Modeling of changes in tumor burden

Skin painting studies on transgenic mice have recently been approved by the Food and Drug Administration (FDA) for carcinogenicity testing. Data consist of serial skin tumor counts on the backs of shaved mice in each of several dose groups. Current methods for assessing the tumorigenicity of test compounds are based on generalized estimating equations and require large samples. This paper proposes a new framework for modeling of the change over time in the papilloma burden in each mouse. A latent variable underlying the observed papilloma response is assumed to follow a generalized linear mixed-effects transition model. The model accounts for heterogeneity among animals and serial dependency in the skin tumor counts. Extensions of existing Markov chain Monte Carlo procedures for Bayesian estimation in generalized linear mixed models are proposed. The methods are applied to data from a National Toxicology Program short-term carcinogenicity study of lauric acid.     

Path analysis of genotype-environment interactions of potatoes exposed to increasing warm-climate constraints

Summary Twenty potato cultivars were tested in replicated trials in three seasons. The weather gradually changed from relatively high humidity and cold air temperatures in February to dry and hot in July. Fresh and dry weights, sucrose, reducing sugar and starch contents were recorded on tubers sequentially harvested over four stages during the growing period of each of the three trials. The data were analyzed for genotype-environment interactions by a path regression model which is composed of a main effect and four multiplicative effects. The model fitted well to the observed data for all traits but reducing sugar. Results of dry tuber weight were used to calculate a heat susceptibility index for each of the cultivars. Four components of the index were identified based on the path model. Comparison of sizes of the components provided information on the degree of response to the environmental stress of each of the cultivars during successive stages of growth. High yielding and heat tolerant cultivars were identified based on the experimental results.     

Development of new sources of tetraploid <Emphasis Type="Italic">Arachis</Emphasis> to broaden the genetic base of cultivated groundnut (<Emphasis Type="Italic">Arachis hypogaea</Emphasis> L.)

Groundnut, an important crop of many countries of the world, is susceptible to a range of diseases and pests. High levels of resistances are not available in the cultivated gene pool as the crop is said to have a narrow genetic base. Narrow genetic base is attributed to the evolution of the crop which took place by the combination of A and B genome species, and later doubling their chromosome number, giving rise to tetraploid cultivated groundnut. Direct utilization of cross-compatible wild relatives, which are diploids, to broaden the genetic base and introduction of useful traits, is not a straight-forward process due to ploidy differences between the cultivated species and wild relatives. Hence amphiploids and autotetraploids were created by not only combining the putative genomes, but many other A and B genome species, thus producing a highly variable population of tetraploid groundnuts also called new sources of Arachis hypogaea. This study describes the development and characterization of newly generated tetraploid groundnuts and the level of molecular diversity as assessed by DArT markers.     

A composite Latin rectangle and nonstandard strip block design

Considered is an unusual split plot design. The whole plot part is a Latin rectangle design, while the split plot part derives from a nonstandard strip block design. For the strip block part, there are two treatment factors that are randomized to strips across the whole plot experimental units, not to strips within each whole plot experimental unit. The result is five split plot error terms, not three as in a standard strip block design. The mixed model analysis and optimal exact tests for all treatment effects are developed geometrically. The analysis is illustrated by example and concluding remarks on replicated designs are offered.     

Tracking the potato late blight pathogen in the atmosphere using unmanned aerial vehicles and Lagrangian modeling

A means for determining the aerial concentration, C (sporangia m⁻³), of plant pathogenic spores at various distances from a source of inoculum is needed to quantify the potential spread of a plant disease. Values of C for Phytophthora infestans sporangia released from an area source of diseased plants in a potato canopy was quantified in three ways: (1) by using Rotorods to sample the air just above the source, (2) by using unmanned aerial vehicles to sample the air at altitudes up to 90 m above the source and at downwind distances up to 500 m from the source, and (3) by using a Lagrangian stochastic simulation of sporangia flight trajectories to tie these two measurements together. Experiments were conducted using three potato crops over two years. Model predictions of time-average, crosswind-integrated concentrations were highly correlated (r = 0.9) with values of C measured using the unmanned aerial vehicles. The model describes the release and dispersal of sporangia from a potato canopy to a downwind distance of 500 m. Thus, it may have utility as a part of an area-wide decision support system by helping to predict risk of disease spread between neighboring or distant potato fields.     

