Master of Science / Department of Biology / Rollie Clem / Apoptosis, or programmed cell death, is a crucial conserved process among organisms for deleting damaged unwanted cells, as well as for development and viral defense, and plays an important role in multiple diseases. Too much apoptosis may lead to Alzheimer’s disease, and too little may result in cancer. Therefore, the ability to understand this process is essential for improved medical knowledge today. Apoptosis has been explored in a number of species and pathways seem relatively conserved among most, with unique aspects contained in each, but little is known about apoptosis in mosquitoes. Improved knowledge and growing interest concerning apoptosis in mosquitoes is necessary considering the vast health effects seen across the globe as a result of diseases transferred by the mosquito vector. The Dengue virus mosquito vector Aedes aegypti was the focus here. A new player named defense repressor 1 was discovered in Drosophila melanogaster (DmDnr1), shown to play a role in apoptosis, and the homolog discovered in A. aegypti (AeDnr1). Silencing Dmdnr1 resulted in cells sensitized to apoptosis but was not enough to induce spontaneous apoptosis. In contrast, silencing Aednr1 in the A. aegypti cell line, Aag2, led to spontaneously induced apoptosis. This showed the importance of AeDnr1 as a member of the apoptotic pathway in this species. Epistasis experiments showed that apoptosis induced by silencing Aednr1 requires the initiator caspase Dronc and the effector caspase CASPS8, whereas apoptosis induced by silencing the inhibitor of apoptosis, Aeiap1, also requires Dronc but acts through the effector caspase CASPS7. Further epistasis experiments showed that apoptosis induced by silencing Aednr1 requires the IAP antagonist Mx, but not IMP. This showed for the first time a gene regulating upstream of an IAP antagonist. Biochemical studies showed that AeDnr1 regulates active CASPS8 but not CASPS7, and interacts with Mx and CASPS8 but not AeDronc, CASPS7 nor AeIAP1. Studies also showed Mx competes effectively with CASPS8 but not CASPS7 for AeIAP1 binding, and IMP competes effectively with CASPS7 but not CASPS8 for AeIAP1 binding. An improved apoptosis pathway for the mosquito A. aegypti emerged involving a potential feedback loop with explanations for the upstream IAP antagonist preference as well as the downstream effector caspase preference resulting from apoptosis induced by Aednr1 silencing. Through the discussed research, multiple unique findings resulted. Studying the mosquito model will allow us to find certain gene relations that are more difficult to uncover in the Drosophila model. Because Dnr1 is found in most systems, this improved pathway may shed light not only on a potential role of Dnr1 in apoptosis in insects but higher organisms as well.

Doctor of Philosophy / Department of Biochemistry and Molecular Biophysics / John M. Tomich / Success for gene therapy clinical protocols depends on the design of safe and efficient gene carriers. Nature had already designed efficient DNA or RNA delivery devices, namely virus particles. However, the risk of insertional mutagenesis has limited their clinical use. Alternatively, safer approaches involving non-viral carriers have been and continue to be developed. While they have been reported to be less efficient than viral vectors, adding genome editing elements to pDNA makes the integration of corrective sequence site specific moving non-viral gene delivery systems closer to clinical applications. Over the last decade, peptides have emerged as a new family of potential carriers in gene therapy. Peptides are easy to synthesize, quite stable and expected to produce minimally immunogenic and inflammatory responses. We recently reported on a new class of Branched Amphiphilic Peptides Capsules (BAPCs) that self-assemble into extremely stable nano-spheres. BAPCs display a uniform size of _20 nm if they are incubated at 4_C and they retain their size at elevated temperatures. In the presence of DNA, they can act as cationic nucleation centers around which DNA winds generating peptide-DNA complexes with a size ranging from 50nm to 100nm. However, if BACPs are not incubated at 4_C, the pattern of interaction with DNA differs. Depending of the peptide/DNA ratios, the peptides either coat the plasmid surface forming nano-_bers (0.5-1 _M in length) or condense the plasmid into nano-sized structures (100-400nm). Different gene delivery efficiencies are observed for the three types of assemblies. The structure where the DNA wraps around BAPCs display much higher transfection efficiencies in HeLa cells in comparison to the other two morphologies and the commercial lipid reagent Lipofectinr. As a proof of concept, pDNA was delivered in vivo, as a vaccine DNA encoding E7 oncoprotein of HPV-16. It elicited an immune response activating CD8+ T cells and provided anti-tumor protection in a murine model.

