Chiral molecule sensing has important biochemical applications for detection of disease, as well as cognitive and neurodegenerative disorders. Circular dichroism (CD) has emerged as a powerful spectroscopic tool for probing post-synthetic ligand exchanges of chiral molecules onto originally achiral quantum confined CdS morphologies, manifesting in chirality corresponding to the electronic transitions of the nanocrystals. In this work, we first describe making water soluble quantum dots (QDs) and nanorods (NRs) via ligand exchange with glycine. After this exchange, aqueous chiral thiol solutions are then titrated into glycine capped achiral CdS, and the optical properties are monitored via UV-vis, photo-luminescence (PL), and CD spectroscopies. Preliminary results show we can controllably produce measurable chirality equal to or exceeding previous literature values whilst using orders of magnitude less L-cysteine than previously reported. Moving forward, we intend to correlate growth in CD with changes in PL across a myriad of cysteine derivatives. Additionally, we plan to examine the impact of NR aspect ratio on normalized maximum CD absorption (g-factor).   

Autism spectrum disorder (ASD) is a neurodevelopmental disorder marked by repetitive behavioral patterns and challenges with social interaction. Gastrointestinal symptoms are a common comorbidity of ASD, and individuals with the disorder tend to have a distinct gut microbial community composition and circulating metabolomes. Elevated levels of gut-derived metabolite 4-ethylphenolsulfate (4-EPS) are associated with ASD mouse models and children with ASD. Administration of 4-EPS to conventional mice induced atypical myelination and anxiety-like behaviors. 4-Ethylphenol (4-EP), its precursor, is produced by gut microbiota before host-mediated sulfation; however, its microbial biosynthetic pathway remains unknown. We propose a pathway involving stepwise conversion of plant-derived complex polysaccharides to 4-EP. My project aims to identify a gut microbial enzyme that completes the first step of this proposed pathway: a hydroxycinnamoyl esterase. After extensive literature review and biochemical study, candidate enzymes from resident gut microbes were identified and selected using bioinformatic tools. In vitro and in vivo experiments will be used to assess their activity towards model and dietary substrates. Remaining substrate and product concentrations will reveal species and strain specific enzymatic activity and substrate uptake. If the results are negative, this bioinformatics to experimental analysis pipeline will be repeated on new candidate enzymes. This work complements ongoing lab investigations to demonstrate the complete enzymatic pathway in a single species. Elucidating the microbial biosynthetic pathway of 4-EPS will contribute to detangling the gut’s role in ASD, regardless of if it is causal to the disorder or simply a biomarker. More importantly, studying the biochemistry and metabolism of gut microbiota supports the efforts to fill fundamental gaps in understanding the gut-brain axis. 

The balance of ions in soil and water directly impacts sustainable agriculture, human health, and livestock well-being. Small family farms, such as the one in this study, often depend on well water for household and agricultural use, making water quality essential for both food safety and long-term farm viability. This study investigates the spatial distribution of key anions, including nitrate (NO₃⁻), nitrite (NO₂⁻), and phosphate (PO₄³⁻), in soil and well water across a small family-operated farm in Woodinville, WA. These ions were selected due to their roles in plant growth, soil chemistry, and potential health effects on humans and animals. The farm sustains 68 animals, including chickens, cows, donkeys, alpacas, llamas, sheep, quails, and horses, and provides food and water for seven residents. Soil and water samples were collected from distinct zones, including livestock pens, vegetable fields, and tap water from the farm’s well, to evaluate how land use influences ion distribution. Soil samples were collected at multiple sites; ions were extracted from the samples using a  common water extraction method. Ion chromatography (IC) was employed to quantify anion concentrations and assess spatial variability. While this study does not determine definitive sources of the ions, analyzing variations in these ion concentrations near crop fields and livestock areas can help assess potential nutrient leaching and runoff. This type of comparative analysis of soil and well water samples helps quantify potential risks to both farm operations and the health of residents and livestock. This research underscores the importance of ongoing water and soil quality monitoring to ensure the sustainability of small-scale farms that rely on well water and homegrown food, while offering insights for improved land and resource management practices

For biomass derived molecules to serve as precursors for biofuel and other related energy sources, more stable and efficient catalysts are needed. Drawing inspiration from enzymes, our group has recently shown that a bifunctional acid–base metal–organic framework (MOF) with co-localized acid and base sites outperforms a MOF with randomly dispersed acid and base sites as a catalyst for the aldol condensation of biomass-derived carbonyls. These active acid–base sites are composed of a primary amine and carboxylic acid. However, to further improve catalytic activity a templated framework with secondary amine and carboxylic acid active sites can be developed. Relative to primary amines, secondary amines should favor the formation of the key enamine intermediate and increase catalytic rates. Framework synthesis and characterization show success of incorporation of the secondary amine, and preliminary catalysis results indicate how successful this secondary amine has been. Overall, this work expands on the previous introduction of metal-organic framework catalysts as an alternative to common industrial catalysts in the biomass upcycling process by exploring the utility of a new templated secondary amine acid–base MOF. 

Indium phosphide (InP) quantum dots are a high-performing semiconductor material used in optoelectronic applications due to their tunable electronic properties and low toxicity compared to cadmium-based quantum dots. However, InP quantum dots are currently synthesized at or above 180°C because of the high energy input required for nucleation and growth of the covalent nanocrystals. This study explores the synthesis of small InP clusters at lower temperatures by investigating reaction conditions that can produce InP with reduced energy consumption. Using the precursors indium carboxylate and P(SiMe₃)₃ in a nonpolar solvent toluene, we systematically investigate the evolution of InP clusters at room temperature and 60°C via UV-Vis absorbance spectroscopy. The formation of atomically precise InP clusters was observed at room temperature after 23 days. To speed up the reaction, we investigate adding a polar aprotic solvent or amines to promote the formation of InP at low temperatures. Including 20% of N-Methylpyrrolidone in the solvent mixture with toluene allows InP to be formed in 2 hours. Amine additives interact with the indium cations to modulate their reactivity, therefore we investigate adding varying equivalents both to the pre-formed atomically precise cluster, and to the indium and phosphorous precursors in toluene. We found that adding up to 100 equivalents of benzylamine per cluster did not promote the growth of InP clusters. Our findings contribute to the understanding of how InP forms at low temperatures for scalable, environmentally friendly production.

