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.

Glycogen synthase kinase-3 (GSK-3) alpha and beta are central regulators of key developmental pathways, including Wnt, Hedgehog and Notch, which control stem cell activities and cellular differentiation. Both forms of GSK-3 are also regulated by receptor tyrosine kinases via the PI3K/Akt growth-promoting pathway and are involved in feedback mechanisms that maintain signaling homeostasis. These signaling systems have critical functions in mammary gland development and aberrations in them have been implicated in breast cancer. However, the role of GSK-3 in breast oncogenesis is unclear. Here, I provide evidence that maintenance of appropriate GSK-3 activity is necessary for normal acinar morphogenesis of mammary cells in the ductal/alveolar epithelium. Inadequate GSK-3 levels result in enlarged structures that often lack hollow lumens and resemble early premalignant breast cancer lesions. A potential contribution for PI3K signaling to this phenotype was identified as a PI3K inhibitor partially reversed the observed morphological defects. Mammary epithelial cell (MEC) identity also requires modulation of signals through the Wnt/beta-catenin pathway. GSK-3-depleted mammary glands not only transdifferentiate into squamous epithelium but also develop highly proliferative adenosquamous carcinomas characterized by activated beta-catenin. Furthermore, beta-catenin appears to be required for both cell fate changes and tumorigenesis in the absence of GSK-3 function. Mammary tissues engineered to enable conditional deletion of beta-catenin in a GSK-3-null background also assumed an epidermoid cell fate with ensuing tumor formation albeit with a significantly longer latency and different histopathology. The metaplastic nature of tumors observed is similar to a rare yet aggressive form of human breast disease, metaplastic breast carcinomas (MBCs). Mammospheres (MS) generated from GSK-3 depleted MECs exhibited a less compact morphology compared to those with activated beta-catenin, which also exhibited an expansion of the CD24:CD49f double positive progenitor population and enhanced self-renewal. No MS were formed by MECs lacking GSK-3 and beta-catenin. ErbB2/Neu-mediated mammary tumor progression has been associated with Wnt/beta-catenin pathway activation. Loss of beta-catenin delayed tumor onset in a constitutively active ErbB2 mouse model but did not alter either the luminal characteristics of the ensuing tumors nor their metastatic potential. Collectively these studies indicate GSK-3 plays important roles in mammary gland function thereby suppressing mammary tumor formation.

Glycogen synthase kinase-3 (GSK-3) alpha and beta are central regulators of key developmental pathways, including Wnt, Hedgehog and Notch, which control stem cell activities and cellular differentiation. Both forms of GSK-3 are also regulated by receptor tyrosine kinases via the PI3K/Akt growth-promoting pathway and are involved in feedback mechanisms that maintain signaling homeostasis. These signaling systems have critical functions in mammary gland development and aberrations in them have been implicated in breast cancer. However, the role of GSK-3 in breast oncogenesis is unclear. Here, I provide evidence that maintenance of appropriate GSK-3 activity is necessary for normal acinar morphogenesis of mammary cells in the ductal/alveolar epithelium. Inadequate GSK-3 levels result in enlarged structures that often lack hollow lumens and resemble early premalignant breast cancer lesions. A potential contribution for PI3K signaling to this phenotype was identified as a PI3K inhibitor partially reversed the observed morphological defects. Mammary epithelial cell (MEC) identity also requires modulation of signals through the Wnt/beta-catenin pathway. GSK-3-depleted mammary glands not only transdifferentiate into squamous epithelium but also develop highly proliferative adenosquamous carcinomas characterized by activated beta-catenin. Furthermore, beta-catenin appears to be required for both cell fate changes and tumorigenesis in the absence of GSK-3 function. Mammary tissues engineered to enable conditional deletion of beta-catenin in a GSK-3-null background also assumed an epidermoid cell fate with ensuing tumor formation albeit with a significantly longer latency and different histopathology. The metaplastic nature of tumors observed is similar to a rare yet aggressive form of human breast disease, metaplastic breast carcinomas (MBCs). Mammospheres (MS) generated from GSK-3 depleted MECs exhibited a less compact morphology compared to those with activated beta-catenin, which also exhibited an expansion of the CD24:CD49f double positive progenitor population and enhanced self-renewal. No MS were formed by MECs lacking GSK-3 and beta-catenin. ErbB2/Neu-mediated mammary tumor progression has been associated with Wnt/beta-catenin pathway activation. Loss of beta-catenin delayed tumor onset in a constitutively active ErbB2 mouse model but did not alter either the luminal characteristics of the ensuing tumors nor their metastatic potential. Collectively these studies indicate GSK-3 plays important roles in mammary gland function thereby suppressing mammary tumor formation.

