Breeding Objectives Indicate Value of Genomics for Beef Cattle

Genomics may have much to offer in the implementation of breeding objectives. Advantages of genomic prediction include increased accuracy of expected progeny differences (EPDs) for traits that have been components of routine genetic evaluations. Perhaps more importantly, genomic prediction makes it possible to include traits that are too costly or too difficult to measure, and traits that are measured too late in life or are sex-limited such that candidates for selection cannot have EBV with high accuracy at the time when selection decisions are made. Genomically enhanced EPDs may also allow for a marked reduction in generation interval, thus accelerating the annual rate of genetic improvement. Here, the value of genomic prediction, on a trait-by-trait basis, is extended to explore the contribution of genomic prediction to selection for a multitrait breeding objective indicative of economic merit. A simple two-trait objective indicative of feed efficiency is illustrated first, followed by objectives for terminal and maternal strains of Angus

Doctor of Philosophy

dissertationCancer is extremely challenging to treat as every patient responds differently to treatments, depending on the specific molecular aberrations and deregulated signaling pathways driving their tumors. To address this heterogeneity and improve patient outcomes, therapies targeting specific pathways have been developed. The use of computational pathway analysis tools and genomic data can help guide the use of targeted therapies by assessing which pathways are deregulated in patient subpopulations and individual tumors. However, most pathway analysis tools do not account for complex interactions inherent to signaling pathways, and are not capable of integrating different types of genomic data (multiomic data). To address these limitations, this dissertation focuses on developing user-friendly multiomic gene set analysis tools, and utilizing bioinformatics tools to measure pathway activation for multiple pathways simultaneously in cancer. Chapter 2 first describes the need for genomics and pathway-based analyses in cancer using the commonly aberrant RAS pathway as an example. Chapter 3 utilizes pathway-based gene expression signatures and the pathway analysis toolkit ASSIGN to interrogate pathways from the growth factor receptor network (GFRN) in breast cancer. Two discrete phenotypes, which correlated with mechanisms of apoptosis and drug response, were characterized from GFRN activity. These phenotypes have the potential to pinpoint more effective breast cancer treatments. Chapter 4 describes the development of Gene Set Omic Analysis (GSOA), a novel gene set analysis tool which uses machine learning to identify pathway differences between two given biologicalconditions from multiomic data. GSOA demonstrated its capacity to identify pathways known to play a role in various cancers, and improves upon other methods because of its ability to decipher complex multigene and multiomic patterns. Chapter 5 describes GSOA-shiny, a novel web application for GSOA, which provides biologists with lack of bioinformatics experience access to multiomic gene set analysis from an easy-to-use interface. Overall, this dissertation presents novel breast cancer phenotypes with clinical implications, provides the research community with gene expression signatures for GFRN components, and presents an innovative method and web application for gene set analysisâ€"all contributing to furthering the field of personalized oncology

Understanding the Illness Experience of Veterans With Dementia

Not all individuals with dementia (IWDs) experience the progression of their illness similarly. Though recent work has given attention to how IWDs experience the cluster of symptoms in dementia, little work has been conducted with the unique population of veterans with dementia. Stressing the ability of IWDs to self-report and guided by the Stress Process Model for Individuals with Dementia, this study examined the relationships between depressive symptoms and various aspects of the illness experience including objective cognition, perceived memory difficulty, perceived functional difficulty, and dyadic relationship strain. The sample includes IWDs with mild to severe dementia who are veterans (N=69). Significant positive correlations emerged between depressive symptoms and several measures of the illness experience: perceived cognition (r=.48,

A long-term study (1949–2015) of the aftermaths of the deliberate experimental introduction of an invasive freshwater amphipod (Crustacea) to a small Island

