In classical electrodynamics, accelerated charges emit electromagnetic radiation. The associated energy loss of the particle can be modeled as a radiation reaction force, proportional to the change in acceleration. Including this force in the usual dynamical equation for a charged particle yields the Abraham-Lorentz-Dirac (ALD) equation. For point particles, solutions to the ALD equation are problematic. First, they require additional initial conditions beyond those needed in regular Newtonian dynamics, but more concerning are the presence of unphysical run-away solutions and acausal trajectories. These problems arise in the point-like limit of the theory, so it is possible that quantum mechanics is the more appropriate framework with which to address the problem. In order to explore the similarities and differences of the classical and quantum frameworks, we compute classical trajectories of charged particles in the presence of a Coulomb field, including radiation reaction. We compare the associated classical cross-section with the quantum field-theoretic cross-section for Coulombic scattering, including radiative corrections. With these calculations, we will be able to assess when the field theoretic formulation of single-photon emission can approximate the classical radiation reaction.

During the formation of the early embryonic zebrafish body, bipotential neuromesodermal progenitor cells (NMPs) that are located at the posterior end begin to differentiate via regulation of the Wnt pathway. Relatively higher Wnt-signaling activates the expression of the tbx16 gene, which in turn inhibits the neural fate and commits cells to a mesodermal (muscle) fate. The aim of this study is to understand the downstream effects of tbx16 on the rate and mechanism of anterior migratory transitions of mesodermal cells as they leave the progenitor region and travel to the somite-forming mesoderm region. We have previously shown that successful anterior migration and differentiation of mesodermal cells is dependent upon tbx16 downregulating the expression level of two Arhgaps, a Rho GTPase-activating protein. Hence, we heat shock hsp70: Arhgap29 and hsp70: Arhgap35 zebrafish transgenic lines at early somite stages in order to compare and contrast the effects of sustained Arhgap activation during the critical period of mesodermal cell anterior migration. At 24 hours post-heat shock, embryos are sorted by wild-type and transgenic, with transgenics having severe defects in their posterior somite formation. Followed by immunocytochemistry for a muscle antibody, confocal imaging on whole-mount embryos captures the shape and number of somites from each transgenic line. My results show that while Arhgap29 affects both the number and morphology of somites, Arhgap35 only affects their morphology. This suggests that these two Arhgaps do not have overlapping roles in the control of mesodermal cell migration. I am currently performing a separate in-situ hybridization experiment to help me understand the role of these Arhgaps on the essential genes involved in muscle cell differentiation. This study contributes to understanding early vertebrate development as a model for human embryogenesis.

Energy efficiency of important industrial chemical reactions is a motivation behind scientific research across a wide range of disciplines as a response to the growing energy crisis. Electrocatalysts play a crucial role in improving energy efficiency in the interconversion of electrical and chemical energy, and are essential components in any sustainable solar fuels conversion scheme. An issue in the widespread use of renewable energy sources is the fluctuation between energy demand and energy supply. This issue can be solved by using the renewable energy source to generate chemical fuels, storing the energy from the sun or wind in energy-dense chemical bonds to be released on-demand. One such fuel is molecular hydrogen, H2. Molecular [Ni(PNP)2]2+ catalysts are highly active catalysts for the hydrogen evolution reaction (HER) that employ pendant amines—an end group that assists with hydrogen production by allowing for efficient proton transfer. However, as molecular species, these catalysts suffer from low stability and low potential for scalability. The primary focus of this research is to develop an efficient nano-scale Ni2P synthesis based off prior syntheses in the literature, that incorporates cooperative ligands for HER on the surface. Our end goal is to determine the best method to synthesize Ni2P nanoparticles with enhanced activity due to the cooperative effects of pendant amine functionalities to create a nanomaterial catalyst with properties that meet and surpass the molecular [Ni(PNP)2]2+ catalysts for HER.

Diverticulitis is a common gastrointestinal condition in both the United States and Europe. Approximately 200,000 people are hospitalized for cases of diverticulitis in the United States alone on a yearly basis. When small pouches called diverticula develop along the sigmoid colon, the lower part of the colon, this initial condition is known as diverticulosis. Diverticulosis turns into diverticulitis when these diverticula, located in the left lower quadrant (LLQ) of the abdomen, become inflamed usually due to a bacterial infection. A common symptom of diverticulitis is when patients generally have LLQ pain sustained over a period of time. We, the Surgical Outcomes Research Center (SORCE), are conducting the Diverticulitis Evaluation of Patient Burden, Utilization, and Trajectory (DEBUT) study to investigate the impact of diverticulitis treatment options on patients and to improve the understanding about how physicians and patients decide to have elective surgery for diverticulitis. Currently, the optimal timing for elective (non-emergency) colectomy surgery to treat diverticulitis is unclear, and diverticulitis affects individuals in many different ways. Through our patient-centered research approach in DEBUT, we hope to determine the impact of treatment decisions on a patient's quality of life, work, and clinical symptoms. These patient-reported outcomes are measured over time among patients who do and do not undergo elective colectomy surgery to treat diverticulitis. Our goals are to better understand how physicians and patients decide to undergo elective colectomy surgery to treat diverticulitis as well as provide higher quality evidence that can help patients and their physicians to make better-informed decisions about the timing of surgery for diverticulitis. Results gained from this study may eventually help inform current medical recommendations for diverticulitis treatment and give current healthcare professionals the tools necessary to develop more effective guidelines for treating patients with diverticulitis.

