DNA origami is the fabrication of biochemical structures using DNA as the building material. Using base pair design principles, DNA can be synthesized to self-assemble into dynamic objects such as a piston. The resulting creations have potential applications in nanotechnology including drug delivery, enzyme immobilization, photolithography, environmental restoration, and biocompatible devices. The goal of this project was to design a nanoscale mechanical spring and determine the parameters for spring constant and size. First, a spring comprised of multiple columns of double-stranded DNA was designed and fabricated. Size measurements were taken and morphology was verified using a transmission electron microscope. To measure the force constant of this structure, the 5’ end of the first column was functionalized with a thiol group which was then bonded to a gold cantilever tip on an atomic force microscope (AFM). This construct was brought very close to a magnesium substrate and allowed to bond. Force measurements for the spring were taken via AFM by slowly retracting the cantilever from the substrate. The spring force constant was calculated from this data using Hooke’s law in order to predict the amount of work that the DNA nanospring can perform when included in a complex nanostructure. The nanostructures created in this project can be used in conjunction with other DNA origami designs in order to create increasingly complex machines on the nanoscale.

Newborns and children are more vulnerable to xenobiotics (foreign chemical substances) partly because little is known regarding the developmental regulation of drug-processing genes (DPGs) by drugs and environmental chemicals. The xenobiotic-sensing nuclear receptors, namely the pregnane X receptor (PXR) and constitutive androstane receptor (CAR), are well-known to up-regulate many DPGs in liver. However, relatively less is known regarding the effect of developmental exposure to PXR- or CAR-activators on the expression of DPGs in intestine, where the biotransformation of orally-exposed xenobiotics takes place. Therefore, the goal of this study was to determine both the acute and the potential long-term effects of neonatal exposure to PXR- and CAR-activators on the regulation of DPGs in neonatal and adult intestine. Wild-type mice were pharmacologically administered the PXR-ligand PCN (the activator of PXR in mice), the CAR-ligand TCPOBOP (the activator of CAR in mice), or vehicle, at 3-day-old neonatal age. Intestines were collected 24h post-dose (whole intestine) or at 60-day-old adult age (duodenum, jejunum, ileum, and colon). Neonatal exposure to TCPOBOP and PCN up-regulated many DPGs 24h postdose. Interestingly, at 60-days adult age, neonatal exposure to TCPOBOP persistently up-regulated many DPGs especially in small intestine, but down-regulated particularly in colon (large intestine). Neonatal exposure to PCN persistently up-regulated 6 DPGs but down-regulated 11 DPGs in specific sections of intestine. In conclusion, this study has demonstrated that neonatal exposure to xenobiotics that activate PXR and CAR not only produce acute induction effect on the DPG expression in newborns, but also lead to persistent alterations on the expression of certain DPGs in adult intestine, and this may potentially alter the pharmacokinetics of orally-exposed chemicals in adults.

 Diabetes affects about 10% of the US population and is the 7th leading cause of death. Diabetes results from either a lack of insulin production (Type 1) or resistance to it (Type 2). The active form of insulin is a 51 amino acid monomer which regulates homeostasis of blood-glucose levels. It is crucial for insulin to be structurally sound and not degraded, especially for people using insulin pumps. However, insulin has a shelf life of about 28 days unopened and only 14 days after opening the container. Efforts to improve the stability of insulin may facilitate the development of implantable pump technologies for insulin delivery and allow for longer storage of insulin. Based on a review of the literature, I hypothesize that solvation in an Ionic Liquid solution will decrease the degradation and increase the shelf-life of insulin. To better understand the stability of the insulin protein, I compared its activity at an air-water interface to an air-ionic liquid interface. The approach consists of modeling the structure of insulin using the simulation software GROMACS and PLUMED. 10 nanosecond trials in different air-liquid interfaces were then analyzed to optimize the best insulin backbone stability. The goal is to extrapolate an ammonium- or imidazolium-based ionic liquid solution that will decrease the aggregation of the insulin monomers. Compared to the bulk insulin form, we found that the ionic liquid-protein solution demonstrates a lower radius of gyration and a root-mean-square deviation value that levels out towards 1 Angstrom representing a stable protein. These results are also supported by a decreased hydrodynamic radius and an increased free energy of unfolding the insulin protein. These findings suggest that insulin in an ionic liquid solution will last longer in vitro than in a water-based solution.

