dsc-4(qm182), a mutation that suppresses the lengthened defecation cycle of clk-1 also suppresses the delay in germline development. dsc-4 encodes a putative orthologue of microsomal triglyceride transfer protein (MTP), a protein essential for the assembly and secretion of apo-B-containing low density lipoproteins (LDL). The effect of dsc-4 on clk-1(qm30), coupled to studies of apoB homologues in worms led to a model suggesting the possibility of using C. elegans in the study of LDL-like lipoprotein particles. The impact of the level of lipoproteins is particularly evident in the germline developmental rate of the worms. / We report here a further elucidation of clk-1 mutants in the study of the biology of LDL-like particles. In particular, we investigated the effect of targeting LDL receptor-like genes by RNA interference (RNAi) on the egg laying rate of clk-1(qm30). We find positive modulating effects by disruption of these putative LDL receptors. In confirmation of our model of lipoprotein metabolism in clk-1 mutants, we find that disruption of these putative LDL receptors produces strikingly different effects in wild-type, clk-1(qm30) or clk-1(qm30); dsc-4(qm182) animals. / In addition, we report unexpected effects of various clk-1 alleles on the phenotypes of animals in which lrp-1 and rme-2 are disrupted. Specifically, we observe an allele specific amelioration of the phenotypes associated with disruption of these genes (abnormal molting and sterility, respectively). We discuss the possible significance of these findings. (Abstract shortened by UMI.)

How behaviors are generated by neural circuits is one of the central questions in neurobiology. Under standard culture conditions, Caenorhabditis elegans travel by propagating sinusoidal waves, moving primarily forward, punctuated by brief runs of backing. How these behaviors are generated and altered is not well understood. Using a combination of behavioral analyses and neuronal imaging, I reveal that an activity imbalance between cholinergic A- and B-motoneurons is the key determinant of directional locomotion. Furthermore, heterotypic gap junctions that couple command interneurons and motoneurons of the backward motor circuit, mediated by innexins UNC-7 in AVA and UNC-9 in A-motoneurons, respectively, establish the B>A activity pattern required for forward movement. Loss of this coupling results in both the hyperactivation of AVA backward interneurons revealing the unregulated, endogenous activity of A-motoneurons. With equal A-motoneuron activity levels as B-motoneurons, innexin mutant animals exhibit irregular body bending (kinking) instead of executing forward motion, as well as increased backing. Through a genetic screen, I identified two stomatin-like proteins as regulators of innexin UNC-9 activity that affect C. elegans’ directional movement. The loss of function of stomatin-like unc-1 leads to the same kinker phenotype as unc-7 or unc-9 mutants. Like UNC-9, UNC-1 functions primarily in the A-motoneurons to allow forward motion, suggesting that UNC-1 is required for effective UNC-7-UNC-9 coupling between AVA and A-motoneurons. Dominant mutations in UNC-1, and another stomatin-like protein STO-6, exhibit genetic interactions with these innexin mutants. These mutations partially restore the forward movement of unc-7 mutants, in an UNC-9-dependent manner, indicating that they regulate UNC-9 channel activity in motoneurons to re-establish the B>A-motoneuron activity pattern in the absence of heterotypic gap junctions between interneurons and motoneurons. These studies describe a role of gap junctions as regulators of circuit dynamics by establishing an imbalanced motoneuron activity pattern that favors forward motion, which can be modulated by upper layer inputs. This study also identifies stomatin-like regulators of innexin hemichannel and gap junction function. Future work will focus on understanding mechanisms through which these stomatins regulate the activity of specific innexin channels in C. elegans motoneurons, as well as their contribution to the dynamic output of the C. elegans motor circuit.

