Skeletal muscle is composed of repeating units called sarcomeres which contain distinct sets of thin and thick filaments that slide past each other during contraction. In addition to these proteins a third filament called titin acts as a molecular spring and prevents overstretching of muscle. In skeletal muscle, titin's spring-like elements include the PEVK sequence which elongates upon stretch and immunoglobulin-like (Ig) domains. A fourth myofilament, nebulin, is anchored into the Z-disk and present along the length of the thin filament. Nebulin is proposed to be a regulator of thin filament length. These large sarcomeric proteins can be differentially spliced to yield proteins of various sizes and properties. During my graduate career I sought to elucidate the role of titin and nebulin in skeletal muscle development and disease. Firstly, I studied if differential splicing of titin and nebulin occurred during development. Early post-natal development is a time of rapid isoform switching and growth, and I hypothesized that these large proteins could be affected. In post-natal development of the mouse, large compliant titin molecules are gradually replaced with shorter, stiffer isoforms through removal of PEVK exons. In nebulin, C-terminal exons present in the Z-disk are differentially expressed between muscle types and throughout development which correlates with differences in Z-disk width. My research has shown that titin and nebulin transcripts are tuned during development with changes in titin affecting the I-band region of the molecule and changes in nebulin affecting the Z-disk region. Secondly, I sought to study the effect of specific titin domains on titin elasticity in skeletal muscle. Changes in titin's stiffness occur in various myopathies but whether these are a cause or an effect of the disease is unknown. To test this, a genetically engineered mouse model was created in which part of the constitutively expressed immunoglobulin-like (Ig) domains of titin (Ig3-11) were removed. Unexpectedly, the deletion of these domains causes additional differential splicing to take place in skeletal muscle and leads to skeletal muscle myopathy. I sought to investigate the mechanism by which this occurs and found that RBM20, a titin splice factor, was significantly increased in IG KO mice and additional differential splicing was reversed in IG KO mice crossed with a mouse with reduced RBM20 activity. Through the use of this model the mechanisms that underlie titin alternative splicing were explored and demonstrated how alternative splicing alters muscle function. My third project was to better understand the mechanisms by which nebulin loss causes the disease nemaline myopathy (NM). We generated a mouse model in which nebulin's exon 55 is deleted (NEBΔex55) to replicate a founder mutation seen frequently in NM patients with Ashkenazi Jewish heritage. The mice phenocopy pathology of severe myopathy with a short lifespan, changes in thin filament length and cross bridge cycling kinetics, and changes in calcium sensitivity. Force generation in this model is improved by the addition of a calcium sensitizer and supports the use of these compounds in treating patients with nemaline myopathy. In my last project, a second mouse model in which nebulin levels are reduced (NEB cKO) was created to study the effects of reduced nebulin levels on survival and pathology of skeletal muscle. NEB cKO mice recapitulate many of the hallmark features of typical congenital NM, and mice have muscle type dependent effects on contractility and trophicity. Most notably, the intact EDL muscle had a 84% reduction in maximal active force compared to that of the soleus muscle which had a 42% reduction in force. These differences can be explained in part by changes in thin filament length, cross bridge cycling kinetics, and muscle fiber disarray. In conclusion, through the use of genetically engineered mouse models, differential splicing of titin and nebulin during development has been characterized and mechanisms by which mutations in these large sarcomeric proteins cause skeletal muscle disease have been elucidated.

Colon cancer is the second leading cause of cancer deaths in the United States of America. It is caused by the accumulation of mutations in tumor suppressors and oncogenes. The APC tumor suppressor is mutated in most diagnosed cases of colorectal cancer. Mutations in the K-RAS oncogene occur at later stages of colon cancer progression. In the present study, the transcriptional regulation of a novel target of these two genes, caveolin-1, was studied. Caveolin-1 is transcriptionally regulated by the APC tumor suppressor gene, via induction of its inducer, FOXO1 and the suppression of its transcriptional repressor, C-MYC. An activated K-RAS oncogene induces caveolin-1 transcription via activation of the P-I3 Kinase pathway. In addition to transcriptional regulation of caveolin-1, the influence of caveolin-1 expression on cellular phenotypes like signal transduction and polyamine uptake were assessed. The present studies demonstrate that caveolin-1 expression affects basal levels of AKT and ERK signaling, with an increased signaling associated with caveolin-1 expression in these colon tumor-derived cells. In addition, caveolin-1 expression positively affects signaling in response to an inflammatory stimulus like TPA. Interestingly, caveolin-1 expression leads to a decrease in the uptake of pro-tumorigenic molecules like polyamines, in the colon cell lines tested. Taken together, the data from this study suggests that caveolin-1 is transcriptionally regulated by the APC and the K-RAS gene at different stages of colorectal tumorigenesis and this in turn, leads to different phenotypes influenced by caveolin-1 expression.