Belted Kingfishers (Megaceryle alcyon) are widely distributed across freshwater and marine environments of North America, but the species’ feeding ecology remains poorly studied in marine habitats. In summer 2017, we investigated the behavior and feeding ecology of Belted Kingfishers in the nearshore marine waters of San Juan Island. Our objectives were to assess differences in feeding strategy and success among birds of different ages, to calculate time budgets, and to examine the effects of dynamic environmental factors such as tide and current speed on kingfisher feeding. We conducted focal behavioral observations of adult and juvenile birds at two locations on San Juan Island. Observations on individual feeding success were collected opportunistically during study periods. Overall, adult birds showed a higher success rate and longer average prey length than was observed for juveniles. Feeding success for all age categories was higher at Jackson Beach than at Friday Harbor Labs, suggesting that prey abundance or accessibility may be site specific. Feeding success was fairly consistent over all current speeds but was highest during low tides. Feeding success also showed a diel pattern (highest from 1200 to 1400), differing from prior research in freshwater habitats. Our results are intriguing and demonstrate the need for continued research on how life stage, currents and tidal stage influence marine based Belted Kingfishers and their role in coastal ecosystems and food webs.

Many children with Autism Spectrum Disorder (ASD) suffer from decreased gut motility that manifests as debilitating chronic constipation, leading to an unhealthy aversion to food. We hypothesized that the same neurological defects that cause the hallmark cognitive impairments in ASD also negatively impact the enteric nervous system controlling gut peristalsis. Within the autism spectrum, we chose to study one particular condition called Phelan-McDermid Syndrome (PMDS), because every patient with the diagnostic chromosome 22 micro-deletion has a dramatic decrease in gut motility. Evidence suggests that the gene-of-interest in the deleted region is SHANK3 because mice with SHANK3 haploinsufficiency show decreased postsynaptic density of neurotransmitter receptors. The overriding goal of this project is to develop novel drug treatments for patients with PMDS and ASD. Finding new compounds that can increase (or bypass) postsynaptic receptor density could alleviate these patients’ gut motility problems. However, models to study the enteric nervous system either involve invasive biopsy procedures to remove enteric tissue from patients or the use of animal models that fail to replicate the pathology observed in humans. Therefore, the objective of this study is to create a human disease-in-a-dish model of enteric nervous system dysfunction by generating stem cells from PMDS patients and differentiating them into enteric neurons (ENs). We predict that molecular characterization of SHANK3-deleted enteric neurons will identify aberrant signaling pathways suitable for therapeutic intervention. Preliminary experiments from our laboratory have demonstrated the feasibility of differentiating patient-derived induced pluripotent stem cells (iPSCs) into neural crest (NC) cells, which are necessary precursors to making enteric neurons. NC plus smooth muscle co-culture experiments will then be used to drive fluorescently labeled normal and SHANK3-deficient NC cells to enteric neurons, thus enabling phenotypic characterization of the disease phenotype in vitro.

For more than a century, Drosophila melanogaster (fruit flies) have been an invaluable and versatile tool to further our understanding of cell signaling and survival mechanisms. To this day, they continue to shed light on the endogenous pathways that cancer cells can hijack in order to proliferate, metastasize, and recur following remission. The molecular conservation of these pathways invites parallels between the germline stem cells in D. melanogaster and the cancer stem-like cells in human carcinoma. In the same way that a tumor can relapse following a period of dormancy, Drosophila germline stem cells are capable of repopulating their niche after insult from Ionizing Radiation (IR). Utilizing this powerful model, we have conducted a small molecule drug screen of 512 compounds that we have narrowed down to eight candidate drugs that appear to increase cell death in Drosophila germline stem cells. Having already characterized the wild type Drosophila germline stem cell response to IR-induced DNA damage, we  probed how drug treatment and gene knockdown affected the germline stem cells' ability to recover from insult. Previous work in the Ruohola-Baker Lab has demonstrated the critical importance of the mechanistic target of rapamycin (mTOR) and the Tie receptor pathways in regulating regeneration after insult in the Drosophila germline. The Tuberous Sclerosis Complex (TSC), a heterodimer comprised of Tsc1 and Tsc2, is a known negative regulator of mTOR. Additionally, the Tie receptor is central to anti-apoptotic signal transduction in the Drosophila ovary. We have screened four candidate drugs to see if they effectively increase stem cell death in Tsc1-knockdown and Tie-null flies, in order to ascertain whether our drugs affect stem cell survival mechanisms through mTOR and/or Tie signaling. Our findings may shed light onto how to mitigate the quiescent threat of tumor relapse.

