Tree lines play a vital role in plant community composition in montane ecosystems. Over the past several decades, increasing annual temperatures have led to shifts in tree lines in montane environments. However, little is known about how local topography may have an effect on tree line advance. My research incorporates historical and repeat, ground based and aerial photography to assess the change of alpine tree line in a range of topographical conditions in Mount Rainier National Park over the past century. My study quantifies changes in tree cover and tree-line elevation in ridge and cove environments of the park. To track treeline change, historical and recent photographs were aligned, and areas of the photograph were broken up into polygons based on their small-scale topography. Random points were overlaid in these polygons to assess the rate of change of tree line shift. By looking at the change in tree cover in each random point relative to the polygon type, we are able to determine the amount of tree thickening that has occurred. We predicted that tree lines on sun exposed ridges will shift more quickly than those in cove environments. Snow is prevalent for longer periods of time in concave valleys limiting the amount by which the trees can shift up. Our results thus far indicate that small-scale ridge regions have the highest rate of change for tree line shift followed by cove. Subalpine meadows often occur in cove topography. Tree thickening in these regions over time may impact the wildflower populations and decrease species richness in subalpine meadows. In all, our research adds to the growing body of evidence that tree lines are moving up in elevation as well as provides the National Park Service with information about tree line influences on the plant communities of the park.

With concern about climate change increasing, assessing how plant reproductive success is impacted by increases in temperature is crucial in order to fully understand how climate change influences ecosystem structure and dynamics. This study measures how population variation and the climate of different elevations affect the capsule size and seed mass of the high-elevation plant mountain monkeyflower, Mimulus tilingii, at Mt. Rainier National Park. If climate is the primary limiting factor determining the range of M. tilingii, plants within the species’ climate range will produce the most abundant capsules and seeds whereas plants grown outside the species’ distributional range will produce smaller amounts. Sample seedlings were planted at two elevation sites: 1)  M. tilingii’s range center and 2) below M. tilingii’s range to mimic the increase in temperature due to climate change. Populations were categorized as either within-population (for crosses within the same elevation site) or between-population (for crosses between the two elevation sites) with equal amounts at both sites. This study quantifies M. tilingii’s reproductive success both in the context of the site as well as the population type, allowing for comparisons on these two levels. Results show that parent plants from the lower site produced more flowers and grew faster, indicating that plants in the lower elevation site might be more successful. These unexpected results suggest that M. tilingii may be better adapted to a warmer environment and that climate change might even be beneficial for this reason. Determining the exact impact of temperature on reproductive success is crucial not only for measuring the species’ fitness but also for understanding how these new adaptations will play an even bigger role in competition for resources among different plant species and how those new interactions will alter the ecosystem as a whole as the climate warms.

Post-traumatic stress disorder (PTSD) is a widely known and generally understood condition, however, in pain medicine, it is often overlooked and not considered in treatments. PTSD has been shown to greatly affect mood and quality of life in the general population but has not been studied extensively in general pain medicine. Data collected from the University of Washington Center for Pain Relief’s web-based questionnaire that patients fill out prior to clinic visits was used to analyze how PTSD correlates with common components of pain such as intensity, interference with common tasks, quality of life, and substance use. PainTracker^TM is a web-based patient reported outcome tool that assesses pain treatment over time. PainTracker incorporates a variety of questions and instruments to effectively understand the various components of pain. This research illuminates the importance of PTSD in chronic pain patients and how it affects the population suffering from chronic pain. Current analysis has indicated that as PTSD severity increases, so does pain intensity, interference in daily life, mood, anxiety, and quality of life. This illustrates the importance of understanding PTSD’s role in pain and may potentially lead to more effective pain treatment by understanding the roots of pain in post-traumatic stress disorder.

Eclipsing binaries are systems in which two stars orbit and pass in front of each other. They are important astrophysical tools we utilize to measure fundamental properties of stars, such as their masses, radii, and temperatures. Here, we analyzed photometric data acquired from the Kepler satellite in order to model the light as a function of time of specific eclipsing binary systems. We selected these targets from the Villanova Kepler Eclipsing Binary Catalog. For each system, we used a least-squares optimization method to determine the best fit solution between the model and the observed light curve. Our light curve model has a total of 13 parameters. They include stellar elements such as sum of radii and flux ratio, as well as orbital elements such as period and eccentricity. In addition to providing orbital solutions, our models can be used to search for the presence of additional bodies in the system, such as a third star or a circumbinary planet.

