Conjugation of the Human Immunodeficiency Virus Transactivator of Transcription (TAT) to active proteins allows transport into the intracellular environment. This feature can be harnessed to deliver combinations of reprogramming factors (RFs) such as c-Myc, Oct4, Klf4 and Sox2 into somatic cells to derive induced pluripotent stem cells (iPSCs). For this project, TAT-fusion proteins including four TAT-conjugated RFs (TAT-RFs) have been produced and purified. All four TAT-RFs can bind specific DNA sequences. Bioactivity was tested in live cells using a novel assay based on an engineered fibroblast cell line that can be induced to express RFs by doxycycline and subsequently generate iPSCs. To test each TAT-RF, reprogramming was blocked by transient silencing of a single RF by siRNA and rescued by the corresponding TAT-RF. The results of this assay suggested that TAT-Klf4 was bioactive in cells; however, definitive evidence could not be obtained for other RFs.

Aquifer storage and recovery (ASR) is a particular scheme of artificial recharge of groundwater by injecting fresh water into aquifers and subsequently recovering the stored water during times of peak demand or extended drought. In the era of combating climate change, ASR, as an effective means for water reuse and sustainable management of water resources in concert with the natural environment, represents a huge opportunity for climate change adaptation to mitigate water availability stress.The success of an ASR scheme is quantified by the recovery efficiency (RE), defined as the volume of stored water that can be recovered for supply purposes divided by the total volume injected. It is not uncommon that RE may be significantly lower than 100% because of the water quality changes as a consequence of the mixing between the injected water and native groundwater and the interaction between injected water and soil. Thus, the key of a successful ASR scheme is (1) to select appropriate aquifers and (2) to design optimal operational processes to build up a bubble of injected water with minimized negative impact from such mixing and interaction. To achieve this, this thesis develops an integrated knowledge base with sound interdisciplinary science and understanding of the mixing processes under operational ASR management in aquifers with various hydrogeological conditions. Analytical and numerical modeling are conducted to improve the scientific understanding of mixing processes involved in ASR schemes and to provide specific technical guidance for improving ASR efficiency under complex hydrogeological conditions. (1) An efficient approach is developed to analytically evaluate solute transport in a horizontal radial flow field with a multistep pumping and examine the ASR performance in homogeneous, isotropic aquifer with advective and dispersive transport processes. (2) Numerical and analytical studies are conducted to investigate the efficiency of an ASR system in dual-domain aquifers with mass transfer limitations under various hydrogeological and operational conditions. Simple and effective relationships between transport parameters and ASR operational parameters are derived to quantify the effectiveness and ascertain the potential of ASR systems with mass transfer limitations.(3) Effects of hydrogeological and operational parameters on ASR efficiency are assessed in homogeneous/stratified, isotropic/anisotropic coastal aquifers. Effects of transverse dispersion are particularly investigated in such aquifers.(4) Finally, we test and study an innovative ASR scheme for improving the RE in brackish aquifers: injection through a fully-penetrated well and recovery through a partially-penetrated well.

This study presents a comprehensive overview of the current state of the Milne Ice Shelf and how it has changed over the last 59 years. The 205 ±1 km2 ice shelf experienced a 28% (82 ±0.8 km2) reduction in area between 1950 – 2009, and a 20% (2.5 ±0.9km3 water equivalent (w.e.)) reduction in volume between 1981 – 2008/2009, suggesting a long-term state of negative mass balance. Comparison of mean annual specific mass balances (up to -0.34 m w.e. yr-1) with surface mass balance measurements for the nearby Ward Hunt Ice Shelf suggest that basal melt is a key contributor to total ice shelf thinning. The development and expansion of new and existing surface cracks, as well as ice-marginal and epishelf lake development, indicate significant ice shelf weakening. Over the next few decades it is likely that the Milne Ice Shelf will continue to deteriorate.

