Doctor of Philosophy / Department of Anatomy and Physiology / A. Philine Wangemann / Pendred syndrome is characterized by sensorineural deafness and post-pubertal goiter. It is caused by mutations in the anion exchanger, pendrin (SLC26A4). The purpose of this study was to understand the etiology of Pendred syndrome using a mouse model. Different methods of amplification from nanogram amounts of starting RNA were evaluated for gene array application. Gene arrays were performed and free radical stress markers were compared between the stria vascularis and the thyroid of the Slc26a4+/- and Slc26a4-/- mice. Hearing loss in Slc26a4-/- mice is linked to the loss of Kcnj10 protein expression and consequently the loss of endocochlear potential. To understand the mechanism of hearing loss in Slc26a4-/- mice, progressive loss of Kcnj10 protein expression in stria vascularis of Slc26a4-/- mice was assessed, the modulation of Kcnj10 protein expression by free radical stress in cultured stria vascularis and in an heterologous expression system was evaluated. To characterize the thyroid pathology, pendrin expression in the thyroid of Slc26a4+/- mice was measured in a developmental study and correlated with serum thyroxine (T4) levels of Slc26a4+/- and Slc26a4-/- mice over a developmental time course. All tested methods of RNA amplification were suitable for gene array application and demonstrated high internal consistency. Intermethod comparisons revealed variations in data, suggesting that a single amplification method ought to be used within a given experiment. Markers of free radical stress were increased in the stria vascularis of Slc26a4-/- mice before the onset of hearing. Progressive loss of Kcnj10 expression was seen in Slc26a4-/- mice at the onset of hearing. Furthermore, free radical stress modulated the expression of Kcnj10 in cultured stria vascularis and in a heterologous expression system. The pendrin mRNA expression was marginal in the thyroid and did not correlate with serum T4 levels. Further, absence of pendrin did not affect free radical stress markers in the thyroid. These data suggest that free radical stress-mediated loss of Kcnj10 expression in stria vascularis contributes to deafness in the Pendred syndrome mouse model and that pendrin is not essential for the function of mouse thyroid gland.

Master of Science / Department of Electrical and Computer Engineering / Masaaki Tamura / Steven Warren / Lung cancer mortality is the highest among all cancer–associated deaths. Despite early detection and treatment, prognosis of this disease remains poor. Therefore, development of new therapeutic agents and effective treatment procedures are urgently needed. Endogenous Angiotensin II (Ang II) type 2 receptor (AT[subscript]2), one of two isoforms of Ang II, has been shown to mediate apoptosis. Nanoparticle delivery systems make possible targeted drug delivery and controlled release of therapeutic molecules and genes. Thus, the aim of this study was to determine the anti-cancer effect of the over-expressed AT[subscript]2 gene on lung adenocarcinoma cells in vitro using adenoviral vector (Ad-) and nanoparticle (NP-) based gene delivery systems. This study showed that over-expression of Ad-AT[subscript]2 induced cancer cell-specific apoptosis in several human lung adenocarcinoma cell lines with minimal effect on normal lung epithelial cells. Ad-AT[subscript]2 significantly attenuated multiple human lung cancers' cell growth (A549 and H358) in vitro compared to the control viral vector, Ad-[Beta]-galactosidase (Ad-LacZ) when examined by direct cell count. The growth attenuation effect was detected as early as 24 hours after Ad-AT[subscript]2 transfection and lasted 12 days. Western Blot analysis revealed the activation of the caspase pathway. Examination for Annexin V by flow cytometry also confirmed activation of the apoptotic pathway via AT[subscript]2 over-expression. Similarly, AT[subscript]2 cDNA encapsulated poly(DL-lactide-co-glycolide) (PLGA) biodegradable nanoparticles (NPs) were shown to be effectively taken up into lung cancer cells. Surface conjugation of the angiotensin II peptide significantly stimulated uptake of the particles. This PLGA vector-dependent AT[subscript]2 transfection was effective in sustained gene expression and resultant cell death. These results indicate that the AT[subscript]2 over-expression effectively attenuated growth of lung adenocarcinoma cells through activation of intrinsic apoptosis. Since PLGA safety has been proven, whereas adenoviral vectors have several drawbacks in safety, the Ang II conjugated PLGA nanoparticles may be a better therapeutic gene delivery system. Therefore, it is concluded that the discovery of AT[subscript]2 DNA encapsulated PLGA conjugated with the Ang II peptide is a potentially useful tool for lung cancer gene therapy.

