Organisms are comprised of many cells with multiple distinct cell types, each of which must be decided precisely to ensure proper formation of a functional organism. In C. elegans, the basic helix-loop helix transcription factor HLH-2 is required for the specification of the anchor cell, or AC. The AC arises from a group of four somatic gonad cells, all of which initially express HLH-2. Two of the four cells, which we call β cells, lose AC competence early and instead become ventral uterine precursor cells, or VUs. We call the remaining two cells α cells. One α cell becomes the AC, while the other becomes a VU. Which α cell becomes the AC is random—50% of the time one α cell becomes the AC, while the other 50% of the time the other α cell becomes the AC. The choice of which cell becomes the AC and which becomes the VU is called the AC/VU decision, and occurs through reciprocal signaling by LIN-12/Notch and its ligand LAG-2/DSL. At first, both α cells express similar levels of lin-12 and lag-2. As the AC/VU decision progresses, the AC expresses higher levels of lag-2, and the VU expresses higher levels of lin-12. By this time, HLH-2 is only present in the specified AC, while it is post-translationally degraded in VUs. The mechanism by which HLH-2 is degraded and the consequences of disrupting its degradation on AC specification are unknown. In this work, we studied the function and regulation of HLH-2 during two stages of somatic gonad development. First, we used long-term fluorescence microscopy to visualize HLH-2 over the course of somatic gonad development. We found that HLH-2 expression begins in the parents of the α and β cells a consistent amount of time after their birth, and that the parent cell that first expresses HLH-2 almost always gives rise to the α cell that becomes the VU, while the second cell to express HLH-2 gives rise to the AC. This led us to study the effect of a loss of hlh-2 activity in the α and β cells. We generated an α and β cell-specific hlh-2(0) allele using genome editing tools and found that LIN-12 protein is not present in the absence of hlh-2 activity. Based on this discovery, we conceived a model where HLH-2 expression biases the first-expressing cell towards the VU fate by endowing it with an edge in lin-12 activity. Next, we focused on restriction of HLH-2 to the AC. Typically, HLH-2 protein is degraded in VUs, which we hypothesized was a crucial step in restriction of the AC fate to a single cell. We found that in a lin-12(0) background, HLH-2 is stabilized in VUs even when the resulting cell does not become an AC, indicating that lin-12 directly promotes HLH-2 degradation. This led us to search for a lin-12-regulated factor that targets HLH-2 for degradation in VUs. We identified seven ubiquitin-related genes whose depletion resulted in stabilized HLH-2 in VUs, but surprisingly did not cause an AC/VU defect. We suspect that HLH-2 degradation in VUs is one of multiple negative regulatory mechanisms that ensure the robustness of the AC/VU decision. The following research contributes new insights into how stochastic cell fate decisions amplify noise to ensure a consistent and reproducible outcome.

Candida albicans is the most common human fungal pathogen. The relationship between C. albicans and Enterobacter bacteria have yet to be explored. The hypothesis of this study is that C. albicans and both E. aerogenes and E. cloacae have a positive relationship and work together to infect the host. In this study, the physical cell-to-cell interaction, molecular components of said interaction, and the impact of the interaction on a live organism were explored. Results indicate that Enterobacter adheres to C. albicans and inhibits growth with unidentified secreted molecules. Als1p has potential involvement in the attachment of E. cloacae to C. albicans. Out of 480 E. cloacae mutants, 6 showed reductions in attachment to C. albicans. The presence of C. albicans in C. elegans may lead to less Enterobacter colonization. Future work involving this interaction should strive to identify the Enterobacter secreted molecules and genes necessary for their production.