The South Pacific Convergence Zone (SPCZ) is the most prominent rain feature of the Southern Hemisphere, but is a very understudied region. Changes in the SPCZ can affect freshwater availability to people living on the islands in the South Pacific. The satellite record shows precipitation patterns from the past 37 years; in the tropics the best way to investigate rainfall before 1979 is to examine lake sediment. We used sediment cores with age models from Barora Lake, a shallow freshwater lake in the Solomon Islands, to obtain a detailed view of past rainfall patterns. This lake’s lack of oxygen one meter below the water’s surface has left its sediment in a uniquely undisturbed state. Because of this, and a high accumulation rate, the sediment provides a record of the rainfall in the Solomon Islands over the last millennium. Lipids are well-preserved in sediment over geologic time, making them an ideal proxy for reconstructing tropical paleoclimate. The lipid dinosterol is produced primarily by a limited group of dinoflagellate microalgae and acts as a “molecular fossil”. The isotopic ratio of deuterium to hydrogen (2H/1H) found in dinosterol reflects the 2H/1H ratio in the lake water, which is dictated by changes in precipitation and evaporation. In the tropics, more rain results in 2H-depleted rain and lake water. After purifying dinosterol from the sediment with column chromatography and high-performance liquid chromatography, we found minor fluctuations in the dinosterol 2H/1H ratios, which implies a fairly stable rainfall pattern at this location during the past millennium.
 

Cholangiocarcinoma, better known as bile duct cancer, is a rare and aggressive form of cancer in the biliary system. Bile duct cancer has the third lowest 5-year survival rate among all forms of cancer in the US. Due to its location, access to the biliary system for detection or diagnosis is difficult without invasive methods. Early detection of bile duct cancer is crucial and could be achieved by using the multimodal scanning fiber endoscope (SFE) developed in our lab. The SFE is able to noninvasively enter the biliary tree through the digestive system and present realistic information about the potential malignancies or disease state. Typically, a phantom is used to mimic the in-vivo presentation of disease state in order to validate the use of a new medical device. To prepare the SFE for this kind of cancer detection, a bile duct phantom with three dimensional (3D) cell culture was developed to test the sensitivity and specificity of the real-time in-vivo imaging. A biocompatible and optically clear polydimethylsiloxane (PDMS) device was first made for the cast of the hydrogel phantom. The device was utilized for structural stability of the phantom like a cast. The phantom was constructed by folding a flat sheet of hydrogel into a cylindrical tube with a lumen that reflects the true diameter of bile duct. The cancer cells were suspended at specific locations in order for spatial validation of SFE. The end result was the development of a 3D cell culture phantom with fluorescent probes targeted to cancer biomarkers. The phantom was imaged with SFE to evaluate its ability to accurately locate malignancies, distinguishing cancer cells from normal cells. Future work will extend to validation of fluorescent probes and ultimately lead to development of a new cancer imaging method with SFE to reduce late diagnosis.

Therapsids (mammal-like reptiles) document the transition to modern mammals and are an important study tool in examining how the past informs the present. Understanding diseases today requires understanding the deep evolutionary history in our fossil ancestors. We present an instance of dental pathology in a gorganopsid therapsid (~260 million years old). Using fossil histological techniques, we examine a gorganopsian canine and preliminary results reveal abnormal mixture of dental tissue next to the functional tooth. These individual ectopically expressed teeth have preserved tissue layers such as enamel, dentine and a pulp cavity. Based off of the histological characters of our specimen as compared to modern clinical studies we hypothesized two possible diagnoses: odontoma and enamel pearls. Enamel pearls show dento-enamel pearl nodules protruding from the enamel of a functional tooth. Odontoma presents as individual teeth with their own histological packaging (i.e. dentine and enamel). These results suggest that our specimen most likely had odontoma. In modern cases, this results in excess dentinal tissue growth and un-alignment of teeth. The cause of this odontoma in modern clinical practices is a result of either trauma or rapid tooth replacement. The canine tooth of this gorgonopsid was prone to trauma since it served to pierce prey and was subjected to intense forces. Alternatively, gorgonopsids replaced their teeth continuously. This continous replacement could have gone awry resulting in this disease. This study presents the oldest possible case of cancer in the fossil record and elucidates the evolution of such pathologies. This study has relevance in dental clinical studies because understanding how diseases operate in humans requires an understanding of how they evolved in our deep evolutionary history. 

