Humans are incapable of regenerating a majority of their major organs and tissues following traumatic injury, often resulting in an irreversible loss of function. Tadpoles of the frog genus Xenopus can regenerate multiple tissue types in response to injury, however this capability is lost after metamorphosis. This stage-specific regenerative capacity makes Xenopus a uniquely powerful model for studying factors that promote regeneration. Tadpoles develop ex-utero and do not develop mouths until days after fertilization. Before tadpoles are able to ingest exogenous food, they rely instead on maternal yolk stores for sustenance. A regenerative refractory period has been described in tadpoles of Xenopus laevis, in which regenerative capacity is transiently lost. In this study we describe a similar refractory period in the closely related Xenopus tropicalis, and observe that the onset of the refractory period aligns with the transition independent feeding. Based on this observation, we hypothesized that the lapse in regenerative capacity could be due to a lack of metabolic fuel. We used immunohistochemistry (IHC) against the yolk protein vitellogenin (vit) to study the utilization of maternal yolk stores during tadpole development. We find that yolk localization is dynamic over the course of development, and that it is ultimately is depleted by the onset of the refractory period. We additionally used IHC against phospho-Histone 3 (pH3), a marker of mitosis, to study proliferation during development and regeneration. We found that proliferation declines across development heading into the refractory period, in both uninjured and amputated contexts. Lastly, we successfully rescued both regeneration and proliferative rates by feeding tadpoles after they develop the ability to eat. As a whole, this work articulates that nutritive stress may contribute to the loss of regenerative capability in the refractory period, and that alleviation of this stress promotes regenerative ability in this context.

Pain and unpleasant stimuli carry a negative hedonic valence, indicating an intrinsic aversiveness useful for avoiding harm. There are instances, however, of unpleasant stimuli carrying positive valence – such as the pleasure from spicy food, suggesting that pain and aversion can be decoupled. The Dhaka lab has discovered a small molecule Analgesic Screen 1 (AS1) which reverses the valence of a number of nociceptive and other aversive stimuli, whereby animals prefer normally aversive stimuli. Behavioral studies with zebrafish indicate that AS1 induces preference for noxious heat, painful chemical (AITC) and normally aversive dark environments. As positive valence or reward is often mediated by the neurotransmitter dopamine, we tested for the affects of dopamine antagonism on AS1-evoked behavior and found that the effects of AS1 are reversed by a D1 dopamine receptor antagonist. We currently propose that AS1 potentiates activity in the dopamine reward system in the presence of nociceptive and other aversive stimuli via D1R activation, thereby creating “pleasure from pain.” Understanding these pathways and the mechanisms underlying AS1 action, could provide a path forward for the development of novel therapeutics to treat debilitating pain disorders.

The direction that plants grow in is dictated by the directions of gravity and light. A mutation in the LAZY-2 (LZ-2) gene in tomato (Solanum lycoperiscum) causes the plant to actively grow downwards, in the direction of gravity. It has been shown that the lz-2 phenotype is dependent on the phytochrome (Phy) protein family; a group of plant proteins that is responsive to red light. In a plant with no functional phytochromes, the lz-2 mutation is restored to wild-type, and the plant will grow upwards as normal. In this project, we discern the roles of three of the five tomato phytochromes, A, B1, and B2, to see if they work together or alone to provide the light cue that initiates the mutant function of lz-2. By gravistimulating combinations of lz-2 and Phy tomato seedlings under red light, we have detetermined that PhyA delays the lz-2 response, while PhyB2 exhibits an additive effect with PhyA and PhyB1 to effectively reverse the lz-2 phenotype. These data expand on previous work to further our knowledge on the relationship between light and gravity sensing in higher plants. 