The goal of the project is to determine whether ma-N 1420 photoresist can be used with Heidelberg laser direct write tool, and to optimize the ma-N photoresist sidewall profile. The process starts by applying a negative photoresist onto a surface of a silicon wafer followed by an exposure to an ultraviolet light using a Heidelberg laser tool. The 410nm laser is applied directly to the photoresist without the use of a photomask, which is normally used for the purposes of exposing the wafers. The Heidelberg process is optimized in a manner that has not been possible previously at UW. This requires studying the thickness of the photoresist using reflectometry and optimizing the spin speed during spin coating. Various exposures on the Heidelberg system are then tested to make sure that the ideal exposure conditions have been achieved. The next step is to deposit a thin metal film on top of the photoresist. The deposition is achieved via an evaporation of metal inside the chamber of the device in which the metal is melted and evaporated by high speed electrons and is then deposited on a cooler silicon surface. The undesired metal is then stripped away from the surface of the wafer by removing the photoresist from under the metal film in a process the engineers refer to as “liftoff.” The optimization part of the project refers to testing different development times to make sure the development gives ideal photoresist overhang for the liftoff process. Finally, the sidewalls of the photoresist mask are analyzed using Scanning Electron Microscope (SEM). An SEM is used as the thickness of photoresist can be thinner than 1µm. The research was performed to verify that ma-N photoresist is suitable to use with Heidelberg system to complete a nanofabrication process.

It is not fully known what controls signal preference in branched signal transduction pathways. One hypothesis is that the configuration and orientation of receptors determines signal preference. We are investigating this hypothesis in the context of the Tie2 receptor pathway which has downstream signaling involved in cell survival via Akt, migration via Dok-R, and sprouting via FAK, among other branches. We are using computer designed protein tools, short-armed claw trimers and nanocages, conjugated to F domains of the canonical Tie2 ligand angiopoietin 1 in our investigation. We have shown that short-armed claw trimers with three conjugated F domains do not yield increased phosphorylation of Akt, suggesting that more than three receptors must cluster together for signal activation. The nanocages are multivalent, for they have multiple F domains conjugated to them. We have different valency nanocages with different percentages of F domain conjugation. We are using these different valency nanocages to investigate which valency is optimal for receptor activation. We have shown that higher valency nanocages yield increased phosphorylation of Akt. We predict that higher valency nanocages cluster more Tie2 receptors together in a specific conformation. Thus, we show a positive correlation between Tie2 clustering and the phosphorylation of Akt due to Tie2 activation. Now we will investigate combination conjugations of F domain and integrin binders to the nanocages as well as other branches of the Tie2 pathway: Dok-R corresponding to wound healing ability and FAK corresponding to tube formation ability. This work has potential to help generate therapeutic compounds for wound healing.

Icelandic wetlands have ecological, climatological, and historical significance. The Millennium Ecosystem Assessment defines ecosystem services as the benefits humans receive from nature. Many of these benefits are not included in the economic market which leaves them out of cost-benefit analysis in decision making. Although the Kyoto Protocol approved wetland restoration as an official climate mitigation activity, wetland restoration activities in Iceland have yet to catch up. Valuing the ecosystem service of carbon sequestration can help clarify for Icelandic policy-makers that the benefits outweigh the costs of restoration. This study conducts an economic valuation of the carbon sequestration service in Úlfarsárdalur to provide the city of Reykjavik with new information to include in a cost-benefit analysis of restoration. Three methods are used to quantify the monetary benefit provided by potential carbon sequestration in Úlfarsárdalur – direct market pricing, damage avoidance cost, and replacement cost. The results relied on physical data provided by the Verkís report of restoration potential in Úlfarsárdalur as well as data collected by Hlynur Óskarsson, a wetland ecology expert. In accordance with claims from the Millennium Ecosystem Assessment, all three methods reflected that the economic benefits of carbon sequestration exceed the costs of restoration by a significant amount. The direct market pricing and replacement cost methods yielded similar values, while the damage avoidance cost came out much lower. These findings suggest that wetland restoration to promote carbon sequestration could serve as a cost-effective climate mitigation measure. Researchers must continue to investigate the accuracy of such valuation techniques as well as their transferability and scalability to larger ecosystems.