Explosive boiling is characterized by an unstable, non-uniform liquid/vapor interface consisting of multiple gaseous lobes. Explosive boiling at microscales is a process of extreme interest in the studies of micromechanical systems and actuation due to the nearly instantaneous pace and large amounts of kinetic energy associated with the process. These characteristics that make the explosive boiling phenomenon highly attractive for certain microscale applications also hinders the study and understanding of the dynamics of the unstable liquid/vapor interface, and thus the prediction of the overall behavior of the process. The objective of my research is to overcome the challenges posed by the small temporal and spatial scales by designing and building an experimental apparatus to observe the explosive boiling phenomenon. This apparatus consists of a test chamber in which the explosive boiling of a droplet of test fluid will be controlled by the host fluid temperature gradient, and a high speed camera used to capture the process in a high level of detail. The experimental results will be compared with theoretical results acquired from direct numerical simulation to elucidate the dynamics of the liquid/vapor interface. The experimental apparatus design and preliminary imaging results are presented.

The Tritium Recoil-Ion Mass Spectrometer (TRIMS) experiment is designed to measure the branching ratio of molecular tritium to the helium-tritium molecular ion after beta decay. Tritium emits very low-energy beta particles and is difficult to detect. My research seeks to measure the background levels of tritium contamination on laboratory and apparatus surfaces by using a gas flow proportional counter. This type of counter consists of a gas filled metal tube with a high voltage wire in the center. Beta particles from tritium decay ionize the gas, and the high electric field causes avalanche multiplication, which is picked up as a signal on the wire. The size of the signal is proportional to the energy of the original particle. This apparatus allows for surveys for tritium contamination initially and throughout the lifetime of the TRIMS experiment, with real time indication.

As magnetohydrodynamic (MHD) systems exhibit incredible nonlinearity, computational models have become increasingly common for parsing difficult engineering problems in plasma experiments. The dynamic mode decomposition (DMD) is a principled, data-driven, equation-free approach to extracting coherent temporal-spatial structures from raw data, with particular success in hydrodynamics and fluid-flow problems. We consider the DMD applied to MHD systems in the particular example of spheromak plasmas simulated in the Helicity Injected Torus experiment. We find that the DMD successfully resolves magnetic field structures in simulated magnetic field measurements that closely match expected physical properties. We further find that, under certain constraints, the DMD provides a powerful tool for further validation of simulation to experiment. Given the nonlinearity of magnetohydrodynamic systems, existing mechanisms for feedback controlling plasmas as instabilities occur are limited. Because the dynamic mode decomposition effectively serves as an approximate, linear reduced order model built from experimental and simulated magnetic field measurements on the fly, it offers considerable promise as a predictive feedback controller. This is significant as the detection of and control over plasma instabilities remains a major barrier to the use of spheromaks for fusion energy.

Imidacloprid (IMI) is being sought as an alternative to the carbamate pesticide, carbaryl to control burrowing shrimp (ghost shrimp, Neotropea californiensis) in Willapa Bay and Grays Harbor. The shrimp destabilize sediments resulting in poor survival and low yields of the commercially harvested Pacific oyster. Previous laboratory tests indicate ghost shrimp are overtly affected (immobilized) when exposed to IMI at concentrations up to 1,500 ppb in artificial seawater (SW), but not killed and subsequently recover. Our objective was to determine the concentrations of IMI in SW that result in mortality of the shrimp and compare these levels to those known to affect other marine invertebrates, particularly Crustacea. Additionally, we quantified time to recovery in shrimp exposed to the concentrations tested. We exposed adult non-gravid females to 0, 10, 100, 1000, 10000, and 1000000 ppb (1,000 ppm) of the active ingredient (a.i.) (Nuprid® 2F) in SW for 48 h (24-h static renewal; 5 individual shrimp per concentration) and quantified overt behavior, survival and water quality. All shrimp at concentrations > 1 ppb were overtly affected, but none died. In the recovery test, 6-8 individual shrimp were exposed to 0, 10, 100, 1000, and 10000 ppb a.i. for 24 h (static) followed by 120 h in clean SW (static renewal). One shrimp exposed to 100 ppb died and time to recovery in survivors was concentration dependent. Results suggest ghost shrimp are very sensitive to IMI in terms of immobilization, but concentrations necessary to kill the shrimp exceed those for other marine invertebrates. The neurophysiology of Crustacea may not match the mode of action of IMI because most neural receptors in these species use glutamate as the neurotransmitter and not acetylcholine. Our results, coupled with the less than desired efficacy in the field, suggest IMI may not be an effective alternative to carbaryl.
 