The ability to track changing distributions and long-term inter actions between native and introduced species provides insights into forecasting impacts of invaders. We used data from deliberate field introduction experiments of a freshwater Gammarus amphipod (Crustacea) to the rivers of a small British island, The Isle of Man. The deliberate introductions commenced in 1949 and re-sampling occurred in the ‘60s, ‘70s ‘80s, ‘90s, 200 5 and finally in 2015. The findings generally confirmed the failure of introductions of Gammarus pulex into sites previously dominated by the native Gammarus duebeni celticus even with high propagule pressure in terms of numbers of individual invaders released and repeated introductions. Despite this, the island-wide 2015 survey revealed that G. d. celticus occurred in fewer sites and G. pulex in more sites than a decade earlier, indicating at this island-wide scale, the displacement of G. pulex by G. d. celticus seems to be continuing. In addition, one of the introduction sites, Arbory Stream which contained G. d. celticus from 1951–2005 contained only G. pulex in 2015, showing that even after six decades, assumptions cannot be made as to the limits of invader range expansion. Multivariate analysis of physico-chemical data from the 2015 island-wide sur vey revealed water quality as a crucial environmental gradient that influences the distributions of the native and invader species, with the former in higher organic water quality sites than sites with the invader or where invader and native co-occurred. The North American amp hipod Crangonyx pseudogracilis had expanded its range since 2005, including invading low biological water quality sites previously devoid of both Gammarus spp.. Pollution from historic metal mining is implicated as a potential major factor excluding amphipods. This deliberate ecological experiment, through long-term monitoring, continues to provide insights into the factors determining the distributions of natives and invaders

Responses to threat in a freshwater invader: Longitudinal data reveal personality, habituation and robustness to changing water temperatures in the ‘killer shrimp’ Dikerogammarus villosus (Crustacea: Amphipoda).

Freshwater biodiversity and ecosystem integrity are under threat from biological invasions. The ‘killer shrimp’ Dikerogammarus villosus is a highly predatory amphipod which has spread readily across Central Europe and recently the U.K. and its arrival has been associated with the significant loss of resident species. Despite this, studies of its behavioural ecology are sparse, even though its behaviour may contribute to its invasion success. For the first time we investigated anti-predator ‘fleeing’ behaviour in D. villosus and how this changed with water temperature. Three key patterns emerged from our analysis. First, within a particular temperature condition there are moderate but consistent among-individual differences in behaviour. These are driven by a combination of mean level among-individual differences and within-individual relative consistency in behaviour, and provide the key marker for animal personalities. Second, the fleeing responses were not influenced by temperature and thirdly, regardless of temperature, all individuals appeared to habituate to a repeated non-dangerous stimulus, indicating a capacity for individual-learning. We suggest that the anti-predator behaviour of D. villosus contributes to its rapid spread and that consistent among-individual differences in behaviour may promote biological invasions across heterogeneous conditions. Robustness to changing water temperatures may also be potentially advantageous, particularly in an era of global climate change, where average temperatures could be elevated and less predictabl

Breeding objectives for Angus and Charolais specialized sire lines for use in the emerging sector of South African beef production

Breeding indigenous cows to terminal sires may facilitate production of calves in the emerging sector that better meet commercial feedlot requirements. Thus, the objective of this research was to develop breeding objectives for Angus and Charolais terminal sires to be used in breeding Afrikaner, Bonsmara, and Nguni cows. An aggregated simulation model that is reliant on user inputs for the phenotypic characterization of the germplasm and economic characterization of the production environment was developed. Relative economic values were calculated by approximating partial derivatives of simulated profit with respect to economically relevant traits. Correlations among the breeding objectives calculated from simulations of Angus and Charolais bulls bred to Afrikaner, Bonsmara and Nguni cows were consistently > 0.9. Thus, an average index could be used for all six scenarios with little loss of selection efficiency. On average, relative emphasis given to breeding values for survival, direct weaning weight, postweaning daily gain, postweaning daily feed intake, dressing percent, and fat depth were 31.1, 31.0, 17.3, 1.4, 19.1, 0.2%, respectively. These breeding objectives may be viewed as an appropriate step in the evolution of multi-trait selection to facilitate poverty alleviation among cattle producers in the emerging sector through wealth creation resulting from their production of calves for industrial feeding. Keywords: Beef cattle, genetic evaluation, selection strategy, crossbreeding, cow-calf production system South African Journal of Animal Science Vol. 37 (1) 2007: pp. 1-1

Simulations of a lattice model of two-headed linear amphiphiles: influence of amphiphile asymmetry