This study presents the first comprehensive assessment of the Petersen Ice Shelf and the Petersen Bay epishelf lake, and examines their current characteristics and changes to their structure between 1959 and 2012. The surface of the Petersen Ice Shelf is characterized by a rolling topography of ridges and troughs, which is balanced by a rolling basal topography, with thicker ice under the surface ridges and thinner ice under the surface troughs. Based on thickness measurements collected in 2011 and area measurements from August 2012, the Petersen Ice Shelf has a surface area of 19.32 km2 and a mean thickness of 29 m, with the greatest thicknesses (>100 m) occurring at the fronts of tributary glaciers feeding into the ice shelf. The tributary glaciers along the northern coast of Petersen Bay contributed an estimated area-averaged 7.89 to 13.55 cm yr-1 of ice to the ice shelf between 2011 and 2012. This input is counteracted by a mean surface ablation of 1.30 m yr-1 between 2011 and 2012, suggesting strongly negative current mass balance conditions on the ice shelf. The Petersen Ice Shelf remained relatively stable until 2005 when the first break-up in recent history occurred, removing >8 km2 of ice shelf surface area. This break-up led to the drainage of the epishelf lake once the ice shelf separated from the southern coast, providing a conduit through which the freshwater from the lake escaped. More break-ups occurred in summers 2008, 2011 and 2012, which resulted in a >31.2 km2 loss in surface area (~63% of June 2005 area). While ephemeral regions of freshwater have occurred along the southern coast of Petersen Bay since 2005 (with areas ranging from 0.32-0.53 km2), open water events and a channel along the southern coast have prevented the epishelf lake from reforming. Based on these past and present observations it is unlikely that Petersen Ice Shelf will continue to persist long into the future.

Our lab recently demonstrated that retargeting an alkylating agent, chlorambucil (Cbl), to the mitochondrion is a viable strategy to restore drug activity and overcome drug resistance in cancer. The mechanism of action of the mitochondria-targeted chlorambucil (mt-Cbl) was studied using a cervical carcinoma model. It was discovered that mt-Cbl bound to mitochondrial DNA and various mitochondrial proteins. A ρ° model revealed that the toxicity of mt-Cbl is largely dependent on its protein targets. Damage induced by mt-Cbl was found to result in the activation of several modes of caspase-independent cell death including necrosis. In contrast, Cbl was found to only activate caspase-dependent cell death that is highly sensitive to caspase inhibition. These results illustrate that the ability of mt-Cbl to activate various orthogonal cell death pathways is what allows mt-Cbl to bypass several drug resistance mechanisms, thus making mitochondrial retargeting a lucrative strategy for future anticancer drug development.

The mitochondrion is an important therapeutic target due to its roles in energy metabolism, reactive oxygen species production, and activation of cell death. The connection of these cellular processes with diabetes, obesity, neurodegenerative disorders, and cancer makes this organelle a potential control point for treatment of these diseases. The advancement of mitochondrial medicine will be accelerated by the development of organelle-specific cellular transporters as well as by strategies to enhance the activity of mitochondrially-active drugs. Here, the discovery and development of a new class of mitochondria-specific agents, mitochondria-penetrating peptides (MPPs), is described. These peptides, exemplified by the sequences (FXY)3 and (FXY)4 where FX=cyclohexylalanine and Y=basic arginine or lysine residues, display hydrophobic and cationic residues critical for access to this organelle, and appear to accumulate within cells and mitochondria through membrane potential-dependent mechanisms. Subcellular localization of the peptides was determined by the interplay of hydrophobicity and positive charge, and necessary lipophilicity “thresholds” for access to the mitochondrion. MPPs can be engineered to have minimal mitochondrial disruptive activity and cytotoxicity through minimization of hydrophobicity and length. Furthermore, MPPs appear to accumulate predominantly in the mitochondrial matrix, a feature which places them within an exclusive class of mitochondria-specific transporters and may enable delivery applications for a number of therapeutically-relevant cargoes. Information gained from MPP studies on the physiochemical parameters that drive mitochondrial localization were applied to improve the activity of the anticancer peptide d-(KLAKLAK)2, an agent that activates apoptosis through mitochondrial disruption. Residue substitutions that increased peptide hydrophobicity, regardless of changes to secondary structure, enhanced mitochondrial localization, activity, and cytotoxicity induced by the peptide. In conclusion, these studies provide important guidelines for how to drive the subcellular localization and activity of peptides, and expand the possibilities for mitochondrially-targeted therapeutics.