The extension of life span by caloric restriction has been studied across species from yeast and Caenorhabditis elegans to primates. No generally accepted theory has been proposed to explain these observations. Here, we propose that the life span extension produced by caloric restriction can be duplicated by the metabolic changes induced by ketosis. From nematodes to mice, extension of life span results from decreased signaling through the insulin/insulin-like growth factor receptor signaling (IIS) pathway. Decreased IIS diminishes phosphatidylinositol (3,4,5) triphosphate (PIP3) production, leading to reduced PI3K and AKT kinase activity and decreased forkhead box O transcription factor (FOXO) phosphorylation, allowing FOXO proteins to remain in the nucleus. In the nucleus, FOXO proteins increase the transcription of genes encoding antioxidant enzymes, including superoxide dismutase 2, catalase, glutathione peroxidase, and hundreds of other genes. An effective method for combating free radical damage occurs through the metabolism of ketone bodies, ketosis being the characteristic physiological change brought about by caloric restriction from fruit flies to primates. A dietary ketone ester also decreases circulating glucose and insulin leading to decreased IIS. The ketone body, d-β-hydroxybutyrate (d-βHB), is a natural inhibitor of class I and IIa histone deacetylases that repress transcription of the FOXO3a gene. Therefore, ketosis results in transcription of the enzymes of the antioxidant pathways. In addition, the metabolism of ketone bodies results in a more negative redox potential of the NADP antioxidant system, which is a terminal destructor of oxygen free radicals. Addition of d-βHB to cultures of C. elegans extends life span. We hypothesize that increasing the levels of ketone bodies will also extend the life span of humans and that calorie restriction extends life span at least in part through increasing the levels of ketone bodies. An exogenous ketone ester provides a new tool for mimicking the effects of caloric restriction that can be used in future research. The ability to power mitochondria in aged individuals that have limited ability to oxidize glucose metabolites due to pyruvate dehydrogenase inhibition suggests new lines of research for preventative measures and treatments for aging and aging-related disorders.

Activity plays diverse roles in shaping neuronal development and function. These roles range from aiding in synaptic refinement to triggering cell death during traumatic brain injury. Though the importance of activity-dependent mechanisms is widely recognized, the genetic underpinnings of these processes have not been fully described. In this thesis, I use the motor circuit of Caenorhabditis elegans as a model system to explore the functional and morphological consequences of modulating neuronal activity. First, I used a gain-of-function ionotropic receptor to hyperactivate motor neurons and asked how increased excitation affects neuronal function. Through this work, I identified a cell death pathway triggered by excess activation of motor neurons. I also showed that suppression of cell body death failed to block motor axon destabilization, providing evidence that death of the cell body and of motor axons can be genetically separated. Secondly, I removed excitatory drive from a simple neural circuit and asked how loss of excitatory activity alters circuit development and function. I identified excitatory motor neurons as master regulators of inhibitory synaptic connectivity. Additionally, I was able to identify previously undescribed activity-dependent mechanisms for regulating inhibitory synapses in both developing and mature neural circuits. Finally, I show data to implicate the highly conserved genes neurexin and neuroligin in determining inhibitory synapse connectivity. Collectively this work has lent insight into activity-dependent mechanisms in place to regulate neuronal development and function, a core function of neurobiology that is relevant to the study of a wide range of neurological disorders.

MicroRNAs play an important role in protecting biological robustness during development. Biological robustness is the ability to maintain a consistent output despite variation in input, such as transcriptional noise or environmental stresses. Here, we show that the conserved microRNAs mir-34 and mir-83 promote the robust migration of the distal tip cells in Caenorhabditis elegans when stressed by changing environmental temperature. Our results show that distal tip cell migration is sensitive to temperature changes occurring within a two hour period during the first larval stage. mir-34 and mir-83 protect distal tip cell migration by regulating potential targets cdc-42, pat-3, and peb-1. cdc-42 and pat-3 are known components of the integrin signaling network controlling pathfinding during migration, while the involvement of peb-1 is a novel finding. Additionally, loss of the two microRNAs leads to a reduction in both fecundity and lifespan, suggesting that the loss of developmental robustness leads to a decrease in fitness. mir-34 and mir-83 are not only conserved in higher organisms, but duplicated. Both have been implicated as tumor suppressor genes in mammalian work. Our work has found a role for both microRNAs in integrin-regulated cell migrations that is potentially conserved in higher organisms. Additionally, our work supports the growing appreciation for the role of microRNAs in both stress response and promoting developmental robustness.