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.

Doctor of Philosophy / Department of Anatomy and Physiology / Michael J. Kenney / It is well established that normal aging is associated with progressive increases in efferent sympathetic nerve discharge (SND). Type II diabetes, obesity, heart failure, and hypertension are pathologies that have been attributed to both the processes of aging and sympathetic dysfunction, exemplifying the importance of understanding central regulation of SND during aging. However, the central mechanisms mediating altered SND with advancing age remain unclear. The rostral ventral lateral medulla (RVLM) is a brainstem region critically involved in setting the basal level of sympathetic outflow and cardiovascular function. Indeed, the RVLM is the only presympathetic region that when bilaterally inactivated results in profound reductions in both SND and arterial pressure. Glutamatergic influences in RVLM activity are powerfully inhibited by tonic GABAergic neural inputs originating from the caudal ventral lateral medulla (CVLM); effects that are mediated by GABAA receptors located on presympathetic neuronal cell bodies within the RVLM. In the present study we proposed that reductions in GABA[subscript A] receptor subunit gene expression may reflect withdrawal of GABAergic tone in the RVLM thereby contributing to the basal sympathetic activation that occurs with advancing age. Therefore, the objective of the current study was to identify age-related changes in the constitutive expression of genes related to GABAergic and muscarinic, nicotinic and dopaminergic receptor systems due to their reported involvement in modulating GABA[subscript A] receptor function, in the RVLM of adult young (3-5 mo. old), middle-aged (12 mo. old), weight stable presenescent (24-25 mo. old) and senescent (>24 mo. old) Fischer 344 (F344) rats using a commercially available real-time PCR array. Real-time analysis revealed nonuniform and age-associated changes in the RVLM GABA, muscarinic, nicotinic and dopaminergic neurotransmitter gene expression profile between young and middle-aged F344 rats. Heterogeneous expression of genes related to these neurotransmitters was also observed between presenescent and senescent F344 rats. Our results suggest that potential changes in neurotransmitter synthesis and degradation, uptake, transport, signaling and receptor subunit composition may account for the sympathoexcitatory state that is commonly observed in the aged.

Doctor of Philosophy / Department of Diagnostic Medicine/Pathobiology / Roman Reddy R. Ganta / Ehrlichia chaffeensis, an emerging tick-borne pathogen, causes human monocytic ehrlichiosis (HME). The relationship between E. chaffeensis and its target cells in ticks and vertebrates is critical as the organism must persist in them. We hypothesize that E. chaffeensis alters gene expression in support of adapting to dual hosts. In support of testing this hypothesis, we developed an ORF-based microarray and performed global transcriptional analysis on the pathogen grown in macrophage and tick cells. The analysis revealed the expression of about 30% of all the predicted E. chaffeensis genes, in macrophages or tick cell. Two-thirds of the transcribed genes are common for both host cell backgrounds. About 20% of the commonly expressed genes also varied in expression levels which ranged from two to five fold. Microarray data was verified by RT-PCR for a subset of randomly selected genes. Together, this is the first report describing the global host cell-specific gene expression patterns in E. chaffeensis. Differential gene expression may be an important adaptive mechanism used by E. chaffeensis for its continued survival in dual hosts. To test this hypothesis, we established many basic protocols and tools needed for performing mutational analysis in E. chaffeensis. Four antibiotic selection markers; gentamicin, chloramphenicol, spectinomycin and rifampin, and two promoters constitutively expressed in E. chaffeensis, genes rpsL and tr, were identified. Two regions of the genome were also identified for performing initial mutational analysis. Several plasmid constructs were also made. The optimal conditions for introducing these plasmids into host cell-free viable E. chaffeensis organisms were also established. The molecular evaluation of several E. chaffeensis transformants using these plasmids suggested that the plasmids gained entry, but failed to get integrated into the genome or remain in the bacteria for longer periods of time. In summary, we demonstrated global host cell-specific differential gene expression in E. chaffeensis by employing microarray analysis. Numerous host-specific expressed genes will be important for studies leading to effective methods of control. We also established several basic protocols and tools needed for performing mutational analysis useful in evaluating the impact of the loss of expression of uniquely expressed genes.

