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. ^

NMR structure of a complex between the VirB9/VirB7 interaction domains of the pKM101 type IV secretion system.

Type IV secretion (T4S) systems translocate DNA and protein effectors through the double membrane of Gram-negative bacteria. The paradigmatic T4S system in Agrobacterium tumefaciens is assembled from 11 VirB subunits and VirD4. Two subunits, VirB9 and VirB7, form an important stabilizing complex in the outer membrane. We describe here the NMR structure of a complex between the C-terminal domain of the VirB9 homolog TraO (TraO(CT)), bound to VirB7-like TraN from plasmid pKM101. TraO(CT) forms a beta-sandwich around which TraN winds. Structure-based mutations in VirB7 and VirB9 of A. tumefaciens show that the heterodimer interface is conserved. Opposite this interface, the TraO structure shows a protruding three-stranded beta-appendage, and here, we supply evidence that the corresponding region of VirB9 of A. tumefaciens inserts in the membrane and protrudes extracellularly. This complex structure elucidates the molecular basis for the interaction between two essential components of a T4S system.

Changes in 911 call volume and type during Hurricane Ike and the implementation and usefulness of the TeleHealth Nurse system for the Houston Fire Department

This study examined both changing call volume and type with resulting effect of TeleHealth Nurse, the Houston Fire Department's (HFD) telephone nurse line, on call burden during Hurricane Ike. On September 13, 2008, Hurricane Ike made landfall in the Galveston area and continued north through Houston resulting in catastrophic damages in infrastructure and posing a public health threat. The overall goal of this study looked at data from Houston Fire Department to obtain a better understanding of the needs of citizens before, during, and after a hurricane. This study looked at four aspects of emergency response from HFD. The first section looked at call volumes surrounding the time of Hurricane Ike in 2008 compared to the same time period in 2007. The data showed a 12% increase in calls surrounding Hurricane Ike compared to previous years with a p value <.001. Next, the study evaluated the types of calls prevalent during Hurricane Ike compared to the same time period in 2007. The data showed a statistically significant increase in chronic health problems such as diabetes and cardiac events, Obstetric calls and an increase in breathing problems, falls, and lacerations during the days following Hurricane Ike. There was also a statistically significant increase in auto med alerts and check patients surrounding Hurricane Ike's landfall. The third section analyzed the change in call volume sent to HFD's Telephone Nurse Line during Hurricane Ike and compares this to earlier time periods while the fourth and final section looks at the types of calls sent to the nurse line during Hurricane Ike. The data showed limited use of the TeleHealth Nurse line before Hurricane Ike, but when the winds were at their strongest and ambulances were unable to leave the station, the nurse line was the only functioning medical help some people were able to receive. These studies bring a better understanding to the number and types of calls that a city might experience during a natural disaster, such as a hurricane. This study also shows the usefulness of an EMS Telephone Nurse Line during a natural disaster.^