Our lab recently demonstrated that retargeting an alkylating agent, chlorambucil (Cbl), to the mitochondrion is a viable strategy to restore drug activity and overcome drug resistance in cancer. The mechanism of action of the mitochondria-targeted chlorambucil (mt-Cbl) was studied using a cervical carcinoma model. It was discovered that mt-Cbl bound to mitochondrial DNA and various mitochondrial proteins. A ρ° model revealed that the toxicity of mt-Cbl is largely dependent on its protein targets. Damage induced by mt-Cbl was found to result in the activation of several modes of caspase-independent cell death including necrosis. In contrast, Cbl was found to only activate caspase-dependent cell death that is highly sensitive to caspase inhibition. These results illustrate that the ability of mt-Cbl to activate various orthogonal cell death pathways is what allows mt-Cbl to bypass several drug resistance mechanisms, thus making mitochondrial retargeting a lucrative strategy for future anticancer drug development.

Near-surface sediments in the vadose zone play a fundamental role in the hydrologic system. The shallow vadose zone can act as a buffer to delay or attenuate surface contaminants before they reach the water table. It also acts as a temporary soil moisture reservoir for plant and atmospheric uptake, and regulates the seasonal groundwater recharge process. Over the past few decades, geophysical methods have received unprecedented attention as an effective vadose zone characterization tool offering a range of non-invasive to minimally invasive techniques with the capacity to provide detailed soil moisture information at depths typically unattainable using conventional point-measurement sensors. Ground-penetrating radar (GPR) has received much of this attention due to its high sensitivity to the liquid water phase in geologic media. While much has been learned about GPR soil moisture monitoring and characterization techniques, it has not been evaluated across highly dynamic natural soil conditions. Consequently, GPR’s capacity to characterize a complete range of naturally occurring vadose zone conditions including wetting/drying and freeze/thaw cycles, is not yet fully understood. Further, the nature of GPR response during highly dynamic moisture periods has not been thoroughly investigated. The objective of this thesis is to examine the capacity of various surface GPR techniques and methodologies for the characterization of soil moisture dynamics in the upper few meters of vadose zone, and to develop measurement strategies capable of providing quantitative information about the current and future state of the shallow hydrologic system. To achieve this, an exhaustive soil moisture monitoring campaign employing a range of GPR antenna frequencies and survey acquisition geometries was initiated at three different agricultural field sites located in southern Ontario, Canada, between May 2006 and October 2008. This thesis represents the first attempt to evaluate multiple annual cycles of soil conditions and associated hydrological processes using high-frequency GPR measurements. Summaries of the seven major works embodied in this thesis are provided below. Direct ground wave (DGW) measurements obtained with GPR have been used in a number of previous studies to monitor volumetric water content changes in the root zone; however, these studies have involved controlled field experiments or measurements collected across limited ranges in soil moisture. To further investigate the capacity of the DGW method, multi-frequency (i.e., 225 MHz, 450 MHz and 900 MHz) common-midpoint (CMP) measurements were used to monitor a complete annual cycle of soil water content variations at three sites with different soil textures (i.e., sand, sandy loam and silt loam). CMP surveys permitted characterization of the nature and evolution of the near-surface electromagnetic wavefields, and their subsequent impact on DGW velocity measurements. GPR results showed significant temporal variations in both the near-surface wavefield and multi-frequency DGW velocities corresponding to both seasonal and shorter term variations in soil conditions. While all of the measurement sites displayed similar temporal responses, the rate and magnitude of these velocity variations corresponded to varying soil water contents which were primarily controlled by the soil textural properties. Overall, the DGW measurements obtained using higher frequency antennas were less impacted by near-surface wavefield interference due to their shorter signal pulse duration. The estimation of soil water content using GPR velocity requires an appropriate petrophysical relationship between the dielectric permittivity and volumetric water content of the soil. The ability of various empirical relationships, volumetric mixing formulae and effective medium approximations were evaluated to predict near-surface volumetric soil water content using high-frequency DGW velocity measurements obtained from CMP soundings. Measurements were collected using 225, 450 and 900 MHz antennas across sand, sandy loam and silt loam soil textures over a complete annual cycle of soil conditions. A lack of frequency dependence in the results indicated that frequency dispersion had minimal impact on the data set. However, the accuracy of soil water content predictions obtained from the various relationships ranged considerably. The best fitting relationships did exhibit some degree of textural bias that should be considered in the choice of petrophysical relationship for a given data set. Further improvements in water content estimates were obtained using a field calibrated third-order polynomial relationship and three-phase volumetric mixing formula. While DGW measurements provide valuable information within the root zone, the characterization of vertical moisture distribution and dynamics requires a different approach. A common approach utilizes normal-moveout (NMO) velocity analysis of CMP sounding data. To further examine this approach, an extensive field study using multi-frequency (i.e., 225 MHz, 450 MHz, 900 MHz) CMP soundings was conducted to monitor a complete annual cycle of vertical soil moisture conditions at the sand, sandy loam and silt loam sites. The use of NMO velocity analysis was examined for monitoring highly dynamic vertical soil moisture conditions consisting of wetting/drying and freeze/thaw cycles with varying degrees of magnitude and vertical velocity gradient. NMO velocity analysis was used to construct interval-velocity-depth models at a fixed location collected every 1 to 4 weeks. Time-lapse models were combined to construct temporal interval-velocity fields, which were converted into soil moisture content. These moisture fields were used to characterize the vertical distribution, and dynamics of soil moisture in the upper few meters of vadose