Atherosclerosis is a disease in which cholesterol accumulates in the walls of arteries, limits blood flow, and causes heart attacks and strokes. Atherosclerosis could be prevented or reversed by expressing therapeutic genes in the artery wall. Gene therapy for atherosclerosis will require high-level therapeutic gene expression for two reasons: 1) to increase efficacy; and 2) to allow use of lower vector doses, thereby minimizing vector-related toxicity. Our goal is to increase expression of an apolipoprotein A-I (apoA-I) transgene, which both prevents and reverses atherosclerosis in rabbits. We used an in silico bioinformatics approach to identify endothelial cell-specific cis-regulatory modules (CRMs). CRMs are short enhancer regions of DNA that are expected – when introduced into endothelial cells – to increase transcriptional activity of a nearby gene. We identified 11 CRMs in the CDH5, EFEMP1, THBS1, and VWF genes. We hypothesize that insertion of these CRMs into a helper-dependent adenoviral vector encoding apoA-I will increase apoA-I expression in endothelial cells. We also hypothesize that the genomic regions surrounding these CRMs contain sequences that, along with the CRMs, could increase transgene expression above levels obtained with the CRMs alone. Our adenoviral vectors have a larger capacity for the insertion of DNA sequences than other gene-therapy vectors. This large capacity allows us to evaluate CRMs in their native genomic context (i.e., with several kilobases of neighboring DNA included). We cloned large CRM-containing regions of the 4 genes listed above and we are inserting the apoA-I gene into the translational start sites of these genes. We will test vectors containing individual CRMs and vectors containing the larger CRM-containing regions in cultured endothelial cells (in vitro) and in rabbit carotid arteries (in vivo) to identify CRM-containing constructs that express the highest apoA-I levels. This project may provide higher-expressing vectors for use in gene therapy for atherosclerosis.

Cancer stem cells are thought to play a role in relapses and metastasis in numerous cancers. The inability of traditional cancer therapies, such as chemotherapy, to eradicate these cancer stem cells prompted a search for small molecules that induced apoptosis in cancer stem cells. Drosophila germline stem cells can be used as a model system to emulate cancer stem cells. Upon irradiation, Drosophila germline stem cells are able to survive apoptosis through a molecular signal released by the apoptotic daughter cells via the TIE receptor. We have conducted an in vivo drug screen of 512 compounds in Drosophila melanogaster to find drugs that would disrupt this protective mechanism and induce apoptosis. In particular, Camptothecin, NSC 125197, and NSC 127458 were effective in killing germline stem cells. To test the effect of the small molecules we fed female flies the compound for 3 days, dissected and fixed the ovaries and stained for an apoptosis marker, activated caspase, and the GSC marker, adducin. We quantified the effect of the drug by analyzing the number of germline stem cells and caspase signaling on a confocal microscope. Through this system we aim to find potentially new, and more powerful anti-cancer drugs that can affect cancer stem cells. Future directions include attempting to understand the mechanism of action of these apoptotic compounds in hopes that they might be useful in the fight against cancer stem cells.

90% of drugs fail in clinical trials. As a result, a successful FDA-approved drug costs an average of $2.6 billion to develop and takes a decade to reach the market. Pharmaceutical companies are unable to comprehensively evaluate drug toxicity before clinical trials because no methods exist to screen the thousands of protein-protein interactions (PPI) that a drug could unintentionally disrupt in the human body. The ability to disqualify drug candidates with off-target effects before clinical trials would greatly increase the speed at which useful drugs are introduced to the market and reduce the expense of developing new therapeutics for those who need them. Here, we demonstrate a novel synthetic biology-based method, SynAg, that enables thorough drug characterization by linking PPI binding strength to the cellular agglutination of engineered S. cerevisiae cells. SynAg is a library-on-library approach that conserves the accuracy of pairwise PPI toxicity screening in a high-throughput, one-pot format. Specifically, we construct a SynAg library to characterize a 20-by-20 protein interaction network involved in cellular apoptosis to demonstrate the accurate profiling of a complex and highly interconnected family of proteins. Finally, we use the SynAg library to characterize the on- and off-target effects of small-molecule cancer therapeutics, which are shown to be consistent with previous studies. 

“Jamming” is characterized by fluid behavioral coordination of musicians unhindered by expectations. The jammers come together without a plan on what they are producing in hopes of finding unification through their music leading to a sense of self-satisfaction. More specifically, a musical jam session, originally coined by the jazz community, is an impromptu gathering of musicians with the purpose of improvising together. Jamming has had an effect on the players, but no qualitative research has been done pertaining to the audience. It is important to look at the relationship between the jammers and the audience because whether one is jamming or a member of the audience, that person is still considered a listener of the music and can, therefore, interpret the musical “conversation” from different perspectives. Listening to people jam increases the listener’s sense of wholeness and it is likely that the players feed off the audience and vice versa. Thus everyone in attendance is involved.