 Eukaryotic cells contain membrane-bound organelles that serve to compartmentalize certain cellular functions. Different organelles contain optimal pH levels necessary for the organelle function. The vacuolar ATPase (V-ATPase) is a highly evolutionarily conserved proton pump that is responsible for acidification of many organelles. This proton pump consists of various protein subunits and loss of any these subunits results in disruption of the entire protein complex, which in return is not compatible with life for most organisms. Within certain conditions, S.cerevisiae (yeast) is able to survive in the absence of a functional V-ATPase, which makes it an ideal model organism to study V-ATPase function. In yeast, the proteins that comprise the V-ATPase are encoded for by vacuolar membrane ATPase (VMA) genes. Loss of any individual VMA gene results in pleiotropic phenotypes including an inability to grow on nonfermentable carbon sources and shortened replicative lifespan. In order to understand more about how the V-ATPase functions, we have performed multiple screens to identify genes that when overexpressed or mutated can suppress the respiratory phenotype of VMA mutants. Our results implicate iron homeostasis as a process that is crucially disturbed when the V-ATPase is disrupted.

Hydrostatic pressure is important to many vascular processes, including endothelial activation (inflammation), vasodilation, vasoconstriction and angiogenesis (branching of new blood vessels from existing ones). The problem of pressure regulation in in vitro studies is usually solved by syringe pump based systems. Harvard Apparatus provides a catalogue of “Constant Pressure Syringe Pumps,” the cheapest of which costs $4500. This is prohibitively expensive for many applications. Thus, there is a need to create an affordable device that can reliably regulate hydrostatic pressure. I present a syringe pump based system that maintains liquid pressure within a flow chamber at a fraction of the cost of commercially available devices. My pump was designed from open-source and off the shelf components, including a pressure transducer and Arduino Microcontroller, at a total cost of ~$350. I have tested the pump’s ability to maintain constant liquid pressure across a high-impedance microfluidic system and have shown that it maintains pressure at a user-defined set point between 0 and 70 cmH2O of gauge pressure. This device illustrates the power of open-source software and hardware, 3D-printing and rapid prototyping to allow labs to design customized hardware to meet specific research needs at a reasonable price. Once completed, I will use it to study the pressure dependence of angiogenesis and vasculogenesis (formation of new blood vessels by endothelial cells embedded in interstitium). We will vary hydrostatic pressure to optimize and document blood vessel network formation. This is relevant to studying embryonic development and tumor vascularization and to engineering grafts to repair the damage from myocardial infarction (heart attack). Other possible applications include eliminating the confounding variable of pressure variation in Doppler echocardiography or in studies of endothelial cell response to variation in microvessel geometries.

In mammals, fundamental differences evolved between the sex chromosomes of males (XY) and females (XX), resulting in specific regulatory mechanisms, which restore a balanced expression of X-linked genes between the sexes. To do this, one of the female’s X chromosomes is silenced (i.e. X inactivation). However, some genes escape this inactivation and remain bi-allelically expressed in females, resulting in higher expression levels potentially contributing to sex differences. The Car5b gene, which encodes a mitochondria carbonic anhydrase important for heart function, escapes X inactivation in both mouse and human. The CCCTC-binding factor (CTCF) often binds near the boundaries between escape and silenced genes. Car5b is inactivated in mouse brain, but it escapes silencing in embryonic kidney (Patski) cells derived from a F1 hybrid female mouse. Selective CTCF binding at a site near Car5b in Patski cells but not in brain suggests the possibility that a chromatin loop that includes the Car5b promoter may facilitate escape in the cell line. To test this looping escape model, we are deleting the CTCF binding site on the inactive X (BL6 allele) and will evaluate its effects on escape. To establish an allelic deletion at the Car5b locus, a CRISPR/cas9 approach (DNA modifier) is being used with two BL6-specific small guide RNAs spanning the CTCF binding site upstream of the Car5b promoter. We’ve completed single-cell cloning for Patski cells transfected with CRISPR constructs. These cell clones are currently being verified for correct deletion by PCR and Sanger sequencing. Results have shown a positive deletion in the cell cloning colony. Allelic expression of Car5b will then be examined in the clones to investigate whether deletion of the CTCF binding site affects its escape (chromatin architecture). If results are conclusive, such an approach will be utilized to examine other escape gene regions.