zone. Although the use of multiple antenna frequencies provided varying investigation depths and vertical resolving capabilities, optimal characterization of soil moisture conditions was obtained with 900 MHz antennas. The integration of DGW and NMO velocity data from a single CMP sounding could be used to assess the nature of shallow soil moisture coupling with underlying vadose zone conditions; however, a more quantitative analyses of the surface moisture dynamics would require definitive knowledge of GPR sampling depth. Although surface techniques have been used by a number of previous researchers to characterize soil moisture content in the vadose zone, limited temporal sampling and low resolution near the surface in these studies impeded the quantitative analysis of vertical soil moisture distribution and its associated dynamics within the shallow subsurface. To further examine the capacity of surface GPR, an extensive 26 month field study was undertaken using concurrent high-frequency (i.e., 900 MHz) reflection profiling and CMP soundings to quantitatively monitor soil moisture distribution and dynamics within a sandy vadose zone environment. An analysis on the concurrent use of reflection and CMP measurements was conducted over two contrasting annual cycles of soil conditions. Reflection profiles provided high resolution traveltime data between four stratigraphic reflection events while cumulative results of the CMP sounding data set produced precise depth estimates for those reflecting interfaces, which were used to convert interval traveltime data into soil water content estimates. The downward propagation of episodic infiltration events associated with seasonal and transient conditions were well resolved by the GPR data. The GPR data also revealed variations in the nature of these infiltration events between contrasting annual cycles. The use of CMP soundings also permitted the determination of DGW velocities, which enabled better characterization of short-duration wetting/drying and freezing/thawing processes. This higher resolution information can be used to examine the nature of the coupling between shallow and deep moisture conditions. High-resolution surface GPR measurements were used to examine vertical soil moisture distribution and its associated dynamics within the shallow subsurface over a 26 month period. While the apparent ability of surface GPR methods to give high quality estimates of soil moisture distribution in the upper 3 meters of the vadose zone was demonstrated, the nature of these GPR-derived moisture data needed to be assessed in the context of other hydrological information. As a result, GPR soil moisture estimates were compared with predictions obtained from a well-accepted hydrological modeling package, HYDRUS-1D (Simunek et al., 2008). The nature of transient infiltration pulses, evapotranspiration episodes, and deep drainage patterns were examined by comparing them with vertical soil moisture flow simulations. Using laboratory derived soil hydraulic property information from soil samples and a number of simplifying assumptions about the system, very good agreement was achieved between measured and simulated soil moisture conditions without model calibration. The overall good agreement observed between forward simulations and field measurements over the vertical profile validated the capacity of surface GPR to provide detailed information about hydraulic state conditions in the upper few meters of vadose zone. A unique DGW propagation phenomenon was observed during early soil frost formation. High-frequency DGW measurements were used to monitor the seasonal development of a thin, high velocity frozen soil layer over a wet low velocity unfrozen substratum. During the freezing process, the progressive attenuation of a low velocity DGW and the subsequent development of a high velocity DGW were observed. Numerical simulations using GPRMAX2D (Giannopoulos, 2005) showed that low velocity DGW occurring after freezing commenced was due to energy leaking across the frozen layer from the spherical body wave in the unfrozen half space. This leaky phase progressively dissipated until the frozen layer reached a thickness equivalent to one quarter of the dominant wavelength in the frozen ground. The appearance of the high velocity DGW was governed by its destructive interference with the reflection events from the base of the frozen layer. This interference obscured the high velocity DGW until the frozen layer thickness reached one half of the dominant wavelength in the frozen ground. While GPR has been extensively used to study frozen soil conditions in alpine environments, its capacity to characterize highly dynamic shallow freeze-thaw processes typically observed in temperate environments is not well understood. High-frequency reflection profiles and CMP soundings were used to monitor the freezing and thawing process during the winter seasonal period at the sand and silt loam sites. Reflection profiles revealed the long-term development of a very shallow (<0.5 m) soil frost zone overlying unfrozen wet substratum. During the course of the winter season, long-term traveltime analysis yielded physical properties of the frozen and unfrozen layers as well as the spatial distribution of the base of the soil frost zone. Short-term shallow thawing events overlying frozen substratum formed a dispersive waveguide for both the CMP and reflection profile surveys. Inversion of the dispersive wavefields for the CMP data yielded physical property estimates for the thawed and frozen soils and thawed layer thickness. It was shown that GPR can be used to monitor very shallow freezing and thawing events by responding to changes in the relative dielectric permittivity of the soil water phase. The works embodied in this thesis demonstrate the effectiveness of high-frequency GPR as a non-invasive soil moisture monitoring tool under a full range of naturally occurring moisture conditions with the temporal and vertical resolution necessary to quantitatively examine shallow vadose zone moisture dynamics. Because this study encompassed an unprecedented range of naturally occurring soil conditions, including numerous short and long duration wetting/drying and freezing/thawing cycles, complex geophysical responses were observed during highly dynamic soil moisture processes. Analysis and interpretation of these geophysical responses yielded both qualitative and quantitative information about the state of the hydrologic system, and hence, provided a non-invasive means of characterizing soil moisture processes in shallow vadose zone environments. In the future, these GPR soil moisture monitoring strategies should be incorporated into advanced land-surface hydrological modeling studies to improve our understanding of shallow hydrologic systems and its impacts on groundwater resources.