Rising atmospheric carbon dioxide levels have driven research into efficient gas separation materials. Polymers of intrinsic microporosity (PIMs) is one promising solution due to their rigid, porous structures and processability, allowing them to be turned into thin films for membrane-based gas separations. My research focuses on enhancing the carbon dioxide selectivity of helicene-based PIMs through post-synthetic modification of these polymers. I have synthesized a small molecule model of the PIM to screen for amine substitution conditions and ensure the viability of post-synthetic modification on the larger helicene-based PIM. Characterization techniques, multinuclear NMR and mass spectrometry, have verified the synthesis and amination of my model system. By incorporating nucleophilic amines into PIMs, these polymers can feature enhanced binding to electrophilic carbon dioxide, thereby increasing the interactions with carbon dioxide over other mixed gases, leading to separation. In my future studies, I will extend these modifications to the helicene-base PIM, fabricate films and evaluate their properties. Surface area measurements using N₂ gas sorption methods and CO₂ absorption isotherms will quantify gas-binding affinity and separation performance.

Multidrug-resistant cancers is responsible for over 90% of the metastatic cancer deaths which show enhanced drug transportation. Our group wanted to know how the acquired drug resistance impacts the flow of the MDR drug class, (Imidazoquinolinone, IMQ) by P-Glycoprotein (transporter protein in helping transport the drug). The experiments were performed by using melanoma cancer cell lines, prostate cells, and mouse genomes as the basis for observation. The cells were then introduced to three derivatives of IMQ, called Imiquimod (IMQ), Resiquimod (RSQ), and Gardiquimod (GDQ). The findings we hope to see were how effective each derivate of IMQ were in transport, hindering cell replication, and rhodamine concentration (compound dye in the cells to see how much of the drug is in the cells) with GDQ expected to have the lowest effect of drug resistance. The future of small molecular immunotherapy prodrugs heavily depends on the research and investigation of candidate compound classes and its derivatives to make sure that it is safe, effective, and the overall quality for the patients.

Erbium(III) doped cerium oxide nanocrystals are promising candidates for spin qubits in quantum computing and information science applications. Our goal is to tune the synthesis and composition of Er-doped CeO2 nanocrystals for monodispersity and desirable optical properties, particularly the intensity and lifetime of near-infrared emission features unique to Er3+. We optimized previously reported methods for making Er-doped CeO2 by altering the concentration of erbium, presence of water, and the amount of time allowed for the reaction to progress. These nanocrystals were then analyzed using several techniques, including transmission electron microscopy, X-ray diffraction, and photoluminescence spectroscopy. Our results indicated that by omitting water from the synthesis, the sizes of the nanoparticles decreased significantly. Additionally, smaller concentration of erbium(III) dopant in the nanoparticles correlated with a longer lifetime of photoluminescence intensity.

The electron transfer energy and the voltage of solar cells can be changed by tuning the energy band gap of photovoltaic materials. In lead perovskites, this is mainly controlled by the particular halides around lead atoms, with the best materials often having mixed halide compositions. Iodide substitution and identification in lead chloride APOSS perovskites to generate mixed-halide perovskites for control of light absorption in solar cells is creatively proposed in this project. In my previous work, I investigated new methods of bromide substitution and found that highly controlled substitution was achieved by heating copper chloride APOSS perovskites, (APOSS)[Cu₄Cl₁₆ ], in the presence of more stable organic bromides as normal methods, which includes highly reactive liquid bromine or trimethylsilyl bromide. Based on this preliminary research, proper experimental procedure and aims are put forward in this project as follows: lead chloride APOSS perovskite is first synthesized according to the synthesis method of copper chloride perovskite, which has already been published. After that, the iodide substitution is performed by exposing (APOSS) [Pb₄Cl₁₆ ] to a solution of relatively stable organic iodide reagents like carbon tetraiodide or diiodoethane at different temperature and concentration. In order to get more understanding about the substitution process on atom level, NMR and Gas Chromatography are performed to identify where the substituted chlorine atoms go.

The ability to pattern three-dimensional microscale cultures opens new avenues for examining the effect of nonplanar mechanical environments on mammalian cells and tissues. Our lab has developed a method for generating suspended tissues with spatial control using open microfluidic principles called Suspended Tissue Open Microfluidic Patterning, or STOMP. STOMP utilizes spontaneous capillary flow and capillary pinning to pattern suspended, multi-region tissues. Using similar microfluidic principles as STOMP, we have developed a method to pattern large (cm-scale) models via semi-open microfluidic channels called Suspended Nonplanar and Planar, or SNaP, geometries. I design these devices with computer-aided design, fabricate components on stereolithography 3D printers, pattern devices with standard pipettes, and culture resulting tissues for short- and long-term time periods to model biological scenarios. With the broad statement that human tissue is generally nonplanar in mind, my research focuses on three different geometries of tissue, 1) a sinusoidal wave, 2) a transwell-like mogul, and 3) a multi-region dome, where each nonplanar geometry enables a different biomedical investigation. The sinusoidal wave construct allows us to ask if cells embedded in tissues with varying frequencies of undulation experience changes to cell morphology due to the topology of their environment; the transwell-like mogul enables investigation of cell proliferation of cells grown at or within an air-liquid interface; and the multi-region dome facilitates the study of tissue interfaces where a diseased region of cells meets a healthy region of cells, all within a single contiguous tissue. I am currently exploring these questions through multiple cultures where different device versions and/or multiple cell types are engaged to collect biological readouts which demonstrate SNaP as a translatable platform for the investigation of questions in biomechanics and regenerative medicine.

Electrochemical water splitting is an effective method for generating hydrogen gas (H2) and an attractive means for energy storage. During this process, hydrogen and oxygen bubbles form on the electrode surfaces often lower the efficiency of gas production. The overarching goal of this study is to probe and better understand the nucleation process of small H2 and O2 nanobubbles on the electrode. To do this, we use ultrasensitive fluorescence microscopy to monitor the transient adsorption and desorption of single fluorophore molecules, such as Rhodamine 6G (R6G), on the nanobubble surface. My project aims to study how different fluorophores interact differently with the bubble surface and how they may interact with each other when multiple fluorophores are co-adsorbed on the bubble surface. This research may help us better understand bubble-molecule and molecule-molecule interactions at confined spaces for enhanced chemical labeling of the nanobubble surface. Moreover, it may also help us better understand the chemical nature of the gas/water interface, which has direct implications for more efficient gas productions and energy conversion and storage.