Humans are incapable of regenerating a majority of their major tissues following traumatic injury. Tadpoles from the frog species Xenopus tropicalis have the ability to regenerate lost spinal cord, vasculature, muscle, and cartilage within a few days following injury. The regulatory mechanisms of gene expression necessary for regeneration have not yet been well defined. My primary interest is in understanding the relationship between stress signaling and gene expression during regeneration. The lab has shown that the stress responsive transcription factor Hypoxia Inducible Factor 1α (Hif1α) is necessary for the expression of Wnt target genes, one of the primary signaling processes necessary for regeneration. While we have found that Hif1α is necessary for Wnt target gene expression, we do not know the epistatic relationship between Hif1α and Wnt. In order to test this relationship, I utilized the drug IWR to antagonize Wnt and found that tadpoles treated with IWR have reduced tail regeneration 72 hours post amputation (hpa). I then supplemented these tadpoles with DMOG to stabilize Hif1α and found that DMOG is sufficient to rescue tail regeneration, suggesting that Hif1α is downstream of Wnt. In order to determine if Hif1α is sufficient for Wnt target gene expression, I extracted RNA from regenerating tails 24 hPa and used quantitative PCR (qPCR) to determine relative gene expression. I also utilized in situ hybridization to see if expression of these genes is restricted to regenerating tissues. As Wnt is a known regulator of neural and muscle development, I investigated how inhibiting Hif1α would impact complex tissue regeneration and found that Hif1α is necessary for regeneration of axons and muscle specifically. By determining the epistatic relationship between Hif1α and Wnt through the analysis of specific gene expression, we continue to improve our understanding of how regenerative organisms convert stress signals to cell fate signals.

Wildfires are known for their destructive capacity towards ecosystems and devastating impacts to human life and property. Regions in the western United States are particularly prone to such events, including large crown fires. However, there is limited research on the potential for smoke from these wildfires to carry and redistribute nutrients in the form of aerosols. Here I show that higher levels of airborne nutrients, specifically iron, phosphorus, and potassium, can be associated both with the timing of active wildfires and a known smoke tracer, elemental carbon. Data from the Interagency Monitoring of Protected Visual Environments (IMPROVE) show a strong correlation with fire presence and local peaks in levels of potassium, with less strong associations with phosphorus and iron. Across a multi-year period, there is also a correlation between the number of acres burned in a particular year and the average concentration of iron and potassium in that region. Using data from the NASA DC-8 airborne laboratory corroborates this information, with calculated potassium concentrations matching those on the ground. These findings indicate the wildfire plumes have a potential to be significant sources of nutrients in the short term. This is especially relevant for areas impacted by wildfires, as these nutrients are key for plant growth and development. These elements may also be carried into the ocean and affect the aquatic biosphere. All of the information gathered will help improve our understanding of the complex networks that make up Earth’s biogeochemical cycles.

Hemoglobinopathies, a hereditary condition involving abnormalities in the structure of hemoglobin, currently require expensive and highly sophisticated medical facilities to treat using gene therapy. The purpose of this study is to provide a highly portable and scalable approach using in vivo hematopoietic stem cell (HSC) gene therapy to potentially overcome these limitations. The main idea of our in vivo HSC gene therapy approach is to mobilize HSCs from the bone marrow, and while they circulate at high numbers in the periphery, transduce them with an intravenously injected HSC-tropic, helper-dependent adenovirus HDad5/35++ gene transfer vector system. The transduced cells return to the bone marrow where they remain long-term. This study followed one animal for 22 weeks after in vivo HSC transduction with a human-γ-globin expressing HDAd5/35++ vector using Sleeping Beauty transposase 100X for integration. Treatment with G-CSF/AMD3100 (a bone marrow stimulant) resulted in efficient HSC mobilization into the periphery blood circulation. The treatment was well tolerated and after in vivo selection, gamma-globin marking in peripheral red blood cells rose to ~90% and was stable during the duration of the study. Enrichment of gene-modified cells by in vivo selection was also reflected by an increase in mgtm and gamma-globin mRNA levels. Our data suggest that in vivo gene therapy with HDAd5/35++ is feasible and side effects can be minimized or prevented with appropriate pretreatment. This is the first proof-of-concept study that in vivo HSC gene therapy could be feasible in humans and provide the necessary portability and accessibility to reach patients in places with limited medical resources. Future studies will involve the optimization of HSC mobilization, gene transfer vectors and in vivo selection.

