Anatolia, in modern Turkey, is a complex assemblage of micro-continents that collided during the Late Cretaceous and the Paleogene, 80 to 25 million years ago. Despite the large volume of work on the numerous Anatolian terranes and collisions, basic questions regarding the timing of collision, style of post-collisional deformation and development of topography remain enigmatic. In western Anatolia, the timing and mechanisms of these successive collisions are poorly understood and do not conform with current continent-continent collision models. This project reconstructs the evolution of the collision zone in order to reconstruct the tectonic evolution of western Anatolia and refine models of collisional tectonics. Here, we present new data from the 160-40 million year old sedimentary archives preserved in the Central Sakarya Basin, a sedimentary basin that formed adjacent to the collision zone. Two methods for sedimentary analysis are employed in this research: detrital zircon dating and sandstone petrography. Detrital zircon ages attained through Uranium-Lead dating techniques are compared to known ages from surrounding mountain ranges to determine the source of sediment through time and apply age constraints to stratigraphic layers. Sandstone petrographic analysis examines the composition of samples to determine sedimentary provenance. The evolution of sediment sources through time provides a robust timeline of collision, post-collisional deformation and topographic development. The results from zircon dating and sandstone petrography show an evolution of sediment provenance where the oldest, pre-collisional sediments are derived from an adjacent volcanic chain. The onset of collision, around 60 million years ago, is marked by a change in sediment composition as collision creates topography and fault systems exhume older, buried rock. In constructing a progression of sediment source, this research determines a precise chronology for the collision and post-collisional evolution of western Anatolia and contributes to modifying current models on collisional margins.

 Many veterans live in rural areas with limited access to traditional face-to-face (FTF) dermatological services. This barrier to care can result in worse health outcomes. Store-and-Forward Teledermatology (SFT) is a program that aims to address this disparity by providing veterans with increased access to dermatological care. Instead of seeing a dermatologist in person, veterans with suspicious lesions first see a primary care physician (PCP) who then arranges for pictures of the lesions to be taken. These pictures are electronically sent to a dermatologist who reviews them remotely and then suggests a plan of care for the patient. SFT allows veterans to both avoid potentially long wait times at in-person dermatology offices and address lesions that may have gone untreated. This study focused on the timeline of care for the treatment of melanoma. Because of its lethality, it is important to diagnose and treat melanoma as quickly as possible. In this study we compared the timeline to treatment – from when the lesion was first discovered to the date of its surgical excision – in groups receiving standard FTF dermatological care and SFT care. Using chart data from patients within the VISN 20 network, we retrospectively gathered the dates of discovery, biopsy, and excision in patients. From there, we calculated the mean days from discovery to biopsy and biopsy to excision in both groups. Upon comparing these timelines to each other we found that the overall timeline for SFT was approximately 12 days longer than that for FTF. We identified sections of the SFT process that may be responsible for the delay as potential quality improvement points in the future.

During the last ice age outburst floods from glacially-dammed lakes incised canyons across eastern Washington, transporting large amounts of sediment ranging in grainsize from silt to boulders. Around Ephrata, floodwater channeled through Grand Coulee escaped the confinement of the canyon and deposited much of this sediment in the Ephrata Fan. Deposited at the mouth of Grand Coulee extending 45 kilometers south across Quincy Basin to the Frenchman Hills, this deposit is up to 90 meters thick. Older, high-standing deposits within the fan are cut across by successively younger scarps and channels to produce a stepped landform that records many episodes of flooding. The aims of my project are to date the deposits forming the oldest surfaces, and to determine the source of the granite boulders contained within these steps.
I made elevation, slope and aspect maps of the Ephrata Fan using digital elevation data and ArcInfo Geographical Information System (ArcGIS) software in order to distinguish the relative age of deposits within the fan. I collected samples from granite boulders on surfaces of different ages for exposure dating with cosmic-ray-produced beryllium-10 (Be-10). I am currently separating quartz from these samples. Quartz will be dissolved, and beryllium will be extracted and purified for isotopic analysis, to determine the concentration of cosmic-ray-produced Be-10. The abundance of this isotope measures the exposure time of the samples. The range of dates from the oldest to youngest surfaces in the fan will constrain the age and duration of the floods epoch. Furthermore, granite samples from the sequence of deposits will be compared to granites exposed in the floor of upper Grand Coulee. If found, the appearance of this specific rock type in the Ephrata Fan deposits will help determine when floods eroded the canyon to its present depth offering an insight into its development.

The Seattle Fault Zone (SFZ) is a region of complex, east-west striking thrust faults in the Puget Sound area in Washington. Radiocarbon dating of landslides has determined that the SFZ most recently ruptured ~1100 years ago. At this time, non-glacial sedimentary rocks from the Blakeley Formation (26-37 Mya) were uplifted up to 7 meters along the hanging wall of the fault. In this study, we use low temperature (U-Th)/He thermochronology to constrain the timing of slip on the main thrust of the Seattle Fault Zone. The dating technique is used on apatite crystals obtained from samples of the Blakeley sandstone to develop a time-temperature cooling history as the rocks were uplifted and subsequently exhumed. The apatite (U-Th)/He thermochronometer records the date that the mineral passed through the approximately 70°C closure temperature. Based on a 25°C/km geothermal gradient, this closure temperature represents the upper 2-3 km of the crust. The samples were collected from a transect along the hanging wall of the fault, from Alki Point, Seattle in the west to East Lake Sammamish, Issaquah in the east. All samples were collected between 0.5 and 1 m from the surface, and at similar elevations in order to account for different exhumation rates. The rate of exhumation along the fault will be determined from plots of the apatite time-temperature cooling history, where younger dates indicate more rapid exhumation rates. From this data, we will back out erosion rates in order to constrain the total fault uplift.

The objective of this study is to evaluate vaping products that contain vitaminB12 (cyanocobalamin). Breathable vitamin supplements claim to be moreeffective than oral and injectable methods. Vitamin B12 is known to bechemically unstable when exposed to certain variables such as heat, light,oxygen, etc. in biochemistry related studies. The recent popularity of usingvaping devices as delivery methods for flavorings and other substances(including vitamins) prompts the need to study the chemical composition ofe-juices after vaping conditions to evaluate their safety.

Dysregulation of the dopamine system is a central mechanism driving substance use disorders. Our laboratory has shown that chronic cocaine consumption decreases dopamine release in the nucleus accumbens of the rat, which is a brain area that is important in reinforcement learning. This study also found that restoring dopamine transmission through the administration of the dopaminergic drug, L-DOPA, decreased their cocaine consumption. Recently, we have also shown that acute administration of L-DOPA decreases ethanol (EtOH) intake. Thus, the present study sought to examine the effects of chronic L-DOPA on operant responding for EtOH in adult male rats. Rats were presented with a 2-bottle choice between an EtOH (20%) solution or water, daily for 21 days. Next, animals made nose poke responses (FR1) for 0.2 mLs of an EtOH (20%) solution over 1-h daily sessions for 35 days. On Days 26-35, rats consecutively received either vehicle or L-DOPA (30 mg/kg) for 5 days, counterbalanced across days, and L-DOPA decreased operant responding for EtOH compared to VEH. We are presently examining the effects of L-DOPA on dopamine release during operant responding for EtOH. Together, these data may suggest the efficacy of L-DOPA as a treatment for patients with alcoholism.

The level of plastid DNA (ptDNA) declines as plastids develop from colorless proplastids to green chloroplasts. The decline in ptDNA is associated with an increase in DNA damage resulting from oxidative stress and ultraviolet (UV) radiation. 8-oxoguanine (8-oxoG) is a lesion in ptDNA that results from the oxidation of guanine. Our lab previously found a reduced amount of ptDNA in light-grown plants compared to dark-grown plants, likely due to increased oxidative stress that increases ptDNA damage. Here, our objective is to quantify ptDNA damage by assessing 8-oxoG lesions during the greening of maize leaves. We hypothesize that as plastids mature, 8-oxoG lesions increase. Our experimental outline involves the quantification of 8-oxoG by the enzyme-linked immunosorbent assay (ELISA), as well as immunofluorescence microscopy using antibodies that target 8-oxoG. We are examining plastids isolated from light-grown and dark-grown stalk and leaf tissues. As 8-oxoG lesions are one of the markers of oxidative DNA damage, our results will be used to assess DNA damage during development of maize plants. This research will provide a better understanding of role of oxidative stress in plant development

Climate change has increased the prevalence and intensity of wildfire events in the Pacific Northwest. Exposure to wildfire smoke has been linked to several adverse health outcomes, most notably respiratory-related morbidity and mortality. Local public health response to reducing a community’s exposure has primarily focused on communicating risks to the public and provide suggestions to reduce exposure risk. Effectively communicating the health effects of wildfire smoke and the interventions possible to reducing exposure is imperative for reducing adverse health outcomes during smoke events. In order to discern the messages the public received, we conducted a content analysis of wildfire smoke risk information communicated by local and state government organizations and by the mainstream media during the August 2018, statewide wildfire smoke event in Washington state. The Extended Parallel Process efficacy and risk framework was used to assess the presence and message content of wildfire smoke risk and efficacy information. Summary statistics were calculated to identify common messages about efficacy recommendations, vulnerable populations, and trusted sources of public health information. With these results, we hope public health jurisdictions will better understand the extent of their wildfire smoke risk messages and improve their standing as trusted sources of information in the community. Through the use of the extended parallel process framework-- a “recipe” for future wildfire season communication can be created.