NCA-1 (putative nematode calcium channel) and NCA-2 are two cation channel-like proteins in Caenorhabditis elegans that function redundantly to regulate locomotion through unknown mechanisms. A recent study from our lab showed that in vivo Ca2+ imaging analyses of egg-laying neurons in nca-1 loss- and gain-of-function mutants implicate that NCA channels regulate Ca2+ flux at synapses, without affecting Ca2+ dynamics in neuron somas. Furthermore, we observed that NCA-1 localizes to non-synaptic region along axons, strongly suggesting that NCA channels propagate electrical signals from cell bodies to synapses. To identify molecular components that function in the nca-1 genetic pathway, I performed a genetic suppressor screen that led to the identification of behavioral suppressors of nca-1 gain-of-function mutant. Possible NCA auxiliary subunits, UNC-79 (uncoordinated) and UNC-80, were identified from this screen. Molecular characterization of other suppressors will help to identify other regulators and downstream signaling components through which NCA channels transmit electrical signals.

lin-11 and let-711 are early-developmental gene expression regulators with no previously known roles in aging regulation. Yet, they show strong aging-correlated expression profiles (Lund, Tedesco et al. 2002). lin-11 is strongly upregulated in very old worm populations, and let-711 is progressively downregulated in aging worm populations. Microarray studies were performed to identify their genome-wide targets, which were then subjected to further lifespan and genetic analysis to investigate their role in C. elegans aging. The results indicate that the target pools of both lin-11 and let-711 are enriched for aging genes, since a significant number of tested genes increased lifespan. This enrichment of aging genes in their target pools provides strong evidence that lin-11 and let-711 are indeed regulating the expression of aging genes in adult C. elegans. The data suggests that increased lin-11 expression as well as reduced let-711 expression may be promoting longevity by downregulating the insulin/IGF-1 pathway. Decreasing let-711 may also be contributing to longevity by downregulating the germline signaling pathway. K11E4.2, R53.5, C49A9.2 and Y82E9BR.5 are four genes from the lin-11 target pool, whose knockdown produced increases inlifespan. These are unannotated genes, and the details of their roles in aging regulation are not known at this point. ins-3 expression was downregulated two-fold upon knockdown of lin-11, suggesting the possible involvement of lin-11 in regulation of the insulin/IGF-1 pathway. An RNAi construct for ins-3 was not available and it is not known whether loss of ins-3 leads to lifespan extension. let-711 knockdown resulted in an almost four-fold reduction in pdk-1 expression. pdk-1 is an integral part of the insulin/IGF-1 pathway and its knockdown by RNAi extended lifespan. Four other genes from the let-711 target pool that increased lifespan, cdc-25.1, gna-2, meg-1 and ooc-3, all have germline specific functions. The extensions in lifespan generated by these genes were completely dependent on DAF-16. Furthermore, for gna-2, meg-1 or ooc-3, they were independent of DAF-2. These results agree with previously established mechanisms for germline regulation of aging, suggesting the involvement of let-711 in regulating the germline-signaling pathway.

Forty-six genomic gene expression studies of free living soil nematode C. eleganshave been published. To facilitate exploratory analysis of those studies, we constructed adatabase containing all the published C. elegans expression datasets. A Perl CGIprogram, called Microarray Analysis Display (MAdisplay), allows gene expressionclustergrams of any combination of entered genes and datasets to be viewed(http://elegans.uky.edu/gl/madisplay). Perl programs were used to preprocess the rawdata from different sources into a common format and to transform the data to displaythe expression changes relative to each experiment's controls. Three hundred lists ofgenes from figures and tables were extracted from the publications and made available inthe GeneLists database, which also contains Gene Ontology and KEGG gene lists. Weused these tools to examine in a systematic fashion the mean expression of gene lists inthe set of microarray and SAGE experiments. Seventy-nine percent of publicationderived gene lists show a strong expression change (p-value andlt;0.001) in more than oneexperiment with the median being fourteen out of the 127 experiments that are derivedfrom the forty-six publications. This indicates that groups of genes identified in onepublication typically show an expression effect in many other experiments.

Since its introduction in 1960's, the model organism Caenorhabditis elegans has played a crucial role towards scientific discoveries because of its relatively simple anatomy, conserved biological mechanisms, and mapped genome. The organism also has a rapid generation time and produces a large number of isogenic progeny, making C. elegans an excellent system for conducting forward genetic screens. Conventional screening methods, however, are labor intensive and introduce potential experimental bias; typically, large-scale screens can take months to years. Thus, automated screening and characterization platforms can provide an opportunity to overcome this bottleneck. The objective of this thesis is to develop tools to perform rapid phenotypical characterization of C. elegans to enable automated genetic screening systems for neural development. To achieve this goal, I developed methods to increase throughput of worm handling using microfluidic devices and demonstrate software modules to phenotype unknown mutants using quantitative and morphological image analysis methods. Microfluidic devices are constructed from PDMS using established soft-lithography techniques. The emphasis on the simplification of existing designs greatly facilitates the adoption of our developed systems by other scientists. This thesis also includes image processing modules using various techniques to determine animal phenotypes. For example, we adapted standard thresholding methods to detect animal motor neurons, developed a modified granulometry algorithm to rapidly characterize large numbers of lipid droplets in 3D, and developed a probability model to determine neuronal process morphology. This work is significant because it increases current capabilities of screening small animals with morphological phenotypes by enhancing throughput and reducing human bias. Genes or gene functions that can be discovered using these methods can further elucidate mechanisms relevant to neural development, degeneration, maintenance, and function; these discoveries in turn can facilitate discoveries of potential therapeutic strategies for human neurological diseases.