The Ayeyarwady River Delta, Myanmar is the third largest fluvial source of sediment to the global ocean. This river is an ideal natural laboratory in comparison to other nearby Southeast Asian rivers. This is due to the lack of construction of dams or other alterations to its flow. The UW Sediment Dynamics Group is investigating three distributaries of the Ayeyarwady: the Pathein, the Bogale, and the Yangon Rivers in the west, central, and eastern regions of the delta respectively. These rivers experience differences in discharge, tides, and waves, resulting in different morphologies. The river experiences high seasonal flow during the summer monsoon and low flow during the winter. During the high flow season, the interface between freshwater tidal river and salty estuary is relatively far downstream, and the deposited bed sediment is sourced from the river. During low flow however, the estuary interface migrates upstream and the tides have a stronger influence on the flow, with bed sediment sourced from the continental shelf. In both seasons, bed sediment was collected along the lengths of each distributary in order to understand the patterns of mud and sand deposition in the delta. Disaggregated samples were analyzed for grain size using a LS13-320 Laser Coulter Counter. The percent mud and median grain size was used to determine where mud is being deposited and what causes it to be deposited there. It is expected that during low flow, sediment gets more muddy towards the mouth of the river, and during high flow the bed sediment will be more sandy. Initial findings show that in the Pathein River, sediment indeed does get muddier with downstream distance, supporting the hypothesis. By examining the spatial patterns, our research group will be able to better understand where and when sediment is retained in this relatively natural deltaic environment.

 The Svoboda Diaries Project (SDP) works with personal diaries written at the turn of the 19th century, capturing over 40 years of the life, politics, and landscape of Iraq through the unique lens of a British steamship employee, on which there exists minimal literature. Undergraduate interns transcribe these diaries and develop open-source tools to make the texts available in a variety of formats and for a variety of audiences, from researchers to the general public. This project builds on fifteen years of work through the University of Washington. This research, in particular, is part of an iterative design process originating in 2019 with the launch of the project’s current website. In order to design and create a more accessible and useful website, the purpose of this user study is twofold: (1) to identify user groups and possible uses for the SDP’s online resources; (2) to test usability on SDP website features for better user experience. Student researchers employ two tactics, user interview and usability testing. We first interview academic professionals to identify their research and pedagogical needs from digital humanities projects such as the SDP, and then record their experience navigating the SDP website through a set of tasks intended to facilitate usability assessment. These research methods act as a critical process and device that can provide detailed user feedback to the team for further development of the website. With this user study, the SDP team aims to better promote the usage of primary source historical documents for a global audience.

Excessive reactive oxygen species (ROS) production in cells induces oxidative stress causing a variety of cell damage that relates to the pathophysiology of more than 200 types of diseases, including Alzheimer's disease and cardiovascular lesion. Many molecules in the ROS family also act as secondary messengers in a series of intracellular signaling mechanisms, such as the neural regulation of opioid addiction. Time-resolved measurements of ROS dynamics is critical to the development of therapeutics for related diseases. The genetically encoded fluorescence indicator (GEFI) can be used as an efficient tool for real-time ROS detection. However, the current ROS fluorescent probes have many downsides hindering their performance, such as the low signal-to-noise ratio, slow responding kinetics, low sensitivity, in vivo incompatibility, and limited potential to target subcellular structures. Thus, we engineer a novel fluorescent protein probe for ROS detection based on the structure-guided protein designing principles and high-throughput variant library screening technique. We first used protein structures to guide mutations for improved allosteric coupling between the ROS binding domain and the fluorescent reporter protein, as well as for strengthening the network of hydrogen bonds surrounding the ROS-binding residues. We also implement a novel engineering platform to optimize the efficiency of screening a large number of mutated variants. Thus far, we have generated multiple sensor variants that demonstrate better fluorescent performance and faster response times to direct ROS stimulation compared to the existing ROS protein probes. Our aim is to monitor the real-time ROS production in the signaling mechanism of behaving mice and the ROS-induced oxidative stress in the pathological neuron and cardiomyocyte cell lines to validate the in vivo and in vitro performance of our sensor.

