Bioinformatics
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Item Impact of cortisol treatment on specific cell types in the regenerating caudal fin in zebrafish.(Wheaton College. (Norton, Mass.), 2022-05-16) Nobrega, Celeste GraceCortisol is a stress hormone that is regulated by the hypothalamic pituitary adrenal axis which is impacted by both circadian rhythms and acute stress. If stress becomes chronic, cortisol levels in the body continually rise instead of having natural oscillations, which can predispose individuals to compromised physical and mental health. Since stress hormone receptors play a role in gene regulatory networks, the effects of chronic stress can be seen through studying gene expression. The effects of chronic stress on zebrafish were investigated by exposing embryos to cortisol and studying the ability of those adults to respond to a stressor later in life (tailfin amputation) using bulk genomics methods (Hartig et al., 2016). However, the main limitation of bulk genomics methods is the loss of single cell resolution. This means that observed differential gene expression patterns could either be due to true differences in gene expression as a response to treatment, or due to the growth patterns of different cell types since each cell expresses a unique transcriptome. Previous work understanding the cellular diversity of the caudal fin and the impacts of chronic early life stress on the regeneration of the caudal fin come together in the present study to indicate what cell types of the regenerating caudal fin are impacted by chronic early-life stress. The goal of this research is to explore the differential cellular responses in adult zebrafish to chronic early life stress by studying the regenerating tailfin. The results reported here indicate that overall, hematopoietic cells in adult zebrafish are most effected by the chronic exposure to cortisol in early development. In addition, these results demonstrate the usefulness of single cell genomics methods to provide cell type context to previously collected bulk genomic data.Item A Comparative Study Mapping the Landscape of Repetitive Elements in Fundulus heteroclitus(Wheaton College. (Norton, Mass.), 2021-05-16) Elkhoury, KevinFundulus heteroclitus has shown to be capable of rapid adaptation in environments lethal to most other species. Comparisons of isolated Fundulus heteroclitus populations in similar polluted environments have been found to contain similar mutations despite their geographic isolation. This thesis aims to identify the potential role transposable elements serve in Fundulus heteroclitus relating to these common mutations. To accomplish this a pipeline is created that annotate genomes for transposable elements and is applied to the Fundulus heteroclitus genome to be used for further study.Item Evolution and diversification in toll-like receptors of fundulus heteroclitus and teleosts based on whole genomic data.(Wheaton College (MA), 2019) Wu, YushengToll-like receptors (TLRs) are a major component of the innate immune system and are pivotal for organismal survival by recognizing a diverse group of pathogens. Compared to mammals, TLRs are found to be more diverse in teleost species, which suggests the essential role of innate immunity in teleosts due to the lack of their diversification in adaptive immunity.The purpose of this study was, 1) to estimate an evolutionary tree of teleosts TLRs, 2) to verify and clarify the number of TLR gene copies in Fundulus heteroclitus, and 3) to test for evidence of positive selection acting on the various TLRs. A gene tree of the TLR family in teleosts was constructed based on the whole genome data from Ensembl database, and it allowed for a clarification in teleost TLRs’ nomenclature and the description of the full complement of TLRs in F. heteroclitus.Positively selected sites were detected in all TLRs with TLR22 found to be under the highest positive selection rate (4.63% of TLR gene sites) among all TLRs. Copy number variation of teleost-specific TLR22 gene moreover suggested gene duplication and diversification potentially to compensate for the lack of other cell surface TLRs. These results suggested that various TLR22 paralogues have likely arisen from positive selection pressure as well as gene expansion and functional diversification in teleost species.Item Analysis of ciliary gene expression in sea urchin development.(Wheaton College (MA), 2019) Olander, Kira E.Cilia are important cellular organelles tied to many disease states due to their pivotal roll in important cellular processes, including early organism development. In this Honors Thesis, cilia were studied in developing Strongylocentrotus purpuratus embryos during the blastula stage of development. The blastula stage is when the sea urchin embryos develop motile cilia. The upstream DNA regions of 37 ciliary genes expressed during the blastula stage of development were analyzed using a motif discovery algorithm MEME and further analyzed with a motif comparison algorithm TOMTOM, in search of shared regulatory elements related to transcription factor binding proteins. This experiment resulted in three promising motifs aligned with known transcription factors Klf6, Klf11, Klf2, and Glis-3. Our data supports a model were Klf6, Klf11, and Klf2 may be transcriptional enhancers of the blastula cluster genes while Glis-3 may be a transcriptional repressor. These transcription factor proteins may play a roll in regulating the ciliary phenotype in S.p..Item Genomics approaches to analyzing ciliary gene functions and regulation.(Wheaton College (Norton, Mass.), 2016) Mullings, Javon R.