The plasma protein von Willebrand Factor (VWF) is secreted by vascular endothelial cells. VWF’s primary function is to recruit platelets to the site of blood vessel injury. The interaction between VWF and platelets happens through binding between the VWF A1 domain and the platelet surface receptor, glycoprotein Ibα (GpIbα). VWF requires shear to be activated. Recently, it has been shown that oxidizing agents increase the platelet-binding activity of VWF, although the exact molecular mechanism is not understood. To explore whether neighboring domains of A1 play a role in the oxidant-induced activation of VWF, we used a flow chamber microscopy assay. Two experimental constructs of VWF, one containing the A1 domain and the neighboring A2 and A3 domains, the second containing A1 and the neighboring D`D3 domain were expressed and bound to separate plates. One control construct containing only the A1 domain was also expressed and bound to plates. Then GpIbα coated beads were washed at different shears over plates that had either been pre-oxidized or not. The movement of beads was recorded. Subsequently, rolling velocities and total number of beads were measured and analyzed using MATLAB. The results showed that, at high shear, both the A1A2A3 and the D`D3A1 constructs were more active in binding to beads when oxidized compared to the unoxidized controls. The control construct did not show a difference in binding to beads when oxidized compared to unoxidized controls. These findings suggest that the A2, A3 and D`D3 domains could have an inhibitory function on the A1 domain and that oxidation removes this inhibition resulting in an increased binding activity of VWF to platelets. Understanding how oxidation alters the function of VWF domains is necessary to explain the increased risk of thrombosis in patients suffering of chronic or acute inflammation.

Anthropogenic carbon dioxide (CO₂) has been identified as a primary driver of climate change, the oceans have been shown to be a large sink of this CO₂. Fjord systems have been identified as potential sinks for the CO₂ in summer due to high primary production, but also in winter due to cool surface waters. Our study focuses on the temperate fjord system of Nootka Sound, BC, Canada, during December 2015. Investigation of this precipitation driven fjord system during a strong El Niño may help us to understand the impacts that warming oceans have on the ability of fjords to act as sinks for atmospheric CO₂. Depth profiles at 12 stations began outside of Nootka Sound and went into the head of Muchalat Inlet. Vertical profiles and water samples at 5 depths were collected using the CTD rosette system onboard the R/V Thomas G. Thompson. Additional samples from the surface 10cm of the water column were collected within 2 of the inner fjords, Muchalat and Tahsis. Analysis of these samples for dissolved inorganic carbon (DIC) and alkalinity allowed for the calculation of pCO₂, a measure of the partial pressure of CO₂ in water. From this and atmospheric pCO₂ data provided by Environment Canada, the flux of CO₂ across the air-sea interface was calculated. Preliminary results of surface samples show effluxes of CO₂ near riverine inputs, while surface waters within the inlets appear to be in near equilibrium with the atmosphere. Preliminary transect results show deep waters have higher pCO₂, further analysis will reveal if a relationship between air-surface fluxes and deep water exists.

Sediment cores were collected from White Lake (15°2.46' S 167°5.35' E) and Red Lake (15°1.97' S 167°5.40' E), located on Thion Island, Vanuatu, to analyze precipitation patterns in the South Pacific Convergence Zone (SPCZ) during the last millennium. The SPCZ is a poorly understood and understudied region of the Tropical Pacific, with a very short instrumental record of rainfall. Extending the record of natural variability in precipitation is important for assessing future risks of freshwater availability to islands in the tropical pacific. Known for high precipitation rates and spanning 3000 km in a NW to SE orientation, the South Pacific Convergence Zone is the most prominent rainfall feature in the Southern Hemisphere. These freshwater lakes contain the dinoflagellate sterol, dinosterol, which acts as a “molecular fossil” or lipid biomarker and is used to infer variations of the deuterium/protium (²H/¹H) isotopic ratio of the lake water over time since algal lipids track changes in environmental water. The fluctuations in the ²H/¹H ratio in both the lake water and dinosterol are linked to changes in SPCZ precipitation since in the tropics, the rainfall rate is correlated with the isotopic composition of rain. Dinosterol was purified using column chromatography and High Performance Liquid Chromatography, identified and then quantified using Gas Chromatography-Mass Spectrometry and Gas Chromatography-Flame Ionization Detection. The ²H/¹H ratio of the purified dinosterol was determined using Gas Chromatography-Isotope Ratio Mass Spectrometry.