Treatment of neurological disease has made little progress due to the inability of many therapeutics to access the brain environment. However, delivery vehicles like nanoparticles can allow therapeutics to overcome brain-specific biological barriers including the blood-brain barrier (BBB), the dense extracellular space (ECS), and cellular targeting. The ability of nanoparticles to overcome these barriers is influenced by surface properties which can be modified through the formulation process. One understudied parameter is the choice of surfactant, molecules which stabilize nanoparticle formation and likely form an interface between the nanoparticle and brain environment. First, we investigated the potential toxicity of several commonly used surfactants on brain cells and slices. We added surfactant solutions to mouse microglial cells (BV2) or cultured brain slices and assessed cell viability two days later with colorimetric assays. Our results showed that while surfactants cholic acid (CHA) and polysorbate 80 (P80) caused toxicity at high doses, they were nontoxic at the low doses involved with nanoparticle formulation. Other surfactants, including Pluronic® F127 (F127) and poly(vinyl alcohol) (PVA), were nontoxic throughout the tested dose range. Interestingly, although the F127 compound is nontoxic on its own, nanoparticles formulated with F127 reduced cell viability. This result was not observed with any other nanoparticle-surfactant combination. Confocal microscopy indicated higher intracellular accumulation of the nanoparticles formulated with F127 compared to all other formulations, suggesting that toxicity is mediated by nanoparticle internalization and surfactant choice. Finally, we used a live cell imaging technique to capture videos of the nanoparticle internalization process. Building off these results, ongoing experiments will evaluate several nanoparticle-surfactant formulations on their ability to accumulate within brain tissue after in vivo administration. Findings from this work will guide nanoparticle design for future clinical translation.

In 2016, Captain America brought comic books to the forefront of national discussion with a single phrase: “Hail Hydra.” These two words proclaimed Captain America’s allegiance to Hydra, one of Marvel Comics' most recognizable villains which has historically been used as an allegory for the Nazi Party. The moment incited a riot not only among comic book super fans, but casual onlookers as well. Many claimed that by aligning Captain America with Hydra, author Nick Spencer disregarded the character’s origin as an anti-Nazi propaganda piece and later history as a defender of American values, and gave fuel to the growing Alt-Right movement in the United States. However, this moment was not the first time that Captain America had joined the other side. In 1979, Captain America was briefly brainwashed into joining the National Force, an organization which acted as a clear allegory for the various white nationalist movements gaining power in the United States at the time. While Hydra and the National Force are comparable villains, the lenses through which the writers of both storylines present them reveal how views of white nationalism have changed in the United States. Through a comparative analysis of these two storylines, this paper examines the ways in which the Captain America comic books have reflected the shift in white nationalist movements from a largely condemned movement to a viable political force. This project provides a new lens to examine the history of white nationalism in the United States while building on the current body of scholarship arguing for the importance of comic books as a historical source.

