Application of stellar photometry to the analysis of microarray images

Improvements in the analysis of microarray images are critical for accurately quantifying gene expression levels. The acquisition of accurate spot intensities directly influences the results and interpretation of statistical analyses. This dissertation discusses the implementation of a novel approach to the analysis of cDNA microarray images. We use a stellar photometric model, the Moffat function, to quantify microarray spots from nylon microarray images. The inherent flexibility of the Moffat shape model makes it ideal for quantifying microarray spots. We apply our novel approach to a Wilms' tumor microarray study and compare our results with a fixed-circle segmentation approach for spot quantification. Our results suggest that different spot feature extraction methods can have an impact on the ability of statistical methods to identify differentially expressed genes. We also used the Moffat function to simulate a series of microarray images under various experimental conditions. These simulations were used to validate the performance of various statistical methods for identifying differentially expressed genes. Our simulation results indicate that tests taking into account the dependency between mean spot intensity and variance estimation, such as the smoothened t-test, can better identify differentially expressed genes, especially when the number of replicates and mean fold change are low. The analysis of the simulations also showed that overall, a rank sum test (Mann-Whitney) performed well at identifying differentially expressed genes. Previous work has suggested the strengths of nonparametric approaches for identifying differentially expressed genes. We also show that multivariate approaches, such as hierarchical and k-means cluster analysis along with principal components analysis, are only effective at classifying samples when replicate numbers and mean fold change are high. Finally, we show how our stellar shape model approach can be extended to the analysis of 2D-gel images by adapting the Moffat function to take into account the elliptical nature of spots in such images. Our results indicate that stellar shape models offer a previously unexplored approach for the quantification of 2D-gel spots. ^

MINERALOCORTICOID REGULATION OF ION CONDUCTIVE PATHWAYS OF THE CORTICAL COLLECTING DUCT

Mineralocorticoids (DOCA) are known to increase Na('+) absorption and K('+) secretion in the rabbit cortical collecting duct (CCD). However, the mechanism of regulation of the apical and basolateral cell membranes and tight junction ion conductive pathways (G('a), G('b), and G('tj), respectively) by mineralocorticoids are only partially understood. Using electrophysiological techniques and microelectrodes it was demonstrated that the apical cell membrane contained a dominant Ba('2+) sensitive K('+) conductive pathway, G(,K)('a), and an amiloride sensitive Na('+) conductive pathway, G(,Na)('a). The basolateral membrane contained a dominant Cl('-) conductive pathway, G(,Cl)('b), and a significant Ba('2+) sensitive K('+) conductive pathway, G(,K)('b). Upon elevating the mineralocorticoid levels of rabbits with intact adrenal glands it was found that V('te) was significantly increased after 1 day with a further increase after 13-16 days. These results indicated both primary and secondary effects of mineralocorticoid elevation. After 1 day of DOCA treatment, G(,Na)('a), I(,Na)('a) and I(,K)('a) increased by more than 2-fold and were maintained at high levels after 13-16 days of DOCA treatment. Secondary (chronic) effects of mineralocorticoids were evident after 4 days or more of DOCA treatment. These included a significant increase in G(,K)('a) from 4.0 to 10.2 mS.cm('-2) and a hyperpolarization of V('b) by -20 mV after 4 days of treatment. After 13-16 days of DOCA treatment V('b) remained hyperpolarized at -98.1 mV and G('tj) decreased from 5.6 to 4.2 mS.cm('-2). The hyperpolarization of V('b) was due to an increase in electrogenic Na('+) pump activity as the pump current, I(,act)('b), increased significantly from 35.7 to 195.2 (mu)A.cm('-2). Whereas net passive K('+) current across the basolateral membrane, I(,K)('b), was near zero in the control group of animals, i.e., K('+) near equilibrium, I(,K)('b) was approximately -40 (mu)A.cm('-2) in chronic DOCA treated animals. These results demonstrate that the initial effect of mineralocorticoid elevation is to increase G(,Na)('a). The ensuing depolarization of the apical membrane increases the driving force for K('+) exit into the lumen. Between 1 and 4 days of elevation, G(,K)('a) more than doubles in magnitude and at the same time the electrogenic activity of the Na('+) pump increases. This results in a hyperpolarization of V('b) which increases the driving force for K('+) uptake from the bath to the cell through a basolateral membrane conductive pathway. After 13-16 days G('tj) decreases thereby serving to maintain high electrochemical gradients across the epithelium. Therefore, the long term effects of mineralocorticoid elevation on the CCD appear to be adaptive mechanisms that serve to maintain high levels of K('+) secretion and Na('+) absorption. ^