Please read the abstract in the thesis. / Thesis (PhD)--University of Pretoria, 2013. / gm2014 / Paraclinical Sciences / Unrestricted

Mosses are small avascular bryophytes with a haploid dominant gametophyte and a diploid sporophyte stage. The gametophyte cells are single layered and lack a protective cuticle, which is the first line of defense in vascular plants. These factors would render them highly susceptible to stress but on the contrary, mosses have flourished on land for the past 450 million years with tolerance to both abiotic and biotic stress. Occurrence of unique lipids in bryophytes was considered as an adaptive means to survive harsh terrestrial condition. A recent study identified a lipid metabolite, anandamide in the Physcomitrella patens. Anandamide (NAE 20:4) belongs to a group of fatty acid ethanolamides or N –acylethanolamines (NAEs). In eukaryotes, NAEs were shown to play an important role in mediating stress responses. In plants, NAE 14:0 has been implicated in biotic stress response; its levels increased up to 50-fold in elicitor-treated tobacco plants, along with induction of defense gene expression and inhibition of alkalization. In animals anandamide acts as an endocannabinoid ligand and mediates several physiological responses including stress. This study aims to use P. patens as the model system because of its available genomic database and prior studies on biotic stress, to examine if NAE 20:4 contributes to their ability to tolerate biotic stress. It is hypothesized that the occurrence of anandamide will play a role in mediating biotic stress tolerance in P. patens. To test this hypothesis, three specific aims are proposed. They are to determine the effect of 1) elicitor-treatment on NAE and fatty acid profile in the moss, 2) anandamide on elicitor-induced morphological and physiological changes in the moss and 3) anandamide on elicitor-induced defense gene expression in moss. Mosses utilize similar defense mechanisms as flowering plants and disease symptoms can easily be studied using microscopy because of their haploid dominant gametophyte stage with monolayer cells. The induction of defense gene expression will be studied by quantitative PCR and changes in lipid profile by selective lipidomics. This study is expected to provide novel insights into the role of anandamide in early land plants, specifically in response to biotic stress.

No description available.

Advances in DNA sequencing of microbial communities have revealed a complex relationship between the human microbiome and our health. Community dynamics, host-microbe interactions, and changing environmental pressures create a dynamic ecosystem that is just beginning to be understood. In this work, we develop methods for investigating the dynamics of the microbiome. First, we develop a model for describing community dynamics. We show that the proposed approaches accurately describes community trajectories over time. Next, we develop a method for modeling and eliminating technical noise from longitudinal data. We demonstrate that the method can accurately reconstruct microbial trajectories from noisy data. Finally, we develop a method for estimating bacterial growth rates from metagenomic sequencing. Using a case-control cohort of individuals with irritable bowel disease, we show how growth rates can be associated with disease status, community states, and metabolites. Altogether, these models can be used to help uncover the relationship between microbial dynamics, human health, and disease.

The Tremarctinae are a subfamily of bears endemic to the New World, including two of the largest terrestrial mammalian carnivores that have ever lived: the giant, short-faced bears Arctodus simus from North America and Arctotherium angustidens from South America (greater than or equal to 1000 kg). Arctotherium angustidens became extinct during the Early Pleistocene, whereas Arctodus simus went extinct at the very end of the Pleistocene. The only living tremarctine is the spectacled bear (Tremarctos ornatus), a largely herbivorous bear that is today only found in South America. The relationships among the spectacled bears (Tremarctos), South American short-faced bears (Arctotherium) and North American shortfaced bears (Arctodus) remain uncertain. In this study, we sequenced a mitochondrial genome from an Arctotherium femur preserved in a Chilean cave. Our molecular phylogenetic analyses revealed that the South American short-faced bears were more closely related to the extant South American spectacled bear than to the North American short-faced bears. This result suggests striking convergent evolution of giant forms in the two groups of short-faced bears (Arctodus and Arctotherium), potentially as an adaptation to dominate competition for megafaunal carcasses.

No description available.

No description available.

Analysis of SIP68: A UDP Glucosyltransferase for Its Role in Plant Growth and Immunity UDP-glucosyltransferases (GTs) are a group of enzymes that play a crucial role in plant metabolism by transferring glucosyl groups from UDP-glucose to various acceptor molecules. SIP68 is a UDP-glucosyltransferase enzyme that has been identified to interact with SABP2 in a yeast two-hybrid screen. Previous research conducted in our lab has demonstrated that SIP68 is involved in salicylic acid (SA)-mediated defense signaling in tobacco plants. In the current study, we aimed to investigate the potential role of SIP68 in plant development and immune response. Our analysis of SIP68 revealed that this UDP-glucosyltransferase has a gene family, and its gene and protein sequence, molecular attributes, gene structure, and localization in the chromosome, exon-intron distribution, cis-regulatory elements in the promoter region, homology modeling of protein, domain architecture, motif analysis, phylogenetic tree, and protein-protein interaction were analyzed to better understand its potential function in plant metabolism. Our in-silico analysis predicted that SIP68 may play a role in the cytokinin-mediated metabolic pathway, which could affect plant growth and cell proliferation. Specifically, our analysis suggested that SIP68 might transfer glucosyl groups to various acceptor molecules involved in the cytokinin-mediated metabolic pathway. This suggests that SIP68 may play a role in regulating plant growth and development by affecting the cytokinin pathway. To investigate the potential role of SIP68 in plant development, we generated SIP68-deficient transgenic tobacco plants by silencing the SIP68 protein. The observed phenotype of these plants was compared to that of wild-type plants. We found that root, shoot, leaf width, and overall biomass development were all affected in SIP68-deficient plants. This suggests that SIP68 plays a crucial role in regulating various aspects of plant growth and development. This agrees with our previous finding that SIP68 is involved in SA-mediated defense signaling in tobacco plants. Our analysis of protein-protein interactions revealed that SIP68 interacts with various classes of flavanols in-vitro. This interaction provides a starting point for investigating potential targets of SIP68 in tobacco plants. However, the specific in-planta substrate(s) of SIP68 has not yet been identified. Therefore, further investigation is needed to determine the intracellular targets of SIP68 and its specific role in plant metabolism. In conclusion, our study provides insights into the potential role of SIP68 in plant development and immune response. Our findings suggest that SIP68 plays a crucial role in regulating various aspects of plant growth and development. Furthermore, our in-silico analysis predicts that SIP68 may play a role in the cytokinin-mediated metabolic pathway, which could affect plant growth and cell proliferation. Future investigation is needed to determine the intracellular targets of SIP68 and its specific role in plant metabolism. Overall, this study highlights the importance of UDP-glucosyltransferase enzymes (SIP68) in plant development and immune response.

No description available.

No description available.