Thesis advisor: John Wing / Presented here is research investigating genes that are involved in the development and maintenance of ciliated nerve endings in the nematode Caenorhabditis elegans. C. elegans utilizes a subset of neurons, referred to as ciliated sensory neurons, to sense certain changes in its environment. There are two amphid sensilla (sense organs) that mediate exposure of these ciliated endings to the animal's external environment. Those ciliated endings that penetrate the cuticle are responsible for a myriad of behaviors that range from chemotaxis to osmotic avoidance, but in general function for the reception of environmental cues and stimuli. The intraflagellar transport (IFT) process facilitates the morphogenesis of these ciliated endings, and animals lacking intact ciliated endings may not be able to detect nourishment, hazardous environments, or other worms for mating. Mutant strains used in this study were generated by EMS mutagenesis of wild-type N2 animals and a subsequent screen of those worms displaying significant cilia dysfunction as evidenced by their dye-filling defective (Dyf) phenotype. Cilia-mediated uptake of lipophilic DiI into six pairs of amphid sensory neurons and two pairs of phasmid sensory neurons is expected in wild-type (N2) animals, but in Dyf animals, this dye-filling is disrupted, either through morphological defects, or deleterious mutations in the IFT process. To investigate the morphogenesis of cilia in C. elegans, we analyzed two specific mutant strains, WX737 dyf-3(og022)IV and PK841 dyf-15(pk841)V, that are defective in the uptake of fluorescent dye DiI and abnormal in sensory cilium structure. Through a variety of genetic mapping techniques, we were able to successfully map experimental gene dyf-15(pk841) to an interval of 2.84cM on chromosome V, and identify og022 as an allele of the gene dyf-3. It has been previously shown that dyf-3 expression is detected in 26 chemosensory neurons, including six IL2 neurons, eight pairs of amphid neurons (ASE, ADF, ASG, ASH, ASI, ASJ, ASK and ADL) and two pairs of phasmid neurons (PHA and PHB). Analysis of cilium malformation and the presence of a recognition sequence for the DAF-19 transcription factor suggest that dyf-3 is involved in the intraflagellar transport system complex B. / Thesis (BS) — Boston College, 2008. / Submitted to: Boston College. College of Arts and Sciences. / Discipline: Biology. / Discipline: College Honors Program.

Thesis advisor: John Wing / Thesis advisor: Stephen Wicks / Molecular biology and genetics, single nucleotide polymorphism genetic mapping, phenotypic assays including behavioral assessment, and fluorescent microscopy of GFP-tagged proteins were used to study ciliary defects in the nematode Caenorhabditis elegans. Mammalian cilia are multifunctional. Some of the physiological roles in which they are involved include sensing developmental signaling molecules and ligands as well as creating flows of mucus and cerebrospinal fluid that function as flow meters and mechanosensors. Due to the multifunctional nature of cilia, it is not surprising that many human diseases can be caused by ciliary defects. Bardet-Biedl Syndrome is a rare genetic ciliopathy characterized by retinal degeneration, polydactyly, obesity, cystic kidneys, mental retardation, and many other ailments. We have identified osm- 12/bbs-7 to be a C. elegans homologue of human BBS7, a gene known to cause Bardet-Biedl Syndrome when mutated. With the help of Michel Leroux’s group, I showed the BBS-7 protein to be localized to the base of cilia and to undergo intraflagellar transport along the ciliary axoneme. Our findings suggest that BBS- 7 plays a role in the assembly and/or functioning of the IFT complex. I also performed a mutagenesis and phenotypic screen for animals defective in the uptake of DiI into a subset of their ciliated neurons in order to identify new components involved in ciliogenesis and IFT. I describe an extended bulked segregant analysis (BSA) mapping methodology, which can save time and resources by filtering out alleles of previously known genes without performing time-consuming interval mapping. In addition, I identified one of the 11 dyefilling defective alleles from the screen to be a novel allele of dyf-3, which encodes a protein required for sensory cilia formation. / Thesis (PhD) — Boston College, 2008. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Biology.