βI = l217 ↑ i218 ↓ a219 ↑ W220 ↓ d221 ↑. However we observe that just after βI there is a charged residue (aspartate D221) which would point outwards disrupting the dimer or at least making it less stable. It is interesting to observe that the requirement for a negatively charged residue at this last position is very high: 96% of all type I NLPs contains an aspartate (D) or glutamate (E) indicating an important role for it, maybe in avoiding dimerization of the NLPs. A second interesting hypothesis is as follows: several cupins are oxygenases, decarboxylases, etc. and use a negatively charged residue, such as aspartate or glutamate as proton donor.¹ Now, if the alternate pattern of side chains of the residues is βI = l217 ↓ i218 ↑ a219 ↓ W220 ↑ d221 ↓, instead of the previous one, then the aspartate or glutamate residue would point to the hydrophobic pocket and would be positioned to interact with the metal ion, as in cupins with enzymatic activity. However, there are no experimental evidences that the NLPs have enzymatic activity.Open in a separate windowFigure 1(A) Three-dimensional structure prediction for type I NLP consensus, (B) Interface between two βI strands in type I NLP consensus. From the left to the right: EF-coil with the conserved residue H162, βC and βH strands (superposed) with the conserved histidines H133 and H135 in βC, H193 and leucine L195 in βH, W220 in βI and W118 in βB. The strands in the right subunit follow the same pattern but rotated.The second type of interaction is salt bridges between charged residues in different subunits. Analyzing all interacting side chains in the 1VJ2 protein (dimer), we verify that the charged side chains of N35 and E57 (numbers in original structure) are only 2.72 Å apart. In the NLPs, this corresponds to N108^36% (Q108^60%) at the border of βB and E138^98%. The negatively charged residue D125 helps to correct the orientation of the subunits in relation to each other avoiding any disorientation. The high conservation level of these residues suggests that NLPs are dimeric structures. However, as we will see next, only hydrophobic and charged interactions are not enough to build a dimer.Garcia et al. (2007)² have used small angle X-ray scattering (SAXS) to show that, in solution, at low concentrations (<2 mg/ml) the two copies of the NLPs of Moniliophthora perniciosa, MpNEP1 and MpNEP2, exist as dimers and monomers, respectively. The same technique showed that at higher concentrations, >5 mg/ml, both proteins exist as dimers, as is the case for PpNPP1.² They also reported, based on electrophoresis analysis, that PpNPP1 and MpNEP1 exist as oligomers and MpNEP2 as monomers.² However, experiments with the PpNPP1 in size exclusion chromatography using myoglobin as size standard suggest that PpNPP1 is a monomer.³ Figure 2 compares MpNEP1, MpNEP2 and PpNPP1, where the most relevant differences in sequence are marked with asterisks (*) and are possibly related to the differences in oligomeric properties between MpNEP1 and PpNPP1 with MpNEP2. These positions are methionine M27 and leucine L35, which occur only in MpNEP2, glycine G250, which occurs only in MpNEP2 and NEP1 (Fusarium oxysporum) and lysine K31, which occurs only MpNEP2, {"type":"entrez-protein","attrs":{"text":"BAB04114","term_id":"10173008"}}BAB04114 (Bacillus halodurans) and {"type":"entrez-protein","attrs":{"text":"AAU23136","term_id":"52003194"}}AAU23136 (Bacillus licheniformis). The other residues are aspartate D28, which occurs 9 times and alanine A37 which occurs 7 times of all investigated NLPs. Thus, the sequence mdHDkiakl at the start of the NLPs seems to explain the monomeric state of MpNEP2, although at higher concentrations they form dimers. Besides the weak hydrophobic interactions, dimeric cupins and bicupins (two β barrels in the same sequence building up a dimeric-like 4d-structure) are stable structures (see Fig. 1 in ref. ⁴). By aggregating the first β-strand in the start domain of one β-barrel to the ABIDG β-sheet of the other β-barrel, composing a big ABIDGY β-sheet (Y is the first β-strand). For instance, using the bicupin 1L3J (oxalate decarboxylase) as template, the low confidence level β-strand at position 26–33 (v in H29D30 avv) in type I NLPs corresponds to the first β-strand. Since this proceeds from both barrels they can build a stable structure (see Fig. 1 in ref. ⁴). The quaternary structure is related to the presence of interaction residues in the BID β-sheet of the cupin structure. These are present in the NLPs and would enable them to form dimers.Open in a separate windowFigure 2Alignment of type I NLP consensus, PpNPP1, MpNEP1 and MpNEP2. Solid line boxes are β-strands, double line boxes are α-helices. The sequence positions marked with asterisks (*) are possibly related to the differences in oligomeric properties between MpNEP1 and PpNPP1 with MpNEP2.