Biodiesel, "an alkyl ester of fatty acid" and type of biofuel, can be used for fueling vehicles and can be produced via transesterification, the process of using the alcohol methanol along with a base catalyst (usually sodium hydroxide) to break down oils and fats that have many triglycerides into fatty acid methyl esters (FAMEs) and glycerol. The viscous triglycerides are broken down into ester bonds and free fatty acids (FFAs), which are not ideal for biodiesel synthesis because FFAs have high melting points, unlike FAMEs. Thus, biodiesel synthesis should be conducted in a manner that reduces the number of FFAs while having a high breakdown of triglycerides into ester bonds. Transesterification that involves alkali/alkyl (like the bases sodium hydroxide (NaOH) and potassium hydroxide (KOH)) as a catalyst can cause soap-FFA reactions, resulting in "emulsification" challenges (Cheng et al 2013) (Hasan et al 2017). KOH and NaOH both can cause soap formation if they interact with triglycerides and esters. Furthermore, KOH produces more soap that NaOH, but KOH also helped produce more biodiesel than that from NaOH at 0.2 mol concentration (Van Gerpen et al 2006). What are the effects of NaOH and KOH on the fuel value of the biodiesel produced over the course of eight weeks? If KOH is used to synthesize biodiesel, then the biodiesel's fuel value form KOH will be higher than that form NaOH. Although the research project is currently in progress, the anticipated result is that KOH better catalyzes transesterification (via causing more heat combustion of ethanol) than NaOH for producing biodiesel. The results' significance determines which catalysts are used to produce more biodiesel. This is because the amount of biodiesel produced can be used for daily life purposes like faster transportation without having to refuel automobiles as frequently.

The small ubiquitin-like modifier protein, SUMO, regulates the activity of many cellular processes through covalent modification of proteins. These modified targets include the protein components of chromatin; histones H2A, H2B, H3, and H4. Chemical modification of histones directly regulates gene expression, necessitating an understanding of the role of each type of modification. The identification and role of histone SUMOylation has been described for H4 in human cells; however, SUMOylation of H2B in human cells has been recently observed but not yet characterized. SUMO is shown to impose a predominantly repressive effect on many cellular processes and proteins that it targets. Therefore, I am working toward identifying the role of H2B SUMOylation to either add to this narrative or describe novel functions of SUMO. To accomplish this, I have purified wild-type histones and SUMO-histone fusions through bacterial expression followed by size-exclusion and affinity chromatography. The purification of several of these proteins has not been described yet; therefore, I designed the purification for these proteins using unique methods, like solubilizing tags, to obtain the product. I reconstituted the purified proteins into octamers, the protein complex that DNA wraps around, and purified the octamers away from other oligomeric forms of the histones via size-exclusion chromatography. I further reconstituted the octamers into mononucleosomes by condensing DNA around them to mimic SUMOylated nucleosomes in chromatin. I hope to then subject the mononucleosomes to in vitro biochemical assays to observe changes in the modifications that regulate other chromatin-associated proteins. A better understanding of the complex dynamics at play during gene expression and repression is needed to identify stronger, safer, and more sustainable therapeutics. Furthermore, SUMO is implicated in a wide array of diseases, such as Alzheimer’s. Therefore, the results of this study will increase our understanding of gene regulation and provide insight towards treating related diseases.

Tyrosine-kinase inhibitors (TKIs), a class of chemotherapeutic drugs, are a kind of targeted therapeutics which work by inhibiting the human epithelial growth factor, a common site of mutation in many cancers. However, TKIs may eventually fail due to accumulation of mutations leading to resistance and tumor heterogeneity. Drug cocktails, or combination regimens, provide a potential way to combat this problem. Combining different classes of drugs allow for the attacking of the issue from different angles. However, it is imperative to carefully understand these combinations before putting them to medical use. Results from a novel, non-invasive imaging technique--stimulated Raman microscopy (SRS)--quantified chemotherapeutic drug uptake with different transport inhibitors. Results from SRS show that the calcium channel inhibitor Verapamil increases TKI drug uptake until a certain point for Lapatinib but indefinitely for Afatinib when compared to using the drugs alone, indicating that there is likely an optimal range for each TKI-inhibitor combination. For this project, I aim to show that this stands within a cell culture environment, continuing to use the two common TKIs Afatinib and Lapatinib, and determining the difference in efficacy with used in tandem other inhibitors, namely Verapamil and Chloroquine, a drug that inhibits the progress of the cell cycle. To do so, I will be using a bulk cell viability assay, which allows for the observation of the difference in the value for which 50% of cells are inhibited, and observing differences in this point to determine the optimal treatment and concentrations for a TKI-Inhibitor treatment. Combining a single-cell, non-invasive spectroscopic technique and a cell viability assay, we can better understand the mechanisms behind how typical non-cancer therapeutics can be used in tandem with chemotherapeutic treatments to increase drug uptake, while at the same time acknowledging that a balance is needed for the best synergistic effect.

Recent advances in ultra-high-resolution frequency comb spectroscopy have enabled the observation of previously unresolved spectroscopic details in small molecular systems. However, current theoretical frameworks are insufficient to fully describe the complex interactions between internal and overall rotational angular momenta, and higher frequency vibrational modes, particularly in molecules with multiple internal rotors. This work focuses on elucidating the coupled torsional, rotational, and vibrational kinematics of dimethyl sulfide (DMS), an asymmetric top with two internal methyl rotors which generate a rich and highly structured spectrum. We develop a general theoretical approach that incorporates torsional angular momenta into the overall molecular framework by systematically coupling the individual degrees of freedom, which are initially described in their well-known primitive bases, into a fully symmetrized torsion-rotation-vibration Hamiltonian. Through this systematic approach, interactions between the overall rotational and internal angular momenta of the methyl groups are explicitly addressed, capturing the effects of intrinsic Coriolis couplings and the tunneling splittings of the rotors. The resulting eigenstates and energy spectrum are analyzed to predict spectroscopic transitions, which are then compared with experimental findings, allowing the assignment of observed peaks to specific ground and excited quantum states. This rigorous treatment provides insights into nontrivial state mixing and previously unresolved splittings observed in high-resolution spectra. The methods developed in this work offer a pathway toward more accurate analysis of complex molecular systems and clusters, with broader applicability to high-resolution spectroscopy in atmospheric, astrochemical, and low-temperature environments.