During the 19th Century, the Tigris River in the Ottoman Empire province of Iraq was an essential conduit for trade and travel between the East and the West. European, Ottoman, and Persian steamships plied the river from Baghdad to Basra and back, transporting goods and passengers. At present, there exists no detailed digital historical map of this significant waterway. Our project began with the Joseph Mathia Svoboda diaries. Joseph Svoboda, a European resident of Baghdad, worked as a purser on British Lynch Company steamships running between Baghdad and Basra. For about 50 years, he kept diaries recording his journeys, stopping places, cargos, passengers, weather, and events on the river. Our research project began by creating a schematic map based on Joseph’s accounts listing a number of stops the steamers made going up and downstream. Our next step is to identify the locations of the steamers’ stopping places on the river. We are exploring two options: the first, referencing 18th and 19th century maps of the river found in online map collections such as the David Rumsey Map Collection and the Library of Congress. The second option is using ArcGIS, a geographic information system with an extensive map database, to identify the places Svoboda mentioned. We expect to develop the map, either by manually plugging in the names in an empty, historically accurate terrain map, or by using the historical map database from ArcGIS to set up an interactive map. The finished digitalized map will be the first of its kind. It will help our project’s other research move forward. For example, the developed map will offer a clear visualization of Svoboda’s journey that could help our transcription team as they work with new diaries. It will also build a more comprehensive guide for scholars who study the history, economy, and geography of the Tigris and Ottoman Iraq in the 19th Century.

Altruism encompasses an ethical principle that places significance on promoting the welfare of someone else, even at a cost to one’s self. In classic studies, young children and nonhuman primates have offered objects or moved items to help others. However, it is unclear whether this is evidence of altruism, because there was low self-cost. A stronger test would be to investigate infants’ willingness to give others high-value objects, such as desirable food. In the new research, we examined whether 19-month-old infants help others by transferring fresh fruit to an adult. This work tested whether infants can act altruistically and the generality of this tendency across trials. Infants (N=96) were randomly assigned to a group, either the experimental group (experimenter accidentally dropped and reached for fruit) or the control group (experimenter intentionally discarded and looked at fruit). In both groups, the fruit started in the experimenter’s hand and landed out-of-reach for the experimenter. Infants’ helpfulness was shown by whether they gave fruit to the experimenter (i.e., banana, grape, blueberry, strawberry). We hypothesized infants would be more likely to help in the experimental than the control group given that past work has shown infants can perceive the goals of others (e.g., reaching for fruit). We analyzed how often infants’ transfer high-value fruit as predicted by group, type of fruit, and test trial. We found that more infants helped in the experimental than the control group; we found that infants helped on the first trial, showing that they readily recognized the experimenter’s need. Infants’ willingness to hand over high-value food suggested that their helping behavior is an early form of altruism. Future research of infant helping behavior could examine the effects of low- versus high-value items on patterns of giving.

Prostate cancer (PCa) is the most commonly diagnosed and second most deadly cancer in men. Almost all of these deaths are the result of a very progressed form called metastatic, castration-resistant prostate cancer (mCRPC), which currently has no cure and is incompletely understood. Cancer-related mutations in the untranslated regions (UTRs) of mRNA transcripts have been found to contain various sequence or structural motifs that contribute to the regulation of these cancer-causing genes. These regions are extremely dynamic in their control over gene expression affecting mRNA stability and translation efficiency which have both been previously implicated in prostate cancer. However, the degree to which these mutations in the UTRs functionally contribute to prostate cancer remains poorly understood – especially in the 3’ untranslated region (3’UTR). A candidate gene list to investigate was constructed from an analysis of patient tumor sequencing data from a broad cohort of 230 localized and metastatic prostate cancer patients. I Gibson cloned wild type (WT) and mutant 3’UTRs from the candidate genes into luciferase plasmid constructs. Subsequent dual luciferase assay data revealed significant changes in protein expression between WT and mutant constructs most notably in the genes NCL and CLEC18B. Nucleolin (NCL) is a protein involved in the synthesis and maturation of ribosomes and is oncogenic in many cancers when overexpressed, while CLEC18B is largely unstudied. Given this existing functional evidence and my preliminary data, further investigation into the differential expression of NCL and the cellular mechanism through which it is achieved is warranted. My project focuses on elucidating the effects of 3’UTR somatic mutations on translational regulatory regions of the human genome, so that we may uncover new patterns in the progression of prostate cancer and subsequently elicit possible novel therapeutic targets with which to better treat these patients.

