The first aim of this thesis is to examine relationships between microRNAs targeting gene networks, combining knowledge from microRNA prediction databases into our microRNA Data Integration Portal (mirDIP). Modeling the microRNA:transcript interactome – referred to as the micronome – to build microRNA interaction networks of signalling pathways, we find genes within signalling pathways to be co-targeted by common microRNAs suggesting an unexpected level of transcriptional control. We identify two distinct classes of microRNAs; universe microRNAs, which are involved in many signalling pathways; and intra-pathway microRNAs, which target multiple genes within one signalling pathway. We find universe microRNAs to have more targets, to be more studied and more involved in cancer signalling than their intrapathway counterparts. The second aim was to undertake a more focused view, analyzing the characteristics of microRNAs within the micronome itself beginning with a focus on the under-examined microRNA terminal loop across the micronome to determine if this region of the microRNA structure might contribute to microRNA functioning. We have identified 2 main classes of microRNAs based on loop structure – perfect and occluded, which show biological relevance. We found regulatory motifs within microRNA terminal loops and found a large number of Frequently Occurring Words (FOWs) significantly overrepresented across the micronome. Set analysis of in vitro secreted microRNAs, microRNA expression across a panel of normal tissues, and microRNAs shown to be secreted in lung cancer shows that specific microRNA loop motifs within these groups are significantly overreperesented – suggesting that microRNA terminal loops harbour sequences bearing microRNA processing and localization signals.

This thesis was inspired by the project funded by Bureau of Safety and Environment Enforcement (BSEE) to study the use of epoxy (or any cement alternative) to plug offshore wells damaged by hurricanes. The project focuses on non-cement materials to plug wells that are either destroyed or damaged to an extent where vertical intervention from the original wellhead is no longer possible. The proposed solution to this problem was to drill an offset well and intersect the original borehole at the very top and spot epoxy (or any suitable non-cement plugging material) in the original well. The spotted epoxy then would fall by gravitational force all the way down to the packer and then settle on top of the packer to plug the annulus of the damaged well permanently. This thesis mainly concentrates on the factors affecting the fall rates and how to correlate them in order to derive an applicable test that can be conducted on the field or lab to calculate the terminal velocity of the known epoxy composition. Determining the settling velocity of the epoxy is crucial due to the fact that epoxy should not set prematurely for a better seal and isolation. The terminal velocity and the recovery for epoxy based plugging fluids were tested by using an experimental setup that was developed for this purpose. The results were also validated by using an alternative experiment setup designed for this purpose. Factors affecting the terminal velocity and recovery of epoxy were studied in this research since the settling velocity of the epoxy is crucial because epoxy should not set prematurely for a better seal and isolation. The study was conducted by using an experiment setup that was specially developed for terminal velocity and recovery calculations for plugging fluids. Results obtained from the experiment setup were successfully correlated to epoxy's composition for estimating the terminal velocity of the mixture.

Plants are stationary and need to adapt to the environment they live in. Integration of environmental cues, such as changes in light and temperature, can occur either directly or through the action of hormones. Hormone and light signaling leads to rapid changes in gene expression, and eventually changes in protein levels. In this thesis I have studied how the epigenetic regulator TERMINAL FLOWER2 (TFL2) is involved in light and hormonal signaling in the model organism Arabidopsis thaliana (thale cress). TFL2 is the only Arabidopsis homologue of HETEROCHROMATIN PROTEIN1 (HP1). HP1 proteins have been shown to be involved in repressing gene expression by maintaining the tight structure of heterochromatin or by forming a heterochromatin like structure in euchromatic regions. Unlike metazoan HP1 which can be localized both to eu- and heterochromatin, TFL2 is uniquely localized to euchromatin. tfl2 mutants have reduced levels of free auxin and a reduced rate of auxin biosynthesis. TFL2 binds to and promotes spatial and temporal expression of the genes belonging to the YUCCA gene family, which are believed to regulate a rate limiting step in the auxin biosynthesis pathway. Further, TFL2 binds to a subset of Aux/IAA proteins to repress auxin regulated genes involved in ovule and carpel development. In a similar way, TFL2 is also involved in repressing two jasmonate responsive genes, VEGETATIVE STORAGE PROTEIN1 and 2. This TFL2 regulated repression might occur through the interaction with the jasmonate responsive protein JAZ6. In light signaling TFL2 is involved in repressing both phytochrome A and B signaling as the response to red and far red light is enhanced in tfl2 mutants. The shade avoidance response and chloroplast biogenesis are also regulated by TFL2 as the hypocotyls of tfl2 are not able to elongate as wt in shade conditions and greening is delayed upon de-etiolation of tfl2 seedlings. This work shows that TFL2 has a repressive function in auxin, jasmonate and light signaling and for the first time we show that TFL2 is directly involved in promoting gene expression.

Dissertation (Ph.D.)--Auburn University, 2006. / Abstract. Includes bibliographic references.

Diss. (sammanfattning) Uppsala : Univ., 2001. / Härtill 6 uppsatser.

Thesis (M.Nurs)--University of Western Sydney, Nepean, 1995. / Includes bibliography.

Thesis (Ph.D.) -- University of Western Sydney, 2005. / Includes bibliography.

Thesis (Ph.D.)--Edith Cowan University, 2006. / Submitted to the Faculty of Computing, Health and Science. Includes bibliographical references.

Diss. (sammanfattning) Göteborg : Göteborgs universitet, 2006. / Härtill 4 uppsatser.

Zugl.: Darmstadt, Techn. Univ., Diss.,