Chromatin-remodelling proteins of the pea aphid, Acyrthosiphon pisum (Harris).

Aphids display extraordinary developmental plasticity in response to environmental cues. These differential responses to environmental changes may be due in part to changes in gene expression patterns. To understand the molecular basis for aphid developmental plasticity, we attempted to identify the chromatin-remodelling machinery in the recently sequenced pea aphid genome. We find that the pea aphid possesses a complement of metazoan histone modifying enzymes with greater gene family diversity than that seen in a number of other arthropods. Several genes appear to have undergone recent duplication and divergence, potentially enabling greater combinatorial diversity among the chromatin-remodelling complexes. The abundant aphid chromatin modifying enzymes may facilitate the phenotypic plasticity necessary to maintain the complex life cycle of the aphid.

A mixture model approach for the analysis of small exploratory microarray experiments.

The microarray is an important and powerful tool for prescreening of genes for further research. However, alternative solutions are needed to increase power in small microarray experiments. Use of traditional parametric and even non-parametric tests for such small experiments lack power and have distributional problems. A mixture model is described that is performed directly on expression differences assuming that genes in alternative treatments are expressed or not in all combinations (i) not expressed in either condition, (ii) expressed only under the first condition, (iii) expressed only under the second condition, and (iv) expressed under both conditions, giving rise to 4 possible clusters with two treatments. The approach is termed a Mean-Difference-Mixture-Model (MD-MM) method. Accuracy and power of the MD-MM was compared to other commonly used methods, using both simulations, microarray data, and quantitative real time PCR (qRT-PCR). The MD-MM was found to be generally superior to other methods in most situations. The advantage was greatest in situations where there were few replicates, poor signal to noise ratios, or non-homogenous variances.

Application of One Sided t-tests and a Generalized Experiment Wise Error Rate to High-Density Oligonucleotide Microarray Experiments: An Example Using Arabidopsis.

MOTIVATION: A formidable challenge in the analysis of microarray data is the identification of those genes that exhibit differential expression. The objectives of this research were to examine the utility of simple ANOVA, one sided t tests, natural log transformation, and a generalized experiment wise error rate methodology for analysis of such experiments. As a test case, we analyzed a Affymetrix GeneChip microarray experiment designed to test for the effect of a CHD3 chromatin remodeling factor, PICKLE, and an inhibitor of the plant hormone gibberellin (GA), on the expression of 8256 Arabidopsis thaliana genes. RESULTS: The GFWER(k) is defined as the probability of rejecting k or more true null hypothesis at a given p level. Computing probabilities by GFWER(k) was shown to be simple to apply and, depending on the value of k, can greatly increase power. A k value as small as 2 or 3 was concluded to be adequate for large or small experiments respectively. A one sided t-test along with GFWER(2)=.05 identified 43 genes as exhibiting PICKLE-dependent expression. Expression of all 43 genes was re-examined by qRT-PCR, of which 36 (83.7%) were confirmed to exhibit PICKLE-dependent expression.

Molecular genetic mapping of three X-linked avirulence genes, vH6, vH9 and vH13, in the Hessian fly.

Three X-linked avirulence genes, vH6, vH9, and vH13 in the Hessian fly, Mayetiola destructor, confer avirulence to Hessian fly resistance genes H6, H9, and H13 in wheat. We used a combination of two- and three-point crosses to determine the order of these genes with respect to each other, the white eye mutation and three X-linked molecular markers, G15-1, 020, and 021, developed from genomic lambda clones, lambda G15-1, lambda 020, and lambda 021. The gene order was determined to be vH9-vH6-G15-1-w-vH13-020-021. In situ hybridization of lambda G15-1, lambda 020, and lambda 021, on the polytene chromosomes of the Hessian fly salivary gland established their orientation on Hessian fly chromosome X1. Based on the size of the Hessian fly genome, and the genetic distances between markers, the relationship of physical to genetic distance was estimated at no more than 300 kb/cM along Hessian fly chromosome X1, suggesting that map-based cloning of these avirulence genes will be feasible.