Phenotypic plasticity of growth trajectory and ontogenic allometry in response to density for eucalyptus hybrid clones and families

BACKGROUND: and Aims Response to density is a crucial aspect of the ecology of trees in forests and plantations. Few studies have investigated the genetics of plasticity in response to density for growth traits such as height and circumference through development. METHODS: Two experiments were carried out in the field, the first with full-sib families of Eucalyptus urophylla x E. grandis hybrids, and the second with clones of E. tereticornis x E. grandis hybrids planted across a range of densities (625, 1111 and 2500 trees ha-1). Height, circumference and stem taper were measured through development in both experiments. Variance components were estimated and a repeated measure approach for plasticity and three different methods were used to compare the variance-covariance matrix across densities. KEY RESULTS: Genetic variance was significantly different from zero but the density x genotype interaction was significant only for clone experiments at the adult stage. Significant plasticity for three traits in both experiments was found. In the clone experiments, a significant clone x time x density interaction was found, suggesting that plasticity for growth and stem form is under genetic control. In both experiments, density did not affect environmental correlation, which remained high throughout tree development. The impact of density on genetic correlation was marked in the clone experiment, with a reduced value at lower density, but was not observed in the family trial. The differences between clones and family are mainly explained by the distribution of genetic variation within and among genotypes. CONCLUSIONS: The results suggest that plasticity for growth traits and form of tropical Eucalyptus species is under genetic control and that the environment changes genetic co-variation through ontogeny. The findings confirm that a tree population with a narrow genetic basis (represented by clones) is sensitive to a changing environment, whereas a population with a broader genetic basis (full-sib family here) exhibits a more stable reaction.     

A non-iterative confidence interval estimating procedure for the intraclass kappa statistic with multinomial outcomes

We obtain the asymptotic sample variance of the intraclass kappa statistic for multinomial outcome data. A modified Wald type procedure based on this theory is then used for confidence interval construction. The results of a simulation study show that the proposed non-iterative approach performs very well in terms of confidence interval coverage and width for samples as small as 50. The procedure is illustrated with two examples from previously published medical studies.     

Exact tests for one sample correlated binary data

In this paper we developed exact tests for one sample correlated binary data whose cluster sizes are at most two. Although significant progress has been made in the development and implementation of the exact tests for uncorrelated data, exact tests for correlated data are rare. Lack of a tractable likelihood function has made it difficult to develop exact tests for correlated binary data. However, when cluster sizes of binary data are at most two, only three parameters are needed to characterize the problem. One parameter is fixed under the null hypothesis, while the other two parameters can be removed by both conditional and unconditional approaches, respectively, to construct exact tests. We compared the exact and asymptotic p-values in several cases. The proposed method is applied to real-life data.     

Global analysis of fluorescence fluctuation data

Over the last decade the number of applications of fluorescence correlation spectroscopy (FCS) has grown rapidly. Here we describe the development and application of a software package, FCS Data Processor, to analyse the acquired correlation curves. The algorithms combine strong analytical power with flexibility in use. It is possible to generate initial guesses, link and constrain fit parameters to improve the accuracy and speed of analysis. A global analysis approach, which is most effective in analysing autocorrelation curves determined from fluorescence fluctuations of complex biophysical systems, can also be implemented. The software contains a library of frequently used models that can be easily extended to include user-defined models. The use of the software is illustrated by analysis of different experimental fluorescence fluctuation data sets obtained with Rhodamine Green in aqueous solution and enhanced green fluorescent protein in vitro and in vivo.An erratum to this article can be found at Victor V. Skakun, Mark A. Hink and Anatoli V. Digris contributed equally to this work.     

Polyacetylenes accumulation in <Emphasis Type="Italic">Ambrosia maritima</Emphasis> hairy root and cell cultures after elicitation with methyl jasmonate

Three lines of hairy root culture of Ambrosia maritima induced by Agrobacterium rhizogenes ATCC15834 were established. Thiarubrine A, thiarubrine A epoxide, thiarubrine A diol and their precursor pentayneene were produced by the hairy roots after elicitation with methyl jasmonate, the common signal molecule in the plant defense and development. Thiarubrine A diol was the main form detected in the medium. Maximum yield was achieved when the 13-day-old hairy root cultures were exposed to 40 M methyl jasmonate for 72 h. Callus and cell suspension cultures were established and maintained on Murashige and Skoog medium supplied with -naphthylacetic acid (NAA) and kinetin. When the cell suspension cultures were elicited with methyl jasmonate, pentayneene was the only polyacetylene produced. The yield of pentayneene in hairy root cultures was much higher (9.6 times) than that of cell suspension cultures.     

