Serial Analysis of Gene Expression (SAGE) on Caenorhabditis elegans RNA from FACS sorted embryonic body wall muscle cells has identified nearly 8000 genes expressed in nematode body wall muscle. Approximately 60% of these are genes are expressed at low levels (<5 tags/~50,000-100,000 tag library). Low-abundance transcripts have typically been overlooked since most are considered experimental or contamination errors. Consequently, research has been focused on transcripts that are most enriched in the particular tissue of interest. Here I focus on the analysis of low-expressed transcripts in the muscle SAGE libraries in order to investigate what percentage of these are in fact expressed in muscle and are not false positives. Most well characterized C. elegans body wall muscle genes are not expressed at low levels, therefore I anticipate that focusing on these rarely expressed genes will allow for the identification of muscle components that have been previously unrecognized. RT-PCR was performed on RNA isolated from purified body wall muscle cells to initially estimate what fraction of these low abundance transcripts present in the SAGE data are indeed expressed in muscle. I examined 128 genes, of which 84 were represented by a single SAGE tag. From this initial list, 38% of the low-expressed transcripts were verified for their presence in body wall muscle. Subsequently, reporter GFP fusions were used to deduce if these low-expressed transcripts are indeed expressed in vivo within muscle. Of the low-expressed genes that tested positive via RT-PCR, 42% showed in vivo expression in body wall muscle. When the results from the RT-PCR and in vivo expression experiments are combined, I can extrapolate that at least 16% of low-expressed genes identified by the SAGE libraries are in fact expressed in muscle and are not false positives. RNAi and knockout analysis were performed in order to investigate the role of low-expressed muscle genes in myofilament structure. RNAi results show that 14/34 (41%) of the genes screened had mild defects in myofilament organization. The SAGE libraries identified 6388 low-expressed transcripts, this work suggests that at least 16% (1022 genes) of these are in fact expressed in muscle and may reveal new components previously overlooked by other approaches.

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.

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.

Serial Analysis of Gene Expression (SAGE) on Caenorhabditis elegans RNA from FACS sorted embryonic body wall muscle cells has identified nearly 8000 genes expressed in nematode body wall muscle. Approximately 60% of these are genes are expressed at low levels (<5 tags/~50,000-100,000 tag library). Low-abundance transcripts have typically been overlooked since most are considered experimental or contamination errors. Consequently, research has been focused on transcripts that are most enriched in the particular tissue of interest. Here I focus on the analysis of low-expressed transcripts in the muscle SAGE libraries in order to investigate what percentage of these are in fact expressed in muscle and are not false positives. Most well characterized C. elegans body wall muscle genes are not expressed at low levels, therefore I anticipate that focusing on these rarely expressed genes will allow for the identification of muscle components that have been previously unrecognized. RT-PCR was performed on RNA isolated from purified body wall muscle cells to initially estimate what fraction of these low abundance transcripts present in the SAGE data are indeed expressed in muscle. I examined 128 genes, of which 84 were represented by a single SAGE tag. From this initial list, 38% of the low-expressed transcripts were verified for their presence in body wall muscle. Subsequently, reporter GFP fusions were used to deduce if these low-expressed transcripts are indeed expressed in vivo within muscle. Of the low-expressed genes that tested positive via RT-PCR, 42% showed in vivo expression in body wall muscle. When the results from the RT-PCR and in vivo expression experiments are combined, I can extrapolate that at least 16% of low-expressed genes identified by the SAGE libraries are in fact expressed in muscle and are not false positives. RNAi and knockout analysis were performed in order to investigate the role of low-expressed muscle genes in myofilament structure. RNAi results show that 14/34 (41%) of the genes screened had mild defects in myofilament organization. The SAGE libraries identified 6388 low-expressed transcripts, this work suggests that at least 16% (1022 genes) of these are in fact expressed in muscle and may reveal new components previously overlooked by other approaches.

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