The coordination of various cellular differentiation and morphogenetic programs during plant embryogenesis is required to establish the basic adult body plan. The molecular basis of these patterning events remains to be fully understood. In particular, little is known about the roles of cell-cell signaling during embryonic pattern formation.I identified two receptor-like kinases, RECEPTOR-LIKE PROTEIN KINASE1 (RPK1) and TOADSTOOL2 (TOAD2), redundantly required for Arabidopsis thaliana embryonic pattern formation. Genetic analysis indicates that RPK1 and TOAD2 have overlapping embryonic functions. The zygotic gene dosage of TOAD2 in an rpk1 background is of critical importance, suggesting that signaling mediated by RPK1 and TOAD2 must be above a threshold level for proper embryo development. The localization of RPK1 and TOAD2 translational fusions to GFP coupled with the analysis of cell-type specific markers indicate that RPK1 and TOAD2 are redundantly required for both pattern formation along the radial axis and differentiation of the basal pole during early embryogenesis.I found that RPK1 and TOAD2 also have overlapping functions required for cotyledon primordia initiation during Arabidopsis embryogenesis. Genetic analyses indicate that cotyledon initiation is sensitive to TOAD2 gene dosage in an rpk1 background. Analysis of cell-specific markers suggest that RPK1 and TOAD2 are primarily required for the differentiation of cell types (i.e. the central domain protoderm) subjacent to the cotyledon primordia, and that the cotyledon initiation defects are caused by defects in the central domain protoderm. In addition, RPK1-GFP and TOAD2-GFP translational fusions had overlapping localization patterns in the central domain protodermal cells when cotyledon primordia were first recognizable. I propose that RPK1 and TOAD2 are primarily required to maintain central domain protoderm cell fate and that the loss of this key embryonic cell type in mutant embryos results in patterning defects throughout the embryo including the failure to initiate cotyledon primordia.This work has identified two putative receptors for cell-cell signals that mediate key patterning events during plant embryogenesis. The future identification of components in the RPK1 and/or TOAD2 signaling pathways will yield further insight into the molecular basis of the generation and assembly of diverse embryonic cell types.

Intersections of distinct biological pathways in cells allow for nodes of metabolic regulation. This work describes the discovery of the intersection of two pathways in yeast mitochondria: RNA processing and fatty acid synthesis and attachment. Analysis of the components of the pathways is presented here along with a model illustrating the connection as a potential mode of regulation of mitochondrial gene expression.A genome-wide screen of respiratory-deficient <italic>Saccharomyces cerevisiae</italic> deletion strains for defects in mitochondrial RNA processing revealed that two novel genes affect processing of mitochondrial tRNAs by RNase P. One gene encodes Htd2, an enzyme in the type II mitochondrial fatty acid synthesis pathway (FAS II). The other gene is described here as encoding Lip3, an enzyme involved in the synthesis and attachment of the co-factor lipoic acid, which is synthesized from a product of the FAS II pathway.RPM1 is the mitochondrial-encoded RNA subunit of mitochondrial RNase P. The multigenic transcription unit containing RPM1 also contains tRNA<super>pro</super>. Maturation of RPM1 necessitates processing of the tRNA by RNase P. Thus, RNase P is required for maturation of its own RNA component, constituting a positive feedback cycle. The present work demonstrates that a product of the FAS II pathway is necessary for the assembly or activity of RNase P, as deletion of any gene encoding an FAS II enzyme results in inefficient processing of tRNApro from the transcript.Analysis of the enzymes involved in the synthesis and attachment of lipoic acid to target proteins is also described here. Disruption of any of these enzymes affects protein lipoylation and tRNA processing. Gcv3, a target of lipoylation, was found to be required for lipoylation as well as for efficient tRNA processing.A second feedback cycle controlling pyruvate dehydrogenase activity and fatty acid synthesis may be functional under certain conditions. Pyruvate dehydrogenase, which provides acetyl-CoA for the FAS II pathway, requires lipoic acid for its activity. It is hypothesized that the two feedback cycles and the role of Gcv3 may provide switch-like regulation of mitochondrial gene expression in response to the nutritional state of the cell.