Doctor of Philosophy / Department of Biochemistry / Anna Zolkiewska / Muscle satellite cells are the primary stem cells of postnatal skeletal muscle. Quiescent satellite cells become activated and proliferate during muscle regeneration after injury. They have the ability to adopt two divergent fates: differentiation or self-renewal. The Notch pathway is a critical regulator of satellite cell activation and differentiation. Notch signaling is activated upon the interaction of a Notch ligand present in a signal-sending cell with a Notch receptor present in a signal-receiving cell. Delta-like 1 (Dll1) is a mammalian ligand for Notch receptors. In this study, we found that Notch activity is essential for maintaining the expression of Pax7, a transcription factor associated with self-renewing satellite cells. We also demonstrated that Dll1 represents a substrate for several ADAM metalloproteases. Dll1 shedding takes place in a pool of Pax7-positive self-renewing cells, but Dll1 remains intact in differentiated myotubes. Inhibition of Dll1 shedding with a dominant-negative form of ADAM12 leads to elevated Notch signaling, inhibition of differentiation and expansion of the pool of self-renewing cells. We propose that ADAM-mediated shedding of Dll1 helps achieve an asymmetry in Notch signaling in initially equivalent myogenic cells and helps sustain the balance between differentiation and self-renewal. Pax7 plays a key role in protecting satellite cells from apoptosis. The mechanism of Pax7 protecting muscle satellite cells from apoptosis is not well understood. In the second part of this study, we show that Pax7 up-regulates manganese superoxide dismutase (MnSOD) at the transcriptional level, suggesting the involvement of MnSOD in Pax7-mediated cell survival. A specific chromosomal translocation involving the Pax7 gene and generation of a fusion protein Pax7-FKHR is found a childhood cancer, rhabdomyosarcoma. Furthermore, the level of the wild-type Pax7 is down-regulated in rhabdomyosarcomas. In the third part of this dissertation, we investigated the dominant-negative effect of Pax7-FKHR fusion protein on the wild-type Pax7, and found that the Pax7 protein level is down-regulated by Pax7-FKHR expression while the Pax7 mRNA level is not affected. We propose a specific microRNA-mediated inhibition of Pax7 mRNA translation by the oncogenic Pax7-FKHR fusion protein.

Master of Science / Genetics Interdepartmental Program / Bikram S. Gill / TILLING (Targeting Induced Local Lesions IN Genomes) is a high-throughput, reverse genetics strategy for scanning mutagenized populations for point mutations in loci of interest. Originally, TILLING was used to investigate gene function in Arabidopsis and has since been similarly applied for gene functional analysis in other organisms. TILLING also allows the generation of novel genetic variation in specific genotypes and, thus, has been implemented as a tool for crop improvement. Ethyl methanesulfonate (EMS) is a widely used mutagen to induce point mutations in most TILLING protocols. M1 plants are then self-pollinated and M2 seed harvested. A single seed is grown from each M2 progeny and tissue taken for DNA isolation. M3 seed is cataloged. DNA is pooled to increase the efficiency and aid in mutation detection. Polymerase chain reaction (PCR) is used to amplify a locus of interest using the M2 DNA pools as a template. The PCR products are digested with an endonuclease that cleaves mismatched, mutant DNA, and the digested products are visualized. The pools for which PCR products are positive for a mutation are deconvoluted to determine which individual plant of the pool was responsible for the mutation. DNA from the positive individual is sequenced to determine the type of mutation (missense, nonsense, synonymous). Individuals with mutations that are more likely to disrupt gene function (nonsense and certain missense) are studied further by growing the corresponding M3 generation. In bread wheat, Triticum aestivum, TILLING is complicated by polyploidy: genes that have homoeologs require that the functionality of each be studied. If functional homoeologs are present for all three genomes, mutants must be identified for each homoeolog, followed by successive intercrossing to produce a triple mutant plant. As a model for wheat genetics, we propose TILLING in diploid wheat. EMS mutant populations were created in diploid wheat (Triticum monococcum ssp. monococcum) and the hexaploid bread wheat cultivar ‘Jagger’. The diploid and hexaploid wheat populations were screened for mutations at the waxy locus, GBSS1, as a validation of our population and for comparative analysis of mutation rates in 2x and 6x wheat. For diploid wheat, GBSSI was screened in 716 M2 plants, and one mutant was found for 1.9 Mb screened. 3 For hexaploid wheat, GBSSI was screened in 518 M2 plants, and 30 mutants were identified within a total of 657 Kb screened, giving a mutation frequency of one mutation per 22 Kb. The reasons for this vast difference in mutation frequency between diploid and hexaploid wheat are discussed. The diploid wheat population was further examined by screening for mutations within four lignin biosynthesis candidate genes, for a total of 2 Mb screened. A single mutant was discovered for both of the lignin genes PAL6 and HCT, giving a mutation frequency of one mutation per 1 Mb screened.