Statistics have revealed that males are more susceptible to significant spinal cord injuries than females. Carlos Ayala, MD-PhD student from the Keck Center of Collaborative Neuroscience at Rutgers University, has found preliminary evidence that males have a heightened immune response comparison to females following injury. This immune response involves an increase in inflammation surrounding the injury site, and the release of damaging cytokines that suppress neuronal growth and promote axon demyelination following injury. At the injury site, there is also an aggregation of M1 macrophages, which are known to have inflammatory properties and are involved in the promotion of cell death in the surrounding tissues. Another type of macrophage present are M2 macrophages, which are known to be anti-inflammatory and promote tissue regeneration, but these macrophages appear to be suppressed at the site of injury due to myelin debris and other chemical signals. Recent studies suggest that human umbilical cord blood (hUCB) has anti-inflammatory properties which could be beneficial in decreasing the inflammatory response that occurs in males. In this study, we propose to investigate the use of hUCB derived monocytes to treat spinal cord injury in male rats to determine whether it causes the polarization of monocytes into M1 or M2 macrophages in vivo. Using the classification of monocytes standard of myself, Carlos Ayala, Cameron Wolf, and Johvany Plaisime of Rutgers Univerity, the next step is to determine which monocytes are precursor cells to M1 (inflammatory) and M2 (anti-infammatory) macrophages. Monocytes are a heterogeneous population with cells found at various stages of life. Some of the critera include size of the cell, amount of and form of cytoplasm (smooth vs jagged), density of the cytoplasm, how indented the nucleus is, number of nuclei the cells have, and cell markers that are present for monocyte/macrophage specific cell membrane receptors. If this study is successful, hUCB could be further studied for possible therapeutic applications for the treatment of  spinal cord injury.

As the nation openly confronts the issue of sexual violence, black women remain confined to the periphery. The emergence of the #MeToo movement continues a centering of white women, most evident in the displacement and erasure of the founder of the movement. While this is just one example, it speaks to a larger history of dehumanization and erasure that renders the victimization of black women as illegible. Through the hyper sexualization of black women, which makes their victimization impossible, and systemic erasure, victims of sexual violence and black women have become a contradiction of terms. In my project I utilize discourse analysis of media representations and interviews with young black women who are sexual assault victims to offer a critical analysis of public conversations about the epidemic of sexual violence on college campuses, focusing on the #MeToo Movement and the lack of media coverage surrounding Daniel Hotzclaw. Through this study, I show how these public discourses contributed to the erasure of black female survivors and, ultimately, a lack of justice and support for these women. This research seeks to better understand reporting methods for young women of color in a rural area, the varying types of sexual assault experiences, accountability of sexual assault perpetrators, the importance of non-profit organizations as means of social support, and the impact of a lack of visibility and resources for sexual assault victims who are minority women. By examining the lack of media and literature coverage of rape and sexual assault against black women, my project aims to identify the faults within sexual assault reporting methods and increase support for black women survivors.

Metalloproteins account for at least one-third of all known proteins and take part in a myriad of redox chemistry. In spite of the long-standing interest, designing metalloproteins from scratch with structural precision and tunable redox properties remains an elusive goal. The underlying hypothesis for this project is to design redox active, iron- sulfur [Fe-S] proteins using protein designing software called Rosetta. Iron-sulfur proteins are nature's modular unit for electron transfer and redox catalysis. We used Rosetta to design classes of iron sulfur proteins including [4Fe-4S] and [2Fe-2S] clusters. We have expressed these designed proteins in E.coli and tested their binding properties to their respective inorganic clusters using biophysical techniques such as ultraviolet–visible spectroscopy (UV-Vis), circular dichroism (CD), and electron paramagnetic resonance spectroscopy (EPR). Initial results show that designed proteins can be expressed in E.coli and bind to [4Fe-4S] clusters as designed. The Cluster incorporation was verified by UV-Vis spectroscopy, which shows absorption centered around 410nm, characteristics of a [4Fe-4S] cluster. We also verified that the holo protein is folded and thermostable using CD. We are currently focusing on crystallizing these holoproteins to verify the accuracy of the design process and investigate their redox properties. These designed proteins will help in explaining the fundamental factors controlling the redox properties of metalloproteins and lay the foundation for designing a new class of metalloenzyme relevant to metabolic engineering.

Hybrid organic-inorganic perovskite films have exhibited power conversion efficiencies (PCEs) over 22% in photovoltaic devices. Despite high PCE, non-radiative recombination at surface defects remains a major material challenge in achieving theoretical efficiency limits. We have recently shown that surface passivation using Lewis bases on model CH3NH3PbI3 perovskite films can increase the external photoluminescence quantum efficiency (PLQE) to 30% and internal PLQE to near unity. This puts CH3NH3PbI3 alongside Gallium Arsenide, currently the highest performance solar cell material, as the only other semiconductor with such high radiative efficiency. Recently, several other alloyed perovskite compositions such as (HC(NH2)2¬)xCs1-xPb(I1-yBry)3 have been investigated for photovoltaic applications due to their increased stability. Preliminary studies have shown that the surface chemistry and effect of Lewis bases on these alloyed perovskites depends on their composition. In order to understand these differences, we investigate the nature of defects, surface chemistry and the effect of Lewis bases on these alloyed compositions. We test a library of Lewis-bases as ligands on alloyed perovskite compositions and use time-correlated single-photon counting and photoluminescence quantum yield measurements to quantify changes in charge carrier lifetimes. We also use glow discharge optical emission spectroscopy to show that the ligands are primarily confined at the surface and thus, act as surface treatments. Furthermore, we use solid-state nuclear magnetic resonance along with X-ray photoelectron spectroscopy to show that the behavior of ligands is consistent with that of a typical Lewis-bases. This study demonstrates the importance of surface defects in alloyed perovskite compositions and the importance of surface passivation in achieving higher optoelectronic quality materials. The information gained in this study will be critical in optimizing the design of alloyed perovskite composition devices.