Doctor of Philosophy / Department of Biochemistry / Michael R. Kanost / Manduca sexta is a large insect species well-suited for biochemical analysis of proteins in the hemolymph (blood) that respond to infection. Insects lack adaptive immunity and rely entirely on innate immunity to prevent and manage infection. Immune response proteins include proteins that bind pathogens and activate serine proteases, which function in proteolytic cascades that trigger effector responses, such as antimicrobial peptide production and prophenoloxidase activation. Phenoloxidase catalyzes melanin synthesis, which leads to microbial killing. I used MALDI-TOF/TOF mass spectrometry and immunoblotting to identify M. sexta proteins present in putative immune complexes. From analyses of high molecular weight gel filtration fractions of plasma activated by microbial polysaccharides, I detected hemocytin, prophenoloxidase, and cleaved serine protease homologs, suggesting prophenoloxidase and serine protease homologs form large complexes in plasma. I used in vitro bacterial binding assays to identify hemolymph proteins that bind either directly or indirectly to the surface of bacteria or curdlan. Prophenoloxidase, annexin IX, and hemocyte aggregation inhibitor protein were found bound to all the samples tested, indicating they play a role in the early stage of immune response. Serpins regulate specific active proteases by covalently binding and forming serpin-protease complexes. Serpin-1, an abundant plasma protein, has an alternatively spliced ninth exon encoding 12 serpin-1 isoforms that differ in inhibitory selectivity. RT-PCR showed that all 12 isoforms are expressed in hemocytes, fat body, and midgut. Comparisons of naïve and immune-challenged hemocytes and fat body indicated the immune-related upregulation of serpin-1A but not the other isoforms. Using immunoaffinity chromatography I isolated two serpin-1-protease complexes from plasma after activation with bacterial lipopolysaccharide. MALDI-TOF/TOF analysis of these serpin-1-protease complexes identified the digestive enzyme chymotrypsin as a specific target of serpin-1K. Nine out of the twelve serpin-1 isoforms were identified from control plasma at the protein level using 2D-PAGE. Serpin-1 protease complexes were identified by 2D-PAGE analysis: serpin-1A, E and J were found to be complexed with hemolymph proteinase-8 and an unidentified isoform of serpin-1 was complexed with hemolymph proteinase-1. Discovering the serpin-1 isoforms that inhibit specific proteases enhances our understanding of the regulation of proteolytic cascades in M. sexta.

Master of Science / Department of Biochemistry / Qize Wei / Proper regulation of mitosis and cytokinesis is fundamentally important for all living organisms. During anaphase, antiparallel microtubules are bundled between the separating chromosomes, forming the central spindle (also called the spindle midzone), and the myosin contractile ring is assembled at the equatorial cortex. Regulators of central spindle formation and myosin contractile ring assembly are mostly restricted to the interdigitated microtubules of central spindles and they can be collectively called midzone components. It is thought that characteristic microtubule configurations during mitosis and cytokinesis are dictated by the coordinated action of microtubule-stabilizing and -destabilizing factors. Although extensive investigations have focused on understanding the roles of microtubule-bundling/stabilizing factors in controlling central spindle formation, efforts have been lacking in aiming to understand how microtubule-destabilizing factors regulate the assembly of central spindles. This dissertation describes the role of a novel microtubule-destabilizing factor termed CCDC69 (coiled-coil domain-containing protein 69) in controlling the assembly of central spindles and the recruitment of midzone components. Endogenous CCDC69 was localized to the nucleus during interphase and to the central spindle during anaphase. Exogenous expression of CCDC69 in HeLa cells destabilized microtubules and disrupted the formation of bipolar mitotic spindles. RNA interference (RNAi)-mediated knockdown of CCDC69 led to the formation of aberrant central spindles and interfered with the localization of midzone components such as aurora B kinase, protein regulator of cytokinesis 1 (PRC1), MgcRacGAP/HsCYK-4, and pololike kinase 1 (Plk1) at the central spindle. CCDC69 knockdown also decreased equatorial RhoA staining, indicating that CCDC69 deficiency can impair equatorial RhoA activation and ultimately lead to cytokinesis defects. Four coiled-coil domains were found in CCDC69 and the C terminal coiled-coil domain was required for interaction with aurora B. Disruption of aurora B function in HeLa cells by treatment with a small chemical inhibitor led to the mislocalization of CCDC69 at the central spindle. Further, vitro kinase assay showed that Plk1 could phosphorylate CCDC69. Taken together, we propose that CCDC69 acts as a scaffold and a microtubule-destabilizing factor to control the recruitment of midzone components and the assembly of central spindles.