Integrating sequence information in microarray data analysis by free energy modeling

Microarray technology is a high-throughput method for genotyping and gene expression profiling. Limited sensitivity and specificity are one of the essential problems for this technology. Most of existing methods of microarray data analysis have an apparent limitation for they merely deal with the numerical part of microarray data and have made little use of gene sequence information. Because it's the gene sequences that precisely define the physical objects being measured by a microarray, it is natural to make the gene sequences an essential part of the data analysis. This dissertation focused on the development of free energy models to integrate sequence information in microarray data analysis. The models were used to characterize the mechanism of hybridization on microarrays and enhance sensitivity and specificity of microarray measurements. ^ Cross-hybridization is a major obstacle factor for the sensitivity and specificity of microarray measurements. In this dissertation, we evaluated the scope of cross-hybridization problem on short-oligo microarrays. The results showed that cross hybridization on arrays is mostly caused by oligo fragments with a run of 10 to 16 nucleotides complementary to the probes. Furthermore, a free-energy based model was proposed to quantify the amount of cross-hybridization signal on each probe. This model treats cross-hybridization as an integral effect of the interactions between a probe and various off-target oligo fragments. Using public spike-in datasets, the model showed high accuracy in predicting the cross-hybridization signals on those probes whose intended targets are absent in the sample. ^ Several prospective models were proposed to improve Positional Dependent Nearest-Neighbor (PDNN) model for better quantification of gene expression and cross-hybridization. ^ The problem addressed in this dissertation is fundamental to the microarray technology. We expect that this study will help us to understand the detailed mechanism that determines sensitivity and specificity on the microarrays. Consequently, this research will have a wide impact on how microarrays are designed and how the data are interpreted. ^

Role of phosphatidylethanolamine in the function and assembly of phenylalanine-specific permease of Escherichia coli

Transmembrane segments of polytopic membrane proteins once inserted are generally considered stably oriented due to the large free energy barrier for topological reorientation of adjacent extra-membrane domains. However, proper topology and function of the polytopic membrane protein lactose permease (LacY) of Escherichia coli is dependent on the membrane phospholipid composition revealing topological dynamics of transmembrane domains (Bogdanov, M., Heacock, P. N., and Dowhan, W. (2002) EMBO J. 21, 2107–2116). The high affinity phenylalanine permease PheP shares many topological similarities with LacY. In this study, mutant E. coli cells lacking phosphatidylethanolamine (PE) as a membrane component were used to evaluate the role of PE in the function and assembly of PheP. Active transport of phenylalanine by cells lacking PE was severely inhibited (both Vmax and Km were altered), whereas the PheP protein level in membranes was unaffected. Cysteine residues were introduced into predicted periplasmic or cytoplasmic segments of cysteine-less PheP, and the topology of the protein was explored using a membrane-impermeable thiol-specific biotinylated probe. Based on the biotinylation patterns of PheP in whole cells, the N-terminus and adjoining transmembrane hairpin of PheP adopted an inverted topological orientation in PE-lacking cells. Introduction of PE following the assembly of PheP triggered a reorientation of the N-terminus and adjacent hairpin to their native orientation associated with regain of wild type transport function. These results coupled with the results for LacY support a specific role for membrane lipid composition in determining topological organization and function of membrane proteins. Several other secondary symporters are compromised for activity in PE-lacking cells suggesting that lipid-assisted topogenesis is a general property of such transporters. The reversible orientation of these secondary transport proteins in response to a change of phospholipid composition might be a result of inherent conformational flexibility necessary for transport function or during protein assembly. ^

Monitoring of industrial exposure for chloracne

This study (1) established comedogenicity dose response curves for the pure compounds of 3,3$\sp\prime$,4,4$\sp\prime$-tetrachloroazobenzene (TCAB) and 3,3$\sp\prime$,4,4$\sp\prime$-tetrachloroazoxybenzene (TCAOB) individually and as a couple-compound using a rabbit ear model; (2) used a rabbit ear model to establish comedogenicity potential for TCAB and TCAOB as they existed in a given industrial herbicide manufacture process; (3) evaluated actual environmental contamination in a herbicide industrial setting by air monitoring and wipe sampling; (4) biologically monitored potentially exposed workers for alterations in follicular orifice size as an index of actual exposure to chloracnegenic compounds; and (5) biologically monitored potentially exposed workers for changes in weight, cholesterol, triglycerides and blood sugar.^ A silastic monomer mold (an objective measure) was used to measure change in follicular orifice size over time. This required taking impressions of (1) skin of the forehead and right and left malar crescents of workers and (2) the skin of the external ear of the rabbit. Molds were stained using a solution of hematoxylin and digitized using a Nikon UFX microscope (magnification 300 X), a drawing tube and a digitizing tablet attached to an IBM Personal Computer. Comedogenicity assays were used to establish dose-response curves for TCAB, TCAOB and the couple-compound TCAB + TCAOB.^ No evidence of chloracne or toxicity was observed in any of the workers. Nor, was there a statistically significant increase in size of follicular orifice means measured over time. This was attributed to extensive personal and environmental hygiene programs along with teaching the workers about chloracne, its cause and its prevention. These programs may have been the greatest factor in preventing the development of chloracne in this group of workers. Monitoring of the plant environment showed relatively high concentrations of the couple-compound (TCAB + TCAOB). Comedogenicity assays showed a linear dose-response relationship over time for TCAB, TCAOB and the couple-compound. An antagonistic action was found for the TCAB/TCAOB of the couple-compound; such action may provide some protection to workers in this type of setting. It is speculated that the observed antagonistic action may be due to the difference in binding affinities of TCAB/TCAOB for receptor sites. ^