Improvement of xylanase production in solid-state fermentation by alkali tolerant Aspergillus versicolor MKU3

AIMS: To optimize the media components for xylanase production by Aspergillus versicolor MKU3 in solid-state fermentation (SSF). METHODS AND RESULTS: Medium optimization was carried out using De Moe's fractional factorial design with seven components. Maximum production of xylanase 3249.9 U g(-1) was obtained in SSF with an optimized medium containing (g l(-1)): NaNO(3), 20; K(2)HPO(4), 20; MgSO(4), 10; FeSO(4), 0.001; KCl, 1; peptone, 10 and yeast extract, 10. Four components namely NaNO(3), MgSO(4), peptone and K(2)HPO(4) significantly increased the xylanase production by A. versicolor MKU3. CONCLUSIONS: Fractional factorial design was used to optimize the seven components in the fermentation medium for SSF. The optimized media increased xylanase production by 3.4-fold. SIGNIFICANCE AND IMPACT OF THE STUDY: Aspergillus versicolor MKU3 produced maximum xylanase after two steps of media optimization under alkaline condition. This medium will be significant value for xylanase production in SSF.     

Extra thin alginate film: an efficient technique for protoplast culture

Summary. This paper reports an efficient protoplast culture technique, the “extra thin alginate film” technique. The development of this improved method of protoplast culture was an outcome of an assessment of the efficiency and shortcomings of various protoplast culture techniques. The efficiency of this technique was evaluated with two model plant systems, viz., Nicotiana tabacum and Lotus corniculatus, and a comparison was made with the “thin alginate layer” technique, another efficient protoplast culture system. Results indicate that the culture technique with extra thin alginate film is as efficient as the technique with thin alginate layer, with many additional advantages. The present innovation overcomes most of the limitations of protoplast culture techniques described so far and can now be applied to a wide variety of crops to check its general applicability. Correspondence and reprints: Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar 143 005, India.     

The use of whole genome amplification in the study of human disease

The availability of large amounts of genomic DNA is of critical importance for many of the molecular biology assays used in the analysis of human disease. However, since the amount of patient tissue available is often limited and as particular foci of interest may consist of only a few hundred cells, the yield of DNA is often insufficient for extensive analysis. To address this problem, several whole genome amplification (WGA) methodologies have been developed. Initial WGA approaches were based on the polymerase chain reaction (PCR). However, recent reports have described the use of non-PCR-based linear amplification protocols for WGA. Using these methods, it is possible to generate microgram quantities of DNA starting with as little as 1mg of genomic DNA. This review will provide an overview of WGA approaches and summarize some of the uses for amplified DNA in various high-throughput genetic applications.     

Response Surface Analysis of Solid State Growth of <Emphasis Type="Italic">Pleurotus ostreatus</Emphasis> Mycelia utilizing Whey Permeate

A novel approach to utilizing whey permeate, the cultivation of mycelia of the edible mushroom Pleurotus ostreatus, is introduced. Response surface analysis (RSA) was successfully applied to determine the combination of substrate concentration, temperature and pH that would result in a maximal mycelial extension rate under solid state cultivation. The conditions to maximize the mycelial extension rate were predicted to be 44 g lactose l⁻¹, pH 6.0 and 24.2 °C. Subsequent verification of these levels agreed with model predictions.     

A new culture system for in situ observation of the growth and development of Eucyclops serrulatus (Copepoda: Cyclopoida)

A practical and convenient method of rearing Eucyclops serrulatus in a microculture environment is described. A complete life cycle of E. serrulatus was maintained in a narrow space on a microscope slide glass on which a cover glass of 22 x 40 mm in size was mounted at a height of 0.8 mm. The culture medium was constituted by bottled mineral water boiled with grains of Glycine max (soybean). Chilomonas paramecium, a free-living protozoan organism, was provided as live food. Growth of nauplii hatched from eggs to the first stage of copepodite took an average of 7.7 days, and the growth of copepodite 1 to the egg-bearing adult female took an average of 20.1 days in the microculture cell with an average life time of 44.7 days. Continuous passage of copepods was successfully maintained as long as sufficient medium and food were provided. The microculture method enables an in situ microscopic observation on the growth and developmental process of helminth larvae experimentally infected to copepods as well as of copepod itself. Furthermore, it does not require anesthetization and, therefore, minimize the amount of stress exposed to copepods during the handling process.