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.

A method will be presented for dating the last time sub-glacial mountains in West Antarctica were fully exposed by measuring the cosmic-ray-produced isotope ⁴¹Ca. The use of ⁴¹Ca will add a new cosmogenic isotope to the existing toolbox to improve surficial dating. The advantage of ⁴¹Ca over other isotopes is its short half-life (99,000 years), which reduces the complication of prior exposure in natural samples. To accomplish this, calcium will be extracted from Antarctic bedrock samples, converted to oxalate, and then further treated by column ion exchange to produce pure calcium, free of problematic potassium contamination. The biggest challenge will be to produce calcium hydride for measurement by accelerator mass spectrometry (AMS) to determine the ⁴¹Ca/⁴⁰Ca ratio. Current AMS capabilities allow ratio measurements in the 10-10 or 10-11 range. Measurements of the hydride should allow us to extend this down to the 10-14 level necessary for geological applications. Successful measurements in this range will open up applications such as tests for whether sub-glacial bedrock in West Antarctica was exposed to cosmic rays during the last warm interglacial climate period, approximately 120,000 years ago. Perfecting this method and making it available to others in the field can open a door into the past to determine if current global warming trends are leading us down a path similar to the last deglaciation, which raised global sea level by several meters. Though we are working on a geological and glaciological issue, the ultimate product of this research touches areas of meteorology, biology, and sociology as the Earth adjusts to increases in global temperature.

TRPV1 is an ion channel of great importance for pain and heat sensing. The EC50 (threshold dose) of the ion channel TRPV1 is highly variable depending on the cell type in which it is expressed. For example, the EC50 of TRPV1 in HEK293T/17 (a cultured mamalian cell line) is ~1 µM whereas the EC50 of TRPV1 in isolated DRG neurons is ~ 100 nM. Numerous explanations have been proposed for this phenomenon, with one possible explanation being the varying lipid contents of the plasma membrane regulating the EC50 of TRPV1. The cholesterol content of the plasma membrane is a candidate for regulating TRPV1, as it is known to vary among types of cells. We measured TRPV1 function with patch-clamp electrophysiology to determine the effect of removing cholesterol from the plasma membrane on channel function. Inside-out excise patches remain stable for tens of minutes, allowing for cholesterol removal and replacement by flowing a Methylated-β-Cyclodextrin, a ring of sugar molecules that bind cholesterol, across the patch. In intact HEK293T/17 cells, we estimated the cholesterol content to be about 30%. Thus, the Methylated-β-Cyclodextrin is expected to produce a very large change in plasma membrane properties as removes cholesterol. Recordings from these patches showed that both the EC50 for activation of TRPV1 by capsaicin and the capsaicin-induced maximum current were unaffected by patch treatment with Methylated-β-Cyclodextrin. These results are significant as they shows that TRPV1 function is unaffected by a large reduction in plasma membrane cholesterol. Because removal of such an abundant component of the plasma membrane likely produces meaningful changes in the bulk properties of the bilayer, these data also indicate that lipid regulation of TRPV1 is caused by lipids which have specific, chemical interactions with the channel, rather than the bulk properties of the plasma membrane.