The ease at which we appear to recognize and assess faces belies the difficulty underlying face recognition. Faces possess similar features (i.e. eyes, nose, mouth), yet we are able to identify separate individuals based on their featural configuration (i.e. T-shaped arrangement of features). Prior research using fMRI shows that featural and configural information is processed in different face-specific brain regions. Evidence suggests that the FFA responds to both featural and configural information, compared to the OFA and fSTS, which only respond to featural modification. However, precise response time of featural and configural face processing is unknown. Featural processing may occur before configural processing, or configural processing may occur before featural processing; conversely, they may occur simultaneously. Using a 2x2 factorial design we assessed the effects of changes in featural information, configural information, as well the interaction between the two. Participants saw four versions of a face: intact faces, faces with removed features, faces with distorted configuration, and faces with both modifications. Stimuli were presented while the brain activity of subjects was recorded using electroencephalography (EEG). This study specifically looked at temporal changes in a face-specific event related potential (ERP) called the N170, which consistently fires when presented with anything that resembles a face. We assessed the magnitude of the N170 to determine whether the face-processing brain regions explicitly processed information regarding features and configuration. In addition, timing of face-processing was assessed to detect any differences in how long it took the brain to process faces with featural or configural modifications. We tied together evidence from fMRI (spatial) and the N170 (temporal) to see how precise timing and location interact in the brain during face perception of facial features and feature configuration.

Degeneration of mechanosensory hair cells in the inner ear leads to complications in hearing and balance. Calcium plays an important role in hair cell function and failure to maintain calcium homeostasis is an underlying cause of hair cell death. We used hair cells in the zebrafish lateral line as our model, to explore the role of endoplasmic reticulum (ER)-mitochondrial calcium flow in hair cell damage. We utilized ER-GCaMP-150 for these studies, a new low-affinity calcium indicator made distinctly to look at calcium concentrations in the ER. Injection of zebrafish embryos with ER-GCaMP-150 expressed under a hair cell specific promoter allowed for visualization of ER Ca²⁺  concentrations under a high-resolution microscope. To date we have confirmed expression of ER-GCaMP in our zebrafish models and quantified Ca²⁺ transfer between the ER and mitochondria. Examining changes in calcium concentrations of hair cell organelles provides the opportuninty to gain more insight into the intracellular mechanisms underlying hearing loss.

Understanding how extracellular environments facilitate the differentiation of stem cells holds much promise for the field of regenerative medicine. Non-muscle myosin II (NMII) plays an important role in cell morphology and also generates forces that alfter biochemical signalling. It has been shown that the activity of NMII controls mechanoreceptors and integrins facilitating stem cell fate. More specifically, mechanotransduction of transcriptional coactivators YAP/TAZ facilitate differentiation of mesenchymal stem cells (MSCs). YAP and TAZ are responsible for upregulating genes associated with stem cell differentiation. Under external stresses mesenchymal stem cells differentiate into osteocytes whereas softer extracellular conditions favor the differentiation into adipocytes through mechanotransduction of YAP and TAZ.To further explore the role of physical forces determining the fate of stem cells, we used a computationally designed self-assembling homo-polymer called 2E01, generated by the Institute for Protein Design (IPD). Mechanical stress and the physical activity of NMII can be mimicked by controlled expression of the length of the E01 protein fiber. We introduced the 2E01 gene under a doxycycline-inducible promoter into the AAVS1 "safe harbor" locus of the induced pluripotent stem cells (iPSC). Expression of the E01 fiber in iPSCs lead to changes in colony morphology and subsequent differentiation of those cells, suggesting that changing the morphology of cells can change their fate. I want to see if I can use the 2E01 fiber as a tool to accelerate differentiation from IPSCs to neuronal cells and cardiomyocytes. In addition, we expressed 2E01 in mesenchymal stem cells, a cell type currently used in lab, and observed the activity of YAP and TAZ as an indicator of differentiation. Utilization of the 2E01 fiber could be benefical to the field of regenerative medicine as a directed agent of physical manipulation towards desired stem cell fate.