Master of Science / Division of Biology / Stella Y Lee / Neuronal Ceroid Lipofuscinoses (NCLs) are a group of lysosomal storage diseases that are characterized by accumulating autofluorescent lipopigments in cells. NCLs are a form of progressive neurodegenerative diseases with symptoms ranging from blindness, loss of speech and motor activities to ataxia and seizures. Patients do not live to adulthood in most cases, making it prevalent in children. Among the many genes that cause NCL, CLN5 leads to different forms of NCL (infantile, late infantile, juvenile, and adult). CLN5 protein resides in the lysosomes but its function has not been established. It is predicted to contain eight N-glycosylation sites, but the role of N-glycosylation on its function and trafficking has not been assessed. We analyzed the role of N-glycosylation on the transport and stability of human CLN5. We created N-glycosylation mutants of each site by changing the Asn to Gln and our analysis of these mutants show that all the eight N-glycosylation sites are used in vivo. We also report effects of abolishing individual N-glycosylation sites on the trafficking of CLN5. While the lack of glycosylation at some sites results in CLN5 being retained in the ER or Golgi, others do not affect CLN5 trafficking. Cycloheximide chase experiments show that one of the mutants (N401Q) in CLN5 leads to lower protein levels in cell pellets with an increased secretion compared to CLN5 wild type, while other mutations show differential stability in cell pellets. These results demonstrate that each N-glycosylation site plays a different role(s) in the stability, transport and/or function of CLN5.

Doctor of Philosophy / Department of Biology / Alexander Beeser / Large-scale genomic approaches have demonstrated many atypical dual specificity phosphatases (DUSPs) are differentially expressed or mutated in cancer. DUSPs are proteins predicted to have the ability to dephosphorylate Ser/Thr and Tyr residues, and the atypical DUSP subgroup contains at least 16 members with diverse substrates that include proteins, nucleic acids, and sugars, and some of the atypical DUSPs function in the cell not as phosphatases but as scaffolds in signal transduction pathways. Of the atypical DUSPs, DUSP12 is one of the most evolutionarily conserved with homologs found in organisms ranging from yeast to humans. DUSP12 is of particular interest as it has been identified to be one of only two candidate genes for the target of a genetic amplification found in liposarcomas. Furthermore, DUSP12 may be an oncogene in that over-expression of dusp12 in cell culture promotes apoptosis resistance, cell motility, and the up-regulation of two established oncogenes, the hepatocyte growth factor receptor (c-met) and integrin alpha 1 (itga1). Additionally, DUSP12 may protect from apoptosis by functioning as a regulator of stress-induced translation repression and stress granule formation that may be due to its interaction with the DEAD Box RNA Helicase, DDX3.

Doctor of Philosophy / Biochemistry and Molecular Biophysics / Jeroen Roelofs / The proteasome is a large protease in the cell that contributes to the controlled degradation of proteins. This 2.5MDa 26S proteasome complex consists of a 19S regulatory particle (RP) that recognizes substrates and a 20S proteolytic core particle (CP) that hydrolyses substrates. To function optimally all 66 subunits of the proteasome complex need to assemble properly. Efficient and accurate assembly of the proteasome is achieved with the help of proteins that can monitor the quality of the proteasome during pre- and post-assembly processes. The work in this thesis described an investigation into two of such quality control mechanisms. Pba1-Pba2 dimer has been known to facilitate the CP assembly by interacting with the top of the α-ring of CP throughout CP maturation. After CP maturation, RP utilizes same surface to form a CP-RP complex. Our data showed that Pba1-Pba2 binds tightly to the immature CP and prevents RP association. Once matured CP has a reduced affinity for Pba1-Pba2 and shows a higher affinity towards RP, resulting the formation of 26S proteasome complex. Our results imply that during maturation, CP undergoes conformational changes that results in this switch in affinity. Mathematical models indicate that during assembly such an 'affinity switch' quality control mechanism is required to prevent immature CP-RP complex formations. These types of wrong dead end products prevent efficient proteasome complex formation. Proteasomes formed with post-assembly defects are enriched with the proteasome associated protein Ecm29. Here Ecm29 is proposed to function as a quality control factor that inhibits such defective proteasomes to avoid aberrant protein degradation. This would require Ecm29 to preferably bind to mutant proteasomes. While we know Ecm29 interacts with RP as well as CP, we still don’t understand well how it binds to proteasomes holoenzyme. Here, we identify that besides the Rpt5 subunit of RP, Ecm29 binds to alpha7. We showed that conserved acidic residues containing unstructured C-terminal region of the CP subunit alpha7 facilitates the Ecm29-Proteasome interactions. Further mapping revealed the importance of phosphorylation of serine residues at the alpha7 C-terminal tail for Ecm29 interaction. We anticipate that this study leads to identification of specificity of the Ecm29 for the defective proteasomes. Overall this will help us to understand the role of Ecm29 in regulation of defective proteasomes in vivo.