Photosynthesis is how plants gather energy from the sun and store it as chemical energy. This pathway involves multiple energy gathering antennae that absorb light and move electrons through photosystems to store the energy in NADPH and ATP and in turn split water into O₂ and 2H₂. There are two mechanisms proposed for the O-O bond forming step catalyzed by the oxygen evolving complex (OEC), Mn^dang-CaMn₃O₅, of photosystem II, and the dangling Mn (Mn^dang) and Ca ions have both been shown to be involved. One mechanism is through nucleophilic attack by an OH^- that is coordinated to the Ca ion at an electrophilic Mn(V)≡O species, and the other is through radical coupling between two Mn(IV)-O• species. Recent data shows that the nucleophilic attack mechanism is the most likely mechanism. Because the O-O bond forming step occurs after the rate-determining step, these intermediates are not observable in photosystem II. This project involves the synthesis and isolation of species that are representative of the Mn^dang-O-Ca fragment, and intermediates involved in one of the proposed mechanisms for O-O bond formation by the OEC. We are using [Mn(II)(N₃S^Me2(tren))]⁺ as our Mn starting material, and [(dipp-DAD)Ca²⁺(OH)₂]^2- as Ca-(OH)₂ source. The reaction between these two compounds will be monitored by UV-Vis, in the presence of an oxidant, to detect changes in the Mn ion’s electronic environment. So far we have been able to isolate the previously reported [(dipp-DAD)Ca²⁺(THF)₃] precursor complex, and our next step will be to generate hydroxide derivative and monitor its reaction with [Mn(II)(N₃S^Me2(tren))]⁺ using the method described above.

HIV remains a major global health problem due to high transmission levels and emergence of drug resistant strains. According to WHO, in 2014, sub-Saharan Africa had 25 million people living with HIV and 70% of new HIV infections globally. A high number of circulating drug resistant HIV remains undetected due to lack of affordable HIV genotyping methods. The lab based oligonucleotide ligation assay (OLA) is a highly sensitive method for detecting HIV drug resistance as an alternative to the expensive and complex complete-genome sequencing, but its reliance on moderately expensive lab equipment prevents its universal access.  Our lab, in collaboration with the Frenkel Lab (Seattle Children’s Research Institute) and the Lai Lab (UW BioE), focuses on developing a simplified OLA-based HIV drug resistance test. The ligation step of the OLA relies on the specificity of DNA ligase to target single nucleotide polymorphisms (SNP’s) that can confer HIV drug resistance. However, ligation currently requires a thermal cycler to cycle between 95 °C to de-hybridize target DNA and 37 °C for annealing of oligonucleotide probes to target DNA. Eliminating the temperature cycling component of ligation would be a key advantage because thermal cyclers are not widely available in low resource settings. We measured ligation at intervals from 25 °C to 70 °C and were able to pinpoint an optimal temperature range for isothermal ligation. We plan to further increase ligation yield, and therefore detection signal, by optimizing the concentrations of salts and cofactors, adjusting probe lengths, and modifying probe sequences.  With the development of isothermal ligation, the OLA will be further simplified for potential widespread use in low resource settings. This will allow HIV infected individuals to be accurately diagnosed and receive the proper line of HIV drugs, controlling transmission rates and reducing the evolution of drug resistant HIV within entire populations. 

Every year bee specialists report detection of larger numbers of bee colonies suffering from colony collapse disorder. One of the suggested causes of colony collapse disorder is the increasing use of neonicotinoid pesticides in farming agriculture. Neonicotinoids like clothianidin, thiacloprid and imidacloprid are effective insect neurotoxins created as a safer alternative to previous insecticides. Neonicotinoid pesticides have many distribution methods including dusting methods and application to soil and root systems; leading to their dispersion in a multitude of matrices. The quantity of these pesticides in water and soil samples needs to be measured to further asses the effect of these pesticides on bees and other species including fish and humans. However, differences in extraction methodology can lead to differences in analyte detection. Water and soil samples are complex matrices to be separated before being assessed through gas chromatography-mass spectrometry or liquid chromatography–mass spectrometry. Here I present my work in comparing methods for extracting imidacloprid, a specific pesticide in the neonicotinoid category. Results from determining a reliable and accurate method of imidacloprid will help to increase the ability for future research to be conducted on collected environmental samples.