The Wanganui-Wilberg landslide lies between Hokitika and Franz Josef townships, at the entrance of Harihari, on the true left bank of the Wanganui River, by State Highway 6. This apparently co-seismic landslide belongs to the class of events called rock avalanches - powerful destructive agents (Keefer, 1984) in the landscape. Other rock avalanches are numerous (Whitehouse, 1983), and widespread over the Southern Alps of New Zealand, and many appear to be co-seismic. De Mets et al. (1994) used the model NUVEL-1A to characterize the motion of the Alpine fault: 37 mm/year at an azimuth of 071° for the strike-slip and a dip-slip of 10 mm/year normal to the strike direction. Although linear when seen from the sky, the detailed morphology of the fault is more complex, called en échelon (Norris and Cooper, 1997). It exhibits metamorphosed schists (mylonite series) in its hanging wall (McCahon, 2007; Korup, 2004). Earthquakes on the Alpine fault have a recurrence time of c. 200-300 years and a probability of occurrence within 100 years of 88% (Rhoades and Van Dissen, 2002). Thought to have been triggered by the AD1220 event (determined by dendrochronology), the Wanganui-Wilberg rock avalanche deposit represents only 20% of its original volume, which was c. 33 million cubic metres. The deposit probably dammed the Wanganui River and, as a result, created a small and short-lived lake upstream. The next earthquake capable of triggering such events is likely to occur fairly soon (Yetton, 1998). Knowledge of historic catastrophic events such as the Wanganui-Wilberg rock avalanche is of crucial importance in the development of future hazard and management plans.

Thesis (Ph. D.)--University of Texas at Austin, 2007. / Vita. Includes bibliographical references.