Skeletal reduction is a common feature among deep-sea fishes that have diversified from shallow-water relatives, such as snailfishes. These skeletal reductions may be an adaptation to environmental conditions of high pressures, low temperatures, declining luminosity and limited food availability. Snailfishes (family Liparidae) are found across a large bathymetric range (0 – >8,000 m), with intertidal ancestors giving rise to a large clade of deep-sea species. We used microcomputed tomography (micro-CT) to estimate average bone mineral density and examine jaw, pectoral girdle, and neurocranium morphology. Our results suggest at least three mechanisms of skeletal reduction: (1) reduction of bone size, (2) reduction of bone density, and (3) loss of skeletal elements. First, using phylogenetic generalized least squares (PGLS) analysis, we found that the change in cranial dimensions with depth was not uniform. While the size of the maxilla, dentary, and pectoral girdle decreased with greater depth, length of the upper premaxilla and the neurocranium did not vary with collection depth. Second, average density of the lower jaw decreased with increasing depth. Lastly, the ventral suction disc has been lost multiple times within the deep-sea lineage. While all three methods are seen in snailfishes, other groups may use some or all of these mechanisms to different extents. Some mechanisms of skeletal reduction may be more advantageous than others. The extent to which a structure is retained in deep-dwelling fishes may indicate its functional importance. Variable skeletal reduction in the family Liparidae provides insights into the physiological adaptations that allow fishes to survive in deep-water environments. We conclude that some skeletal elements are maintained at the expense of others as fishes balance the functional demands of life in the deep sea.

Establish-Maintain-Restore (EMR) is a professional development training for teachers to strengthen their relationships with their students. Previous studies have shown that the strategies presented in the training have significantly improved academically engaged time and reduced disruptive behavior among elementary and middle school students. The proposed study will examine 9th grade high school student perceptions of the appropriateness and effectiveness of the EMR strategies to improve student-teacher relationships within the school context. Additionally, this study will analyze whether there is a significant difference in these perceptions between the genders of students. It is predicted that male students will tend to perceive the EMR strategies as less effective and appropriate in improving student-teacher relationships compared to their female peers. A focus group was held to present the EMR strategies to 9th grade students at a racially/ethnically diverse high school in the Pacific Northwest. After the strategies were presented, students were asked to provide ratings and comments regarding the appropriateness and effectiveness of each individual strategy. The students were asked about the following items for each of the EMR strategies: appropriateness for school context, appropriateness for both students and teachers, and effectiveness at improving relationships with high school students. Findings from this study will offer insight for improving student-teacher relationships with consideration for the students’ genders. Research has shown that strong student-teacher relationships can serve as a protective factor against high school dropout, and this study may help provide information about culturally responsive strategies to reduce the dropout rates among students of color and male students.

The most recent National Vital Statistics Report reports that approximately 9.85% of babies in the United States are born preterm, with 72% of those born late-preterm (at 34-36 weeks of gestation). Using neonatal ferrets at age 17 days old, the Juul lab in the Division of Neonatology at the University of Washington Medical Center has developed a preliminary model of brain injury to mimic late-preterm neonatal injuries. In this species-specific adaptation of the Vannucci Model, the left carotid artery is permanently ligated, along with a temporary (4h) occlusion of the right carotid artery. Ferrets are then exposed to periods of hypoxia and hyperoxia. By looking at data and outcomes from our surgeries, I aim to examine the effects of certain surgical parameters on ferret mortality. These parameters include: time the animal is exposed to isoflurane, the length of surgery, and the amount of time the animal is given to recover between surgery and hypoxia. Aside from mortality, I will also analyze the effects of these parameters on respiratory rate after surgery as well as gross brain injury and data from behavioral testing in an attempt to discern the level of injury in living animals and the most common predictors of death in those that died prior to their determined endpoint.

Promotores are local trusted community members in Latino/a communities who often provide lay health education. Multiple studies have shown improved health outcomes when promotores are involved in providing education to communities. Occupational health and safety training materials are needed to better support promotores within rural agricultural communities. For this project, results are being compiled from several data sources to create a framework for an occupational safety and health curriculum for promotores in WA state. The data sources are as follows: 1) Needs assessment polls which were set up for attendees to vote on occupational safety topics at three different events in central WA in 2017/2018 (mobile clinic events, safety and health agricultural-focused conferences, and conferences for health professionals and agricultural workers); 2) A survey project funded by the UW Population Health Initiative to identify health disparities of farmworkers in Skagit and Whatcom counties by asking participants about previous training and preferred training topics; 3) A comprehensive report on health risks associated with climate change in Washington state, titled An Unfair Share: Exploring the Disproportionate Risks from Climate Change Facing Washington State Communities. The framework will be presented as well as examples of participatory educational materials that may be included as part of the curriculum.

Women and people of color are underrepresented in classrooms as both instructors and students, as well as in the field of physics. A lack of diversity limits the ideas that evolve and creates disadvantages for systemically nondominant groups. The goal of this research is to understand how we can make students feel more empowered to change the culture in physics. Students in introductory, calculus-based physics classes from both a two-year college and a four-year university participated in a similar equity unit, which focused on increasing awareness of the systemic marginalization of women and people of color in physics. At the end of the unit students brainstormed how to raise awareness of, and then ultimately remove, this inequity. We analyzed and coded students’ responses using key words and phrases coinciding with similar ideas. The themes were tested for reliability by the authors who addressed discrepancies through discussion, after independently categorizing these responses. Students from both populations (two-year and four-year colleges) concluded that learning about their own bias and having intentional conversations about equity issues are both important steps in physics for changing societal structures. One theme unique to the two-year college setting was to develop coping strategies that combat inequities in physics. Future work will involve acquiring more data from different student populations and using that data to better support students in various physics learning contexts. By following students’ suggestions from the equity unit, we can take action to create an inclusive and diverse physics culture.

The impacts of war can include political gains, emotional turmoil of those in a warzone, destruction of land, and loss of money and resources. Belligerent occupation has very similar effects, but can last for a longer duration of time and be life altering for those living in the occupied land. Since 1967 Palestine has been occupied by Israel, during which there has been active conflict, construction of military bases and Israeli settlements, and loss of land and cherished spaces. This thesis focuses on the destruction of Palestinian buildings and cities that has occurred throughout the duration of the occupation. Many of these destroyed spaces remain as ruins in Palestine that have not been reconstructed, removed, or repurposed. This paper will begin by establishing an understanding of the extent, including duration and frequency, to which Palestinians are exposed to wreckage. It will then convey the reasons behind this rubble’s repetitive and prolonged presence in the country, exposing the debilitating permitting process that Palestinians face. Once this context has been established, the results of this rubble will be explored in terms of the health effects of prolonged exposure to rubble, the psychological aspects of losing property, and the impact on communities involved in this devastating destruction. Various villages and cities in the region of West Bank, Palestine will serve as illustrations of these effects as the West Bank has experienced intense and well-documented destruction throughout the occupation. This paper will ultimately develop a unique understanding as to why these ruins must no longer be permitted to remain in Palestine and ultimately propose solutions to removing the rubble and/or lessening its negative effects.

Secondary metabolite chemicals are specialized chemicals produced by plants that serve specific roles in plant survival beyond aiding in growth or development. Sometimes, the presence of these chemicals negatively impacts surrounding species, a phenomenon known as allelopathy; an example of this is the inhibition of germination of neighboring species. One common non-native species that is known to have high concentrations of leaf secondary metabolite chemicals is Plantago lanceolata (ribwort plantain). Focusing specifically on prairies ecosystem implications, this experiment aims to test the allelopathic effects of Plantago leaf secondary chemicals on the germination of native prairie species. The predicted outcome of this experiment was that increased concentrations of Plantago extract would lead to decreases in germination quantity. To accomplish this, numerous extraction concentrations (including a controlled no-extract treatment) of Plantago leaf chemicals was applied to several prairie species. These species were additionally tested in the presence of high concentrations of yarrow and lettuce extracts; yarrow is another species that contains high concentrations of secondary chemicals, while lettuce leaf material lacks substantial secondary metabolites. Prairie seeds germinated in the presence of secondary chemical extracts include yarrow, Oregon sunshine, Roemer's Fescue, Blue wildrye, and Plantago. 1,400 seeds per species were placed in petri dishes and germinated in either spring or summer growth chambers based on each species' germination requirement. Germination data were analyzed to determine the significance of germination inhibition by each leaf extract. Because Plantago is a non-native and potentially invasive species, it is important to understand the potential for native ecosystem disruption. Additionally, since yarrow and Plantago seeds were germinated in the presence of extracts from their own species, we could determine whether extracts have stronger effects on disparate species than on the species that the extract is derived from. 