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.

The oxygen evolving complex (OEC) is the enzyme in Photosystem II responsible for oxidizing water into oxygen gas. The OEC, a Mn₄O₅Ca cofactor, has one manganese “dangling” off a cubane, and it undergoes several conformational changes as photons provide energy for the splitting of water. The mechanisms and intermediates for the transitions between states are not fully understood, so research into manganese dioxygen chemistry will illuminate this important biological process. In order to characterize intermediates more successfully, we use synthetic, small molecule, ligand framed analogues that emulate the properties of the enzyme. Synthetic analogues have a distinct advantage in characterizing intermediates because the enzyme is limited to activity under conditions of a living organism such as temperature and solvent. By tuning the conditions and coordination sphere of our manganese complexes, we can stabilize metastable intermediates in order to spectroscopically characterize them. Our target is to synthesize a mononuclear manganese superoxo complex modeling the dangling manganese, which has been previously reported as an active site in oxygen evolution. A superoxo must be the last intermediate in oxygen evolution, so by characterizing our complex, we can determine viable mechanisms for the evolution of oxygen off the dangling manganese. We designed the ligand to be sterically bulky and have a low coordination number so there is a selective open coordination site for dioxygen binding. The lower coordination number raises the manganese’s Lewis acidity which allows for reversible oxygen binding. A trans thiolate is incorporated into the ligand framework as it has been previously shown that the sulfur to metal charge transfer band is in the visible region, giving the complex an easily identifiable spectroscopic property. By synthesizing our superoxo complex then characterizing its properties, we can better understand the complex mechanisms of oxygen evolution.

Copper-doped semiconductor nanocrystals (NCs) combine the large effective Stokes shifts and broad PL spectra of bulk copper-doped semiconductors with the solution-processability of colloidal semiconductor nanocrystals. These properties make copper-doped NCs attractive materials for applications such as luminescent solar concentrators and light-emitting diodes. Copper-doped CdSe NCs are particularly desirable materials because their tunable absorption spans the visible spectrum, and they provide a useful model system for studying the photophysics of copper-doped semiconductor NCs. However, both fundamental studies and applications of copper-doped CdSe NCs have been limited by the inability to simultaneously control the NC diameter, size dispersity and copper dopant concentration during synthesis, This poster reports a new one-pot synthesis of copper-doped CdSe NCs that enables precise control of NC size and copper concentration while maintaining a narrow size distribution. This level of synthetic control is achieved by separating the nanocrystal growth and copper-doping steps, and tuning the reactivity of the copper precursor. Post-synthetic treatments with various surface ligands are also used to tune copper dopant concentration. Fundamental photophysical studies enabled by access to the high-quality copper-doped CdSe NCs provided by this new synthetic method will also be discussed.

Microplastics are a marine pollutant estimated to be in the range of 4-8 million tons released annually in to the world’s oceans. Microplastics have been shown to bio-accumulate in marine life, specifically fish and bivalves. Due to the hydrophobic properties of plastics, non-polar organic pollutants will interact chemically and physically. Adsorption of pollutants allows plastics in the marine environment to act as a distribution vector. This project focuses on the microplastic content in food grade sea salts, specifically those made from solar evaporation. Due to the nature of how sea water is concentrated down to form sea salt, these salt crystals are at risk of harboring microplastics. We have investigated the potential for microplastic bound organic molecules in sea salts. To address this we analyzed four kinds of commercially available salt. These salts were dissolved in water and filtered through 2 micron filters, and analyzed by Fourier transform infrared (FT-IR) spectroscopy and scanning electron microscopy (SEM) to characterize the filtrate. Following this, we washed the filtrate with dichloromethane and analyzed this with Gas Chromatography Mass Spectrometry (GC-MS). SEM analysis showed particles of 5-500 m diameter present in teh filtered salt solutions. When microplastics were washed with dichloromethane, phthalic acid was identified in the eluted fraction by GC-MS. Thus, preliminary results indicate the presence of organic pollutant absorbed to the surface of microplastics in sea-salt. Future work will focus on improving extraction of persistent organic pollutants. With microplastics becoming an ever more present pollutant in the global marine environment, the continuation of our research should include the health hazards of ingestion of large quantities of microplastics that have been exposed to the marine environment.

