Geometric morphometrics reveals shifts in flower shape symmetry and size following gene knockdown of CYCLOIDEA and ANTHOCYANIDIN SYNTHASE

Peer reviewe

Local Antibiotic Discovery

This project discovers potential antibiotic producing bacteria within soil in hopes of finding a new antibiotic. Various tests and diagnostics are used in the process of isolating candidates, finding zones of inhibition across tester strains, and determining the characteristic and genome of a specific bacteria species. The isolation process takes place through the collection of a soil sample, serial dilutions of sample, and acquiring a master plate. Isolated candidates are then tested for zones of inhibition across several tester strains through a series of Kirby-Bauer tests. Characteristics and Genome of the primary candidate for antibiotic potential are found through Gram Stains and DNA sequencing/Metabolic testing. These results shall determine the properties and origins of a bacterium that present such findings

Duplication and Functional Divergence in the Floral Organ Identity Genes

Thesis (Ph.D.)--University of Washington, 2015Among all extant land plant lineages, the flowering plants, or angiosperms, are by far the most abundant and diverse. A leading force in their speciation has been attributed to morphological changes in flowers, a key reproductive innovation. The floral organ identity genes are thus a logical focus to gain insight into the angiosperm radiation, since alterations to both the structure and regulation of developmental genes are known to underlie morphological diversity. Genetic studies on flower development in the model plants Arabidopsis and Antirrhinum have yielded the ‘ABC model’, which predicts that the four types of floral organs (sepals, petals, stamens and carpels) are specified by the products of four gene classes, A, B, C, and the subsequently added E class, that act in combination. All but one of these transcription factors belong to the MADS-box family, their function analogous to the metazoan body patterning of HOX genes. Plant genomes are prone to duplication and paralogs are particularly widespread in the floral organ identity genes. My aim was to elucidate the function of representatives of an early clade of duplicated floral organ identity genes, with a focus on determining the degree of redundancy vs. divergence amongst them and of conservation in relation to the later-diverging models. To that end, I use the species T. thalictroides, from the clade sister to all other eudicots, with two C class gene orthologs and three B class gene orthologs. In the C class genes, one paralog showed deep conservation of the dual C class function, affecting both reproductive organ identity and meristem determinacy, while the second revealed specialization to ovule identity. This sub-functionalization is unlike the fate of the B class genes following duplication, which retained partial redundancy, showed deep conservation in stamen identity, and gained a novel role in ectopic petaloidy. Taken together, these studies illustrate the different fates that floral organ identity gene paralogs can assume following duplication that can ultimately be relevant to the generation of biodiversity. Moreover, they underscore the need to survey the functional relevance of all branches of a gene’s evolutionary history

Gene Duplication and Transference of Function in the paleoAP3 Lineage of Floral Organ Identity Genes

The floral organ identity gene APETALA3 (AP3) is a MADS-box transcription factor involved in stamen and petal identity that belongs to the B-class of the ABC model of flower development. Thalictrum (Ranunculaceae), an emerging model in the non-core eudicots, has AP3 homologs derived from both ancient and recent gene duplications. Prior work has shown that petals have been lost repeatedly and independently in Ranunculaceae in correlation with the loss of a specific AP3 paralog, and Thalictrum represents one of these instances. The main goal of this study was to conduct a functional analysis of the three AP3 orthologs present in Thalictrum thalictroides, representing the paleoAP3 gene lineage, to determine the degree of redundancy versus divergence after gene duplication. Because Thalictrum lacks petals, and has lost the petal-specific AP3, we also asked whether heterotopic expression of the remaining AP3 genes contributes to the partial transference of petal function to the first whorl found in insect-pollinated species. To address these questions, we undertook functional characterization by virus-induced gene silencing (VIGS), protein–protein interaction and binding site analyses. Our results illustrate partial redundancy among Thalictrum AP3s, with deep conservation of B-class function in stamen identity and a novel role in ectopic petaloidy of sepals. Certain aspects of petal function of the lost AP3 locus have apparently been transferred to the other paralogs. A novel result is that the protein products interact not only with each other, but also as homodimers. Evidence presented here also suggests that expression of the different ThtAP3 paralogs is tightly integrated, with an apparent disruption of B function homeostasis upon silencing of one of the paralogs that codes for a truncated protein. To explain this result, we propose two testable alternative scenarios: that the truncated protein is a dominant negative mutant or that there is a compensational response as part of a back-up circuit. The evidence for promiscuous protein–protein interactions via yeast two-hybrid combined with the detection of AP3 specific binding motifs in all B-class gene promoters provide partial support for these hypotheses

Development of a field bioassay for rapid detection of Candidatus Liberibacter solanacearum (Lieft.) in potato (Solanum tuberosum L.) leaves and tubers

Candidatus Liberibacter solanacearum (CaLso) is vectored by Tomato/Potato Psyllid (Bactericera cockerelli Sulc.). The bacterium spreads throughout the phloem and eventually infects underground tubers, which exhibit brown flecking throughout the perimedullary tissue. Upon deep-drying of tuber cross-sections in oil, this results in a characteristic zebra pattern, giving rise to the common name, Zebrachip. Currently, the only way to determine whether plants are infected with CaLso is by time-consuming and expensive PCR testing. Here, we developed an inexpensive bioassay that can be performed rapidly in the field. CaLso is known to degrade starch into amylose and amylopectin. The latter stains dark purple in iodine. Potato laminas were sliced parallel to, but 2 mm away from, the midrib. The smaller piece of the lamina was immersed in 3% iodine solution for 30 sec., rinsed for 5 sec in distilled water and cut surfaces photographed immediately. Similarly, cross-sections of tubers were stained in 3% iodine for 10 sec., rinsed in distilled water for 5 sec and photographed. Cut surfaces that stained dark purple were thought to be infected with CaLso. 100% of plants with dark flecked tubers had positively stained leaves and tubers. Of the healthy-looking plants, 25% of them were suspect for CaLso as those leaves and tubers exhibited partial staining of cut surfaces. PCR of all leaves and tubers were undertaken to confirm the presence or absence of CaLso. Results of the PCR study will be presented, along with a confidence interval for accuracy of the bioassay