The experiments reported here describe mechanisms involved in the establishment of the dorsal-ventral axis in the mud snail, Ilyanassa obsoleta. Ilyanassa and other spiralians utilize an embryonic organizer to induce dorsal identity, and thus establish the bilateral axis. The D macromere embryonic organizer in Ilyanassa is specified at the four-cell stage by the inheritance of the polar lobe, but does not function as an inductive center until the 24-cell stage. Previously it was assumed that the D macromere of Ilyanassa functioned autonomously through its inheritance of the polar lobe. I have found this is not the case. Rather, I describe the role that the micromeres play in the activation of the D macromere organizer. Specifically, I have found that micromeres of the first and second quartet are necessary for at least three known characteristics of the D macromere: the activation of MAPK in the D macromere, the division of the D macromere, and the inductive capacity of the D macromere. Thus, while the polar lobe is necessary for D macromere function, its inheritance does not provide the D macromere with functional autonomy.The localized activation of MAPK was the first molecular component of dorsal-ventral patterning to be identified in Ilyanassa and other spiralians. In addition to being activated in the D macromere organizer, MAPK is also activated in the micromeres that are induced by the D macromere. I undertook a pharmacological screen to identify other components involved in dorsal-ventral patterning. I have found that a member of the Protein Kinase C (PKC) family is also involved in the establishment of the dorsal-ventral axis in Ilyanassa. Inhibition of PKC disrupts patterning, resulting in a radialized animal. In addition, I have found that PKC functions in the same path as MAPK. PKC is necessary for the proper activation of MAPK in the D macromere organizer and the micromeres. These results suggest that either the same transduction pathway is used repeatedly in the establishment of the dorsal-ventral axis or that patterning is the result of one global signal. These results drastically change our view of dorsal-ventral patterning during spiralian development.

The polyamines positively charged molecules that are able to affect nucleic acid structure. Investigation of polyamine and RNA interaction shows that the two are able to form aggregates and these aggregates may be responsible for the inhibition of RNA decapping that is seen in the presence of polyamines. The polyamines are also responsible for a post-translational modification of a protein, eukaryotic initiation factor 5a (eIF5A). This protein is known to affect translation and RNA decay. This investigation shows that eIF5A is able to affect the formation of foci by Dhh1 but does not affect DCP1 or DCP2 foci formation. This investigation also shows that eIF5A mutation leads to a depression of polysome profiles and 35S-met incorporation and therefore eIF5A may truly be a translation initiation factor. This study also describes unique interactions of eIF5A with Dhh1p and eIF5A-independent effects of the polyamines on gene expression. The inhibition of eIF5A's hypusine modification leads to an increase in phoshorylation of eIF2&amp;#945; and this may contribute the induction of apoptosis and inhibition of protein synthesis associated with inhibition of eIF5A's hypusine modification.