The South Fork Tolt River is regulated by a dam that provides an essential source of drinking water and hydroelectric power for the City of Seattle. While hydroelectricity is a greener energy alternative, there are still environmental considerations of the influence of dam operations on rivers. Seattle City Light (SCL) has an active program to monitor and mitigate the effects of dam operations on the ecology of streams and rivers within their management domain with a focus on stream flow. In 2003, in response to the new Washington Department of Ecology (WA DOE) water quality standards, SCL developed an improved management plan to emulate natural water conditions on the South Fork Tolt utilizing variable water release heights to meet the new temperature and flow requirements. Initially, temperature data from United States Geological Survey (USGS) river gages were used to monitor how the water releases influenced temperature. In 2015, following an unprecedented dry and hot spring and early summer after a low snowpack winter, SCL installed their own network of temperature loggers in the Tolt Watershed to better understand how operations on the South Fork Tolt translate further downstream and to improve the overall spatial resolution of the data. Sensor data obtained from SCL, along with temperature data from USGS Stream Gages will be analyzed to determine the zone of influence resulting from varying water release heights on the South Fork Tolt. Findings from this analysis will assist SCL in ensuring that the utility is minimizing adverse impacts of hydroelectric operations on stream temperature and will assist in understanding how dams may be used to offset increasingly warmer trends and decreasing snowpack in the future.

Lakes cover a greater fraction of boreal and arctic landscapes than anywhere else on the planet. Collectively, northern lakes re-mineralize massive quantities of organic material into the greenhouse gases (GHGs) carbon dioxide and methane, forming an important link between the biosphere and the atmosphere. Rapid climatic changes in northern circumpolar environments are changing the physical structure of many boreal and subarctic lake ecosystems, and in many cases are substantially shortening the duration of ice cover. A clear understanding of contemporary, under-ice GHG production is needed to fully appreciate future trajectories of change in northern lake carbon cycling. Yet the field, in general, is missing direct, ecosystem-scale estimates of greenhouse gas production, especially during frigid and dark periods of ice-cover when field sampling is particularly challenging. Here, to provide a better understanding of greenhouse gas cycling in northern circumpolar lakes, we conducted a cross-lake survey of under-ice methane and carbon dioxide production in twelve lakes of the Alaskan portion of the remote Yukon River basin. We use this survey to first quantify rates of GHG buildup from fall to late winter. Second, we identify the physical and chemical lake features that best explain the cross-lake differences in rates of gas accumulation. Ultimately, these findings will help to improve our understanding of carbon cycling in remote and understudied northern aquatic ecosystems and will help to constrain northern carbon biogeochemical budgets.

Synthetic nucleocapsids have the potential to be a novel class of drug delivery vehicle that represent a happy medium between viral and polymeric delivery systems. They were recently engineered by the Baker lab to encapsulate their own RNA. RNA encapsulation provided the genotype-phenotype linkage required for evolution. Nucleocapsids were then evolved to have relatively long circulation times (4.5 hours), which gives them the potential to deliver nucleic acids to many cell types in vivo. My project focuses on attaching pH-responsive proteins to the surface of nuclecapsids to mediate RNA delivery. Since the endosome is typically the first compartment the nucleocapsids enter, it is vital that the nucleocapsids escape the endosome before being trafficked to the lysosome and degraded. The pH-responsive proteins are proven to rupture membranes upon pH changes similar to those found in the transition from endosome to lysosome. This would allow the cages to break out of the endosomal pathway and deposit their RNA cargo into the cell cytoplasm. Once the RNA is deposited, native cellular machinery can transcribe the desired proteins. We aim to program the packaged RNA to either induce apoptosis or slow cell growth in tumor-related cells. This revolutionary delivery vehicle could be utilized for more precise and effective biologics delivery. 

Autoimmune diseases are characterized by one’s own immune system attacking healthy cells in the body. Current treatments for autoimmune diseases require regular intravenous injections. The objective of this project is to develop a new generation of oral protein therapeutics. As a proof of concept, we computationally designed inhibitors against the inflammatory cytokine IL-17 in order to inhibit its activity in autoimmune conditions. IL-17 elicits its effect by triggering a signal cascade through heterodimerization of its cognate receptors. Our goal is to selectively occlude this dimerization to prevent the progression of disease. We have designed our inhibitors to bind in the same location as the native receptor, preventing downstream signaling that leads to autoimmune diseases. Historically, binders have been created by using existing protein interfaces grafted onto native protein shapes. However, we succeeded in designing IL-17 binders without using any prior protein interface information through de novo protein scaffolds. This project could revolutionize the way protein therapeutics are developed. Our goal is to analyze the biophysical characterization of our binders. In order to create a new standard in protein design our binders should have accurate size and folding in relation to the designed model which we are analyzing through mass spectrometry and circular dichroism spectroscopy. In order to become an effective drug candidate the binders must have successful binding to the IL-17 target which we are analyzing using octet binding analysis. In the end we hope to test our successful IL-17 binders in mouse models of multiple sclerosis, eventually transitioning to human clinical trials.