Morality has significant social importance as it influences the way we interact with others. We know that adults and children (aged 3-11) expect all groups to follow moral norms such as fairness, but only in-group members to follow non-moral norms like certain food preferences (Liberman, 2017). It remains unknown if this applies to infants. Studying infants’ moral sensitivities will shed light on the origins of morality, and it will give us insights on its socialization. We are investigating infants’ expectations about in-group and out-group members performing actions that are consistent/inconsistent with moral norms (i.e., distributing resources fairly/unfairly) and actions that are consistent/inconsistent with non-moral norms (i.e., using an object according to its established function or unconventionally). In Study 1, 24-month olds (N=32, testing ongoing) are first familiarized to a storyteller speaking English (in-group) or Spanish (out-group). Infants are then shown the storyteller doing a fair (equal) or an unfair (unequal) distribution of cookies to two third parties. We are measuring, via infants’ visual attentiveness, whether they expect fair or unfair resource distributions. We predict that infants will show enhanced attentiveness to the unfair event, thereby suggesting what they saw violated their expectations. During piloting, infants in both conditions looked longer at the unfair distribution (English-Unfair: M=32.44 seconds (SE=9.09), Fair: M=28.8 seconds, (SE=15.4), Spanish-Unfair: M=27.8 (SE=15.2), Fair: M=17.3 (SE=5.39), providing preliminary support for our hypothesis. We are also testing how non-moral norms translate across group boundaries. After the same familiarization events as before, the test trial shows an unconventional action (ie. brushing your hair with a fork) pitted against a convention one (ie. eating with a fork). We predict that non-moral norms will be group-specific because they should be seen as culturally dependent and not encompasing. In sum, these findings will provide important new insights into the origins of morality.

In the US more than 100 million people are living with diabetes or pre-diabetes. The economic burden caused by these conditions, including medical costs, is approximately $327 billion annually. Conventionally, transgenic Escherichia coli has been the primary source of commercial insulin production, a process that requires extensive purification to ensure shelf stability and complete removal of contaminants. This study seeks to establish an alternative mode of insulin production using polyethelyne glycol (PEG) and agrobacterium to transform the oyster mushroom, Pleurotus ostreatus, with the human insulin gene. P. ostreatus is a valuable target for genetic transformation due to its lack of endotoxins, rapid growth, and fully sequenced genome. P. ostreatus was transformed using PEG and agrobacterium with a plasmid containing the human insulin gene and a carboxin resistance gene. Transformed cells were selected using carboxin, extracted, and regenerated on plates composed of yeast extract, malt extract, and glucose (YMG). Integration of the human insulin gene in to the mushroom genome was confirmed through PCR analysis of the transformants. Successful transformation of P.ostreatus offers a new avenue for insulin production, potentially diversifying the market and treatment options for diabetics.

Geothermal flux, the amount of heat from the Earth’s interior that reaches the Earth’s surface, is an important boundary value used when modeling ice sheets in Antarctica and estimating future sea level rise. However, geothermal flux is difficult to measure directly. This research project used a numerical ice and heat flow model to estimate the upper bound for geothermal flux under ice domes in Antarctica. We applied this model to ice domes with identifiable Raymond arches, structures in the internal stratigraphy which form only when the ice is frozen to the bed. We estimated the geothermal flux at which an ice dome’s modeled basal temperature reaches the melting point, thus setting an upper bound, using site-specific values for the accumulation rate, surface temperature, and ice thickness. Where measured basal temperatures are known, we made more precise estimates of geothermal flux. Uncertainty values for the modeled flux values were derived by testing the uncertainty of each input value. Model estimates were compared with Martos et al. (2017) and An et al. (2015) geothermal flux estimates derived from remotely sensed data. Comparisons show that in regions such as the Siple Coast, estimates disagree significantly, while they mostly agree in the Antarctic Peninsula. The results of this project set an upper limit on geothermal flux values that can be used to support past and future geothermal flux estimates at these locations.

Understanding prosocial behavior, the concern for the welfare of others, is critical to navigating the social world. Here, we investigated the nature of infants’ understanding of prosociality by asking whether they expect those who are fair (i.e. those who distribute resources equally) to also be trustworthy (i.e. respect someone else’s property). We showed 32 22-month-olds videos of two actors, one who distributes goods fairly (3:3) and another who distributes goods unfairly (5:1). Using eye-tracking, we captured infants’ active and passive expectations about the trustworthiness of these actors when both were warned by a third character, a toy-owner: “Don’t touch my toy”. When she left the room and came back to find the toy missing, she asked “Where is my toy?”. We predicted that more infants would give anticipatory looks towards the unfair actor than towards the fair actor, suggesting that infants expected the unfair actor to have stolen the toy (i.e., active expectations). Next, infants either saw the fair actor steal the toy (n=16) or the unfair actor steal the toy (n=16). Here, we predicted infants would look longer at display when the fair actor stole the toy, a signal that this event violated their expectations (i.e. passive expectations). Additionally, we were interested in how social-environmental factors may influence infants’ expectations. Thus, we also investigated the influence of siblings on infants’ expectations. Findings revealed that infants with siblings looked anticipatorily at the unfair actor while infants without siblings looked anticipatorily at the fair actor. Additionally, infants who saw the unfair actor steal the toy looked longer at the display. This may be explained by infants looking longer at the actor whose behavior they found most interesting. Together, these findings provide insight into infants’ understanding of various sociomoral traits and how this understanding may be influenced by social-environmental factors.

In the last decade, a large amount of studies have been done using virtual environment (VE) because of the increased control over the sensory stimuli used and the detailed observation of the associated behavioral and sometimes neuronal responses. In this study, we placed honeybee in a VE and exposed them to visual stimulus in closed-loop. We showed that honeybees are able to fixate the stimulus regardless of the level of feedback fed to the sensors(e.g., the gain between the animal motion and the stimulus motion on the VE). Our next step is to investigate how different neuromodulators such as the octopamine and dopamine, may be important for fixation and adaptation to the different level of sensor feedback. Octopamine (OA) is key in modulates physiological process in invertebrates including honeybees. Recent studies have identified OA neurons that are critical for visual behaviors and that increase their activity during active behavioral state. To identify the effects on octopamine and dopamine (DA) on honeybee’s ability to fixate, we are injecting bees with OA, DA or their respective antagonists in a visual processing brain area. Potential results of this study will impact the fields of neuroethology, providing insights on the modularity of neural processes and the feedback between sensory and motor pathways.

Electroencephalograms (EEGs) are commonly used for measuring electrical activity in the brain for neuroscience research. In order to better control experimental studies animals can be anesthetized, however there is minimal research done on how the anesthetics may actually change the response the brain has to stimuli. Two commonly used anesthetics are isoflurane and dexmedetomidine. It is currently hypothesized that isoflurane produces a slow wave brain state similar to sleep and dexmedetomidine produces a persistent active brain state similar to an awake animal. This study aims to determine the differences in activation from visual and focused ultrasound stimulation through intra-cranial EEG monitoring in mice. Studies were conducted with a surgery to implant intracranial electrodes in A1, S1, and V1 on both sides of the brain under 3% isoflurane. Isoflurane was then reduced to 1.5% and a recording of the brain was taken for 10 minutes. This was followed by a light stimulus in the right eye with an LED. Focused ultrasound was aimed in V1 left. After the isoflurane trials were completed, the mice were injected with dexmedetomidine and the previously mentioned trials of base line, light, and focused ultrasound were performed again for every animal. Analysis included examining the EEG traces of individual events, averages of 10 events in one animal, and averages of 60 events in an animal. Continuous wave transformation plots were also produced to determine the frequency contribution in the evoked response. Preliminary results show that there is increased activation in V1 left under each anesthesia with some activity appearing in A1 left, however this may be a result of the proximity of the areas. Further research is needed in order to determine the similarities between the brain states and fully awake animals and animals that are in a natural sleep state.

The goal of this project was to determine if mitochondrial biogenesis in zebrafish cone photoreceptors is circadian and/or regulated by light. Photoreceptors use more energy in darkness compared to light, and at night the number of mitochondria in zebrafish cones increases. We hypothesized that mitochondrial biogenesis would correlate with increased energy needs and increased mitochondrial number.  Zebrafish retinas from light/dark and dark-only cohorts were collected over a 24-hour cycle. Retinas were fixed and sectioned at 20 µm for immunohistochemistry. Sections were incubated with primary antibodies against mitochondrial biogenesis genes and cytochrome oxidase and imaged with confocal microscopy. Length measurements were taken from the center of single cone mitochondrial clusters. Retinas were also analyzed by Western blotting to assess cone mitochondrial protein content. 21 genes involved in mitochondrial biogenesis were analyzed via qPCR, in addition to ratios of mitochondrial DNA (mtDNA) to nuclear DNA (nDNA). Experiments were conducted in triplicate with three biological replicates and the ΔΔCt method was used to determine relative expression.  Immunohistochemistry revealed that cone mitochondrial clusters elongate 30% following dark onset. Western blot analysis is ongoing. mRNA transcripts for two genes involved with mitochondrial biogenesis, PolG1 and TFAM, increased roughly 6-fold and 3-fold respectively in the hours leading up to dark onset; transcripts for the mitochondrial fusion factor, Mfn2, increased 3-fold just prior to light onset. Cone mitochondrial clusters enlarge at night, and this is preceded by upregulation of mitochondrial biogenesis genes. Lastly, mitochondrial fusion prior to light onset may be followed by a decrease in mtDNA number. These effects occurred independently of light exposure. Overall, these results highlight a possible mechanism in photoreceptors to increase energy production in the dark while following the circadian clock.