<p> Manipulating the phenylpropanoid (Pp) pathway has been of great focus to bio-engineers as this pathway is responsible for production of many compounds that are important to human health for their known antioxidant, anti-viral, anti-inflammatory, anti-allergenic and vasodilatory properties. The secondary by products of the Pp pathway are important for the physiological well-being of the plant as it contributes to plant&rsquo;s ability to tolerate changing environment. Plant bio-engineering, involves manipulating gene expression of proteins that regulate functional proteins which are known to attribute to stress tolerance. Our research focused on one such regulatory protein called the 14-3-3 lambda (14-3-3&lambda;) protein and its effects on anthocyanin production in two different plants: a plant model <i>Arabidopsis thaliana </i> (<i>A. thaliana, Columbia-0</i>), and a naturally drought tolerant resurrection plant <i>Selaginella lepidophylla</i> (<i> S. lepi</i>). Due to their structural characteristics the family of 14-3- 3 proteins bind to many different client proteins and hence can function as signaling factors in eukaryotes. Anthocyanins are anti-oxidants produced in plants that alter plants physiology to resist stress. The goal of this study was to establish which nodes in the anthocyanin synthesis pathways are influenced by 14-3-3&lambda; in both <i>A. thaliana</i> and <i>S. lepi </i>. Data from this study established the steps in the Anthocyanin pathway that 14-3-3&lambda; affects to alter anthocyanin production during normal hydration and drought stress states. Based on our published studies and experimental data we have identified that the 14-3-3&lambda; isoform is playing a significant role in the anthocyanin pathway during drought stress. Using a reverse genetics approach, the amounts of secondary anthocyanin metabolites produced in a 14-3-3&lambda; knockout mutant were compared to the wild-type <i> A. thaliana</i> during normal hydration and drought conditions. Analytical techniques such as high performance liquid chromatography (HPLC) and liquid chromatography-Mass Spectrometry (LC-MS/MS) in combination with open access databases were used for metabolite profiling. The metabolite profile lead to candidate metabolites that differed between the drought-treated and hydrated groups in the knockout mutants and wild-type. Identification of these metabolites determined the nodes of Pp pathway that were affected by 14-3-3&lambda;, namely the enzymes chalcone synthase and chalcone isomerase. These findings in <i> A. thaliana</i> were expanded in the naturally drought resistant plant <i> S. lepi</i> using similar analytical approaches employed in <i> A. thaliana</i>. The results proved that 14-3-3&lambda; affects biosynthesis of anthocyanin during drought stress in <i>A. thaliana</i> and <i> S. lepi</i> in a similar manner, hence suggesting a similar role of 14-3-3&lambda; in the production of anthocyanins in both the plants.</p><p>

<p> The eukaryotic cytoskeleton is composed of varying proteinaceous filaments and is responsible for intracellular transport, cell proliferation, cell morphogenesis, and cell motility. Microtubules are one of three cytoskeletal components and have a unique polymer structure. The hollow cylinders undergo rapid polymerization and depolymerization events (<i>i.e.</i> dynamic instability) to promote assembly at the leading edge of the cell and disassembly in the rear of the cell to drive the cell front forward and facilitate directional migration. High-resolution light microscopy and automated tracking allow visualization and quantification of microtubule dynamics (<i>i.e.</i> growth speeds and growth lifetimes) during time-lapse imaging. These techniques were used to understand how the physical environment influences molecular control of endothelial cell morphology. The ultimate goal of this work is to test hypotheses relevant to vascular development and diseases associated with endothelial cell angiogenesis &ndash; defined as the development of new blood vessels from pre-existing vessels. Angiogenesis is of particular relevance because it is a commonality underlying many diseases affecting over one billion people worldwide, including all cancers, cardiovascular disease, blindness, arthritis, and Alzheimer's disease.</p><p>

