Automated analysis of tissue microarrays.

The analysis of protein expression in tissue by immunohistochemistry (IHC) presents three significant challenges. They are (1) the time-consuming nature of pathologist-based scoring of slides; (2) the need for objective quantification and localization of protein expression; and (3) the need for a highly reproducible measurement to limit intra- and inter-observer variability. While there are a variety of commercially available platforms for automated chromagen-based and fluorescence-based image acquisition of tissue microarrays, this chapter is focused on the analysis of fluorescent images by AQUA(R) analysis (Automated QUantitative Analysis) and the solutions offered by such a method for research and diagnostics.

Nitrocellulose: a tried and true polymer finds utility as a post-genomic substrate.

High-throughput techniques for genomics and proteomics differ greatly from traditional bio-molecular research techniques in the amount of data that can be obtained from a given experiment. However, many of these novel techniques rely heavily on the traditional concepts of molecular immobilization followed by hybridization, binding or analysis. These concepts, which predate even traditional blotting techniques, have become so widely used that the complexity of their fundamental precepts is often overlooked.

Expression microarray hybridization kinetics depend on length of the immobilized DNA but are independent of immobilization substrate.

Expression microarrays are often constructed by the immobilization of PCR products on two-dimensional modified glass slides or on three-dimensional microporous substrates. In this study we investigate whether the length of the immobilized species and the substrate choice influence hybridization dynamics. Using a simple bimolecular mass action controlled model to describe hybridization, we observed that the extent of hybridization and the initial velocities were directly dependent on the length of the immobilized species.

FAST slides: a novel surface for microarrays.

We have evaluated FAST slides, a glass slide with a microporous polymeric surface that is a suitable substrate for microarray technology. The surface is a nitrocellulose-based polymer that binds DNA and proteins in a noncovalent but irreversible manner. FAST slides are compatible with robotic systems currently used to create microarrays and can easily accommodate volumes of 0.