Doctor of Philosophy / Department of Chemistry / Paul E. Smith / In the past several decades, molecular dynamics (MD) simulations have played an important role in providing atomic details for phenomena of interest. The force field used in MD simulations is a critical factor determining the quality of the simulations. Kirkwood-Buff (KB) theory has been applied to study preferential interactions and to develop a new force field. KB theory provides a path from quantities determined from simulation data to the corresponding thermodynamic data. Here we combine KB theory and molecular simulations to study a variety of intermolecular interactions in solution. First, a force field for the computer simulation of aqueous solutions of alcohols is presented. The force field is designed to reproduce the experimentally observed density and KB integrals for a series of alcohols, allowing for an accurate description of alcohols’ activity. Other properties such as the translational diffusion constant and heat of mixing are also well reproduced. Second, the newly developed force field is then extended to more complicated systems, such as peptide or mini-proteins, to determine backbone dihedral potentials energetics. The models developed here provide a basis for an accurate force field for peptides and proteins. Third, we have then studied the surface tension of a variety water models. Results showed that different simulation conditions can affect the final values of surface tension. Finally, by using the Kirkwood-Buff theory of solution and surface probability distributions, we attempted to characterize the properties of the Gas/Liquid interface region. The same approach is then used to understand the relationship between changes in surface tension, the degree of surface adsorption or depletion, and the bulk solution properties.

Doctor of Philosophy / Department of Biology / Rollie J. Clem / Apoptosis is an extremely conserved process among metazoans. This dissertation will describe apoptotic regulation in two orders of insects, Lepidoptera and Diptera. In the lepidopteran host Trichoplusia ni, we describe phenotypes of infection with the baculovirus AcMNPV lacking the caspase inhibitor gene P35. In the lepidopteran host Spodoptera frugiperda, infection with this mutant virus results in apoptosis, which dramatically hinders spread of the virus in the host. In T. ni, however, infection with this mutant virus is similar to wild-type with normal spread, but the end result of liquefaction does not occur. Experiments indicated that infection of T. ni cells with the P35 mutant virus (P35Δ) resulted in caspase activation, and the P35Δ virus lacked the ability to inhibit these active caspases. With the P35Δ virus a slower entry phenotype was observed, but when the P35Δ virus was grown in the presence of a caspase inhibitor the entry phenotype was rescued. This indicated that caspases have detrimental effects on budded virions, and illustrated that P35 is needed to make robust virions. With regards to Diptera, apoptosis-regulatory genes were annotated in the yellow fever mosquito, Aedes aegypti. The genes annotated included multiple caspases and caspase regulators. Phylogenetic relationships were determined among the caspases from Anopheles gambiae, Ae. aegypti and Drosophila melanogaster, expression patterns were determined for all the annotated genes in Ae. aegypti, and one of the genes, an IAP antagonist named IMP, was functionally characterized. Further characterization of the phylogenetic relationships of caspases from fifteen dipteran species was performed by obtaining gene models for caspases of recently sequenced genomes for twelve Drosophila species and three mosquito species. Furthermore, several Drosophila and mosquito species were found to contain caspase genes with substitutions in critical active site residues. These genes were proposed to encode caspase-like decoy molecules. While these have been found in humans and nematodes, this is the first report for these molecules in insects. One of the caspase-like decoy molecules was found to increase the activity of its paralog caspase.