Serotonin is a very important neuromodulatory agent that affects many physiological and behavioral responses of both vertebrates and invertebrates. In helminths, especially parasitic ones, not much is known about the biosynthesis and mode of action of serotonin or any of the related biogenic amine neurotransmitters, such as catecholamines (dopamine and noradrenaline). In this study, we cloned two full length cDNAs from Schistosoma mansoni encoding tryptophan hydroxylase (TPH) and tyrosine hydroxylase (TH). TPH and TH catalyze the rate limiting steps in the biosynthesis of serotonin and catecholamines, respectively. Both enzymes were expressed in Escherichia coli and the purified proteins were shown to have TPH and TH activities. This indicates that S. mansoni, and possibly other parasitic helminths, may be capable of synthesizing serotonin and catecholamines endogenously. In the second part of our studies, we looked at the mode of action of serotonin in helminths, in particular the molecular properties of serotonergic G protein-coupled receptors (GPCR). We cloned two helminth GPCRs, one from the free living nematode Caenorhabditis elegans and the second from S. mansoni. The C. elegans receptor (5-HT2Ce) was shown to encode a functional serotonin receptor with structural and signaling properties similar to those of mammalian 5-HT2 receptors. However, its agonist I antagonist binding profile differed from previously characterized serotonin receptors. The cloned S. mansoni receptor (SmGPCRx) was found to represent a new structural class of receptor, which shared about the same level of amino acid sequence homology with various biogenic amines receptors, such as serotonin, catecholamines, and octopamine receptors. Additional sequence analysis and immunolocalization studies confirmed that SmGPCRx possesses structural characteristics of a GPCR. SmGPCRx is the first GPCR ever cloned from a parasitic flatworm. Taken together, these studies mark an important first step to

Understanding gene function and genetic relationships is elemental in our efforts to better understand biological systems. Here, I describe a reliable high-throughput approach, Systematic Genetic Interaction analysis (SGI), capable of revealing both weak and strong genetic interactions in the nematode Caenorhabditis elegans. I also present evidence that UNC-73 functions cell-autonomously in an UNC-40 pathway to direct muscle arm extension in C. elegans. Previous efforts to systematically describe genetic interactions between redundant genes on a global scale either have focused on core biological processes in protozoans or have surveyed catastrophic interactions in metazoans. I investigated synthetic genetic interactions between eleven ‘query’ mutants in conserved signal transduction pathways and hundreds of ‘target’ genes compromised by RNAi. A network of 1246 genetic interactions was uncovered through an unbiased global analysis of the interaction matrix, establishing the largest metazoan genetic interaction network to date. To investigate how genetic interactions connect genes on a systems-wide level, the SGI network was superimposed with existing networks of physical, genetic, phenotypic and co-expression interactions. Fifty-six putative functional modules were identified within the superimposed network, one of which regulates fat accumulation and is coordinated by bar-1(ga80)/β-catenin interactions. This led to the discovery that SGI interactions link distinct functional modules on a global scale, which is a previously unappreciated level of organization within metazoan systems. In addition, I present evidence that the properties of genetic networks are conserved between C. elegans and S. cerevisiae, but that the connectivity of the interactions within the current networks is not. Although the buffering between functional modules may differ between species, studying these differences may provide insight into the evolution of divergent form and function. In C. elegans the postsynaptic membrane of the neuromuscular junction reaches its destination through an active process of guided cell extension. The worm has 95 body wall muscles (BWMs) that extend projections called 'muscle arms' to motor axons. The muscle arms harbour the postsynaptic elements of neuromuscular junctions. The stereotypical pattern of muscle arm extension was exploited in a forward genetic screen for new genes required for guided cell migration by looking for mutations that caused a reduction in the number of arms that extend to the motor axons. One of the resulting mutants was tr117, which extended half the number of arms compared to wild type animals. Genetic mapping, complementation tests, and sequencing revealed that tr117 was a mutation in unc-73/Trio, which encodes a guanine nucleotide exchange factor. Expression of UNC-73 specifically in the BWMs rescued the muscle arm development defects of unc-73(e936) mutants, indicating that UNC-73 functions cell-autonomously to regulate muscle arm extension. UNC-73::CFP was localized to muscle arm termini in a pattern similar to that of UNC-40/Dcc, which directs muscle arm extension. UNC-73 over-expression suppressed the Madd phenotype of unc-40 null worms and unc-73(e936) suppressed ectopic myopodia induced by UNC-40 over-expression. These results indicate that UNC-73 functions downstream of UNC-40 in a pathway that regulates muscle arm extension.

