Bayesian Methods for Genomic Prediction and Genome-Wide Association Studies combining Information on Genotyped and Non-Genotyped Individuals

Genomic prediction involves using high-density marker genotypes to characterize the impact on performance of every region of the genome, and using that information to predict performance of genotyped selection candidates. This is a relatively new technology and is now gaining traction in personalized medicine and in various livestock industries. Our new approach promises to overcome serious limitations with existing techniques for genomic prediction

On the Optical Activity of Steroidal 5,7-Dienes

Circular dichroism (CD) data are reported of a series of 9,10- stereoisomeric steroidal 5,7-dienes. In general the effects in the longest wavelength transition (270-280 nm) are large (Mm" 10---30) and consignate with respect to the diene helicity rule. The magnitude of the CD appears to vary markedly with the substituent at C-3 and at C-17, and with solvent. In the case of the 9a,10p-H dienes, variation of solvent and temperature can affect even the sign of the Cotton effect. This is explained from a change of geometry of the diene ring: solvation, substitution and temperature can affect the average geometry of the ring including the values of the angle of twist of the diene (ef> (6-7». The relevance of the observed chiroptical data for the theoretical description of the optical activity in the So-+ Sl transition of homoannular cisoid dienes is discussed

'Unbearable suffering': a qualitative study on the perspectives of patients who request assistance in dying

BACKGROUND One of the objectives of medicine is to relieve patients' suffering. As a consequence, it is important to understand patients' perspectives of suffering and their ability to cope. However, there is poor insight into what determines their suffering and their ability to bear it. PURPOSE To explore the constituent elements of suffering of patients who explicitly request euthanasia or physician-assisted suicide (EAS) and to better understand unbearable suffering from the patients' perspective. PATIENTS AND METHODS A qualitative study using in-depth face-to-face interviews was conducted with 31 patients who had requested EAS. The grounded theory approach was used to analyse the data. RESULTS Medical, psycho-emotional, socio-environmental and existential themes contributed to suffering. Especially fatigue, pain, decline, negative feelings, loss of self, fear of future suffering, dependency, loss of autonomy, being worn out, being a burden, loneliness, loss of all that makes life worth living, hopelessness, pointlessness and being tired of living were constituent elements of unbearable suffering. Only patients with a psychiatric (co)diagnosis suffered unbearably all the time. CONCLUSIONS Unbearable suffering is the outcome of an intensive process that originates in the symptoms of illness and/or ageing. According to patients, hopelessness is an essential element of unbearable suffering. Medical and social elements may cause suffering, but especially when accompanied by psycho-emotional and existential problems suffering will become 'unbearable'. Personality characteristics and biographical aspects greatly influence the burden of suffering. Unbearable suffering can only be understood in the continuum of the patients' perspectives of the past, the present and expectations of the future.This study was supported by the Dutch Cancer Society (grant number KUN2007-03736)

Recognising and defining a new crown clade within Stromboidea Rafinesque, 1815 (Mollusca, Gastropoda)

This paper defines a new crown clade Neostromboidea to separate the Strombidae, Rostellariidae, and Seraphsidae from their sister families Struthiolariidae and Aporrhaidae. There is significant value to understanding evolutionary processes within Stromboidea to recognise the universal similarity in the position of the eye on the end of peduncles and a diminished cephalic tentacle that arises from the middle to the end on that peduncle. This is in contrast to other members of the Stromboidea where the eye is located at the base of the cephalic tentacle. These physiological differences represent two set of organisms with divergent and independent evolutionary life histories and therefore these differences need to be identifiable within the nomenclature to bring meaning to the way we name things

Improved Accuracy of Genomic Prediction for Traits with Rare QTL by Fitting Haplotypes

Genomic prediction estimates breeding values by exploiting linkage disequilibrium (LD) between quantitative trait loci (QTL) and single nucleotide polymorphisms (SNPs). High LD cannot occur when QTL and SNPs have different minor allele frequencies (MAF). Marker panels tend to use SNPs with high MAF and will have limited ability to predict rare QTL alleles. In practice, increasing SNP density has not improved prediction accuracy. A possible reason is that many traits are characterized by rare QTL. In that case, linear models fitting haplotypes could have advantage because haplotypes can be in complete LD with QTL alleles. SNP genotypes were simulated to resemble 600K chip for the bovine genome. Genomic breeding values were predicted using either SNP genotypes or non-overlapping haplotypes. When QTL had low MAF, the haplotype model had significantly higher accuracy than the SNP model. Results show that fitting haplotypes can improve the accuracy of genomic prediction for traits controlled by rare QTL

Genetic parameters and genomic regions associated with piglet response to vaccination for porcine reproductive and respiratory syndrome (PRRS) virus and co-infection with PRRS virus and porcine circovirus type 2b (PCV2b)