Biodiesel fuel is a renewable and biodegradable fuel that is produced from a variety of sources, such as animal fats or vegetable oils. With its potential to replace petroleum diesel in engines, biodiesel can act as a cleaner and more environmentally friendly fuel. To create biodiesel fuel, a substance, like oil or fat, must react with a catalyst, which allows for a transesterification reaction, converting these substances into biodiesel fuel. Washington alone is home to over 4,000 coffee shops, and as a result, there is significant waste from discarding coffee grounds daily. Spent coffee grounds, the substance being used in this experiment, is a potential upcoming form of effective biodiesel fuel. In order to turn spent coffee grounds into biofuel, the oil within it must be extracted first. Oil is extracted using a method involving a solvent, Hexane, and following that, the oil is presented to two separate catalysts for comparison: KOH (potassium hydroxide) and NaOH (sodium hydroxide). Comparisons can then be made of what catalyst yielded the best fuel burn efficient level, depending on what catalyst the oil was presented to. This ultimately brings up the question of what catalyst is more efficient, in addition to how efficient spent coffee ground oil is as biofuel. Our goal is to answer these questions and contribute to the advancing research of using spent coffee grounds to produce biodiesel fuel. 

In this experiment we will look into the relationship between different mushroom species' toxicity and copper concentrations. Due to their wide variety of biochemical characteristics, mushrooms can be either extremely toxic or edible. Mushrooms contain different amounts of copper, an essential trace element that may affect a mushroom's toxicity. Using Atomic Absorption Spectroscopy, we evaluated the amount of copper of several mushrooms. Our early results show that mushrooms with higher copper concentration tend to be more toxic. This shows that copper content may be a useful marker of the toxicity of mushrooms, giving foragers important information and assisting in the development of food safety protocols. Our research is to be continued as we’re going to test on more mushrooms to get a better understanding on how copper could affect the production of toxic compounds.

Fuels are comprised of thousands of compounds and many compound classes. Olefinic compounds in fuels are known to increase the formation of polyaromatic hydrocarbons (PAHs) and gum formation in engines. The formation of the gums leads to premature engine degradation and lessened fuel efficiency. Various methods, such as molecular bromination, have been developed to detect and analyze these gum-forming olefins. Bromination via molecular bromine has been used in the past, but it has limitations, including high cost and potential environmental harm. As an alternative to bromination, I am using silver-ion solid-phase extraction (SPE) to separate alkenes from other compounds in fuels. Silver ion chromatography selectively retains alkenes, allowing for other compounds to be removed. Selective separation of a compound class will allow me to accurately detect and quantify olefins in fuel. My preliminary results show that olefins can be separated from aromatic compounds, polar compounds, and alkanes with silver ion SPE. I accomplished this by collecting the SPE effluent in measured fractions and analyzing each fraction by gas chromatography mass spectrometry to observe analyte breakthrough. I am developing this method to selectively detect trace olefins in fuels.

Recent studies have reported that certain tampon brands contain traces of various metals, raising public safety concerns about regular tampon use. Exposure to metals such as lead may pose detrimental effects on cognitive function, the nervous system, and reproductive health, yet little is known about the extent to which these metals are absorbed into the bloodstream from these products.  This project aims to investigate the presence of heavy metals within tampons. We hypothesized that tampons made from cotton would contain higher traces of metals compared to ones that are made with viscose rayon. We selected five widely available brands of varying absorbances and material, categorizing them as either organic (cotton) or non-organic (viscose rayon). To quantify the total lead content, 0.300 g of each sample was digested using a mixture of hydrogen peroxide and nitric acid. To determine the extractable quantity of lead, each sample was submerged in a simulant solution for 24 hours, replicating the acidity of vaginal fluids. To ensure the presence of lead within the sample, tampons with measurable lead concentration were spiked with known amount of lead quantity. Using AA Spectroscopy, quantifiable total lead contents were found in three out of the five tampon samples; Tampon C exhibited the highest lead content of 1.363 µg/g of tampon. Additionally, only one in five tampon samples was found to have significant extractable lead content, with Tampon C containing 0.2184 µg/g of tampon. Our results indicate a higher proportion of detectable traces of total and extractable lead in non-organic tampons compared to organic tampons. Despite these findings, further research is needed to establish whether there are adverse health effects to lead exposure from tampon use.

The kidney plays an important role in blood filtration, regulation of blood pressure, acid/base homeostasis, and electrolyte balance. Studying the different kidney compartments provides critical insights into the metabolic mechanisms underlying these essential functions. Ziyu Guo, my research mentor has recently developed a highly multiplexed fluorescence microscopy using semiconducting polymer dots (Pdots) that allows one round of immunostaining and imaging of up to 21 targets. However, this technique is restricted to thin samples (50-100 µm), which may oversimplify biological systems by lacking depth and structural integrity. To overcome this limitation, my research integrates multiplexed fluorescence imaging with ELAST, a technology to transform thick tissues into elastic hydrogels, reinforcing the tissue's structure while allowing for better antibody penetration. This approach allows for simultaneously labeling multiple targets in the thick tissue while preserving tissue architecture. Overall, my project seeks to improve our understanding of kidney architecture in their natural spatial 3D context and further provide insights into disease mechanisms and potential therapeutic targets.

The rising impacts of climate change driven by fossil fuel consumption highlight the need for sustainable alternative energy sources, such as biodiesel. Biodiesel is a biodegradable diesel fuel made primarily from vegetable oil or animal fats. Currently, biodiesel production predominantly relies on vegetable oils, which contribute to over 85% of production costs and raise concerns regarding higher consumer costs and environmental sustainability. To mitigate this issue, this study examines the potential of using animal waste, specifically beef tallow,  as an alternative feedstock for biodiesel production. The United States produces 20% of beef in the world, leaving large amounts of waste that go unutilized. Instead of relying on plants and crops for biodiesel, which requires large-scale cultivation of crops like soybean and palm that contribute to increased greenhouse gas emissions, beef tallow offers a resourceful alternative due to its widespread availability. The production of biodiesel from vegetable oil and beef tallow is done through transesterification with the catalysts NaOH and KOH to facilitate the conversion of the fats to biodiesel. Upon synthesizing the biodiesel, a soda can calorimeter is used to analyze how much of the biodiesel is able to be burned and the amount of heat released from the reaction to determine the fuel value. The aim of this study is to evaluate the fuel value of beef tallow to determine its potential as a more viable alternative to vegetable oils for biodiesel production.