Doctor of Philosophy / Department of Biology / Susan J. Brown / RNA interference (RNAi) is a natural gene-silencing phenomenon triggered by dsRNA (dsRNA). While RNAi is an endogenous process that plays essential roles in regulating gene expression it can also be harnessed as a tool for the study of gene function. Introducing dsRNA that is homologous to target mRNA into a cell triggers the RNAi response causing the destruction of the homologous mRNA and a loss of function phenotype. In some organisms, such as the nematode Caenorhabditis elegans, once dsRNA is introduced into the body cavity, the RNAi effect is seen throughout the organism because the dsRNA is taken up by individual cells and is then spread from cell to cell. This process has been termed the systemic RNAi response. For other organisms, such as the fruit fly Drosophila melanogaster, introduction of dsRNA into the body cavity does not result in a systemic RNAi response. This may be due to the cell’s inability to take up dsRNA or spread that dsRNA from cell to cell. For other organisms, including mammals, introduction of dsRNA into the body cavity does not result in a systemic RNAi response because the immune response causes dsRNA destruction before it can be utilized in the RNAi pathway. For organisms that do not exhibit a systemic RNAi response, complex genetic methods are needed to introduce dsRNA into cells to induce the RNAi response. Therefore, one of the challenges in utilizing RNAi as a genetic tool is introducing the dsRNA into individual cells. In recent years, systemic RNAi responses have been documented in both model and non-model organisms, making RNAi an accessible genetic tool. The red flour beetle, Tribolium castaneum is an emerging model organism that has a robust systemic RNAi response. However, the mechanism of systemic RNAi and the specific parameters required to obtain a strong systemic RNAi response in this organism have not been thoroughly investigated. The aim of this work is to provide data that can allow RNAi to be better utilized as a genetic tool in Tribolium and to use this information as a basis for the use of RNAi in other insects in which it can be performed. Specifically we provide data on the essential parameters necessary to achieve an effective systemic response in Tribolium, we describe differences in the systemic RNAi response between Drosophila and Tribolium, we analyze the conservation and function of RNAi machinery genes in Tribolium and we provide information on the genes critical for a systemic RNAi response in Tribolium.

Doctor of Philosophy / Department of Biochemistry / Karl J. Kramer / Subbarat Muthukrishnan / Chitin, a linear homopolymer of beta-1,4-linked N-acetylglucosamine, is the second most abundant biopolymer next to cellulose. It is the major structural polysaccharide in the insect’s exoskeleton and gut lining. An extensive study of two of the major genes encoding enzymes involved in chitin metabolism, chitin synthases (CHSs) and beta-N-acetylglucosaminidases (NAGs), was undertaken. CHS genes from the tobacco hornworm, Manduca sexta, and NAG genes from the red flour beetle, Tribolium castaneum, were identified and characterized. In general, chitin deposition occurs in two major extracellular structures of insects, the cuticle that overlays the epidermis, and the peritrophic membrane (PM) that lines the midgut. Only two CHS genes were identified in M. sexta using Southern blot analysis. Extensive expression studies of both M. sexta CHS genes, MsCHS1 and MsCHS2, suggest a strict functional specialization of these two genes for the synthesis of epidermal and PM-associated chitin, respectively. Furthermore, two alternatively spliced transcripts of MsCHS1, MsCHS1a and MsCHS1b, were identified. Analysis of the levels of these transcripts in different tissues and stages of development indicated that the MsCHS1a transcript predominates in the integument during the feeding and pupal stages, whereas the MsCHS1b transcript is more abundantly present in the tracheae, foregut, and hindgut during all developmental stages tested. Four genes encoding putative NAGs (TcNAG1, TcNAG2, TcNAG3, and TcNAG4) were identified by searching the Tribolium genomic database. The full-length cDNAs for all four NAGs were cloned and sequenced, and the exon-intron organizations were determined. Studies on developmental expression patterns of each gene indicated that they are expressed during most developmental stages with TcNAG1 being the predominant one. The function of each NAG was assessed by down regulating the level of each transcript at various developmental stages using RNA interference. Selective knock down of each transcript, without significant reduction in the expression levels of the other NAG transcripts, was verified and the resulting phenotypes were documented. Knockdown of TcNAG1 interrupted larval-larval, larval-pupal, and pupal-adult molting, and the insects were unable to completely shed their old cuticles.