Although Asians and Asian Americans are often classified as belonging in the same social category, these two groups may perceive and think about the world differently. This project examined whether UW students who are Asians and Asian Americans hold different viewpoints regarding social identities and social statuses. Primarily, we examined group differences in Status Legitimizing Belief, Perceived Racial Discrimination, and Racial Identification. Status legitimizing belief is a set of beliefs (measuring protestant work ethic, perceived system permeability, and system legitimacy) asserting that if individuals work hard, are motivated, and are talented, they can improve their social statuses. Perceived racial discrimination measures the extent to which racial minorities believe that they are targets of discriminations. Racial identification measures individuals’ beliefs and perceptions that their racial group matters and is central to how they perceive themselves. Through meta-analyses of self-report surveys across 13 academic quarters, we found significant differences between Asian Americans and Asians across all measured variables. First, we found that Asians have higher status legitimizing belief than Asian Americans. Asians also perceive lower racial discrimination than their Asian American counterparts. And finally, Asians are less likely to identify with their racial in-group than Asian Americans. This research demonstrates that while both groups are often classified or perceived as the same social group, they, in fact, hold different perspectives regarding their identities as well as their statuses. Understanding how these two groups rationalize and perceive legitimacy and discrimination offers insight into intergroup relations.

Fossil Fuels are associated with contemporary energy crises and climate change. The combustion of fossil fuels is leading to increased greenhouse gas emissions, which in turn have increased the overall earth’s temperatures and is predicted to grow at an alarming rate. Fuel cells are alternative, sustainable sources of energy that uses hydrogen (or hydrogen-rich fuel) and oxygen to generate electricity through electrochemical processes. I conducted a survey, focused on Bellevue College’s (BC) Chemistry Department, that indicated broad support for a simple hydrogen proton exchange membrane (PEM) fuel cell lab to be incorporated into the introductory chemistry curriculum. I will design a lab that will spark student interest in sustainability and expose students to real-world electrochemistry applications while addressing electrochemical, thermodynamic, transport phenomena, and clean energy concepts. The educational goals of this lab are to promote a deeper conceptual understanding of electrochemistry, to improve quantitative reasoning, and to improve explanations of observed scientific phenomena. I collaborated with BC’s Chemistry Department to determine learning outcomes and a systematic process to quantifiably assess fuel cell labs from other institutions. This information was used to design an effective lab and lesson plan surrounding fuel cells. Four fuel cell labs were evaluated: (1) A pre-constructed Hydrogen PEM Fuel Cell from Horizon Fuel Cell Technologies (2) A microbial fuel cell, (3) A fuel cell using platinum electrodes that is bathed in an acid solution (4) A fuel cell using graphite electrodes that is immersed in an acid solution. This research produced an economical and introspective laboratory experience that utilized basic laboratory equipment and materials. The results were presented in an engineering framework that details how aspects of the lab promote critical thinking and engagement, addresses learning objectives, and was cost-effective.

Extracorporeal membrane oxygenation (ECMO) is used to maintain adequate blood-gas exchange in patients experiencing cardiac or cardiopulmonary failure. Close therapeutic drug monitoring of anticoagulants is required to prevent thrombosis within the ECMO circuit or in vivo bleeding from mucosal membranes. The goal of this research was to implement a laboratory developed test for bivalirudin quantification based on plasma diluted thrombin time (dTT). The assay was run on the Diagnostica Stago STA compact. Two calibrations were performed each with R2=0.99. The analytical measurement range was 0.0 to 2.9 ug/mL with a limit of detection of 0.1 ug/mL. Clotting times strongly correlated with the current standard of measurement. Although further testing must be performed, using this calibrated plasma diluted thrombin time assay would improve efforts for safe therapeutic drug monitoring of bivalirudin.

Merkel cell carcinoma (MCC) is a rare and aggressive skin cancer with a recurrence rate of ~40%. The Merkel cell polyomavirus (MCPyV) is causally linked to 80% of MCC cases, while the remaining 20% are caused by UV-induced mutations. A blood test has been developed to detect antibodies to the MCPyV oncoprotein, as these antibody levels have been shown to correlate with disease burden. This test is a useful tool for tracking disease recurrence in patients who produce antibodies and is recognized by the 2018 National Comprehensive Cancer Network (NCCN) Guidelines for this purpose. However, as systemic immunotherapies are increasingly integrated into the standard of care for patients who develop metastatic disease, it is critical to understand the impact of immuno-stimulatory drugs on oncoprotein antibody levels. Using a Seattle-based MCC repository of 1,444 patients, I identified 64 patients who produced antibodies to the MCPyV oncoprotein and received immuno-therapeutic treatment. Eighteen of these patients had serial antibody tests during treatment, providing sufficient data for analysis. To establish a comparison for measuring disease status, I identified imaging studies from patient medical charts, such as PET/CT and MRI, or clinical evaluations administered within 45 days of the antibody test. The imaging studies were used as comparison due to their efficacy and reliability in disease detection. Among all 18 patients, those with increasing tumor burden, had increased antibody titers, while those with decreasing tumor burden had falling or low antibody titers. These results suggest that this antibody test is also an effective indicator of recurrence in MCC patients who are receiving immunotherapy.

Zea mays (maize, corn) is an essential crop plant; important to global agriculture and the U.S. economy. However, maize productivity and yield can be drastically affected by abiotic environmental stress. Therefore, a priority for many plant breeding programs is to select for crops displaying phenotypic traits of enhanced tolerance to abiotic stress. A subset of abiotic stresses induce the plant hormone, abscisic acid (ABA). The mediator of paramutation1 (mop1) gene encodes an RNA-dependent RNA polymerase that functions in the RNA-directed DNA methylation (RdDM) pathway. The mop1-1 mutation results in the loss of DNA methylation which in turn causes a variety of genes to be expressed abnormally. We determined how a mutation in a mop1-1 affects RNA expression under abiotic stress by conducting a computational analysis of multiple RNA-seq datasets of stress-treated maize seedlings. We compared RNA-seq data from mop1-1 and WT seedlings treated with exogenous ABA control (no ABA treatment) with a publicly available dataset of WT maize plants treated with heat, cold, drought, salinity, and control (no stress treatment). Genes commonly down-regulated in the four stresses and in MOP1 WT ABA, but up-regulated in mop1-1 ABA represent genes potentially silenced under stress that require MOP1 for gene silencing. The presence of these genes in the given stress treatment allows us to identify the abiotic stress responsive genes that require ABA and MOP1 mediated regulation.

Chronic stress induces the release of neuropeptides including dynorphin, which activates kappa opioid receptors (KOR) to encode the dysphoric components of the stress response. Dynorphin/KOR actions on dopamine neurons have been shown to underlie aversive learning, and it is hypothesized that potentiation of cocaine reward following stress is likely to occur through similar neural mechanisms. In this study, we investigate the neural substrates underlying stress-mediated enhancement of cocaine reward. First, we verified the reliability of a KOR (KT2) antibody. Immunostaining specificity was verified using KOR-Cre mice which express Cre-recombinase in KOR-containing neurons. By combining cell-specific targeting using Cre-dependent viral expression of fluorophores and immunohistochemistry staining, we confirmed the specificity of anti-KT2 to KOR containing neurons. Using this antibody and an anti-tyrosine hydroxylase antibody, we examined the co-localization of KOR and dopamine in the ventral tegmental area (VTA). Immunohistochemical analyses showed that KORs were expressed in a majority of dopamine neurons in the medial and lateral VTA. Furthermore, we investigated dynorphin-KOR circuitry in the mouse brain. Dynorphin-containing neurons projecting from the prefrontal cortex (PFC) and dorsal raphe nucleus (DRN) to the VTA were identified by injection of a retrograde virus (CAV2-DIO-ZsGreen) into the VTA of prodynorphin-Cre mice. In a separate cohort, an excitatory opsin (Channelrhodopsin2) was injected into the DRN of pDyn-Cre mice with an optic fiber implant. The DRN region was then optically stimulated and resulting KOR phosphorylation was measured in the VTA thereby verifying dynorphin-releasing projections from the DRN to the VTA. This projection was further investigated by examining the effect of DRN dynorphin on stress-induced potentiation of cocaine conditioned place preference (CPP). We found that deletion of dynorphin from the DRN, but not PFC, blocked stress induced enhancement of cocaine CPP. In conclusion, this experiment demonstrates a functional dynorphin/KOR circuit from the DRN to the VTA that mediates stress-induced increases in drug reward.

Hawaii is situated at the crossroads of the Pacific, and remains a unique place where people of different cultures and ideas mix. This project focuses on the development and identity of Honolulu in the decade after statehood. On August 21, 1959 Hawaii was officially recognized as the 50th state to enter the Union. By this time, the character of Honolulu's built environment reflected a 'Territorial Style,' which proliferated in the early-twentieth century. In addition, Hawaii's earlier progress towards a 'modern architecture' was interrupted with the abrupt changes caused by the Depression and World War II. In the years following statehood, Honolulu had developed into a hotbed of unchecked economic, social and political wealth. As a result, the character and identity of Honolulu's 1960s built environment was seen as a hodgepodge collection of buildings and projects reflecting various practices and themes in architecture. At the same time, visiting US mainland architects and firms were given opportune chance to participate in the development and growth of Honolulu's future. As the state capital of Hawaii, Honolulu has developed into a city onto itself. Honolulu's rapid post-statehood growth now poses new questions regarding its future, today. This project explores the early phase of statehood in order to understand how Honolulu's new identity as a state capital was established architecturally amidst the growth of commercial development. This project characterizes the ecological, cultural and technical dimensions of Honolulu's built environment in the 1960s, and explores the tensions between Western modernization and the natural and historical contexts of its Pacific Island location. 