Morphological control in nanocrystal synthesis is crucial for tailoring material properties in magnetic, thermoelectric, catalytic, and renewable energy applications. In this study, we explore the synthesis of anisotropic single-phase Cu2Se nanorods (NRs) via cation exchange from CdSe NRs. Transmission electron microscopy and X-ray diffraction were employed to characterize the resulting nanocrystals. The synthesis of Cu2Se NRs remains challenging due to limited Se precursors suitable for shape control and identifying the kinetic conditions that lead to morphological selectivity. We have since shifted our focus to reaction conditions required to perform Cd-to-Cu cation exchange. Our work aims to refine synthetic parameters, including solvent compositions, hot injection temperatures, and concentration of Cd precursor to establish a reliable pathway for monodispersed nanorod formation and demonstrate precise morphological control. These insights will contribute to the Cossairt Lab’s broader efforts to advance nanoparticle synthesis for classical and quantum light emission, catalysis, renewable energy, and magnetooptical technologies.

Superatoms are (often inorganic) clusters of several to several hundred atoms in size, that mimic the chemistry of elemental atoms by exhibiting a high degree of valence electron delocalization, effectively creating a unified valence shell over the entire superatom. Our lab works with M₃(solv)_xCo₆Se₈L₆ (M = Cr, Mn, Co, Zn; solv = thf, py; L = PPh₂NTol)  clusters, leveraging the molecular nature of the Co₆Se₈ core to attach three metal “edge sites” held in place by phosphine ligands, arranged such that they serve as an interface between the exterior chemical environment and the inner superatomic core. By swapping the edge metal, we are able to modify properties of the overall metalated cluster, imparting a degree of chemical and electronic tuneability. While investigations into these compounds have shed light on their electronic structure and reactivity, applying these properties in a practical sense has been an elusive and ongoing area of study. In 2021, however, the Nuckolls lab demonstrated a mixture of Co₆Se₈(PEt₃)₆, Cr₆Te₈(PEt₃)₆, and C₆₀ that formed an isotropic crystal structure capable of up to 100-fold increased conductivity compared to crystals of Cr₆Te₈(PEt₃)₆ or Co₆Se₈(PEt₃)₆ mixed with C₆₀ alone. In this work, I am investigating the conductivity of mixtures of various M₃(solv)_xCo₆Se₈L₆ clusters via a 2-probe method. In previous work, our lab has demonstrated the occurrence of charge transfer in the solution phase between clusters metalated with Co and Cu; building off of this, I intend to determine whether such a phenomenon can be observed in the solid state, and to a degree of reversibility that facilitates improved conductivity through the mixture. The observation or lack thereof of such behavior could hold implications for the applicability of metalated clusters in future semiconductor or materials technologies.

Current methods of cancer immunotherapy, such as CAR T-cell therapy, can treat blood cancers. However, treating solid tumors with T-cells remains a challenge, as the necrotic cores of solid tumors are a toxic environment for human immune cells. Bacteria are inexpensive, easy to genetically modify, and have many species which can colonize tumors. Bacteria, therefore, have potential to be an effective alternative to T-cell based treatments. Our challenge is to engineer E. coli bacteria to secrete immunomodulatory payloads upon colonizing the tumor microenvironment. This could be a useful avenue for immunotherapy, especially if the bacteria could produce multiple cargos with synergistic effects. However, we have limited data on what therapeutics E. coli can secrete, and whether it can secrete multiple therapeutics simultaneously. In the fall, I tested whether known E. coli secretion tags could export immunomodulatory minibinder proteins designed by the Baker lab. These minibinders interact with cytokine receptors on tumor cells and are hypothesized to reduce rates of tumor metastasis, which could make them effective anti-cancer therapeutics. Through western blot analysis, I successfully detected secretion of one of these candidate minibinders. My next step is to test whether it can be secreted together with another designed cytokine, Neo-2/15. I anticipate that combining cargos might lower each individual therapeutic’s secretion, since expressing multiple proteins may increase the cell’s burden past its secretion capabilities. If secretion or expression is observed, I will work on optimizing secretion of each therapeutic. The results of this experiment will broaden our understanding of E. coli’s potential as a delivery mechanism for individual and combined therapeutics, open future avenues to test more human immunomodulatory therapeutics and combinations thereof, and hopefully someday facilitate more effective forms of cancer immunotherapy.

Nitrogen is often a limiting resource in marine ecosystems, and its availability is heavily influenced by human activities, sometimes causing eutrophication. The study of phytoplankton metabolism under nitrogen-limited and replete conditions is of interest due to eutrophication's ecological and economic implications and the prevalence of nitrogen limitation on marine primary productivity. To investigate the metabolic effects of rapid nitrogen addition on phytoplankton metabolism, 15N-nitrate was traced into polymerized and free amino acids in two treatments of the microalgae Tisochrysis lutea with either initially limiting or replete nitrate concentrations. Using acid digestion, derivatization, and GCMS analysis we found that the culture with a lower initial nitrate concentration incorporated more 15N into alanine, valine, serine, and threonine. This suggests that phytoplankton under nitrogen-limited conditions exhibit greater increases in metabolism than those under replete conditions following rapid nitrogen influxes. Heavy nitrogen incorporation into other metabolites was also detected. This work provides a foundational method for future studies into phytoplankton metabolism under varying environmental conditions.

