The E(NK) model: extending the NK model to incorporate gene-by-environment interactions and epistasis for diploid genomes

The haploid NK model developed by Kauffman can be extended to diploid genomes and to incorporate gene-by-environment interaction effects in combination with epistasis. To provide the flexibility to include a wide range of forms of gene-by-environment interactions, a target population of environment types (TPE) is defined. The TPE consists of a set of E different environment types, each with their own frequency of occurrence. Each environment type conditions a different NK gene network structure or series of gene effects for a given network structure, providing the framework for defining gene-by-environment interactions. Thus, different NK models can be partially or completely nested within the E environment types of a TPE, giving rise to the E(NK) model for a biological system. With this model it is possible to examine how populations of genotypes evolve in context with properties of the environment that influence the contributions of genes to the fitness values of genotypes. We are using the E(NK) model to investigate how both epistasis and gene-by-environment interactions influence the genetic improvement of quantitative traits by plant breeding strategies applied to agricultural systems. © 2002 Wiley Periodicals, Inc.

Play Preferences and Behavior of Preschool Children with Autistic Spectrum Disorder in the Clinical Environment

The play of children with autistic spectrum disorder (ASD) is a valuable medium for assessment and intervention, and its analysis has the potential to aid diagnosis. This study investigated spontaneous play behavior and play object preferences for 24 preschool children with ASD in a typical occupational therapy clinical environment. Play behavior was rated and choice of play object noted at 10-second intervals from a 15-minute video recording of unstructured play. Statistical analyses indicated that play behavior was consistent with descriptions in the literature. In addition, the children demonstrated clear preferences for play objects in the form of popular characters (e.g., Thomas the Tank Engine) and those with sensorimotor properties. We propose that the inclusion of preferred play objects in a clinical environment may increase intrinsic motivation to play, and thereby enhance assessment and intervention.

The mouse secretome: functional classification of the proteins secreted into the extracellular environment

We have developed a computational strategy to identify the set of soluble proteins secreted into the extracellular environment of a cell. Within the protein sequences predominantly derived from the RIKEN representative transcript and protein set, we identified 2033 unique soluble proteins that are potentially secreted from the cell. These proteins contain a signal peptide required for entry into the secretory pathway and lack any transmembrane domains or intracellular localization signals. This class of proteins, which we have termed the mouse secretome, included >500 novel proteins and 92 proteins

Antigen-specific suppression of a primed immune response by dendritic cells mediated by regulatory T cells secreting interleukin-10

Antigen-specific suppression of a previously primed immune response is a major challenge for immunotherapy of autoimmune disease. ReIB activation is required for myeloid DC differentiation. Here, we show that antigen-exposed DCs in which ReIB function is inhibited lack cell surface CD40, prevent priming of immunity, and suppress previously primed immune responses. DCs generated from CD40-deficient mice similarly confer suppression. Regulatory CD4(+) T cells induced by the DCs transfer antigen-specific Infectious tolerance to primed recipients in an interleukin10-dependent fashion. Thus CD40, regulated by ReIB activity, determines the consequences of antigen presentation by myeloid DCs. These observations have significance for autoimmune immunotherapy and suggest a mechanism by which peripheral tolerance might be constitutively maintained by RelB(-) CD40(-) DCs.

Genotype and environment effects on dynamics of harvest index during grain filling in sorghum

An approach based on a linear rate of increase in harvest index (141) with time after anthesis has been used as a simple means-to predict grain growth and yield in many crop simulation models. When applied to diverse situations, however, this approach has been found to introduce significant error in grain yield predictions. Accordingly, this study was undertaken to examine the stability of the HI approach for yield prediction in sorghum [Sorghum bicolor (L.) Moench]. Four field experiments were conducted under nonlimiting water. and N conditions. The experiments were sown at times that ensured a broad range in temperature and radiation conditions. Treatments consisted of two population densities and three genotypes varying in maturity. Frequent sequential harvests were used to monitor crop growth, yield, and the dynamics of 111. Experiments varied greatly in yield and final HI. There was also a tendency for lower HI with later maturity. Harvest index dynamics also varied among experiments and, to a lesser extent, among treatments within experiments. The variation was associated mostly with the linear rate of increase in HI and timing of cessation of that increase. The average rate of HI increase was 0.0198 d(-1), but this was reduced considerably (0.0147) in one experiment that matured in cool conditions. The variations found in IN dynamics could be largely explained by differences in assimilation during grain filling and remobilization of preanthesis assimilate. We concluded that this level of variation in HI dynamics limited the general applicability of the HI approach in yield prediction and suggested a potential alternative for testing.

Evaluating plant breeding strategies by simulating gene action and dryland environment effects

Functional genomics is the systematic study of genome-wide effects of gene expression on organism growth and development with the ultimate aim of understanding how networks of genes influence traits. Here, we use a dynamic biophysical cropping systems model (APSIM-Sorg) to generate a state space of genotype performance based on 15 genes controlling four adaptive traits and then search this spice using a quantitative genetics model of a plant breeding program (QU-GENE) to simulate recurrent selection. Complex epistatic and gene X environment effects were generated for yield even though gene action at the trait level had been defined as simple additive effects. Given alternative breeding strategies that restricted either the cultivar maturity type or the drought environment type, the positive (+) alleles for 15 genes associated with the four adaptive traits were accumulated at different rates over cycles of selection. While early maturing genotypes were favored in the Severe-Terminal drought environment type, late genotypes were favored in the Mild-Terminal and Midseason drought environment types. In the Severe-Terminal environment, there was an interaction of the stay-green (SG) trait with other traits: Selection for + alleles of the SG genes was delayed until + alleles for genes associated with the transpiration efficiency and osmotic adjustment traits had been fixed. Given limitations in our current understanding of trait interaction and genetic control, the results are not conclusive. However, they demonstrate how the per se complexity of gene X gene X environment interactions will challenge the application of genomics and marker-assisted selection in crop improvement for dryland adaptation.