Exposure to particulate matter (PM) is associated with adverse health effects including asthma, cardiopulmonary diseases, and lung cancer. These adverse health effects are responsible for the premature death of 7 million people worldwide each year. To reduce the consequences of air pollution, real-time individual exposure data is essential for health risk assessment and tailored intervention strategies. Portability and cost are significant barriers for consistent and personalized tracking. Unfortunately, the only accurate data regarding levels and types of air pollutants come from static monitoring stations that do not allow personalized analysis. Aero-Spec was developed to provide real-time analysis of air quality particles while also delivering a compact and low-cost approach. It is a wearable exposure monitor that combines real-time measurements of PM using an optical particle sizer (OPS). The OPS sensor allows for individual particle sizing and error reduction associated with the particles’ optical properties. Personal PM exposure data is provided to the user through a smartphone application such that intervention actions could be triggered given the detection of poor air quality. For personalized analysis, indoor localization is used over the global positioning system (GPS) for a more accurate and localized diagnosis. Aero-Spec utilizes this network technology to track the wearable sensors and report back localized air particle data. In conclusion, using a portable and low-cost approach to real-time air particle analysis, Aero-Spec delivers an effective and personalized solution for air quality monitoring. Recently, in a movement to monitor their employees’ exposure to particle data in real-time, Boeing has collaborated with the Sensors, Energy, and Automation Laboratory (SEAL) for further research.

Interferon-gamma Enzyme-Linked Immunosorbent Spot Assay (IFNγ ELISpot) is a laboratory technique that quantifies the number of cells producing interferon gamma (IFNγ) by utilizing antibodies that selectively bind to IFNγ molecules, resulting in spot formation corresponding to individual IFNγ-producing cells. Since cytotoxic T cells (CD8 T cells) and their helper Th1 cells (CD4 T cells) produce IFNγ to activate macrophages and inflammatory responses, quantifying IFNγ-producing cells allows for characterization of host immune responses. Our lab utilized a canine IFNγ ELISpot to test for immune responses against novel proteins expressed following gene therapy in dogs. Currently, we used a routinely given vaccine for canine flu, distemper, adenovirus, and parvovirus as a biological positive control. However, we tested our experimental proteins with peptides, making a whole-protein positive control, which required internal processing, flawed. Our goal was to optimize this ELISpot by identifying peptides from the vaccine that stimulates an IFNγ immune response in peripheral blood mononuclear cells (PBMCs) and splenocytes. Utilizing a commercially available canine IFNγ ELISpot, we stimulated PBMCs and splenocytes. These cells included lymphocytes (T cells) and macrophages, which acted as antigen presenting cells. We compared stimulation with the entire vaccine and various vaccine peptides in order to identify peptides that can be used as a biological positive control. These were compared to traditionally used mitogens that indiscriminately activated all lymphocytes. This optimization allows for greater confidence in the results obtained from our canine IFNγ ELISpot. The improved technique serves as a powerful tool to assist in preclinical trials of vaccine production and gene therapy. It is utilized in our lab to test for CD8 T cell-mediated immune responses against novel dystrophins following gene therapy in Duchenne muscular dystrophy dogs.

Wound healing in the elderly can be a serious health issue because of a delay in tissue repair and compromised immune response. In these circumstances successful treatment can be challenging. New drugs and preclinical animal models are needed to develop alternative treatment strategies. This study was designed to investigate the effectiveness of a novel mitochondrial specific peptide, designated as SS20, in enhancing wound healing in an aging mouse model using a novel and relatively noninvasive ear punch wound. Ten C57BL/6 female mice 26 months of age were ear punched through and through in the central area of both ears using a 2 mm dermal biopsy punch. C57BL/6 mice were chosen due to them being well defined aging models both genetically and physiologically, allowing us to compare aging parameters in the same background. Five mice were randomly selected for daily topical treatment directly on the wound with SS20 at 3mM concentration in a volume of 10 ul. Five mice were treated daily with topical saline in the same manner. Two individuals separately and independently measured diameter of the wounds in two directions (because the wounds were more elliptical than circular) on days 1, 7 and 14 when treatment was stopped. Wound surface areas were then calculated and average change over the 2 weeks was determined between mice with SS20 and saline. A significant decrease in surface area was seen in the left ears of mice treated with SS20 but not with saline as measured by both individuals. Interestingly there was no difference in change in surface area in the right ears of mice treated with SS20 or saline over the 14-day period, confirmed by both individual measurements. These observations suggest that SS20 can prevent a delay in wound healing in very old mice by targeting mitochondrial activity. Additional studies are needed, not only for SS20 effects, but also to investigate utility of the ear punch in aging mice as a model of age-related wound healing.

Cardiovascular disease (CVD) continues as the leading cause of death worldwide. The underlying cause of CVD is atherosclerosis, characterized by fatty plaques in the inner walls of the artery, and exacerbated by oxidative stress, inflammation and immune cells. The high-density lipoprotein (HDL)-associated enzyme paraoxonase-1 (PON1) plays a significant role in protecting against CVD. However, the mechanism of PON1’s protection is not well understood. Our laboratory and others have reported a progressive decrease of PON1 activity in several diseases. Our goal is to understand how PON1 prevents oxidative stress and its potential measurement as an early biomarker of risk of disease. Our hypothesis is that oxidative stress inhibits PON1 enzymatic activity, leading to progression of the atherosclerotic process in CVD. The objective of this research is to generate a mouse model to allow us to study the human enzyme PON1 in induced atherosclerosis in vivo.  Starting from two strains of knockout (KO) mice, we have generated the Pon1/apolipoprotein E (apoE) double KO mouse, known to be susceptible to atherosclerosis. We are now crossing this double KO mouse with Pon1 KO mice that express human PON1 (transgenic human PON1 mice, tgHuPON1). We collect ear punches for DNA extraction and blood from the saphenous vein for activity assays. We use polymerase chain reaction (PCR) genotyping methodology, which amplifies DNA, to identify mice that are KO for mouse Pon1 and apoE and that express human PON1. We run enzymatic assays to determine activity levels of the human PON1 in mice. Once we have created the tgHuPON1/apoE KO mouse, we will feed mice with an atherogenic diet, which will induce subclinical atherosclerosis. This knowledge will contribute to understanding the relationship between PON1 and CVD, and will likely generate a useful biomarker for risk of disease.      

My research project involves the AP-3 (adaptor protein) complex, which plays a key role in membrane trafficking cells. Within all eukaryotic cells, there are membrane-bound sections of the cell that interact with each other in various ways to drive the cell's function. Vesicles mediate the transport of proteins and lipids among cellular organelles. These vesicles are created in various ways by proteins throughout the cell that form a "coat" around the vesicle as it travels to its destination. AP-3 is a protein complex that mediates vesicular transport from the Golgi apparatus to the lysosome. The current aim of my project is to analyze evolutionarily conserved features of the AP-3 complex by mutating subunits of the complex and observing resultant phenotypes in our model organism, Saccharomyces cerevisiae (baker’s yeast). In doing so, we utilize a gene reporter system called GNSI to analyze AP-3 function in different genetic strains. This reporter system is mainly analyzed through a colorimetric assay (chemical test to determine components), using qualitative observations of the intensity of colored halos around yeast colonies on a gel plate. We also use fluorescence microscopy by using signals from the Green Fluorescent Protein (GFP) to determine whether AP-3 was successful in trafficking to the lysosomal vacuole. So far, our results have shown that targeted truncations of proteins within the AP-3 subunit Apl6 yielded loss of function in trafficking. We are continuing our analyses by focusing on other proteins within AP-3. These basic studies will further our understanding of membrane trafficking and may provide insight into diseases linked to AP-3 function, including HIV-1 particle assembly and human genetic disorders.

Despite possessing only one photopigment in its retina, a feature which should render an animal colorblind, the octopus, like other cephalopods, possesses an unrivaled capacity to camouflage itself with its surroundings. A recent theory suggests that cephalopods discriminate color in their environment through exaggerated chromatic aberrations, or the focusing of different wavelenths of light at different points behind a lens, caused by morphological changes in the eye. By monitoring the blurring of different wavelengths of light upon the retina from the visual field in response to the shape of the pupil, a cephalopod can still perceive color with only one photopigment. We test this theory using conditioning to a two-toned visual stimulus and its two differently-colored halves, to look at whether strobing between the two differently colored stimuli evokes the same response as that paired to the combined stimulus or one of its halves. Evoking the response of the combined stimulus would suggest that they can see the two differently colored halves simultaneously, and that a morphological change is not needed to see two different wavelengths of light. This would present a model for color perception with one photopigment that could be explored in various other vertebrates and invertebrates previously thought to be colorblind.

Short-term exposure to diesel exhaust particulate matter can cause headaches, dizziness, and irritation of the nose, throat, and eyes. Prolonged exposure has been shown to increase the risk of developing cardiovascular disease, respiratory disease and lung cancer. Because heavy machinery is often fueled by diesel, occupations such as coal miners, truck drivers, railroad workers, and construction workers are at high risk of exposure. Non-occupational exposures are also of concern, especially in locations impacted by high volumes of vehicle traffic. A potential way to determine diesel exhaust exposure is by measuring the amount of nitrated polycyclic aromatic hydrocarbons (NPAHs) in household dust. There is no current method for measuring NPAHs in dust. We conducted a literature review of methods for measuring related chemicals in household dust and measuring NPAHs in other matrices. We tested three different methods before establishing the optimized sample preparation and cleanup process using silica gel solid phase extraction followed by analysis using high performance liquid chromatohraphy with tandem mass spectrometry detection (HPLC/MS/MS). To evaluate method performance we analyzed replicates of spiked and unspiked household dust and silica gel. The method was used to analyze 42 household dust samples collected in two communities – one with expected high and one with expected low traffic-related air pollution. Future research should include comparisons between dust NPAH measurements and other measures of diesel exhaust exposure, including NP (nitropyrene) metabolites in urine, air filter NP, or a priori predicted exposure based on home location.