LIN-12/Notch is a conserved transmembrane receptor that is required during animal development for proper cell-fate decisions and specification. In Caenorhabditis elegans, activation of LIN-12 occurs through binding to ligand expressed by an adjacent cell. This binding event triggers two cleavage steps and results in the release of the LIN-12 intracellular domain [LIN-12(intra)], which translocates to the nucleus to form a ternary complex with two other proteins: LAG-1/Su(H)/Cbf1 and SEL-8/Mastermind/Mastermind-like. This ternary complex will then transcriptionally activate target genes via LAG-1 Binding Sites (LBSs). LAG-1 is the sole DNA-binding component within the complex, and in the absence of LIN-12(intra), can act as a transcriptional repressor. LIN-12 signal transduction can be studied in the C. elegans Vulval Precursor Cells (VPCs), which exhibit precise spatiotemporal patterning regulated by LIN-12 activity. Here, I show that LAG-1 is positively autoregulated by LIN-12 activity in cells where LIN-12 activity is high. Autoregulation is mediated by an enhancer element that contains a cluster of 18 LBSs that are located within a conserved high occupancy target region, which is a span of DNA that is pulled down promiscuously in ChIP-Seq experiments. Mutation of the LBSs abrogates preferential expression mediated by the enhancer in cells with high LIN-12 signal transduction. When the HOT region is deleted from the endogenous lag-1 locus, expression in the VPCs is strongly reduced and no overt Lag phenotype occurs. Instead, cold-sensitive vulval and egg-laying defects, reminiscent of phenotypes seen in lin-12 hypomorphs, are found. Autoregulation of lag-1, therefore, appears to contribute to the robustness of LIN-12 cell fate specification in response to stochastic environmental and genetic perturbations. Under adverse environmental conditions, C. elegans enter a state of diapause in which they form dauer larvae, which are long-lived and stress-resistant. The VPCs of dauer larvae remain developmentally arrested indefinitely until favorable conditions are reintroduced. Experimentally, this arrest can be relieved by depletion of the Forkhead transcription factor DAF-16. I show that expression of the components of the LIN-12/SEL-8/LAG-1 ternary complex are downregulated during the L2d-dauer molt (prior to dauer entry) and that this downregulation is not relieved by DAF-16 depletion. Instead, DAF-16 depletion leads to resumption of LIN-12 signaling and expression of ternary complex only in completely formed dauer larvae. These observations suggest that DAF-16 is required for the maintenance but not the initiation of blocking LIN-12 signaling. The components of the ternary complex are required to effect LIN-12 signaling. This work contributes to better understanding how these components are regulated and how their expression can affect LIN-12 -mediated cell fate decisions.

The reciprocal evolutionary effects pathogens and their hosts have on each other are one of the most powerful selective forces in evolution, leading to adaptive phenotypic and genetic changes of both antagonists. In nature, bacterial infections often consist of more than one genotype. Since the host represents a limited resource, an interaction between the co-infecting genotypes is likely and potentially has fundamental effects on the interaction with the host. Nevertheless, most studies focus only on the interaction of parasite and host, ignoring within-host dynamics between co-infecting parasite genotypes. In my thesis, I focussed on both, the consequences of long-term host-parasite evolution for the interaction with a host and for parasite-parasite interactions. The first chapter is a comprehensive theoretical overview presenting the effects of multiple infections on virulence towards the host. It summarizes not only potential social interactions between the different co-infecting genotypes, but also discusses the relevance of their relatedness and resulting consequences for virulence. In the second chapter I present the results from a long-term evolution experiment using Caenorhabditis elegans as a multicellular host, singly infected with one of two different strains of its microparasite Bacillus thuringiensis. I found that both, coevolution with and adaptation to the host, led to rapid diversification of the clonal parasite populations into distinct clones. These clones showed strain specific phenotypic changes (i.e., killing rate and production of antagonistic substances) not only within, but also between replicate populations. In the third chapter one of these evolved clones was compared to its ancestral, non-evolved clone on the molecular level. By using next generation genome sequencing, I analysed the underlying genetic mechanisms that led to diversification within the clonal population presented in chapter two. In this study I demonstrated the importance of bacterial genomic plasticity for adaptation: the results revealed that changes were mainly caused by mobile genetic elements (MGEs), especially transposases and plasmids. Overall this thesis shows that the evolutionary selection pressure mediated by a multicellular host causes phenotypic diversification of the parasite. This change within and between parasite populations is reflected on both, the phenotypic and the genetic level.

