An a posteriori strategy for enhancing gene discovery in anonymous cDNA microarray experiments

Representation of Individual Gene Expression in Completely Pooled mRNA Samples

Designing microarray experiments, scientists are often confronted with the question of pooling due to financial constraints, but discussion of the validity of pooling tends toward a sub-pooling recommendation. Since complete pooling protocols can be considered part of sub-pooling designs, gene expression data from three complete pooling experiments were analyzed. Data from complete pooled versus individual mRNA samples of rat brain tissue were compared to answer the question whether the pooled sample represents individual samples in small-sized experiments. Our analytic approach provided clear results concerning the Affymetrix MAS 5.0 signal and detection call parameters. Despite a strong similarity of arrays within experimental groups, the individual signals were evidently not appropriately represented in the pooled sample, with slightly more than half of all the genes considered. Our analysis reveals problems in cases of small complete pooling designs with less than six subjects pooled.

Seasonal reorganization of the xylem transcriptome at different tree ages reveals novel insights into wood formation in Pinus radiata

*Seasonal wood development produces earlywood (EW) and latewood (LW) with distinct properties. The molecular mechanisms controlling EW and LW formation at different tree ages are poorly understood. *Seasonal reorganization of the xylem transcriptome was investigated in Pinus radiata at four tree ages using cDNA microarrays. Transcriptome profiles were compared with seasonal wood variation measured by SilviScan (CSIRO, Clayton, Australia). *The xylem transcriptome was considerably reorganized during seasonal change, and this reorganization showed a maturation-related pattern. The greater reorganization occurred at the transition (30%) and juvenile (21%) stages, but it declined with tree maturity (11-13%). However, this pattern does not correlate well with maturation-related patterns of seasonal wood variation. In total, 319 seasonal-responsive xylem candidate genes were identified. Many transcripts involved in primary and secondary wall biosynthesis were preferentially accumulated in EW and LW, respectively. A large proportion (45-81%) of the candidate genes are preferentially regulated at a single age and their transcript abundance may influence maturation-related patterns of seasonal wood variation. *Seasonal reorganization of the xylem transcriptome is significantly affected by tree age. Physiological changes at the transition stage may contribute to its greater seasonal transcriptome reorganization. Identified stage-preferential xylem transcripts could influence seasonal wood variation at different tree ages.

Impact of microarray technology in nutrition and food research

Microarrays have become standard tools for gene expression profiling as the mRNA levels of a large number of genes can be measured in a single assay. Many technical aspects concerning microarray production and laboratory usage have been addressed in great detail, but it remains still crucial to establish this technology in new research fields such as human nutrition and food-related areas. The correlation between diet and inter-individual variation in gene expression is an important and relatively unexplored issue in human nutrition. Therefore, nutritionists changed their research field dramatically from epidemiology and physiology towards the "omics" sciences. Nutrigenomics as a field of research is based on the complete knowledge of the human genome and refers to the entire spectrum of human genes that determine the interactions of nutrition with the organism. Nutrigenetics is based on the inter-individual, genetically determined differences in metabolism. Nutrigenomics and nutrigenetics carry the hope that individualized diet can improve human health and prevent nutrition-related diseases. In this article we give an overview of current DNA and protein microarray techniques (including fabrication, experimental procedure and data analysis), we describe their applications to nutrition and food research and point out the limitations, problems and pitfalls of microarray experiments.