Long non-coding RNAs (ncRNAs) play a significant role in transcriptional regulation; therefore, mutations in their sequences can lead to human disease. An example is provided by the promoter associated non-coding RNA (paRNA) that, when bound with Argonaut 1 (Ago1) and a miRNA, plays a key role in coordinating gene silencing of the tumor suppressor CDH1 in epithelial cells. The paRNA expression can be implicated with cancer. This is due to a single nucleotide polymorphism (SNP) at positions -160(C/A) relative to the CDH1 promoter. The -160(A) isoform favors a unique secondary structure of the paRNA, distinct from more common -160(C), which favors over-suppression of CDH1 and leads to increased cancer risk. To better understand how the -160(A) isoform mechanistically drives increased suppression of CDH1, our lab is applying NMR-based methods to determine the 3D structure of the paRNA. However, the T7 RNA polymerase used to synthesize RNA is prone to producing heterogeneous products in longer RNAs such as this one. Having exact lengths of the transcript is important for improving signal-to-noise and peak sharpness in NMR spectra, which is critical for 3D structure determination. To overcome this problem, I designed a pUC19 plasmid containing the paRNA -160(A) sequence with a downstream self-cleaving hepatitis delta virus (HDV) ribozyme. Following transcription, the HDV ribozyme undergoes self-cleavage, producing homogenous ends at the 3’ end of the paRNA. My results show that HDV incorporation produces a single species of RNA with no 3’ overhang and improves NMR spectra quality. This cloning tool is easily adaptable to other large RNAs, facilitating data collection for other large RNAs used in our lab. Ultimately, our ability to predict the 3D structure of this paRNA could someday lead to its use as a potential drug target.

My research has worked to develop an automated system that utilizes techniques that will modernize pathology and reduce diagnosis times from days to hours. The current method of diagnosing cancer (histopathology) requires a tissue biopsy that is fixed with formalin for 6-72 hours, dehydrated and embedded with wax, then manually sectioned, mounted on slides, and stained for imaging. This manual process is extremely time and labor-intensive and is the reason diagnoses can take up to ten days. The preferred, and least invasive, way to obtain tissue from a patient is the core needle biopsy (CNB), which is taken by inserting a needle into a region where cancer is suspected to exist, and removing a cylindrical section of tissue. Although CNBs are rapidly becoming the standard-of-care, their small diameters make it difficult to prepare and section the tissue for use in conventional histopathology. My research project over the past year has been to develop CoreView, a device designed to handle CNBs, automatically staining and imaging their entire surface for more complete images used to diagnose cancer. We use deep ultraviolet light to image the outer 2-3 cell layers of fluorescently stained tissue in a lab-built microscope to produce sharp images that can be equivalent to standard histology images from thin sections. I used LabVIEW to develop the rotational and imaging control to image the tissue at different focal points so the biopsy surface stays in focus during rotation. Along with designing necessary components of our system, I have worked on improving processing techniques for staining fixed porcine liver to produce clearer images with high contrast between the nuclei and the cytoplasm/cell boundaries. Our collaborating pathologist has confirmed that these images are at diagnostic quality, proving that CoreView and my improved techniques for processing tissue have the opportunity to revolutionize current histopathology.

Asymmetric cell division (ACD) is an integral process that multicellular organisms use to create cellular diversity. For instance, stem cells use ACD to form differentiating sibling cells while recreating the stem cell in order to maintain the stem cell pool. Defects in ACD can result in a variety of diseases ranging from neurodevelopmental disorders to cancer. Using Drosophila melanogaster neural stem cells (neuroblasts) as a model to study cellular asymmetries, we recently found that hydrostatic pressure is an important factor contributing to ACD. However, the mechanisms and proteins that regulate hydrostatic pressure are unknown. Based on our previous results, I hypothesized that Na+/H+ antiporters are involved in establishing hydrostatic pressure. To examine this hypothesis, I tested the function of four Na+/H+ channels in Drosophila using RNAi knock-down experiments and subsequent live cell imaging. This imaging allowed visualization of fluorescently tagged myosin and microtubules--two critical components of the cell division process. I found that knocking down each of the four antiporters results in a bent mitotic spindle, delayed division times, and centrosome abnormalities. I conclude that the four antiporters play a role during ACD in fly neural stem cells. To validate these results, I will use CRISPR/Cas9 gene editing to develop deletion mutants and EGFP-tagged versions of the four antiporters—two crucial steps in studying the regulation of Na+/H+ channels. Further in the future, I will use CRISPR/Cas9 to create optogenetically controllable Na+/H+ antiporters, such that I can use light to control hydrostatic pressure in Drosophila neuroblasts. I also plan on measuring the  intracellular pH using genetically edited Drosophila, as disruptions in pH could cause the described phenotypes. These studies will provide mechanistic and functional insight into how hydrostatic pressure contributes to successful ACD.

Information warfare is not a new Russian Federation tactic, or its predecessor state the USSR, but the digital age has allowed for a severe increase in the ease and ability to carry out operations. Information war, an overarching term that includes cyberwar, influencing policy outcomes with ill-gotten information, and propaganda campaigns. Russia’s operations are expanding and increasing in number with Russian state affiliated hackers, troll armies, and bots influencing the globe. In spite of the prevalence of this action, there is a lack of databases that track all Russia’s entire information campaign in its entirety. I am building a dataset using open source methods, including research in English, Russian, and French. The dataset currently contains 78 incidents spanning 30 countries. My initial findings indicate that Russian policymakers have three overarching objectives; (1) re-establishing Russian dominance in the post-communist/Russian sphere of influence, (2) undermining western economic, political, and cultural influence globally, and (3) expanding Russia’s political, economic, and military hegemony to all corners of the globe. I have found that although Russia's overall global strategy may seem somewhat straightforward, how that plays out in each region and country differs. The ways which Russia’s goals are customized on the basis of political landscape, historical background, culture, and religion. Often times, Russian actors will choose a simple disinformation campaign through the local media, but in other circumstances more intensive measures are used by way of hacker groups.

IC 10 is an irregular galaxy located in the constellation Cassiopeia. Despite its relative proximity to our own galaxy, it is difficult to study because it lies near the plane of the Milky Way, where interstellar matter obscures visibility. Most notable is the fact that IC 10 is the only known starburst galaxy in the Local Group of galaxies, meaning it is undergoing an exceptionally high rate of star formation in comparison to the average long-term rate. Within these formed stars, our research project aims to find red supergiant stars. Using stellar evolutionary theory, estimates can be made about how many RSGs are expected, based upon analyzation of known facts such as size, age, and metal content. The research conducted will allow for a comparison between observational data to theoretical expectations. RSG's are massive stars with a supergiant luminosity class; they are the coolest of the supergiant’s and have spectral types of K and M; hence temperatures below 4,100 K. Typically, they can be up to a thousand times the radius of the sun, and are therefore highly luminous. We begin our search by collecting the Two Micron All-Sky Survey data of point sources for IC 10 through the VizieR Astronomical catalogue database, and downloading important values such as color band magnitudes and distances, into a table. To determine the temperatures and luminosities within the galaxy, the All-Sky Survey colors are transformed to the Bessell & Brett photometric system, and then de-reddened by taking into account the value for IC 10’s reddening. Temperature of the point sources is then determined, and applied to find the bolometric correction and magnitude, from which luminosity can be identified. Furthermore, to visualize this data we will plot the luminosity and temperature to construct an HR Diagram which will allow us to identify the RSGs.

Sexual harassment is pervasive yet many people underestimate its prevalence or often do not believe victims when they come forward. The current research examines a potential source of this bias. Specifically, we theorize that people assume and misperceive victims of sexual harassment as prototypical women (i.e., those who fit the stereotypical, idealized image of women), and those who deviate from this prototypicality are less likely to be believed as victims. In this study, participants read a vignette describing a woman named Anna who was either sexually harassed by a male boss or not (control group). Importantly, we manipulated her prototypicality using photographs obtained from previous research. After reading the vignette, participants rate how likely they think Anna experienced sexual harassment. This is a 2 (prototypical vs non-prototypical images) x 2 (harassment vs control) between-subject design. We are primarily interested in the interaction between the two conditions. If the interaction is significant, then we will examine the non-prototypical vs prototypical within the harassment condition as well as in the control condition. We are trying to see how the interaction effect works for women who are prototypical or not when they have been harassed because we believe that prototypical women will be more likely to be believed than non-prototypical women. We do not expect this pattern to repeat in the control condition because prototypicality should not influence women who are not harassed. This research will allow us to understand how perception of harassment can be influenced by women’s resemblance to the prototypical image of womanhood.