Electronic cigarettes use a heating coil to aerosolize a liquid made of ingredients which are only approved safe by oral consumption. However, there remains a question as to whether these components may react or decompose to form other, potentially harmful or toxic, substances when exposed to the high temperatures of the vaporizer. Gas chromatography and mass spectrometry (GC/MS) were used to identify chemicals in generic e-liquid and in the vapor produced from the e-cigarettes. A replica of an electronic cigarette was constructed in order to have better control over the temperature coil and produce vapor in a range of 200-700 ⁰C. Seven of the common and commercially available e-liquids were investigated in this study. The chemicals were quantified in a low parts per million (ppm).The nature and the toxicity of the identified chemicals were then discussed based on the available literature information.

Factors such as temperature, pressure, presence of a catalyst, and reactant concentration are all known to affect the rate of chemical reactions and are well exploited in industry to drive chemical synthesis to favor certain mechanistic pathways. Here we consider the effect of using magnetism to control the rate of reaction for the Briggs Ruascher reaction. This reaction was chosen as a model for magnetic manipulation because it is mediated by both radical and non-radical pathways that compete with oscillatory behavior to produce the same product. Dramatic color changes serve as a visual cue to indicate which path is dominating. Here we put forth magnetic radical arrest hypothesis for the Brigg’s Ruascher reaction. It is known that electrons act like tiny magnets that pair with opposite spins. Because radical species carry a lone unpaired electron, presumably their magnetic fields are not concealed. We proposed that due to the exposed nature of the unpaired radical electrons in the Briggs Ruascher reaction, the progress of the reaction would be affected by the application of a magnetic field. Upon exposure to strong magnets, the radical intermediates of the Briggs Ruascher reaction were expected to aligned their spins with the applied magnetic field affecting their reactivity. Several types of neodymium magnets with various strengths were applied to the reaction in order to determine whether magnetism could prevent or greatly reduce the velocity of the color phase changes for the radical mediated portion of the reaction. We also built an electromagnet to expose the reaction to in order to achieve even greater field strength. The Brigg’s Rouscher reaction was found to be significantly robust and there was insufficient evidence to suggest that the reaction was affected by neodymium fields below a range of 5.8 mT. Results of exposure to the electromagnet are still in progress. The color changing cycles of the Briggs Ruascher reaction were found to follow a decreasing sigmoid mathematical model before going to completion after 9-10 oscillations.

Chelating agents are widely used in plants and human industries to capture metal ions and control free metal ion concentrations. Constituent ions in soils (e.g. Ca²⁺, Mg²⁺) influence the exchange of a metal ion between two chelating agents. Predicting changes in reaction pathways and the magnitude of kinetic effects is fundamental to understanding dynamic metal speciation where strong chelating ligands control metal ion speciation. This research focuses on the influence of calcium ions on the exchange rate of Ni between nitrilotriacetic acid (NTA) and 1,2-cyclohexylenedinitrilotetraacetic acid (CDTA). Capillary electrophoresis was used to monitor the changes in free chelating agent and nickel-chelating agent complex concentration with time at different pHs and reactant concentrations. Reaction rates and order were compared to those in the absence of calcium ion. The presence of calcium ions reduces overall exchange rates and alters reaction order under the conditions studied. Kinetic modeling is used to support a proposed mechanism for the influence of calcium on this exchange reaction. Knowledge about dynamic metal speciation is fundamental to understanding the ideal soil compositions for plants’ uptake of essential metals and developing remediation methods for hazardous waste sites.