Environmental mechanical stress within a biological system is integral to proper cell fate, function and disease. These complex processes are affected by mechanotransduction, or the transfer of mechanical stimuli into biochemical signals. This occurs through the activation of mechanosensor proteins which transduce physical signals to the nucleus, leading to the activation of certain genes and cellular remodeling. Commonly used 2D cell culture techniques fail to replicate these forces, and are thus unable to activate mechanotransductive pathways seen in vivo. We have developed a method to apply physical stresses to 3D tissue models for investigating how these pathways impact functionality of the human physiological microenvironment. Our method was inspired by methodology created previously by our lab known as STOMP (suspended tissue open microfluidic patterning), which uses surface forces to pattern 3D hydrogel-based culture models. We use our method to create a cell-laden hydrogel suspended between two rows of disconnected rungs, referred to as tissue hooks. The hydrogel can then be transferred to a secondary device, where it is stretched to varying degrees, generating mechanical stress on the tissue. We use confocal fluorescent microscopy to observe cellular remodeling and use image analysis techniques and qPCR to quantify the activation of mechanotransduction pathways. While it is important to investigate how static mechanical stress on tissue impacts functionality, the human body is a dynamic environment. We created a system to dynamically stretch tissue cultures to further investigate cellular contractility within 3D tissue models. Instead of a static stretch, the cell-laden hydrogel is patterned to hooks with serpentine-style springs on the side. As the cell embedded hydrogel compacts, it pulls on the springs, allowing us to quantify the contractile forces. We plan to apply these models to study highly contractile tissue, such as skeletal muscle, and subsequent disease pathways shown in mechanotransduction.

Lys-R type transcriptional regulators (LTTRs) are one of the largest families of bacterial transcriptional regulator proteins with over 850,000 known members.  Many of these LTTRs are enriched in our gut microbiota, whose metabolic processes affect human health outcomes. LTTRs regulate gene expression through the binding of specific ligands to their ligand binding domain. Currently, less than 500 of them have been studied which represents a severe knowledge gap that conventional methods of characterization are unable to keep up with.  We aim to create a high throughput methodology to characterize LTTRs by their corresponding ligands that regulate gene expression. We are currently developing an assay to use chimeric LTTRs, or engineered LTTRs that share the same DNA binding domain yet a variable ligand binding domain. The use of chimeric LTTRs, which will all bind to the same DNA promoter, will potentially allow dozens of LTTRs to be tested in one assay. Our work thus far has demonstrated that chimeric LTTRs can be expressed in E.coli cells and purified using affinity chromatography and magnetic bead purification. We have also demonstrated that their ligand binding domains are functional and specific via differential scanning fluorimetry, and that their DNA binding domains are functional using an electromobility shift assay using SYBR green and SYPRO ruby dyes. Future work will explore their ability to regulate gene expression when their proper ligands are introduced with a substrate-induced gene expression reporter assay. Then uncharacterized LTTR candidates to be made into chimeras will be selected via a bioinformatic sequence similarity network analysis for assay piloting. If successful, this assay has potential to elucidate new metabolic pathways of our gut microbiota allowing for better understanding of their complex relationship with the human body.

We explore the Earth in order to discover and understand the ecosystems present on it. Representing 70% of the surface of the globe, the oceans are arguably the place we struggle the most to explore due to their size and depth (we know more about space than we do about our oceans). Dissolved organic compounds, produced by diverse marine organisms for a wide variety of reasons, are present in very low concentration in the oceans. This research was done in order to develop, design, and ameliorate existing techniques to detect and analyze dissolved organic compounds (amino acid in this case) present in seawater. Cation exchange chromatography, derivatization and gas chromatography mass spectrometry were used. The results were not as expected but the methodology is very promising. With some ameliorations, that methodology will be able to help us detect and analyze known and unknown particles at very low concentration in our vast oceans.

Glycogen Synthase Kinase 3 (GSK3) is a well-studied enzyme that is implicated in many diseases due to its regulatory role in numerous signaling pathways, both known and unknown. The scaffold protein Axin binds to GSK3 and the substrate β-catenin (Bcat), specifying GSK3 so that it primarily acts within the cancer-implicated Wnt signaling pathway. My project seeks to determine if GSK3 is recruited to other potentially unknown signaling pathways by other scaffold proteins that compete with Axin and each other to bind GSK3 at its Axin-binding site. A previous proteomics and computational experiment identified five proteins that potentially interact at this interface of GSK3. Five peptides were designed from the theorized binding sites of the proteins to evaluate whether these proteins compete with Axin. I am using an engineered mammalian cell line to indirectly measure cellular levels of GSK3's substrate, Bcat, and test whether the peptides are capable of displacing Axin from GSK3. When GSK3 is both active and bound to Axin, it causes degradation of Bcat; when GSK3 is inactivated or unbound from Axin, Bcat builds up in the cell. Lithium chloride is a known pathway-independent GSK3 inhibitor that will be used to compare the effect of the peptides on the amount of Bcat, and thus the effect on the amount of Axin-bound GSK3. Displacement of Axin by these peptides indicates that the proteins specify GSK3 for signaling pathways in a similar mechanism to Axin, and that in normal cell states, some equilibrium exists between pools of pathway-recruited GSK3. Understanding the equilibrium between these binders and their associated signal pathways would give insight into how overexpression of one can cause the development of disease states such as cancer.

Polymer networks, materials comprised of interconnected polymer chains, have been the subject of research interest for decades and have, particularly in recent years, found use cases in a variety of applications. Despite their broad use cases these materials are limited by their inherent tendency toward brittleness. One strategy for increasing the toughness of polymer networks is to introduce mechanochemically reactive groups in the crosslinks of a network instead of in the load-bearing primary polymer chains. Previously reported scissile crosslinkers have typically relied on strained ring structures or unusually weak covalent bonds for selective bond scission, introducing challenges such as difficult synthetic procedures and high design complexity. My collaborators at Johns Hopkins University have developed a novel, synthetically accessible crosslinker design that allows for selective mechanochemical bond scission via the replacement of a single carbon atom with silicon. They demonstrated that this scissile crosslinker doubles the toughness of a polymer network prepared by controlled polymerization. In my project I incorporated this crosslinker into a liquid resin compatible with free radical vat photopolymerization, 3D printed this new material, and mechanically characterized it through tensile testing. My work demonstrated that the same toughening effect occurs on polymer networks that are much less controlled and that this strategy for network toughening is compatible with 3D printing, which allows for the fabrication of more complex constructs. In conjunction with the expedient synthesis of this new crosslinker my project demonstrates that this approach to network toughening has the potential for large-scale applications.