Spatial variation in soil abiotic conditions at plant range limits may be important in determining how plant range limits will respond to climate change. One reason for this is that plants are known to change many characteristics of the soil around their roots in ways that influence the growth of other plants.The range limit of subalpine fir is expected to shift into subalpine meadows as the climate warms. Our goal for this project is to describe the abiotic soil qualities of a subalpine forest habitat and a subalpine meadow habitat on Mount Rainier to explore how these characteristics may affect the predicted range shift. We hypothesize that soils from subalpine meadows will have less organic matter and therefore less phosphorus, a lower carbon to nitrogen ratio, and less water holding capacity than soils from the subalpine forest. We will develop a protocol for measuring water availability and implement it on soil samples obtained from around the roots of subalpine fir trees in both the forest and meadow sites on Mount Rainier. We will use standardized tests to obtain the organic matter and phosphorus measurements. If our hypothesis of lower nutrient availability and water retention in meadow soils is supported, this may suggest that subalpine fir growing in the meadows have a greater dependency on fungal symbionts for obtaining soil resources. This would have important management implications given that suitable fungal symbionts are expected to be rare or absent at range limits.

Through the use of virtual and augmented reality technology, we want to record clinical interactions within the respective environments on acute stroke patients to help us design more acceptable gaming technologies for a wide range of ages and backgrounds in future studies. With the combined efforts of the computer science and electrical engineering team, we were able to produce two games; "Dolphin Days" for the augmented reality environment and "Apollo" for the virtual reality environment. "Apollo" will be available for play during the duration of the symposium. The purpose of exposing patients to these environments is to promote neuroplasticity in the recovery process. Neuroplasticity is when the brain can reform or grow new nerve endings to reconnect with the affected areas in order to accomplish a function. Clinically, our experience has been that patient motivation is key to obtaining good clinical outcomes. Stroke rehabilitation therapies can often be tedious and difficult to maintain interest in. These types of interventions, by incorporating the desired exercises into a motivating and game-like environment, could potentially address this issue. Additionally, these systems offer the potential advantage of not requiring the immediate presence of a skilled occupational and physical therapist. Cost and insurance limitations often mean patients get a limited number of skilled therapy sessions. Therapists skilled in the rehabilitation of stroke are often less available in rural regions and patients often struggle to travel to therapy appointments. All of these factors limit the patient’s overall access to skilled therapeutic interventions. Our results found the overall patient census enjoying the environments while also having them engaged with the technologies. We believe using these technologies would further motivate patients undergoing stroke therapy to continue participation and ultimately reach a state where the patient feels confident physically and mentally to resume their daily tasks pre-stroke.

Individuals with hearing loss have a much greater difficulty understanding speech in noisy environments than their normal hearing counterparts, leading to reduced participation in communicative activities and a lower quality of life. Audibility explains some of the difficulty this population experiences, but even with audibility recovered by hearing aid amplification, impairments exist in spectral and temporal processing. The extent of spectral and temporal processing impairment is captured in detection of spectro-temporal modulations, which is closely related to speech understanding in noise. This study explores the potential effect age has on STM sensitivity, while controlling for severity of hearing loss. In order to investigate, we measured STM sensitivity in participants with a hearing loss across a wide age range. In the STM test, they are asked to listen to two sounds, a broadband noise and the same broadband noise with spectro-temporal modulation applied, and identify which sound contained modulations. The modulation applied will adaptively change based on response accuracy until the listener can no longer discriminate between the two sounds. A multiple linear regression model is used to analyze the data, with predictors of hearing loss severity and age. We expect to see a decline in STM threshold with age, independent of hearing loss status. The results are discussed in terms of potential for future clinical application and the ability to better the quality of hearing aided listening.

Differences in the morphology (size and shape) between sexes in mammals is common and serve to provide advantages in various contexts. Size differences can be allometric (Rensch’s rule), where females are typically larger in smaller species and vice versa. In bats, females are generally larger, although this does not follow an allometric pattern. Instead, it is suggested that selection for mobility and efficient parenting drive sexual dimorphism in bats. Ralls’ ‘Big Mother’ hypothesis suggests that larger size in female bats is due to a need for mobility during reproduction. Bat flight behavior is highly influenced by wing morphology. Therefore, in addition to size differences, females may have different wing shapes, which reduce the load of the fetus during pregnancy. Consistent with the big mother hypothesis, size typically varies more in the wings (e.g., forearm length) as opposed to other body size measurements (e.g., skull length). In this study, I compare cranial, body, and wing size differences between male and female little brown bats (Myotis lucifugus). I also analyze shape differences in the wings between the sexes, using a geometric morphometric approach. Using digital photographs, I placed 14 homologous anatomical landmarks on the wings and body of 83 bats (33 female, 50 male). I use a generalized procrustes analysis in order to obtain shape variables from the digitized landmark configurations. I used t-tests to compare cranial and body size measurements, and I use a procrustes anova to test for differences in the wing shape between males and females. I found significant female-biased differences in forearm (p < 0.01), wingspan (p < 0.01), and total length (p < 0.05) measurements. Wing shape measurements are still in progress. Our results may contribute to growing evidence that sexual dimorphisms in bats are related to selection for mobility during pregnancy and lactation.

Venezuelan equine encephalitis virus (VEEV) is a mosquito-borne New World alphavirus, causing encephalitic disease in mammals. Increased circulation of VEEV in the Americas underlines the need to characterize alphavirus replication and develop countermeasures. The VEEV genome is a single-stranded RNA of positive polarity (+ssRNA). MicroRNA (miRNA) are small, cell-specific non-coding RNAs that aid in post-transcriptional regulation of gene expression. Previous studies have demonstrated that host miRNA can affect viral replication and pathogenesis by directly binding to the viral genome. Recent work on host miRNA in related alphavirus Eastern equine encephalitis virus (EEEV) found miRNA binding sites in the EEEV 3’ non-translated region (NTR). Binding of the host miRNA enhanced pathogenesis. Prediction software miRDB identified potential miRNA binding sites in the 3’ end of VEEV genome, including one for miRNA hsa-miR-1268. In this study, the impact of miRNA interaction with its putative binding site on VEEV pathogenesis was investigated. We performed site-directed mutagenesis of VEEV strain TC-83 to engineer point mutations at the hsa-miR-1268 binding site in the 3’ end. We are currently testing the impact of these mutations on viral replication by analyzing growth kinetics of wild-type and mutant viruses in cell culture. We anticipate that a mutation disrupting the interaction between hsa-miR-1268 and the predictive binding site on the +ssRNA genome will result in the decreased ability to replicate the viral genome and subsequently infect the host. Understanding the impact of the interaction may lead to novel mechanisms to prevent RNA virus replication.

Through mapping the complexities of spatial inequality, I examined the geographic differences in economic and socio-cultural inequality across the state of Indiana. I grew up in Indianapolis, Indiana in an upper-middle class neighborhood that undoubtedly limited my ability to see inequality. Examining inequality in my home state provided me with a deeper understanding of the gap between rich and poor within the state, how Indiana fits into the growing wealth gap in the United States, and how income inequality further impacts access to education, housing, and healthcare. I collected data from the US Census Bureau for Indiana and Indianapolis, as well as the three richest and poorest cities in the state, St. John, Zionsville, Carmel, Gary, East Chicago, and Muncie. Across the state and the seven cities studied, I measured educational attainment, employment status, health insurance coverage, housing costs, and income in the past 12 months. In Indiana, less than 25% of the population over 25 has a Bachelor’s degree. Rates of health insurance coverage vary greatly across the cities studied, but are fairly consistent across racial lines within cities. Income distribution varies drastically across the state, and by race across the seven cities in this study; however, single mothers, regardless of their race or ethnicity, are far more likely to be impoverished compared to the average in each city. In the three richest cities, populations are almost entirely white, while populations in the three poorest cities are almost entirely African American. Economic differences are not the only indicator of inequality in Indiana; socio-cultural differences also underlie many aspects of poverty and inequality. Mapping how inequality varies in terms of race, gender, and location provided a stronger sense of how geography affects the distribution of wealth and resources, and who is impacted the most.

Sleep deprivation has serious health consequence with disturbances in cognitive function and metabolism, and increased risk for age-related diseases such as Alzheimer’s disease. Intervention strategies are therefore of interest, especially in individuals unable to routinely obtain healthful sleep time hours. This study was designed to investigate the effects of the repurpose drug phenylbutyrate (PBA) on learning impairment in a mouse model of short-term sleep deprivation. Histone deacetylase (HDAC) is activated by neuronal stress resulting in decreased gene expression and under-acetylation of histones linked to decreased cognitive function. As an HDAC inhibitor, PBA would be expected to alleviate cognitive dysfunction associated with sleep deprivation. Further rationale for testing PBA was provided by showing the drug enhanced expression of acetylated histones in mouse and human neuronal cell cultures. Nine CB6F1 male mice, 17 months of age, were started on treatment with PBA in the drinking water at a concentration of 6 g/L for twelve weeks. Nine control mice were provided drinking water with diluent only. During the last week of treatment, mice were maintained in an awake state 4 hours during the day for 4 days using a non-stressful protocol. All mice were then immediately tested in a box maze learning paradigm consisting of four successive trials to find an escape hole. Control mice had variable escape times over the four-trial test, while mice treated with PBA showed a consistent decrease in escape times with each successive trial. This observation suggests that pretreatment with PBA can prevent learning impairment induced by short term sleep deprivation in mice. Since PBA is already clinically approved to treat urea cycle disorders in children, there are intriguing implications for repurposing this drug for experimental trials in individuals with primary or secondary sleep disorders.