Master of Science / Department of Entomology / David C. Margolies / Yoonseong Park / Phytoseiulus persimilis (Acari: Phytoseiidae) is a specialist predator on tetranychid mites, especially on the twospotted spider mite, Tetranychus urticae Koch (Acari: Tetranychidae). The foraging environment of the predatory mites consists of prey colonies distributed in patches within and among plants. Quantitative genetic studies have shown genetic variation in, and phenotypic correlations among, several foraging behaviors within populations of the predatory mite, P. persimilis. The correlations between patch location, patch residence, consumption and oviposition imply possible fitness trade-offs. We used molecular techniques to investigate genetic variation underlying the foraging behaviors. However, these genetic studies require a sufficiently large amount of DNA which was a limiting factor in our studies. Therefore, we developed a method for obtaining DNA from a single mite by using a chelex extraction followed by whole genome amplification. Whole genome amplification from a single mite provided us with a large quantity of high-quality DNA. We obtained more than a ten thousand-fold amplified DNA from a single mite using 0.01ng as template DNA. Sequence polymorphisms of P. persimilis were analyzed for nuclear DNA Inter Transcribed Spacers (ITS1 & ITS2) and for a mitochondrial 12S rRNA. The sequence comparisons among individuals identified a number of polymorphisms in the 12S sequences. The foraging gene (for) associated with rover-sitter behavioral strategies of Drosophila is known to have role in feeding behaviors of honeybee and other arthropods. We surmised that the same or a similar gene may be present in P. persimilis. Among the foraging behavior(s) exhibited by this predatory mite, we were particularly interested in resource/prey-dependent dispersal behavior. We isolated a partial sequence that is presumed to be the orthologue of the foraging (for) gene. We named the putative foraging gene as Ppfor (for Phytoseiulus persimilis foraging gene). We used a fragment of Ppfor gene as a molecular marker between populations and among individuals and, further, to help understand behavioral phenotypes.

Doctor of Philosophy / Department of Biology / Susan J. Brown / All arthropods share a segmented body plan. Detailed studies on segmentation mechanisms in the long-germ insect Drosophila melanogaster identified a segmentation hierarchy composed of maternal, gap, pair-rule, and segment polarity genes. In this hierarchy, pair-rule genes play an important role to translate gradients of regional information from maternal and gap genes into segmental expression of segment polarity genes. However, our understanding of the role of pair-rule genes in other short-germ insects and basally branching arthropods is still limited. To gain insights into the role of pair-rule genes in short-germ segmentation, I analyzed genetic interactions as well as expression patterns and functions of homologs of Drosophila pair-rule genes in the short-germ insect Tribolium castaneum. Interestingly, despite the pair-rule like expression patterns of Tribolium homologs of almost all eight canonical Drosophila pair-rule genes, only five have a segmentation function. Knock-down of primary pair-rule genes caused asegmental and truncated phenotypes while knock-down of secondary pair-rule genes caused typical pair-rule phenotypes. Epistatic analysis between the genes revealed that primary pair-rule genes form a gene circuit to prepattern a two-segmental unit, and secondary pair-rule genes are downstream targets of the gene circuit. The typical pair-rule phenotypes observed in secondary pair-rule gene RNAi embryos led to a detailed comparative analysis of the role of paired (prd) and sloppy-paired (slp) between Drosophila and Tribolium. This study revealed that prd is functionally conserved while the functional parasegmental register for Tribolium slp is opposite that of Drosophila slp. The fact that the register of slp function has evolved differently in the lineages leading to Drosophila and Tribolium reveals an unprecedented flexibility in pair-rule patterning. Despite this flexibility in pair-rule patterning between Drosophila and Tribolium, segmental expression of engrailed (en) and wingless (wg) at parasegmental boundaries is conserved in both insects. Analysis of double and triple RNAi for pair-rule genes in Tribolium revealed that the primary pair-rule genes even-skipped and runt are redeployed to directly regulate en and wg with prd or slp at parasegmental boundaries. This redeployment of primary pair-rule genes seem to compensate for the apparently fewer number of functional secondary pair-rule genes in Tribolium segmentation.