Master of Science / Department of Biology / Tonia L. Von Ohlen / The Drosophila embryonic nervous system develops from an array of neural precursor cells called, neuroblasts. These neuroblasts give rise to all the cell types that populate the mature central nervous system (CNS). The CNS originates from a bilateraly symmetric neurectoderm that is subdivided into three domains along the dorso-ventral (DV) axis. One of these domains is defined by the expression of the Homeodomain protein ventral nervous system defective (vnd). Regulation of neuroblast designation is very precise and controlled. Extensive research has been done on neuroblast formation along the anteroposterior axis, most of which indicates that neuroblast selection within a cluster of neurectodermal cells is controlled by segmentation genes. However, much more research is required to elucidate the function of genes along the DV axis. Early studies indicate that vnd is required for neuroblast formation in the ventral column. Here, we show that vnd function, but not expression, is dependent on MAPK activity downstream of Drosophila EGF-R (DER). Specifically, we show that vnd activity is eliminated in EGF-R mutant embryos in a stage specific manner by evaluating vnd’s ability to inhibit intermediate neuroblast defective (ind), muscle segment homeobox (msh), and the newly identified neural tube development player, neu3. Finally, we show that DER functionality in the ventral column is entirely dependent on the processing protein rhomboid (rho) in later stage embryos.

Master of Science / Department of Chemistry / Christopher T. Culbertson / Capillary isoelectric focusing (cIEF) is one of several electrophoretic separation techniques for proteins and various other bio - molecules widely used in biochemistry laboratories. A wide range of analytes separable by the different modes of Capillary Electrophoresis (CE) includes from a small organic or an inorganic molecule to the complex bio-molecules such as protein, peptides, cell organelles, and live microorganisms (e.g. bacteria and viruses). Of the various modes of electrophoresis, Isoelectric focusing (IEF) is a good method for the separation of large amphoteric molecules such as peptides and proteins because of the attainment of overall surface charge depending up on its environment pH. This thesis mainly focuses on application of cIEF for proteins separation and viruses’ detection, which is one of the biggest concerns of human and animal health because of viral outbreak causing loss of thousands of lives and property every year. In chapter one of this thesis, the principles and mechanisms of separation of CE, cIEF, comparative advantages of dynamic coatings over static coating, and advantages of Whole Column Imaging Detection (WCID) over On - olumn Single Point Detection have been discussed. Chapter two includes experimental procedure and calculations for EOF determination. The results of cIEF experiments with standard proteins to develop calibration curve followed by UV absorbance detection of two bacteriophage viruses TR4 and T1 are presented in the chapter three. Final chapter four includes the conclusion and discussion on future direction for the project. The main motivation for this work was to develop a method which is less labor intensive and requires shorter detection time compared to traditional detection methods such as virus culture in serology (7days), polymerase chain reaction (PCR) and gel electrophoresis (6hrs to 2days). A commercially available dynamic coating reagent, EoTrol LN® copolymer used our CE experiments found to be more convenient and efficient than commonly used surface modifiers for example silane-based reagents. Preliminary determination of the pIs of these T1 and TR4 by cIEF was 3.1 ± 1.0 and 6.8 ± 1.0 respectively. The pI of viruses can differ by their strains and the phase of virus - growth. The viruses, though closely related, are easily distinguishable by their different pIs.