<p> Genome instability is a hallmark of human cancers. Patients with Bloom&rsquo;s syndrome, a rare chromosome breakage syndrome caused by inactivation of the RecQ helicase BLM, result in phenotypes associated with accelerated aging and develop cancer at a very young age. Patients with Bloom&rsquo;s syndrome exhibit hyper-recombination, but the role of BLM and increased genomic instability is not fully characterized. Sgs1, the only member of the RecQ family of DNA helicases in <i>Saccharomyces cerevisiae,</i> is known to act both in early and late stages of homology-dependent repair of DNA damage. Exo1, a 5'&ndash;3' exonuclease, first discovered to play a role in mismatch repair has been shown to participate in parallel to Sgs1 in processing the ends of DNA double-strand breaks, an early step of homology-mediated repair. Here we have characterized the genetic interaction of <i>SGS1</i> and <i> EXO1</i> with other repair factors in homology-mediated repair as well as DNA damage checkpoints, and characterize the role of post-translational modifications, and protein-protein interactions in regulating their function in response to DNA damage. In <i>S. cerevisiae</i> cells lacking Sgs1, spontaneous translocations arise by homologous recombination in small regions of homology between three non-allelic, but related sequences in the genes <i>CAN1, LYP1,</i> and <i>ALP1.</i> We have found that these translocation events are inhibited if cells lack Mec1/ATR kinase while Tel1/ATM acts as a suppressor, and that they are dependent on Rad59, a protein known to function as one of two sub-pathways of Rad52 homology-directed repair.</p><p> Through a candidate screen of other DNA metabolic factors, we identified Exo1 as a strong suppressor of chromosomal rearrangements in the <i> sgs1&Delta;</i> mutant. The Exo1 enzymatic domain is located in the N-terminus while the C-terminus harbors mismatch repair protein binding sites as well as phosphorylation sites known to modulate its enzymatic function at uncapped telomeres. We have determined that the C-terminus is dispensable for Exo1&rsquo;s roles in resistance to DNA-damaging agents and suppressing mutations and chromosomal rearrangements. Exo1 has been identified as a component of the error-free DNA damage tolerance pathway of template switching. Exo1 promotes template switching by extending the single strand gap behind stalled replication forks. Here, we show that the dysregulation of the phosphorylation of the C-terminus of Exo1 is detrimental in cells under replication stress whereas loss of Exo1 suppresses under the same conditions, suggesting that Exo1 function is tightly regulated by both phosphorylation and dephosphorylation and is important in properly modulating the DNA damage response at stalled forks.</p><p> It has previously been shown that the strand exchange factor Rad51 binds to the C-terminus of Sgs1 although the significance of this physical interaction has yet to be determined. To elucidate the function of the physical interaction of Sgs1 and Rad51, we have generated a separation of function allele of <i> SGS1</i> with a single amino acid change <i>(sgs1-FD)</i> that ablates the physical interaction with Rad51. Alone, the loss of the interaction of Sgs1 and Rad51 in our <i>sgs1-FD</i> mutant did not cause any of the defects in response to DNA damaging agents or genome rearrangements that are observed in the <i>sgs1</i> deletion mutant. However, when we assessed the <i>sgs1-FD</i> mutant in combination with the loss of Sae2, Mre11, Exo1, Srs2, Rrm3, and Pol32 we observed genetic interactions that distinguish the <i>sgs1-FD</i> mutant from the <i>sgs1 </i> deletion mutant. Negative and positive genetic interactions with <i> SAE2, MRE11, EXO1, SRS2, RRM3,</i> and <i>POL32</i> suggest the role of the physical interaction of Sgs1 and Rad51 is in promoting homology-mediated repair possibly by competing with single-strand binding protein RPA for single-stranded DNA to promote Rad51 filament formation.</p><p> Together, these studies characterize additional roles for domains of Sgs1 and Exo1 that are not entirely understood as well as their roles in combination with DNA damage checkpoints, and repair pathways that are necessary for maintaining genome stability.</p><p>

Breast cancer is the most frequent tumor type among women. Heightened susceptibility of the breast to tumor development has been associated with early menarche, nulliparity, exposures to ionizing radiation, and family history, but the underlying molecular mechanisms are poorly understood. Unfortunately, the etiology of breast cancer is complex and is complicated by the fact that it is a heterogeneous disease. The p53 tumor suppressor gene was altered in a large proportion of these spontaneous breast tumors implicating its involvement in the progression of breast cancer development. The aim of this dissertation was to determine the regulation of p53 in the normal mammary gland and whether it is involved in suppressing the development of mammary tumors. To evaluate the effect of p53 on mammary tumor formation, the first component of this work involved the characterization of BALB/c- p53-deficient mice. BALB/c-p53+/− and p53−/− mice were examined for tumor spectrum and mammary abnormalities. Mammary transplants were performed to evaluate the role of p53 in tumor suppression in the mammary gland. This work demonstrated that p53 is critical in suppressing mammary tumorigenesis in the mammary gland as BALB/c mice deficient in p53 readily develop mammary carcinomas. The second element of this project examined the expression, localization and activity of p53 in normal mammary tissues. Since the mammary gland is a tissue that is sensitive and responsive to local and systemic hormones, the last chapter of this dissertation focused on the hormonal effects on p53 activity. Results from these experiments demonstrated that p53 was expressed at high levels localized to the cytoplasm of the ductal epithelium of the quiescent mammary gland. P53 was not responsive to radiation-induced DNA damage suggesting its function is compromised in the nulliparous mammary gland. Further experiments demonstrated that the functional state of wild type p53 in the mammary epithelium could be regulated by hormonal stimuli.