published_or_final_version / Zoology / Master / Master of Philosophy

published_or_final_version / Community Medicine / Master / Master of Public Health

published_or_final_version / abstract / Pathology / Master / Master of Philosophy

published_or_final_version / abstract / Surgery / Master / Master of Philosophy

published_or_final_version / abstract / Zoology / Doctoral / Doctor of Philosophy

published_or_final_version / Paediatrics / Doctoral / Doctor of Philosophy

published_or_final_version / Electrical and Electronic Engineering / Master / Master of Philosophy

Plants modulate their growth and development according to the prevailing light conditions. To detect light signals plants have an array of photoreceptors including the phytochromes which monitor the red and far-red light regions of the light spectrum. Phytochromes regulate gene expression in response to light in part by physically interacting with nuclear-localized bHLH transcription factors called PHYTOCHROME INTERACTING FACTORS (PIFs). PIFs are known to function as negative regulators of photomorphogenesis. Here we show that PIF1, the PIF family member with the highest affinity for phys, is degraded after pulses or continuous red, far-red or blue light in a phytochrome dependent manner. In etiolated seedlings, phyA plays a dominant role in regulating the degradation of PIF1 after a pulse of red, far-red or blue light; while phyB, phyD and other phys also influence PIF1 degradation after prolonged illumination. PIF1 interacted with phyA and phyB in a blue light-dependent manner, and the interactions with phys are necessary for the light-induced degradation of PIF1. In response to red, far-red or blue light treatments PIF1 is rapidly phosphorylated, poly-ubiquitinated and degraded via the ubiquitin/26S proteasomal pathway. In addition, we show that PIF1 negatively regulates photomorphogenesis at the seedling stage. The overexpression of a light-stable truncated form of PIF1 causes constitutively photomorphogenic phenotypes in the dark. pif1 seedlings displayed more open cotyledons and slightly reduced hypocotyl length compared to wild type under diurnal (12h light/12h dark) blue light conditions. Double mutant analyses demonstrated that pif1phyA, pif1phyB, pif1cry1 and pif1cry2 have enhanced cotyledon opening compared to the single photoreceptor mutants under diurnal blue light conditions. Taken together, these data suggest that PIF1 functions as a negative regulator of photomorphogenesis and that light-activated phys induce the degradation of PIF1 through the ubi/26S proteasomal pathway to promote photomorphogenesis. / text

This measurement study examined the construct validity of the retell component of the Texas Middle School Fluency Assessment (Texas Education Agency, University of Houston, & The University of Texas System, 2008a) within a confirmatory factor analysis framework. The role of retell, provided after a one-minute oral reading fluency measure, was investigated by comparing the fit of a three-factor model of reading competence to the data collected on a diverse sample of seventh- and eighth-grade students (N=394). The final model demonstrated adequate to mediocre fit (χ2 = 97.316 {32}; CFI = 0.958; TLI = 0.941; RMSEA = .081). Results suggest that retell was a significant contributor to comprehension (Δχ2=16.652{1}, p < .001), fluency (Δχ2=10.882{1}, p = .001), and word identification (Δχ2=7.84{1}, p = .005). However, the χ2 difference was greater for comprehension, as was the factor loading for comprehension (.250, p < .001) compared to fluency (.194, p < .001) and word identification .167, p < .001). Retell did, however, have a large residual variance (.938), suggesting it did not function well as a measure of comprehension in its current state with low inter-rater reliability (K = .37). Narrative retell scores (.352, p< .001) were better predictors of comprehension than expository retell scores (from .2221 to .264, p < .001) or the combination of all three scores (Δχ2=134.261{19}; p < .001), but average retell scores produced a more parsimonious model than narrative retell scores alone (ΔAIC = 58.275; ΔBIC = 58.275). Average retell was only weakly correlated to other measures of comprehension (from r = .155 to r = .257, p < .01). However, the relationship was stronger than the relationship between retell and other measures of fluency (from r = .158 to r = .183, p < .01) or word identification (r = .132, p < .05). In addition, retell did not demonstrate differential item functioning when student characteristics (e.g., primary language, socioeconomic status, ability level) were entered as covariates, even though there were overall latent differences. / text

Plant embryogenesis is an intriguing developmental process that is controlled by many genes. AGAMOUS Like 15 (AGL15) is a MADS-domain transcriptional regulator that accumulates preferentially during this stage. However, at the onset of this work it was unknown which genes are regulated by AGL15 or how AGL15 is regulated. This dissertation is part of the ongoing effort to understand the biological roles of AGL15. To decipher how AGL15 functions during plant development, a chromatin immunoprecipitation (ChIP) approach was adapted to obtain DNA fragments that are directly bound by AGL15 in vivo. Putative AGL15 targets were isolated, and binding and regulation was confirmed for one such target gene, ABF3. In addition, microarray experiments were performed to globally assess genes that are differentially expressed between wild type and agl15 young seeds. Among them, a gene, At5g23405, encoding an HMGB domain protein was identified and its response to AGL15 was confirmed. Preliminary results suggest that the loss-of-function of At5g23405 might have an effect on somatic embryogenesis, consistent with AGL15 repression of the expression of this gene. Lastly, to address the question about how the regulator is regulated, the cis elements controlling the expression of AGL15 must be identified. Deletion analysis of the AGL15 promoter indicated the presence of putative positive and negative cis elements contributing to the expression of AGL15. Further analysis suggested that AGL15 regulates the expression of its own gene and this regulation may partially be explained by the direct binding of the protein to the AGL15 promoter. The data presented in this dissertation demonstrate that ChIP can be used to identify previously unsuspected targets of AGL15. Based on ChIP, a ChIP-chip technique is being developed in the lab to allow a more global analysis of in vivo binding sites. The identification of target genes and cis elements in AGL15 promoter is a step towards characterization of the biological roles of AGL15.