Master of Science / Department of Anatomy and Physiology / Masaaki Tamura / Previous studies have shown that both human and rat umbilical cord matrix mesenchymal stem cells (UCMSC) possess the ability to control the growth of breast carcinoma cells. Comparative analysis of two types of UCMSC suggest that rat UCMSC-dependent growth regulation is significantly stronger than that of human UCMSC. Accordingly, the present study was designed to clarify their different tumoricidal abilities by analyzing gene expression profiles in two types of UCMSC. Gene expression profiles were studied by microarray analysis using Illumina HumanRef-8-V2 and RatRef-12 BeadChip for the respective UCMSC. The gene expression profiles were compared to untreated naïve UCMSC and those co-cultured with species-matched breast carcinoma cells; human UCMSC vs. MDA-231 human carcinoma cells and rat UCMSC vs. Mat B III rat carcinoma cells. The following selection criteria were used for the screening of candidate genes associated with UCMSC-dependent tumoricidal ability; 1) gene expression difference should be at least 1.5 fold between naive UCMSC and those co-cultured with breast carcinoma cells; 2) they must encode secretory proteins and 3) cell growth regulation-related proteins. These analyses screened 17 common genes from human and rat UCMSC. The comparison between the two sets of gene expression profiles identified that two tumor suppressor genes, adipose-differentiation related protein (ADRP) and follistatin (FST), were specifically up-regulated in rat UCMSC, but down-regulated in human UCMSC when they were co-cultured with the corresponding species’ breast carcinoma cells. The suppression of either protein by the addition of a specific neutralizing antibody in co-culture of rat UCMSC with Mat B III cells significantly abrogated UCMSC ability to attenuate the growth of carcinoma cells. Over-expression of both genes by adenovirus vector in human UCMSC enhanced their 4 ability to suppress the growth of MDA-231 cells. In the breast carcinoma lung metastasis model generated with MDA-231 cells, systemic treatment with FST-over-expressing human UCMSC significantly attenuated the tumor burden. These results suggest that both ADRP and FST may play important roles in exhibiting stronger tumoricidal ability in rat UCMSC than human UCMSC and imply that human UCMSC can be transformed into stronger tumoricidal cells by enhancing tumor suppressor gene expression.

Doctor of Philosophy / Department of Biochemistry and Molecular Biophysics / Anna Zolkiewska / The ADAM (A Disintegrin and Metalloprotease) family of multi-domain proteins modulates a number of cellular signaling pathways in both normal and cancerous cells. ADAM12 has been shown to be a candidate cancer gene for breast cancer and its expression is up-regulated in breast tumors. The human ADAM12 transcript is alternatively spliced. One of these splice variants encodes a transmembrane ADAM12 isoform, ADAM12-L, which has been demonstrated to release cell signaling molecules from the cell surface. Another variant encodes a secreted protease, ADAM12-S, which cleaves extracellular matrix proteins and other secreted proteins. Although these variants are expressed from the same promoter, their relative expression levels are highly discordant. Here, I demonstrate variant-specific regulation of ADAM12 transcripts by microRNAs. Members of the microRNA-29 and microRNA-200 families target the unique 3’UTR of the ADAM12-L transcript and cause transcript degradation. Additionally, I show the presence of a novel ADAM12 splicing event in which 9 additional nucleotides are inserted in the region encoding the autoinhibitory pro-domain. I demonstrate that this novel variant is expressed in breast epithelial cells and breast cancer cell lines. The resulting protein isoform does not undergo proteolytic processing to activate the protease. Additionally, trafficking of the novel isoform to the cell surface is impaired and this isoform is localized to the endoplasmic reticulum. Finally, I determined a role for ADAM12-L in the progression of triple negative breast cancers (TNBCs). These tumors are lacking expression of hormone receptors and the HER2 receptor. HER2 is a member of the epidermal growth factor receptor (EGFR) family and the loss of the HER2 receptor causes tumors to rely on EGFR for propagating pro-growth signals. I show here that, in TNBC tumors, ADAM12-L expression is strongly correlated with poor patient prognosis and increased activation of EGFR. These data suggest that in TNBCs, ADAM12-L enhances tumor growth via EGFR activation. Collectively, the data presented here demonstrate (a) transcript-specific regulation of ADAM12 in breast cancer, (b) the existence of a novel splice variant and protein isoform with impaired cellular trafficking, and (c) an important role of the ADAM12-L isoform in EGFR activation in TNBC.