Nonsense mediated decay is a pathway that selectively degrades mRNAs that contain premature termination codons (PTCs). The purpose of this study is to research the evolution of NMD in Parabasalia and infer whether they have a normal, functioning nonsense-mediated decay pathway. Parabasalia are single-celled, flagellated protists that have undergone evolutionary transitions as they become obligate symbionts of termites. The key proteins involved in nonsense-mediated decay, ATM, ATR, UPF1, SMG1, UPF2, UPF3A, UPF3B, were researched and used in order to build phylogenetic trees to analyze what other species of eukaryotes have these same genes and where they branch relative to the nonsense mediated decay proteins present in Parabasalia. The main question being asked in this research is if Parabasalia have enough of the main nonsense mediated decay proteins to have a functional nonsense-mediated decay process and if not, which proteins have been lost over evolutionary history. To carry out this research, phylogenic trees were built using transcriptomes from many different types of eukaryotes that contained the main proteins involved in the nonsense-mediated decay pathway. These transcriptomes were taken from the National Center for Biotechnology Information (NCBI) database using the BLAST algorithm, trimmed using TrimAl, aligned by utilizing AliView which utilizes Muscle. Sequoia was then used to remove redundant species from the trees, and IQ-TREE was used to form the phylogenic trees. This process was repeated four times to create well-rounded trees with various eukaryotic species present. The results of this research found that ATM, ATR, UPF1, SMG1, and UPF2 are present in Parabasalia as well as across many eukaryotic groups, whereas UPF3A and UPF3B were not found in many of the eukaryotes researched. This points to Parabasalia having a normal and functioning nonsense-mediated decay pathway as they have the majority of the essential proteins needed for a functional pathway.
In this study, analysis of high resolution topography suggests asymmetric morphology of the SGB basin slopes are partially attributed to structural growth and fault zone damage. Spatial distributions of rock damage, from site mapping and fault perpendicular transects within SGB and Alkali Wash, are seemingly asymmetric with pulverization dominantly between fault strands or in the NE fault block. Remapping of the SJFZ through Alkali Wash indicates the fault is not isolated to a single strand along the main geologic boundary as previously mapped. Displacement measurements within SGB are analogous to those from the most recent large earthquake on the Clark fault. Geologic models from both a 3D shear wave velocity model (a product from the dense seismic array analysis) and lithologic and structural mapping from this study indicate surface observations and shallow seismic data compare well. A synthetic three-dimensional fault zone model illustrates the complexity of the structure at SGB for comparison with dense array seismic wave products. Results of this study generally agree with findings from seismic wave interpretations suggesting damage asymmetry is controlled by a NW preferred rupture propagation.
I employ the full suite of modern geomorphic tools provided by terrestrial cosmogenic nuclides - surface exposure dating, conventional burial dating, isochron burial dating, quantifying millennial-scale upland erosion rates using detrital TCN, quantifying paleo-erosion rates using multiple TCN such as Ne-21/Be-10 and Al-26l/Be-10, and assessing sediment recycling and complex exposure using multiple TCN - to quantify the rates of landscape evolution in southeastern Arizona and northern Chile during the Late Cenozoic. In Arizona, I also use modern remnants of the pre-incision landscape and digital terrain analyses to reconstruct the landscape, allowing the quantification of incision and erosion rates that supplement detrital TCN-derived erosion rates. A new chronology for key basin high stand remnants (Frye Mesa) and a flight of Gila River terraces in Safford basin provides a record of incision rates from the Pliocene through the Quaternary, and I assess how significantly regional incision is driving erosion rates. Paired nuclide analyses in the Atacama Desert of northern Chile reveal complex exposure histories resulting from several rounds of transport and burial by fluvial systems. These results support a growing understanding that geomorphic processes in the Atacama Desert are more active than previously thought despite the region's hyperarid climate.
In western Grand Canyon, I use comparative geomorphology between the Grand Canyon and the Grand Wash Cliffs (GWC). We propose the onset of erosion of the GWC is caused by slip on the Grand Wash Fault that formed between 18 and 12 million years ago. Hillslope angle and channel steepness are higher in Grand Canyon than along the Grand Wash Cliffs despite similar rock types, climate and base level fall magnitude. These experimental controls allow inference that the Grand Canyon is younger and eroding at a faster rate than the Grand Wash Cliffs.
The Grand Staircase is the headwaters of some of the streams that flow into Grand Canyon. A space-for-time substitution of erosion rates, supported by landscape simulations, implies that the Grand Canyon is the result of an increase in base level fall rate, with the older, slower base level fall rate preserved in the Grand Staircase. Our data and analyses also support a younger, ~6-million-year estimate of the age of Grand Canyon that is likely related to the integration of the Colorado River from the Colorado Plateau to the Basin and Range. Complicated cliff-band erosion and its effect on cosmogenic erosion rates are also explored, guiding interpretation of isotopic data in landscapes with stratigraphic variation in quartz and rock strength.
Several hypotheses for the erosion of Desolation Canyon are tested and refuted, leaving one plausible conclusion. I infer that the Uinta Basin north of Desolation Canyon is eroding slowly and that its form represents a slow, stable base level fall rate. Downstream of Desolation Canyon, the Colorado River is inferred to have established itself in the exhumed region of Canyonlands and to have incised to near modern depths prior to the integration of the Green River and the production of relief in Desolation Canyon. Analysis of incision and erosion rates in the region suggests integration is relatively recent.