CdCr₂X₄ and ZnCr₂X₄ (X = S, Se) spinels are ferromagnetic semiconductors, with reported bandgaps between 1.3-2.5 eV. With the advent of spintronic devices, a renewed technological interest in materials with coupled magnetic and optical properties has caused a resurgence in the study of these magneto-optically active spinels. Despite prevailing interest in their magnetic structure, the semiconductor luminescence of these materials is not well studied. We have prepared these materials in-house to study the magneto-optical coupling of this bandgap transition. We are also beginning to prepare these materials as nanocrystals for the first time as a way of accessing alloyed and shelled varieties. We started by synthesizing the non-magnetic In³⁺-based analogous sulfide and selenide spinels as nanocrystals, establishing a starting point to prepare the Cr³⁺-based spinels. We then introduced Cr³⁺ ions, which occupy the In³⁺ sites, into the lattice during the solution-phase synthesis. We aim to make the pure chromium-based nanocrystal spinels, along with a concentration range of Cr³⁺ ions in the In³⁺-based lattice. Our goal is to explore the relationship between the Cr³⁺ concentration gradient and the magneto-optical properties of these materials. We have characterized the composition and optical bandgap energies of these spinels with X-ray diffraction, photoluminescence, and UV-Vis absorption spectroscopy. We have begun tuning the bandgap energy of the nanocrystals by preparing mixed anion alloys with different ratios of Se and S ions (i.e. CdCr₂(Se_1-xS_x)₄; ZnCr₂(Se_1-xS_x)₄) and examining the bandgap shift with photoluminescence excitation spectroscopy. Future work includes utilizing magnetic circularly polarized luminescence (MCPL) to probe the magnetization of the lattice emission, letting us conclude how the optical properties of the semiconductor are coupled to its magnetism.

Less than 10% of drugs successfully transition from preclinical to clinical trials, principally due to the inability of currently used 2-dimensional models to simulate the 3-dimensional structure and function of human tissues. To develop 3D in vitro models of human vasculature for more efficacious screening of anti-atherosclerosis drugs, I created a device for constructing a perfusable tissue containing a lumen by leveraging open microfluidic patterning methods developed by our group: suspended tissue open microfluidic patterning (STOMP). The device can be used to pattern tissue with a hollow luminal structure lined with endothelial cells, which can be perfused via hollow posts the tissue is suspended between. Using surface tension-driven flow, a liquid hydrogel precursor solution flows through the open microfluidic channel and around the two hollow posts. After gelling, the tissue anchors to the post, contracts away from the sides of the microfluidic channel, and the STOMP device is removed. By adding a second STOMP device that can surround the first tissue another cell-laden hydrogel can be patterned around the first tissue, encapsulating it. To form a lumen in cardiac tissue, I will pattern the inner region with human umbilical vein endothelial cells (HUVECs) in an enzymatically degradable polyethylene glycol hydrogel, surrounded by human induced pluripotent stem cell-derived cardiomyocytes in fibrin hydrogel. Enzymatic degradation of the core region will form a cavity through which HUVECs will remodel the cavity walls, forming an endothelial lining. I will assess lining formation by adding fluorescent dextran to cell media being perfused through the device and measuring fluorescence through confocal microscopy in the surrounding region over time, allowing me to evaluate the permeability of the membrane to compare with physiological values. This model can then be used to screen treatments for atherosclerosis to study how drugs interact with cells in a 3D microenvironment. 

Technologies like CRISPR-Cas9 have emerged as promising tools for gene regulation and single nucleotide editing. The field has recently developed mRNA responsive base editors that can edit a genomic scratch pad and record mRNA expression and abundance in bacterial cells over time. RNA responsive base editors can let us retroactively study gene expression that can result in phenotypic differences. However, in complex heterogeneous communities, such as biofilms, monitoring the phenotype and expression of individual cells in real time is challenging. Pairing fluorescence signals to levels of mRNA can convey spatial information about how individual cells behave differently in complex communities. Our goal is to achieve mRNA-responsive base editing to generate fluorescent reporter output. To accomplish this, we will utilize the two existing systems, Rptr, which performs mRNA-responsive base editing, and CRISPR activation (CRISPRa), which can activate a fluorescent signal. These two systems will simultaneously perform base editing and CRISPR activation within the same cell. For this purpose, we will prototype orthogonal CRISPR systems that can independently recruit either activators or base editors through RNA hairpins attached to the guide RNA. My work focuses on designing synthetic fluorescence reporters with installed stop codons that can be modified with base editing and then activated with CRISPRa. My reporters will allow for rapid prototyping of mRNA responsive base editing with RNA hairpin recruitment. We can then find our best performing RNA-recruited base editing system to use in a multiplexed effector system. Ultimately, this integrated approach will couple mRNA expression with a fluorescent reporter read out, allowing us to monitor individual bacterial cells within complex populations.

The future of clinical research is expanding towards sampling that can be completed from the comfort of a participant's home. Blood samples allow for the collection of ribonucleic acid (RNA), which is relevant for gene sequencing that can track the progression of a disease. However, venous blood draws require trained phlebotomists at a healthcare facility, which may not be readily accessible in some areas. Dried blood spots are an existing remote sampling method, but rapid degradation of RNA and low blood volume can limit the scope of analyses that are possible. Previously, our lab developed homeRNA, which interfaces with the Tasso-SST (Tasso Inc.), a lancet-based device that draws blood from the upper arm. The addition of the engineered, spill-resistant container creates a channel through which participants can draw their own blood, stabilize the blood with RNAlater (Thermo Fisher Scientific), and ship the sample to a laboratory for analysis. The homeRNA+ project improves upon the original homeRNA by integrating a commercially available blood collection tube for better compatibility and doubling the maximum blood collection volume. Feedback from study participants over the United States across all age and race demographics generally find the blood collection process painless and the stabilization easy to perform. We expect samples to also have sufficient RNA integrity and yield for downstream analysis. The project serves a number of nationwide and global collaborators, including academic institutions like New York University and Boston University. I assist in receiving and processing biological samples from remote collection, ensuring proper handling by safely unpackaging, logging, and preserving returned samples in cold storage for future analysis. Additionally, I serve as a study coordinator by meeting with collaborators, manufacturing high volumes of kits in a timely manner, and managing inventories.