Citation: Dunkelberger, J. R., Serao, N. V. L., Kerrigan, M. A., Lunney, J. K., Rowland, R. R. R., & Dekkers, J. C. M. (2016). Genetic parameters and genomic regions associated with piglet response to vaccination for porcine reproductive and respiratory syndrome (PRRS) virus and co-infection with PRRS virus and porcine circovirus type 2b (PCV2b). Journal of Animal Science, 94, 52-53. doi:10.2527/msasas2016-112Objectives of this research were to estimate genetic parameters and to identify genomic regions associated with PRRS viral load (VL), PCV2b VL, and average daily gain (ADG) in nursery pigs vaccinated or non-vaccinated for PRRS virus (PRRSV), followed by co-infection with PRRSV and PCV2b. Data used included 396 commercial crossbred pigs from two PRRS Host Genetics Consortium trials, all from the same genetic supplier. Pigs were sent to Kansas State University after weaning and randomly sorted into two rooms. All pigs in one room were vaccinated for PRRS, and 28 d later, pigs in both rooms were co-infected with PRRSV and PCV2b, followed for 42 d, and genotyped using the 80K BeadChip. PRRS VL after vaccination and post co-infection and PCV2b VL were calculated as area under the curve of serum viremia from ?28 to 0, 0 to 21, and 0 to 42 d post co-infection, respectively. Genetic parameters were estimated by fitting multivariate animal models in ASReml4 with litter and pen (trial) as additional random effects. Trait-specific fixed effects of trial and weight and age at vaccination were also fitted. Genome-wide association (GWA) studies were performed by fitting SNPs as fixed effects one at a time in bivariate animal models for the non-vaccinated (Non-Vx) and vaccinated (Vx) groups for each trait. Heritability estimates following vaccination were 0.31, 0.07, and 0.10 for ADG Non-Vx, ADG Vx, and PRRS Vx, respectively. During the co-infection period, heritability estimates were slightly higher at 0.53, 0.57, 0.56, 0.20, 0.18, and 0.15 for ADG Non-Vx, ADG Vx, PRRS Non-Vx, PRRS Vx, PCV2b Non-Vx, and PCV2b Vx, respectively. Standard errors ranged from 0.14 to 0.22. A strong, positive genetic correlation (0.95 ± 1.01) was observed for PRRS VL post-vaccination with PRRS VL Non-Vx. Unique genomic regions were identified between Vx and Non-Vx pigs for each trait, the most significant of which was identified for PCV2b VL and located near the major histocompatibility complex, an important region for response to infection. The chromosome 4 region, which has been associated with VL following PRRSV-only infection, was associated with PRRS VL Non-Vx but not PRRS Vx or PRRS VL post-vaccination. Together, these results suggest that selection for improved performance under co-infection of PRRS and PCV2b is possible. Additionally, identification of unique genomic regions between Vx and Non-Vx pigs may enable selection of pigs with better response to vaccination. This research was supported by USDA-NIFA grants 2012–38420–19286 and 2013–68004–20362

Improved nutrient digestibility and retention partially explains feed efficiency gains in pigs selected for low residual feed intake

Residual feed intake (RFI) is a unique measure of feed efficiency (FE) and an alternative to traditional measures. The RFI is defined as the difference between the actual feed intake of a pig and its expected feed intake based on a given amount of growth and backfat. Therefore, selecting pigs with a low RFI (LRFI) results in a more feed-efficient animal for a given rate of growth. Our objective was to determine the extent to which apparent total tract digestibility of nutrients and energy use and retention may explain FE differences between pigs divergently selected for LRFI or high RFI (HRFI). After 7 generations of selection, 12 HRFI and 12 LRFI pigs (62 ± 3 kg BW) were randomly assigned to metabolism crates. Pigs had free access to a standard diet based on corn (Zea mays) and soybean (Glycine max) meal containing 0.4% TiO2, an exogenous digestibility marker. After a 7-d acclimation, total urine and feces were collected for 72 h. Nutrient and energy digestibility, P digestibility, and N balance were then measured and calculated to determine differences between the RFI lines. As expected, ADFI was lower (2.0 vs. 2.6 kg; P \u3c 0.01), ADG did not differ, and FE was higher in the LRFI (P \u3c 0.001) compared to the HRFI pigs. The digestibility values for DM (87.3 vs. 85.9%), N (88.3 vs. 86.1%), and GE (86.9 vs. 85.4%) were higher (P ≤ 0.003) in the LRFI vs. HRFI pigs, respectively. The DE (16.59 vs. 16.32 MJ/kg DM) and ME (15.98 vs. 15.72 MJ/kg DM) values were also greater (P \u3c 0.001) in LRFI pigs. When correcting for ADFI, P digestibility did not differ between the lines. However, the LRFI pigs tended to have improved N retention (P = 0.08) compared to HRFI pigs (36.9 vs. 32.1 g/d). In conclusion, the higher energy and nutrient digestibility, use, and retention may partially explain the superior FE seen in pigs selected for LRFI