Estimation of nitrogen use efficiency for ryegrass-fed dairy cows: model development using diet and animal-based proxy measures

This study aimed to identify suitable predictors of nitrogen (N) use efficiency (NUE; milk N/N intake) for cows that differed in breeds and were fed with ryegrass pasture, using existing data from the scientific literature. Data from 16 studies were used to develop models based on the relationships between NUE and dietary and animal-based factors. Data from a further 10 studies were used for model validation. Milk urea N (MUN) and dietary water-soluble carbohydrate-to-crudeprotein ratio (WSC/CP) were the best and most practical animal- and diet-based proxies to predict NUE. The results indicate that it might be necessary to adopt separate models for different breeds when using WSC/CP to predict NUE but not when using MUN

Evaluation of Clustering and Genotype Distribution for Replication in Genome Wide Association Studies: The Age-Related Eye Disease Study

Genome-wide association studies (GWASs) assess correlation between traits and DNA sequence variation using large numbers of genetic variants such as single nucleotide polymorphisms (SNPs) distributed across the genome. A GWAS produces many trait-SNP associations with low p-values, but few are replicated in subsequent studies. We sought to determine if characteristics of the genomic loci associated with a trait could be used to identify initial associations with a higher chance of replication in a second cohort. Data from the age-related eye disease study (AREDS) of 100,000 SNPs on 395 subjects with and 198 without age-related macular degeneration (AMD) were employed. Loci highly associated with AMD were characterized based on the distribution of genotypes, level of significance, and clustering of adjacent SNPs also associated with AMD suggesting linkage disequilibrium or multiple effects. Forty nine loci were highly associated with AMD, including 3 loci (CFH, C2/BF, LOC387715/HTRA1) already known to contain important genetic risks for AMD. One additional locus (C3) reported during the course of this study was identified and replicated in an additional study group. Tag-SNPs and haplotypes for each locus were evaluated for association with AMD in additional cohorts to account for population differences between discovery and replication subjects, but no additional clearly significant associations were identified. Relying on a significant genotype tests using a log-additive model would have excluded 57% of the non-replicated and none of the replicated loci, while use of other SNP features and clustering might have missed true associations

Anisotropic Scaling in Threshold Critical Dynamics of Driven Directed Lines

The dynamical critical behavior of a single directed line driven in a random medium near the depinning threshold is studied both analytically (by renormalization group) and numerically, in the context of a Flux Line in a Type-II superconductor with a bulk current $\vec J$. In the absence of transverse fluctuations, the system reduces to recently studied models of interface depinning. In most cases, the presence of transverse fluctuations are found not to influence the critical exponents that describe longitudinal correlations. For a manifold with $d=4-\epsilon$ internal dimensions, longitudinal fluctuations in an isotropic medium are described by a roughness exponent $\zeta_\parallel=\epsilon/3$ to all orders in $\epsilon$, and a dynamical exponent $z_\parallel=2-2\epsilon/9+O(\epsilon^2)$. Transverse fluctuations have a distinct and smaller roughness exponent $\zeta_\perp=\zeta_\parallel-d/2$ for an isotropic medium. Furthermore, their relaxation is much slower, characterized by a dynamical exponent $z_\perp=z_\parallel+1/\nu$, where $\nu=1/(2-\zeta_\parallel)$ is the correlation length exponent. The predicted exponents agree well with numerical results for a flux line in three dimensions. As in the case of interface depinning models, anisotropy leads to additional universality classes. A nonzero Hall angle, which has no analogue in the interface models, also affects the critical behavior.Comment: 26 pages, 8 Postscript figures packed together with RevTeX 3.0 manuscript using uufiles, uses multicol.sty and epsf.sty, e-mail [email protected] in case of problem

Evolution of Robustness to Noise and Mutation in Gene Expression Dynamics

Phenotype of biological systems needs to be robust against mutation in order to sustain themselves between generations. On the other hand, phenotype of an individual also needs to be robust against fluctuations of both internal and external origins that are encountered during growth and development. Is there a relationship between these two types of robustness, one during a single generation and the other during evolution? Could stochasticity in gene expression have any relevance to the evolution of these robustness? Robustness can be defined by the sharpness of the distribution of phenotype; the variance of phenotype distribution due to genetic variation gives a measure of `genetic robustness' while that of isogenic individuals gives a measure of `developmental robustness'. Through simulations of a simple stochastic gene expression network that undergoes mutation and selection, we show that in order for the network to acquire both types of robustness, the phenotypic variance induced by mutations must be smaller than that observed in an isogenic population. As the latter originates from noise in gene expression, this signifies that the genetic robustness evolves only when the noise strength in gene expression is larger than some threshold. In such a case, the two variances decrease throughout the evolutionary time course, indicating increase in robustness. The results reveal how noise that cells encounter during growth and development shapes networks' robustness to stochasticity in gene expression, which in turn shapes networks' robustness to mutation. The condition for evolution of robustness as well as relationship between genetic and developmental robustness is derived through the variance of phenotypic fluctuations, which are measurable experimentally.Comment: 25 page

Estimation of nitrogen use efficiency for ryegrass-fed dairy cows: Model development using diet- and animal-based proxy measures

This study aimed to identify suitable predictors of nitrogen (N) use efficiency (NUE; milk N/N intake) for cows that differed in breeds and were fed with ryegrass pasture, using existing data from the scientific literature. Data from 16 studies were used to develop models based on the relationships between NUE and dietary and animal-based factors. Data from a further 10 studies were used for model validation. Milk urea N (MUN) and dietary water-soluble carbohydrate-to-crudeprotein ratio (WSC/CP) were the best and most practical animal- and diet-based proxies to predict NUE. The results indicate that it might be necessary to adopt separate models for different breeds when using WSC/CP to predict NUE but not when using MUN

Density of Common Complex Ocular Traits in the Aging Eye: Analysis of Secondary Traits in Genome-Wide Association Studies

Genetic association studies are identifying genetic risks for common complex ocular traits such as age-related macular degeneration (AMD). The subjects used for discovery of these loci have been largely from clinic-based, case-control studies. Typically, only the primary phenotype (e.g., AMD) being studied is systematically documented and other complex traits (e.g., affecting the eye) are largely ignored. The purpose of this study was to characterize these other or secondary complex ocular traits present in the cases and controls of clinic-based studies being used for genetic study of AMD. The records of 100 consecutive new patients (of any diagnosis) age 60 or older for which all traits affecting the eye had been recorded systematically were reviewed. The average patient had 3.5 distinct diagnoses. A subset of 10 complex traits was selected for further study because they were common and could be reliably diagnosed. The density of these 10 complex ocular traits increased by 0.017 log-traits/year (P = 0.03), ranging from a predicted 2.74 at age 60 to 4.45 at age 90. Trait-trait association was observed only between AMD and primary vitreomacular traction (P = 0.0009). Only 1% of subjects age 60 or older had no common complex traits affecting the eye. Extrapolations suggested that a study of 2000 similar subjects would have sufficient power to detect genetic association with an odds ratio of 2.0 or less for 4 of these 10 traits. In conclusion, the high prevalence of complex traits affecting the aging eye and the inherent biases in referral patterns leads to the potential for confounding by undocumented secondary traits within case-control studies. In addition to the primary trait, other common ocular phenotypes should be systematically documented in genetic association studies so that adjustments for potential trait-trait associations and other bias can be made and genetic risk variants identified in secondary analyses