Genetic mutation is the ultimate source of new phenotypic variation in populations. The importance of mutation cannot be understated, and constitutes a significant evolutionary force. Although single mutations may have little to no impact on organismal performance or fitness, when multiplied across the total number of potential sites within the genome, mutation can have a large impact. Accurate measurement of the rates, molecular mechanisms, and distributions of effects of mutations are critical for many applications of evolutionary theory. Despite the importance of both deleterious and beneficial mutations, their genome-wide patterns and phenotypic consequences are poorly understood when considering the mitochondrial genome. Mitochondria are organelles that are essential for eukaryotic life. They contain their own genome and generate bioenergy (ATP) necessary to sustain life via the electron transport chain (ETC). Because of their role in eukaryotic physiology, understanding how mitochondrial genetic and phenotypic variation can impact populations and evolutionary outcomes is essential. Past studies have implicated DNA-damaging oxidative stress as a source of mutations within somatic tissue, but there is a gap in knowledge regarding its role in heritable damage within the germ line. In this thesis, I aimed to test this possibility by characterizing the phenotypic and mutational consequences of high intracellular ROS levels caused by mitochondrial ETC genetic damage. I performed experiments using Caenorhabditis elegans ETC mutant, gas-1, and mutation-accumulation (MA) lines generated from this ancestral genotype. I quantified organismal fitness (fecundity and longevity), reactive oxygen species (ROS) levels, mitochondrial membrane potential (delta psi m), and ATP levels in these lines, and compared the results to those from a set of wildtype control lines. I begin with a general introduction to the hypothesis and the C. elegans system in Chapter I. In Chapter II, I report the findings from this work. In short, I found that while gas-1 MA lines began the experiment with low lifetime fecundity in comparison to the wildtype strain, their fecundity showed no further decline as expected, and even exhibited higher fecundity levels on days 3-5 of reproduction relative to the gas-1 progenitor. The gas-1 progenitor exhibited higher rates of ROS compared to wildtype, whereas the MA lines reverted back to wildtype levels; a similar pattern was observed for delta psi m, while ATP levels were low in the gas-1 progenitor and remained low in the MA lines. I interpret these findings in light of high-throughput sequencing results from these lines showing that, while nuclear and mitochondrial DNA mutation rates were equal to wildtype in these lines, the genomic pattern of mutation was highly nonrandom and indicative of selection for beneficial or compensatory sequence changes. Because ROS levels declined to wildtype in the evolved (MA), this study was unable to address whether ROS is a major contributor to heritable mutation in this system. I hypothesize that, in addition to their putatively compensatory genetic changes, gas-1 lineages experienced physiological compensation allowing them to survive, and that this was associated with a "slow living" phenotype. In Chapter III, I summarize general conclusions and implications of this study and end by providing suggestions for further study.

ABF -1 is a human class II bHLH transcription factor that is expressed predominantly in activated B cells and EBV immortalized cell lines. A portion of this study sought to characterize the homolog of ABF- l in Caenorhabditis e/egans. The nematode gene product, ceABF -1, is capable of forming heterodimers with E2A gene products and binding E box binding sites. HeLa cells transfected with ceABF-1 reveal that it is capable of blocking E2A mediated gene transcription. In order to maintain full repression capabilities, two conserved amino acid residues within helix I ofthe HLH domain are required. These results show a conserved mechanism of gene repression between invertebrates and vertebrates. This study also sought to analyze ABF-1 mediated regulation of both ld3 and cellular growth. Using a human ABF-1 stably transfected cell line, ID3 protein levels and transcript levels were shown to increase in response to overexpression of ABF-1 via western and northern blot, respectively. Flow cytometry analysis and Real-time PCR revealed that ABF-1 programs a slow down in the cell cycle, however this growth arrest is not mediated by ID3.

The helix-loop-helix (HLH) family of transcription regulatory proteins are fundamental regulators in the processes of cell proliferation and differentiation, cell lineage determination, myogenesis, neurogenesis, and sex determination in a wide range of multicellular organisms. A gene encoding a novel class II HLH protein has recently been identified from a human B-cell eDNA library using a yeast two-hybrid screen. The predicted human ABF -1 polypeptide sequence was used to search the Caenorhabditis elegans genome database for a C. elegans ABF-1 homolog. This bHLH protein, called C. elegans ABF -1 (CeABF -1 ), has a bHLH domain that shares 72% amino acid similarity with its human ABF-1 relative. The expression of the CeABF-1 mRNA has been detected in larval stages L2, L3, L4, and adult, however the mRNA is most highly expressed at the L3 and L4 stages. CeABF -1 protein is capable of heterodimerizing with the human E2A gene product, E4 7. Like human ABF -1, CeABF -1 expression in the presence of the E4 7 protein results in a reduction in E2A mediated gene activation. It has therefore been concluded that CeABF -1 , like human ABF -1 , also acts as a transcriptional repressor. Because C. elegans shares many conserved genes with higher eukaryotic organisms it has become a model organism for in depth genetic studies. It has therefore become increasingly desirable to investigate the possibility of alternative protein-protein interactions that can potentially occur within C. elegans, so it was necessary to construct a C. elegans eDNA library along with the appropriate bait vector expressing the CeABF- 1 protein. The titer ofthe primary library was calculated to be 9.7 x I06 clones, 10-fold greater than minimum titer requirement of I x I 06 clones for a good representational library. Sequencing of the CeABF -I insert confirmed successful construction of a mutation-free bait construct suitable for use in yeast two-hybrid screening. Yeast-two hybrid analysis revealed two new interactors, one of which was identified as an aldose reductase homolog, while the other remains uncharacterized.