Biofortification of tomato (Solanum lycopersicum) fruit with the anticancer compound methylselenocysteine using a selenocysteine methyltransferase from a selenium hyperaccumulator

Methylselenocysteine (MeSeCys) is an amino acid derivative that possesses potent anticancer activity in animals. Plants that can tolerate growth on soils with high Se content, known as Se hyperaccumulators, do so by converting inorganic Se to MeSeCys by the enzyme selenocysteine methyltransferase (SMT). A cDNA encoding the SMT from a Se hyperaccumulator was overexpressed in tomato (Solanum lycopersicum). Transgenic plants were provided with selenite or selenate to the roots during fruit development, and liquid chromatography-mass spectrometry was used to show that MeSeCys accumulated in the fruit but not in the leaves. Depending on the transgenic line and Se treatment, up to 16% of the total Se in the fruit was present as MeSeCys. MeSeCys was produced more effectively from selenite on a percentage conversion basis, but greater accumulation of MeSeCys could be achieved from selenate due to its better translocation from the roots. MeSeCys was heat stable and survived processing of the fruit to tomato juice.     

Spatial structure of microbial biomass and activity in prairie soil ecosystems

Management of soil ecosystems requires assessment of key soil physicochemical and microbial properties and the spatial scale over which they operate. The objectives were to determine the spatial structure of microbial biomass and activity and related soil properties, and to identify spatial relationships of these properties in prairie soils under different management histories. Soil were sampled along a transect at 0.2 m intervals in each of five long-term treatments, namely, undisturbed, cattle grazed at two intensities, and cultivated with either wheat (Triticum aestivum L.) or cotton (Gossypium hirsutum L.). Contents of organic carbon (C_org), dissolved organic C (DOC), soluble nitrogen (N_sol), and microbial biomass C (C_mic) and N (N_mic) as well as dehydrogenase activity (DH) in 70 samples were evaluated. Results showed that long-term soil management altered the spatial structure and dependence of C_org and microbial biomass and activity. Cultivation has contributed to high nugget variance for C_org, C_mic, N_mic and DH which interfered with detection of spatial structure at the sampling scale used. Contents of C_org were spatially connected to microbial biomass and activity and to DOC in the uncultivated but not in the cultivated soils, indicating that various factors affected by management may operate at different spatial scales.     

Cryptic genetic diversity in “widespread” Southeast Asian bird species suggests that Philippine avian endemism is gravely underestimated

Mistakenly classifying morphologically cryptic endemic species as populations of widespread species potentially interferes with the conservation of biodiversity because undetected endemics that are imperilled may lack appropriate protection. It also impedes the reconstruction of the evolutionary history of a taxon by obscuring the number and distributional limits of species. Here, we present genetic and phylogenetic evidence corroborated by morphology that Philippine populations of seven widespread, non-migratory passerine birds might represent unrecognized, distinct species. An extrapolation based on this finding suggests that the proportion of endemic bird species in the Philippines could be much higher than currently estimated. This high degree of cryptic diversity in a well-studied, volant taxon implies that large numbers of unrecognized species can be expected in less thoroughly studied groups. We predict that genetic investigations of insular populations of widespread species will frequently reveal unrecognized island endemics, and because of the vulnerability of island habitats and their biota, these taxa may be particularly susceptible to extinction.     

Economic benefits of large-scale remediation of contaminated marine sediments—a literature review and an application to the Grenland fjords in Norway

Purpose  

As input to a cost-benefit analysis of large-scale remediation measures of contaminated sediments in the Grenland fjords in Norway, we conducted a contingent valuation (CV) survey of a representative sample of households from municipalities adjacent to these fjords.     

The response of organic matter mineralisation to nutrient and substrate additions in sub-arctic soils

Global warming in the Arctic may alter decomposition rates in Arctic soils and therefore nutrient availability. In addition, changes in the length of the growing season may increase plant productivity and the rate of labile C input below ground. We carried out an experiment in which inorganic nutrients (NH₄NO₃ and NaPO₄) and organic substrates (glucose and glycine) were added to soils sampled from across the mountain birch forest-tundra heath ecotone in northern Sweden (organic and mineral soils from the forest, and organic soil only from the heath). Carbon dioxide production was then monitored continuously over the following 19 days. Neither inorganic N nor P additions substantially affected soil respiration rates when added separately. However, combined N and P additions stimulated microbial activity, with the response being greatest in the birch forest mineral soil (57% increase in CO₂ production compared with 26% in the heath soil and 8% in the birch forest organic soil). Therefore, mineralisation rates in these soils may be stimulated if the overall nutrient availability to microbes increases in response to global change, but N deposition alone is unlikely to enhance decomposition. Adding either, or both, glucose and glycine increased microbial respiration. Isotopic separation indicated that the mineralisation of native soil organic matter (SOM) was stimulated by glucose addition in the heath soil and the forest mineral soil, but not in the forest organic soil. These positive ‘priming’ effects were lost following N addition in forest mineral soil, and following both N and P additions in the heath soil. In order to meet enhanced microbial nutrient demand, increased inputs of labile C from plants could stimulate the mineralisation of SOM, with the soil C stocks in the tundra-heath potentially most vulnerable.