Using a 2D lattice model, we conduct Monte Carlo simulations of micellar aggregation of linear-chain amphiphiles having two solvophilic head groups. In the context of this simple model, we quantify how the amphiphile architecture influences the critical micelle concentration (CMC), with a particular focus on the role of the asymmetry of the amphiphile structure. Accordingly, we study all possible arrangements of the head groups along amphiphile chains of fixed length $N=12$ and 16 molecular units. This set of idealized amphiphile architectures approximates many cases of symmetric and asymmetric gemini surfactants, double-headed surfactants and boloform surfactants. Consistent with earlier results, we find that the number of spacer units $s$ separating the heads has a significant influence on the CMC, with the CMC increasing with $s$ for $s<N/2$. In comparison, the influence of the asymmetry of the chain architecture on the CMC is much weaker, as is also found experimentally.Comment: 30 pages, 17 fgure

Signatures of Coronal Loop Opening via Interchange Reconnection in the Slow Solar Wind at 1 AU

The opening of closed magnetic loops via reconnection with open solar flux, so called “interchange reconnection”, is invoked in a number of models of slow solar wind release. In the heliosphere, this is expected to result in local switchbacks or inversions in heliospheric magnetic flux (HMF). When observed at 1 AU, inverted HMF has previously been shown to exhibit high ion charge states, suggestive of hot coronal loops, and to map to the locations of coronal magnetic separatrices. However, simulations show that inverted HMF produced directly by reconnection in the low corona is unlikely to survive to 1 AU without the amplification by solar wind speed shear. By considering the surrounding solar wind, we show that inverted HMF is preferably associated with regions of solar wind shear at 1 AU. Compared with the surrounding solar wind, inverted HMF intervals have lower magnetic field intensity and show intermediate speed and density values between the faster, more tenuous wind ahead and the slower, denser wind behind. There is no coherent signature in iron charge states, but oxygen and carbon charge states within the inverted HMF are in agreement with the higher values in the slow wind behind. Conversely, the iron-to-oxygen abundance ratio is in better agreement with the lower values in the solar wind ahead, while the alpha-to-proton abundance ratio shows no variation. One possible explanation for these observations is that the interchange reconnection (and subsequent solar wind shear) that is responsible for generation of inverted HMF involves very small, quiet-Sun loops of approximately photospheric composition, which are impulsively heated in the low corona, rather than large-scale active region loops with enhanced first-ionisation potential elements. Whether signatures of such small loops could be detected in situ at 1 AU still remains to be determined

Evaluation of Variation Attributable to Lab and Technician for Measurements of Beef Carcass Traits Made Using Ultrasound

National cattle genetic evaluations assume technician and imaging lab do not contribute to phenotypic variation when measuring carcass traits by ultrasound. The objective of this study was to estimate variance components of ultrasound carcass measurements, specifically variance contributed by ultrasound technician and imaging laboratory. Accounting for technician and imaging lab variation may increase accuracy of genetic predictions for carcass traits. Ultrasound carcass predictions for ribeye area (REA), percent intramuscular fat (IMF), and backfat (BF) were provided by the American Angus Association (AAA; n=281,982 animals), American Hereford Association (AHA; n=49,602), and American Simmental Association (ASA; n=59,576) for a total of 391,160 animals. Data provided by each association included ultrasound carcass measurements, contemporary group, technician ID, imaging lab, and a three-generation pedigree for each animal with ultrasound measurements. Variance contributed by additive genetics, technician, and contemporary group on ultrasound carcass measurements were estimated for each breed separately. Because technician and lab were confounded, the contribution of lab to ultrasound carcass variation could not be separated from technician. Therefore, we assessed whether lab contributed to ultrasound carcass variation by estimating genetic correlations between laboratories for ribeye area, percent intramuscular fat, and backfat. This analysis separated carcass traits by laboratory and treated measurements interpreted by each lab as a separate trait. Technician explained 12-27%, 4-23%, and 4-27% of variance for IMF, BF, and REA respectively across all three breeds. On average, the variance contributed by technician was greater than the variance contributed by additive genetics but less than that explained by contemporary group. Genetic correlations between labs across breeds ranged from 0.79 to 0.95 for IMF, 0.64 to 0.94 for BF and 0.78 to 0.98 for REA. Technician contributed to variance in ultrasound measurements, but high genetic correlations between labs suggest lab plays a lesser role in contribution of variance to ultrasound measurements