Browsing by Author "Pleasants T"

Now showing 1 - 5 of 5
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    Assessing the genetic variation of tolerance to red needle cast in a Pinus radiata breeding population
    (Springer-Verlag GmbH Germany, part of Springer Nature, 2018-06-27) Graham NJ; Suontama M; Pleasants T; Li Y; Bader MKF; Klápště J; Dungey HS; Williams NM
    Breeding for disease resistance or tolerance is a viable option for disease management programmes and is important for the continued success and resilience of planted forests. Red needle cast (RNC) is a disease that affects radiata pine (Pinus radiata) and is caused by Phytophthora pluvialis. Knowledge is still very limited regarding the potential for genetic tolerance to this pathogen. The application of controlled screening techniques is clearly required. Using a detached needle assay, we screened 392 clonally replicated individuals (clones) from an elite P. radiata population for quantitative tolerance to RNC. Data was highly skewed and required logarithmic data transformation and Poisson distributions for the estimation of best linear unbiased predictions. These estimates revealed a broad range in susceptibility/tolerance to RNC, and enabled the identification of clones that were clearly susceptible and clones that were clearly tolerant. There was a high correlation between the number and length of lesions that developed in response to inoculation with P. pluvialis. Broad-sense heritability estimates were low to moderate, indicating that there is potential for improving tolerance through breeding. These results provide evidence that breeding for tolerance to P. pluvialis is possible, although continued work into understanding and minimising causes for variance are required.
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    Linear models with perturbed and truncated Laplace response functions: The asymptotic theory of MLE with application to epigenetics
    (Hindawi Publishing Corporation, 20/11/2012) Hassell-Sweatman CZW; Wake GC; Pleasants T; McLean CA; Sheppard AM
    The statistical application considered here arose in epigenomics, linking the DNA methylation proportions measured at specific genomic sites to characteristics such as phenotype or birth order. It was found that the distribution of errors in the proportions of chemical modification (methylation) on DNA, measured at CpG sites, may be successfully modelled by a Laplace distribution which is perturbed by a Hermite polynomial. We use a linear model with such a response function. Hence, the response function is known, or assumed well estimated, but fails to be differentiable in the classical sense due to the modulus function. Our problem was to estimate coefficients for the linear model and the corresponding covariance matrix and to compare models with varying numbers of coefficients. The linear model coefficients may be found using the (derivative-free) simplex method, as in quantile regression. However, this theory does not yield a simple expression for the covariance matrix of the coefficients of the linear model. Assuming response functions which are 2 except where the modulus function attains zero, we derive simple formulae for the covariance matrix and a log-likelihood ratio statistic, using generalized calculus. These original formulae enable a generalized analysis of variance and further model comparisons.
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    Mitochondrial oxidative capacity and NAD+ biosynthesis are reduced in human sarcopenia across ethnicities
    (Springer Nature Limited, 2019-12-20) Migliavacca E; Tay SKH; Patel HP; Sonntag T; Civiletto G; McFarlane C; Forrester T; Barton SJ; Leow MK; Antoun E; Charpagne A; Seng Chong Y; Descombes P; Feng L; Francis-Emmanuel P; Garratt ES; Giner MP; Green CO; Karaz S; Kothandaraman N; Marquis J; Metairon S; Moco S; Nelson G; Ngo S; Pleasants T; Raymond F; Sayer AA; Ming Sim C; Slater-Jefferies J; Syddall HE; Fang Tan P; Titcombe P; Vaz C; Westbury LD; Wong G; Yonghui W; Cooper C; Sheppard A; Godfrey KM; Lillycrop KA; Karnani N; Feige JN
    The causes of impaired skeletal muscle mass and strength during aging are well-studied in healthy populations. Less is known on pathological age-related muscle wasting and weakness termed sarcopenia, which directly impacts physical autonomy and survival. Here, we compare genome-wide transcriptional changes of sarcopenia versus age-matched controls in muscle biopsies from 119 older men from Singapore, Hertfordshire UK and Jamaica. Individuals with sarcopenia reproducibly demonstrate a prominent transcriptional signature of mitochondrial bioenergetic dysfunction in skeletal muscle, with low PGC-1α/ERRα signalling, and downregulation of oxidative phosphorylation and mitochondrial proteostasis genes. These changes translate functionally into fewer mitochondria, reduced mitochondrial respiratory complex expression and activity, and low NAD+ levels through perturbed NAD+ biosynthesis and salvage in sarcopenic muscle. We provide an integrated molecular profile of human sarcopenia across ethnicities, demonstrating a fundamental role of altered mitochondrial metabolism in the pathological loss of skeletal muscle mass and function in older people.
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    Population growth as a nonlinear process
    (1/12/2003) Soboleva TK; Pleasants T
    The evolution of the probability density of a biological population is described using nonlinear stochastic differential equations for the growth process and the related Fokker-Planck equations for the time-dependent probability densities. It is shown that the effect of the initial conditions disappears rapidly from the evolution of the mean of the process. But the behaviour of the variance depends on the initial condition. It may monotonically increase, reaching its maximum in the steady state, or have a rather complicated evolution reaching the maximum near the point where growth rates (not population size) is maximal. The variance then decreases to its steady-state value. This observation has implications for risk assessments associated with growing populations, such as microbial populations, which cause food poisoning if the population size reaches a critical level.
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    Pre- and Postnatal Nutritional Histories Influence Reproductive Maturation and Ovarian Function in the Rat
    (Public Library of Science, 25/08/2009) Sloboda DM; Howie GJ; Pleasants T; Gluckman PD; Vickers MH
    While prepubertal nutritional influences appear to play a role in sexual maturation, there is a need to clarify the potential contributions of maternal and childhood influences in setting the tempo of reproductive maturation. In the present study we employed an established model of nutritional programming to evaluate the relative influences of prenatal and postnatal nutrition on growth and ovarian function in female offspring.