Secondary scholarship on life in Iraq during the period of direct rule by the Ottoman Empire from the mid-19th century to World War I is minimal. A few primary historical texts have survived - these “forgotten texts” are largely individual accounts of daily life and business, which illuminate the events of a period of which little has been written. A study of such texts can prove valuable, allowing us to get to know individuals dwelling in Iraq and their lives. In this project, I explore the social networks of Joseph Mathia Svoboda, a British steamship purser living in Baghdad, through a collection of his diaries written between 1865-1908. Due to his family ties, profession, and vibrant social life, Joseph interacts with a wide variety of groups, from family, friends, religious and political leaders, to individuals of diverse backgrounds who he encounters throughout his travels; thus, his writings provide a fascinating viewpoint from which to study the Ottoman Empire. I conduct text and social network analyses of Joseph’s diaries, which involve visually mapping ties between people and analyzing the dynamics of the resulting structures. In my presentation, I will review the use of network analysis and entity detection methods in various contexts, such as literature, history, and the social sciences, and explore how these techniques can be applied to automate the extraction of persons mentioned from the diaries, and then subsequently visualize this information. In particular, I focus on Diary 47 of Joseph Svoboda’s diaries as a case study. In the future, the insights gained from this could be applied to the rest of the collection. As the diaries were written from Joseph’s young adulthood to old age, his narratives provide a unique opportunity to study societal relations in Ottoman Iraq.

Hidden bias, also known as implicit or unconscious bias, affects attitudes, thinking, and behaviors in everyday interactions. It contributes to poor continuity and quality of care, and mistrusting relationships between health care providers and patients. Patients may not be treated equitably due to different identities (race, ethnicity, gender, etc) or different diseases (obesity, diabetes, hypertension, etc). These negative outcomes lead to health disparities and inequities. Despite this evidence, training strategies to detect and address hidden bias in patient-provider interactions are not well characterized and do not fully utilize innovative informatics and technology approaches. Can we leverage innovative technology to identify implicit bias from nonverbal cues in interpersonal interactions? Can we then provide feedback that raises awareness of those biases? The UnBIASED project will develop computational sensing tools to assess nonverbal communication signals associated with implicit bias and provide feedback to patients and providers. This approach could shape the next generation of training strategies for hidden healthcare bias. Documenting the range and utility of strategies in prior work upon which this innovative approach expands is important. To characterize existing training strategies for hidden bias and ways that technology can help, I report on a literature review of existing interventions and recommendations to combat implicit bias in clinical settings. Using dimensions, such as format of intervention- paper, technology, interactional (e.g., standardized patients), I characterize training strategies and their utility from prior work. Through this literature review, I aim to identify the gaps in existing work that illustrate opportunities for informatics and technology innovations for addressing implicit bias in healthcare. This review will provide practical insights for academic medical systems and programs on ways that technology can extend medical education curriculum to address implicit healthcare bias.

Graphical dashboards have become a common way for patients to manage their quality of life following cancer treatment. Line charts have proven to help patients track trends in the severity of symptoms following cancer treatment. However, little is known about how to design such resources for people who have limited experience with traditional graphics (i.e., limited numeracy and graph literacy). The purpose of this project is to design and develop a web prototype that communicates prostate cancer quality of life over time for patients with limited numeracy and graph literacy. We define “quality of life” as a self-reported function after prostate cancer treatment. The quality of life data conveyed in prototypes are patient-reported function scores from the Expanded Prostate Cancer Index Composite (EPIC) survey. We are designing prototypes that do not require a high numeracy or graph literacy skills for comprehension through the use of audio, animation, pictographs, isotypes, and other formats. Our ultimate goal is to inform the design of innovative tools that accurately convey EPIC scores over time in ways that facilitate understanding and healthcare engagement among patients with limited numeracy and graph literacy. In this project, we focus specifically on combining (1) design activities and (2) web prototyping activities to create a set of functional prototypes for usability testing and feedback from underserved prostate cancer patients. We will use findings to enhance the design of a revised set of prototypes that better meet the needs of this important but often overlooked group.