Rachel Stupay (Hauswirth lab)

Academic TitleRachel Stupay

Graduate Student

Contact Information

(352) 273-8784


I graduated from the University of Alabama at Birmingham majoring in Molecular Biology with a concentration in Genetics and Biochemistry. I am a member of Alpha Epsilon Delta (the pre-med/pre-health honors society), The Golden Key National Honors Society, the National Society for Collegiate Scholars, Pi Sigma: Biology Honors Society, and AMSA (American Medical Student Association). I began my research in the lab of Dr. Bradley K. Yoder working on a mutagenesis screen to identify novel ciliopathy genes and alleles. We uncovered a novel allele for MKS-5 (RPGRIP1L, NPHP8) that resulted in an alternately spliced transcript and lead to a premature stop codon. We further established that there is a hierarchical relationship among the known proteins that localize to the ciliary transition zone (TZ), and MKS-5 is a key component to anchor many other proteins to the TZ. I received a Genetics Internship in 2009 and placed 3rd in the poster competition, a SIBS internship in 2010 and placed 2nd in the poster competition, and won 1st place in the University of Alabama’s Biology University of Alabama Systems Honors Research Conference at University of Alabama at Birmingham in 2011.

I began Graduate school at UF in the fall of 2011, and I am currently a Graduate Fellow in the lab of Dr. William W. Hauswirth on an Ophthalmology Training Grant. My project involves studying an Usher Syndrome Type III mouse model in order to define a retinal phenotype and establish a therapeutic approach for treatment. Usher type 3 is caused by mutations in the clarin-1 gene, which codes for a four-transmembrane-domain protein that is expressed at very low levels and whose function and retinal localization are currently unknown. Through previous work, clarin-1 has been seen to localize to the photoreceptor inner segment, connecting cilium, and synapses. In humans, clarin-1 mutations lead to both blindness and deafness, however the currently available Usher III mouse models (N48K knock-in and clarin knockout) display no apparent retinal phenotype. I am performing light driven translocation experiments to test the validity of a potential retinal phenotype in N48K mutant and clarin knock-out mice. The translocation experiments have shown a significant difference in the pattern of Arrestin movement in the mutants relative to the control mice. Restoration of Arrestin localization will be examined following AAV-mediated clarin delivery. Establishing a phenotype in these mouse models of Usher III is crucial for testing the therapeutic potential of the currently available clarin AAV vectors in the retina. I am further assessing the toxicity involved in the overexpression of clarin in the retina and using cell-type specific promoters to define where the toxicity is coming from. I am also hoping to identify the true cellular localization of clarin through the use of more specific antibodies for clarin-1, in situ hybridization using highly specific RNA probes, and protein truncations to assess which amino acid sequences target clarin for its proper localization.


  • “The Journal of Cell Biology” (JCB) (March 21, 2011) “MKS and NPHP modules cooperate to establish basal body/transition zone membrane associations and ciliary gate function during ciliogenesis” Williams, C. L., Li, C., Kida, K., Inglis, P. N., Mohan, S., Semenec, L., Bialas, N. J., Stupay, R. M., Chen, N., Blacque,O. E., Yoder, B. K.., and Leroux. M. R.. 192:1023-1041. doi:10.1083/jcb.201012116
  • “The Inquiro, Undergraduate Research Journal” (2010)“A screen designed to target MKS-like genes yields a novel allele of MKS-5, possibly the core MKS protein” Stupay, R.M., Williams, C. L., Masyukova, S. V., and Yoder, B. K. (p. 55-62, Vol. 4, 2010)
  • “The Inquiro, Undergraduate Research Journal” (2009) “A Caenorhabiditis elegans Mutagenesis Screen to Identify Candidate Human Cystic Kidney Disease Genes” Stupay, R.M., Williams, C. L., Masyukova, S. V., and Yoder, B. K. (p. 37-45, Vol. 3, 2009)