The goal of our project is to create an electronic device capable of early detection of pancreatic cancer (PC) with high selectivity and sensitivity. PC projects a very low survival rate often due to late-stage cancer diagnosis. Recent research has established that there are PC biomarkers prevalent throughout the body for several years before symptoms emerge. The consequent wider time window presents an opportunity for these biomarkers to be detected at their initial low concentrations thus allowing for early diagnosis. Our device uses a modular sensing construct consisting of an immobilized probe molecularly bound to the surface of the sensor device. Detection occurs when a target biomarker specifically binds to the probe and changes the electrical properties of the sensing surface that is measured quantitatively. Validating the functionality of the sensing construct and its properties is accomplished through a variety of molecular adsorption and binding techniques that assess each step; from probe immobilization to target detection. Using this modular design, research is underway to develop an array of sensors, thus potentially revolutionizing rapid medical diagnostics to provide long-term health monitoring of PC and other cancers. 

In scientific research labs, in general, experiments are generally treated as a black box: a prepared sample goes in, something happens, and one gets results that are then obtained via elaborate characterization steps. Several important dependent or correlated parameters are either discarded or ignored because of a lack of coherent dependency analyses that require critical thinking, linking, and pattern recognition. In this research we are working to stop treating experiments and computational simulations as black boxes, and create a cohesive platform where materials used, processes and parameters utilized and results achieved can be brought together as separate but related sets of databases. In the next step, the relationships between all the different parameters can then be connected, analyzed and visualized. Machine learning and AI techniques can then be used to predict results using these databases, thereby reducing experiment time, and taking away the traditional ‘trial and error’ method of experimentation. The research involves creation of a software interface, with numerous image and signal processing tools and applications running on libraries made customizable to research fields, types of experiments, etc. Assorted variety of services such as parallelization, compression, data analysis, and visualization, caching (among others) are also provided. We are improving the accuracy of time series data analysis and using fingerprinting to depict all parameters for improved predictability, flexibility and accuracy. When fully developed, we anticipate that the program will enable experimental and computational researchers to extensively use, customize and apply data analytics, machine learning and AI even in niche research in the hard sciences at the intersection of biology and genetics, materials science (physics, chemistry) and engineering, and computational modeling and informatics, enabling faster and accurate cross disciplinary innovation in technology and medicine. The research is supported by NSF-DMREF (DMR-1629071) program at GEMSEC-MSE, as part of National Materials Genome Initiative.

This project is to structurally verify computationally designed genetic fusions between helical bundle and repeat protein sets. With the use of this computational method, Rosetta, combining two discrete numbers of proteins can generate a much larger library of protein scaffolds. By biochemically characterizing and solving X-ray crystal structures of the designs, my work aims to experimentally validate this new computational protocol so that the designed proteins can be used with confidence for downstream applications. The wet lab protocol I will be performing follows common standard protein purification procedure. First, I will transform plasmid of genes containing the designed fusion proteins into an Escherichia coli strain, which is capable of over-expressing proteins of interest. After growing large cultures of these bacteria, the cell will be harvested and lysed. Following with the technique of immobilized metal affinity chromatography to purify the hexahistidine- tagged proteins- that binds to the nickel- charged resin—out of the soluble fraction of the cell lysate. The method of size exclusion chromatography (SEC) will be performed after purification takes place. This is going to further purify as well as giving information of the protein designs. I will perform this protocol on close to one hundred designs to calculate a “success rate” for the computational protocol. In greater picture, the overall goal of this project will be researching self- assembled protein design for crystallization from the computational design. Aiming for the result of producing various proteins have the ability of forming crystal in various solution conditions that confirm the structural characterization of designed protein and also validate both experimental and computational protocols. This research provides an avenue for greatly expanding the database of proteins can be utilized in fields such as materials engineering and creating binders of chemical molecules.

Current diagnostic techniques for bacterial infections are time-consuming, and lead to over prescription of wide spectrum antibiotics. Surface plasmon resonance (SPR)-based biosensors can be used to reduce these diagnostic times, but often suffer from diffusion-limited mass transport. Dielectrophoresis (DEP), the movement of dielectrically polarized particles due to application of electrical inhomogeneous fields, can be used to overcome these mass transfer limitations in SPR devices. Current DEP-enhanced SPR devices separate particles with different dielectric properties by generating an electric field gradient and inducing positive DEP (p-DEP) force and negative DEP (n-DEP) force simultaneously. Depending on the dielectric properties of the particles, the particles are collected either in negative DEP at the center of electrodes or in the positive DEP at the edges. My research focuses on fabricating DEP-enhanced SPR biosensors for rapid detection and separation of pathogenic bacteria. Interdigitated electrodes are chosen to reduce detection limits and increase sensitivity. The structures of electrodes are fabricated by soft lithography techniques. To optimize the performance of DEP, electrode patterns with various gap widths are tested. Ultimately, the DEP-enhanced SPR sensors developed in my research could serve as a powerful diagnostic platform for rapid and sensitive detection of pathogenic bacteria by reducing the time of diagnosis and minimizing morbidity and mortality from infectious diseases.