Microfluidics has enabled researchers to engineer environments with precisely controlled fluids in submillimeter scale, making it an essential tool in biomedical research. Moreover, the study of fluidic dynamics in both closed and open channels has been a major focus in the field of microfluidics. This study specifically examines capillary flow dynamics in open microfluidic systems where capillary flow refers to the spontaneous flow of liquids in narrow spaces without the assistance of external forces. The Lucas-Washburn-Rideal (LWR) law is commonly used to describe capillary flow dynamics in closed and open channels, microporous media, and threads that assumes a viscous regime in which capillary forces are counterbalanced by friction with the solid channel walls. However, in conditions beyond the viscous domain, inertial forces become significant, leading to an imbalance between wall friction and capillary force (e.g. the inertial regime at the onset of capillary motion). This study proposes a straightforward criterion for identifying inertial effects using the Lucas-Washburn-Rideal (LWR) law. This criterion is derived by analyzing the plot of a characteristic function, F, that is defined as the product of the cross-sectional area at the meniscus location, the travel distance, and the meniscus velocity. To validate this criterion, we present four different examples: open-channel devices with converging and diverging channel configurations, an open channel separated into two daughter channels in a symmetrical or asymmetrical configuration, and a two-phase capillary flow experiment in which pentanol pushes a plug of water in an open channel. These experiments successfully validate the proposed criterion for identifying inertial effects in capillary-driven flow within open channels. Furthermore, we also demonstrate that the Bosanquet equation can serve as an accurate model for open capillary flows in rectangular channels with progressively decreasing cross-sections. This study could impact the design of microfluidic systems that traditionally assume negligible inertial effects.

In our biochemistry teaching labs, students conduct 10-week projects using recombinant protein expression and purification protocols, adapted from Fred Hutch, distributed and tracked via GENI-ACT.org, to identify immunoproteins of research or biomedical interest. We hypothesize they can produce antigen fragments for antibody studies and siderocalin proteins, which bind bacterial siderophores, yielding different amounts and results. In Winter 2023, students modeled antibody fragments with I-TASSER, expressed top constructs with His-tags, and purified them using Ni-NTA resin. In Winter and Fall 2024, siderocalins were expressed as GST-tagged constructs in BL21 and DH5alpha cells using longer expression. The human siderocalin in DH5alpha formed an orange solution, consistent with known siderocalin-enterobactin-Fe complexes. Unexpectedly, other species’ siderocalins appeared yellow, pink, or blue, suggesting functional diversity. Students produced enough immunoproteins for viability tests and are now expressing homologs of the blue siderocalin. They participated in all stages, developing spectroscopy and protein crystallization skills for research careers.

Microbial volatile organic compounds (mVOCs) are small molecules produced by microorganisms during biosynthetic pathways that easily diffuse through the air, interacting with other nearby organisms despite not physically touching. One method to measure this mVOC communication was the previous iteration of our co-culture device, a bottomless glass vial sealed onto a chip with two separated culture wells, where mVOCs could be released into the headspace. However, spores, a non-mVOC aerosol, also diffused through the headspace, and the device’s structure made it difficult to ensure a fully intact seal. We are developing a device that supports a co-culture that communicates through mVOCs only, uses an intact vial to improve encapsulation, and allows for solid-phase microextraction (SPME) coupled with gas chromatography-mass spectrometry. To test its efficacy, we use the sporulating fungus Aspergillus fumigatus and the bacteria Pseudomonas aeruginosa as model organisms, which are opportunistic pathogens often co-infecting cystic fibrosis patients. We assemble the device by inserting two layers of CNC milled polystyrene platforms containing wells into a vial. We add 1-octen-3-ol or isopentanol, mVOCs produced by A. fumigatus, to the first layer, and P. aeruginosa cultures to the second. The second layer contains polytetrafluoroethylene (PTFE) membranes that only mVOCs can diffuse through. We incubate the vials, plate the P. aeruginosa cultures onto agar, incubate, and observe their growth to assess mVOC communication. We anticipate higher concentrations of mVOCs to inhibit P. aeruginosa growth, demonstrating that the mVOCs interacted with microorganisms in the upper layer. In the future we will co-culture A. fumigatus and P. aeruginosa in the device to study their mVOC interaction, and explore using different biomarkers to determine their effects. This device could be used with other co-infecting pathogenic microorganisms to study their mechanisms and explore therapeutic possibilities.

Understanding complex disease processes requires visualizing both nanoscale details and their impact on larger structures. The Vaughan group has developed a method that achieves this using conventional optical microscopes by physically expanding tissue via hydrogel chemistry, enabling sub-diffraction-limit resolution. This approach preserves physiological context through fluorescent labeling of macromolecules (DNA, proteins, carbohydrates). Using mouse renal glomeruli—spherical kidney filtration units (~70-100 µm in diameter)—as a model, I demonstrate the method’s ability to capture nanoscale features, specifically global variations in basement membrane thickness (100-2000nm), with validation that the expansion process does not introduce significant distortion.

Fat, oil, and grease (FOG) in residential wastewater presents significant environmental challenges, contributing to the formation of fatbergs that disrupt wastewater systems, increase treatment costs, and heighten public health risks. Traditional methods, like commercial enzymes, are only temporarily effective and require constant maintenance. The goal of this research is to develop Engineered Living Materials (ELMs) comprising a yeast strain, Yarrowia lipolytica, within polymeric matrices for sustained FOG degradation. Y. lipolytica is known for its ability to efficiently degrade hydrophobic FOG components due to its diverse lipase enzyme expression. I encapsulated engineered Y. lipolytica strains in UV-cured poly(ethylene glycol) diacrylate (PEGDA) hydrogels. The findings showed sustained lipase activity and robust cell growth, confirmed by enzyme assays and confocal microscopy. However, over 28 days, significant degradation of the PEGDA-based ELMs occurred, likely due to the breakdown of ester bonds by lipolytic enzymes. To address this, I switched to a thiol-ene polymer network composed of tetra-PEG-allyl and PEG-dithiol, which is expected to resist degradation more effectively. I confirmed the viability and lipase production in these thiol-ene ELMs using the same methods. Varying polymer chain lengths in the thiol-ene network influenced Y. lipolytica growth patterns and morphology, including a shift toward hyphal growth—a filamentous form typical of its dimorphic nature. These changes were influenced by the polymer network’s architecture and material stiffness. Moving forward, I will investigate how hyphal growth impacts FOG degradation and assess the long-term mechanical properties of these thiol-ene ELMs. I expect these ELMs to remain stable over time and reduce FOG concentrations in simulated wastewater. Ultimately, this research aims to provide a sustainable solution for wastewater treatment, addressing the environmental, economic, and infrastructural impacts of fatbergs.