During neuronal development, the axonal and dendritic projections are polarized and oriented along specific body axis. To further explore the molecular basis of neuritogenesis in vivo, we used the nematode Caenorhabditis elegans as a developmental model and performed a forward genetic screen to identify genes that specify the polarity of neurite outgrowth. We examined the VC4 and VC5 neurons, members of the six VC motor neurons using the Pcat-1::gfp transgene cyIs4. The VC motor neurons are ventrally located neurons that extend two processes. VC1, VC2, VC3, and VC6 extend axons along the anterior-posterior (A/P) axis; VC4 and VC5 extend axons around the vulva along a mediolateral left-right (L/R) axis perpendicular to the A/P axis. We identified and showed that vang-1/Van Gogh, a core component of planar cell polarity (PCP) signalling pathway, acts cell-autonomously in VC4 and VC5 neurons and non-autonomously from the epithelial cells to restrict neurite formation along the A/P axis. vang-1 mutant animals display ectopic neurites along the A/P axis. Using a candidate gene approach, we further identified and revealed two additional core members of PCP signalling, Prickle (PRKL-1) and Dishevelled (DSH-1), to play a role in A/P-directed neurite suppression. We also showed prkl-1 and dsh-1 genetically interact with vang-1 and VANG-1 is required to suppress A/P-directed neurite outgrowth from larval stage 4 to adulthood. Overexpression of VANG-1 results in a loss-of-function (lof) phenotype, suggesting that an appropriate level of VANG-1 activity is important. Additionally, vang-1/prkl-1, and dsh-1 may interact in parallel pathways. Our findings implicate PCP genes to play a previously unidentified role in maintaining polarized neuronal morphology by inhibiting neuronal outgrowth responses to environmental cues.

Stachybotrys elegans (Pidopl.) W. Gams is a destructive mycoparasite of the soilborne plant pathogen Rhizoctonia solani. It colonizes effectively all types of cells of R. solani, and is considered as an effective biological control agent (BCA). Monitoring the presence of this mycoparasite in the field trials requires the development of a reliable and sensitive diagnostic assay that is able to detect and differentiate the BCA from their target host. To achieve this, designed SCAR (sequenced characterized amplified regions) primers designated as SE-13F and SE-13R were generated from informative RAPD markers. They were tested in conventional PCR assays alone or in conjunction with the recently developed SCAR primers (SBU-177/336) designed for Rhizoctonia solani (Kuhn) on several types of DNA. These included DNA extracted from pure cultures, co-cultures of the BCA and the pathogen, plant tissue and several types of soils inoculated with both the BCA and the pathogen. Irrespective of the type of the biological samples from which the DNA was extracted, the primers SE-13F/SE-13R successfully amplified only S. elegans. No cross-reaction was observed when the primers were used to amplify DNA of other fungi, bacteria and plant tissues. Likewise, the primer pair SBU-177/336 detected only its target organism, i.e., R. solani. The detection limit using these primers on amplified DNA was as little as 1 pg DNA extracted from pure cultures of S. elegans, 100 pg DNA extracted from greenhouse soil and 33 pg DNA extracted from natural soil. This work is the first report on the development of SCAR markers for the BCA, S. elegans. These molecular markers offer not only an alternative diagnostic assay to conventional detection methods, but also the possibility of being used in ecological studies.