Author's School

Graduate School of Arts & Sciences

Author's Department/Program

Biology and Biomedical Sciences: Molecular Genetics and Genomics


English (en)

Date of Award

January 2011

Degree Type


Degree Name

Doctor of Philosophy (PhD)

Chair and Committee

Michael Lovett


Vertebrates, particularly birds, show extremely variable species-specific morphology in craniofacial structures. Cranial neural crest cells give rise to all the cartilage and bone of the face, and transplantation experiments have shown that these cells contain species-specific patterning information. First, I employed custom cross-species microarrays to analyze the spectrum of developmental signaling pathway and transcription factor gene expression changes in neural crest cells of the developing beaks for the chicken, duck, and quail, both before and after morphological variation is evident. I found that neural crest cells have established a species-specific gene expression profile that predates morphological variation. In addition to expression changes in the Bmp and Calmodulin pathways, previously associated with morphological variation in Darwin's finches, I observed dramatic changes in a number of Wnt signaling components in the broad-billed duck. Second, given that deletion of the microRNA processing gene DICER in neural crest cells results in loss of nearly all facial structures, I utilized high-throughput sequencing to describe the microRNAs that are expressed and/or differentially expressed among the same neural crest samples used for the microarray analysis. In remarkable contrast to relatively unchanged pattern of transcription factor gene expression, microRNA expression is highly dynamic during stages when avians acquire species-specific morphology. The microRNA expression profiles also suggest that the transition from multipotent, proliferative neural crest cells into cells differentiating to form the tissues of the face may be delayed in the duck relative to the chicken and quail. This prolonged period of proliferation in duck neural crest may contribute to the increase in beak size and width of the adult duck bill versus the chicken beak. Finally, I illustrate examples of how these genomic data sets can initiate new avenues of investigation and testable hypotheses. I found that the Wnt pathway acts upstream of the Bmp pathway and induces regional changes in growth of the developing beak. I also correlate changes in expression of miR-222 in the frontonasal prominence with alterations in protein: but not mRNA) levels of one of its target genes, the cell cycle regulator p27(KIP1). I then identified seven mature microRNAs that appear to be specific to the avian lineage. Using PCR, I confirmed that two of these, miR-2954 and miR-2954*, are conserved across the avian lineage, from ratites to songbirds.


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