Search

A number of transcriptome datasets for differential expression (DE) genes have been widely used for understanding organismal biology, but these datasets also contain untapped information that can be used to develop more precise analytical tools. With the use of transcriptome data generated from poplar/canker disease interaction system, we describe a methodology to identify candidate reference genes from high-throughput sequencing data. This methodology will improve the accuracy of RT-qPCR and will lead to better standards for the normalization of expression data. Expression stability analysis from xylem and phloem of Populus bejingensis inoculated with the fungal canker pathogen Botryosphaeria dothidea revealed that 729 poplar transcripts (1.11%) were stably expressed, at a threshold level of coefficient of variance (CV) of FPKM < 20% and maximum fold change (MFC) of FPKM < 2.0. Expression stability and bioinformatics analysis suggested that commonly used house-keeping (HK) genes were not the most appropriate internal controls: 70 of the 72 commonly used HK genes were not stably expressed, 45 of the 72 produced multiple isoform transcripts, and some of their reported primers produced unspecific amplicons in PCR amplification. RT-qPCR analysis to compare and evaluate the expression stability of 10 commonly used poplar HK genes and 20 of the 729 newly-identified stably expressed transcripts showed that some of the newly-identified genes (such as SSU_S8e, LSU_L5e, and 20S_PSU) had higher stability ranking than most of commonly used HK genes. Based on these results, we recommend a pipeline for deriving reference genes from transcriptome data. An appropriate candidate gene should have a unique transcript, constitutive expression, CV value of expression < 20% (or possibly 30%) and MFC value of expression

Abstract: The relation between branch growth characteristics and initial plantation spacing were observed in young Douglas-fir (Pseudotsuga menziesii [Mirb.] Franco var. menziesii). Trees were sampled from Nelder plots ranging in initial density from 309 to 18,730trees/ha and grown in either 1:2 or 1:1 rectangular spacing geometry. Data were derived using 3919 branches from 56 trees, 19 and 21years old, at two sites in western Oregon. Branch diameters in the lower basal log and lower crown were measured outside bark, as well as number of years of radial and terminal growth of branches. Mean and maximum nodal branch diameter increased with decreasing initial tree density, as in previous studies. Within operational planting densities, 469trees/ha (4.6×4.6m) to 1682trees/ha (2.4×2.4m), mean branch diameter outside bark for the basal 5-m log ranged from 28 down to 16mm and maximum branch diameter outside bark ranged from 36 down to 22mm. Rectangularity of space had no effect on branch diameter. The number of nodal branches/m, living and dead, as well as years of radial and terminal branch growth increased with decreasing initial tree density, resulting in larger and more persistent branches. The number of years that lower branches remained alive without radial branch growth ranged from 0 to 8years, but averaged about 1year. Branch diameter was highly correlated with initial tree densities, allowing managers opportunities to improve wood quality through density management in young Douglas-fir plantations. [Copyright &y& Elsevier]

We studied heartwood and sapwood variation in western redcedar (Thuja plicata) at three sites, including a 95-year-old naturally regenerated, unmanaged stand, a 35-year-old planted spacing trial, and a 30-year-old naturally regenerated stand to which thinning and fertilization treatments had been applied. In the 95-year-old stand, we studied within-tree variation in heartwood and sapwood. In the thinning/fertilization trial and the planted spacing trial, we studied effects of cultural practices and growth rate on heartwood and sapwood. In the trees that we studied, sapwood width was generally fairly narrow, rarely exceeding 3.5cm. Heartwood formation in western redcedar appeared to begin at a relatively small stem diameter (7cm) and at a young age, probably 10–15 years. The amount and proportion of heartwood increased with distance downward from the top of the tree, with the implication that older trees will contain a greater proportion of heartwood than younger trees. For any given age, it appears that cultural treatments that favor rapid growth will result in stems with greater amounts of both sapwood and heartwood, and a greater proportion of heartwood. [Copyright &y& Elsevier]

To assess the relationships among pressure ulcer prevalence, body mass index (BMI), and weight, this report analyzed the US data from the 2006 and 2007 International Pressure Ulcer Prevalence Surveys. Findings indicated an overall reduction in pressure ulcer prevalence from 2004 and 2005 to 2006 and 2007; there was a higher prevalence of pressure ulcers in patients with low BMI and patients with both low and high weights. One in 10 patients were extremely obese. [ABSTRACT FROM AUTHOR]

Abstract: Cellulose is usually isolated from the other components of plant material for analysis of carbon stable isotope ratios (δ 13C). However, many studies have shown a strong correlation between whole-wood and cellulose δ 13C values, prompting debate about the necessity of cellulose extraction for tree-ring studies. The δ 13C values were measured in whole wood, extractive-free wood, purified cellulose, acetone/water-soluble extractives and hot water-soluble extractives of Douglas-fir sapwood. Cellulose and acetone/water-soluble extractives from heartwood from the same trees also were compared. Although the various materials showed different absolute δ 13C values, the components of the same samples, including the extractives, were correlated. The correlations of carbon isotope ratios of cellulose, extractive-free wood and extractives, and the relatively low concentration of the extractives in the wood, suggests that extraction of purified cellulose from Douglas-fir wood samples may not be necessary for some tree-ring analyses. [Copyright &y& Elsevier]

Consider repeated measures data with many zeros. For the case with one grouping factor and one repeated measure, we examine several models, assuming that the nonzero data are roughly lognormal. One of the simplest approaches is to model the zeros as left-censored observations from the lognormal distribution. A random effect is assumed for subjects. The censored model makes a strong assumption about the relationship between the zeros and the nonzero values. To check on this, you can instead assume that some of the zeros are 'true' zeros and model them as Bernoulli. Then the other values are modeled with a censored lognormal. A logistic model is used for the Bernoulli p, the probability of a true nonzero. The fit of the pure left-censored lognormal can be assessed by testing the hypothesis that p is 1, as described by Moulton and Halsey. The model can also be simplified by omitting the censoring, leaving a logistic model for the zeros and a lognormal model for the nonzero values. This is approximately equivalent to modeling the zero and nonzero values separately, a two-part model. In contrast to the censored model, this model assumes only a slight relationship (a covariance component) between the occurrence of zeros and the size of the nonzero values. The models are compared in terms of an example with data from children's private speech. [ABSTRACT FROM AUTHOR]

Murray Aitken, Dorothy Anderson, Brian Francis, and John Hinds. Oxford, U.K.: Clarendon Press, 1989. xi + 374 pp. $75 (cloth); $35 (paperback). This book is a welcome addition to the [...]