Atomic Layer Deposition (ALD) is a process whereby thin films of a material, ranging from dielectric materials to metals, are deposited onto a substrate. ALD reactions operate using two vapor phase chemical precursors that react with the substrate material sequentially one at a time, slowly forming the thin film. Because of the sequential nature of ALD, the process is self-limiting and offers exceptional control of thin film thicknesses, film composition, and high conformity on high aspect ratio features, such as trenches and sidewalls, making ALD an extremely useful process for the fabrication of semiconductor devices. The purpose of this project was to develop processes and refine process parameters for thin film deposition using an industry grade ALD machine. Thin films were deposited onto silicon substrates with etched features. The films were then examined and characterized using ellipsometry and sidewall conformity was measured using a scanning electron microscope.  This data was used to refine processes and parameters that were then employed by research staff and industry users in the fabrication of semicondctor devices.  Overall, this data can be employed by the semiconductor industry to better understand this process and utilize it to manufactor silicon devies with  greater uniformity and efficiency.

Parkinson’s Disease (PD) is a neurodegenerative movement disorder characterized by muscular rigidity, slow movement of the limbs and resting tremor. The onset and progression of PD is attributed to the combined effect of environmental and genetic risk factors, with several specific disease-causing genes having been identified. PD onset is determined by the loss of more than 80% of dopamine-synthesizing neurons from the substantia nigra as well as formation of α-synuclein protein aggregates, called Lewy Bodies. Recent research has identified several potential pathogenic variants in the LRP10 gene on chromosome 14, suggesting that LRP10 may be a novel PD causative gene. It has been shown that the LRP10 protein is implicated in vesicular transport and that it may regulate α-synuclein aggregation, intracellular trafficking, and cell-to-cell transmission. The goal of my project was to analyze the association between LRP10 and PD by sequencing the regions on LRP10 that harbor these variants described in other families and check for co-segregation in the relatives of mutation carriers. DNA samples from 188 PD familial patients were sequenced. LRP10 regions of interest that were examined included exons 1-7 (protein coding regions) and intron 5 (a non-protein coding region). These LRP10 regions in patient DNA were amplified by polymerase chain reaction and sequenced subsequently using Sanger Sequencing. Relatives of LRP10 mutation carriers were then analyzed for co-segregation between the variant and PD. It was expected that certain LRP10 variants would be found to segregate with the disease in inheritance or increase the likelihood of its onset. The molecular function of both the normal and mutated LRP10 protein are still largely unknown and future research into their mechanisms will provide valuable insight into their specific role in Lewy Body formation and dopaminergic neuronal loss.

Research has shown that positive outcome expectancy (i.e., anticipated positive consequences as a result of engaging in a behavior) and positive affective responses to exercise play an important role in predicting exercise behavior as well as future exercise intentions. Unlike most research in which the valence (i.e., positive - negative) of outcome expectancy and affective responses are typically assessed through survey items whose valence is predetermined, the current study used a spontaneous word association test (WAT) to examine the subjective meaning of exercise-related outcome expectancy and mood before exercise, and how they are related to exercise intentions and behaviors. One-hundred and eleven undergraduate and graduate students (74 females; 64 undergraduate students) performed an exercise-related WAT in which they were asked to write down the first word or a short phrase that comes to mind when they thought of (a) things that might happen from exercising and (b) their mood right before exercising. Subsequently, they were instructed to rate their subjective valence (i.e., positive-negative) to each of their responses to the WAT. They also completed a series of online self-report surveys that included assessments of exercise intentions and past exercise behavior. Path analyses will be conducted to test our hypotheses that the subjective valence of their mood right before exercising is expected to be directly associated with exercise behavior whereas the subjective valence of outcome expectancy is expected to be indirectly associated with exercise behavior through exercise intentions. This study examines the potential value and usefulness of a spontaneous word association procedure to more accurately measure affective evaluations of an individual’s feelings and thoughts toward exercise behavior.

Mitosis is an essential cellular process in which a cell divides to produce two genetically identical daughter cells. When this process becomes dysregulated cells divide uncontrollably leading to diseases such as cancer. Polo-like kinase 1 (Plk1) is a key enzyme that is necessary for coordinating numerous events during mitosis. When Plk1 becomes dysregulated or mislocalized, mitotic spindle assembly, protein organization, and mitotic timing impairments may occur. One of the many subcellular locations where Plk1 carries out essential mitotic functions is the kinetochore. The kinetochore is the interface between the chromosomes and the mitotic spindle and is critical for ensuring proper DNA to microtubule attachments early on in mitosis. Historically, the small-molecule inhibitor drug BI2536 has been used to inhibit the activity of Plk1 in order to study its role in regulating various mitotic processes. However, traditional inhibitor drugs turn off entire protein kinase populations, inhibiting the activity of Plk1 all throughout the cell, not just at the kinetochore. This can lead to unwanted side effects and limits our understanding of Plk1’s role at specific subcellular locations. To improve the specificity of BI2536 drug delivery, we utilized SNAP-tag, a tool in which a self-labeling enzyme can irreversibly react with substrates linked to a chloropyrimidine (CLP) functional group. By genetically manipulating human bone cancer (U2OS) cells, we expressed a kinetochore localizing SNAP. We also generated a BI2536 conjugated to a CLP group. By treating our genetically modified cells with CLP-BI2536, we can target Plk1 inhibiting drug to the kinetochore to study Plk1’s role at this specific location. Using super-resolution structured illumination microscopy (SIM), we demonstrate that we can effectively target fluorescently labeled CLP substrates to kinetochores in our cell line. In future work, we will target our CLP-BI2536 drugs to the kinetochore and investigate how local Plk1 inhibition affects mitotic timing.

With our rapidly changing climate, plant communities are predicted to experience more variable conditions. Climate change predicts that there will be longer periods of drought followed by heavy rainfall at unpredictable intervals. With this, plants may experience selective pressures to combat the stress that come with these variable conditions, which ultimately may influence plant evolution. Phenotypic plasticity and epigenetic modification are two factors we believe may strongly influence the adaptative ability of plants. I predict that these variable conditions will promote phenotypic plasticity and epigenetic “memory” (where plants’ stressful experience can be inherited from parent to offspring), and potentially help offspring plants cope with the same abiotic stress. We have implemented an experimental design mimicking the predicted variable conditions of climate change. For two generations, we exposed plants to either drought or non-drought conditions. Then in the third generation, we took seeds from parents that experienced those conditions and exposed them to either drought, non-drought, or variable watering in a cross-replicated design. I hypothesize that there is inherited epigenetic memory, and that the different treatment groups will pass memory that will benefits plants if the offspring was exposed to the same condition its parent experienced.

As our society moves into the future, queerness is becoming more mainstream and acknowledged by heteronormative institutions, like the government, and popular culture. Same-sex marriage is now legal in 30 countries and some, like Chile, are taking measures to ensure that trans-kids are protected. But as queerness becomes more accepted by society today, queer spaces are adapting from their artificial birthplace—the dark and hidden interiors of the 19th C middle class. Now as queer space transitions from its past private realm and into the public eye, so does its definition and past implications: "Queer space is not one place: it is an act of appropriating the modern world for the continual act of self-construction. It is obscene and artificial by its very nature. It creates its own beauty. It allows us to be alive in a world of technology. There we can continually search within ourselves as we mirror ourselves in the world for that self that has a body, a desire, a life. Queer space queers reality to produce a space to live." Queer spaces were born out of a need to be hidden from the society that has ignored queers and their needs, but as times change and the world becomes more accepting of queerness, what happens to these queer spaces? I will be investigating queer spaces today as they have moved from the private realm to the public realm and looking at the architecture of two gay neighborhoods, Seattle’s Captiol Hill and Chicago’s Boystown for case studies of what queer space is, in our modern world.

Marine mammal strandings can serve as an indicator of marine ecosystem and mammal population health, providing an opportunity to learn about the life of individual animals prior to their deaths. Existing stranding networks are focused on response to opportunistic reports of stranded or beached marine mammals, which limits their usefulness in establishing baseline data. The Coastal Observation and Seabird Survey Team (COASST) engages volunteers along the western coast of the United States in collecting and reporting data for two effort-based programs, beached birds and marine debris. Looking to the future, COASST hopes to complement information gathered by marine mammal stranding networks by expanding their effort-based surveys to include marine mammals. COASST has already begun this process by asking volunteers to report sightings of marine mammals along with pictures of their beached bird or marine debris finds. These pictures can be used for species identification, and by looking at these photos in correspondence to other survey data such as region, beach, and survey date we can learn about species distribution along the western coast of the United States. We found at least 300 beached pinnipeds, through photo identification we were able to place them into at the least the families Otariidae or Phocidae. Using current literature on marine mammals, pinnipeds specifically, and their identifying characteristics, I aim to map pinniped species distribution and locate hotspots to ultimately test a pinniped species identification key that will be used by COASST volunteers. With this distribution and hotspot identification we will be able to idenify whether pinnipeds follow already established beaching patterns of beached birds or if they differ. These differentiations could lead to more information about the death of marine mammals and allow future research on the death of these animals in more focalized areas. 

Maternal exposure to persistent environmental toxicants polybrominated diphenyl ethers (PBDEs) is associated with many human diseases, notably hepatotoxicity, thyroid disorders, and reproductive toxicity. PBDEs, previously seeded into manufactured products as flame retardants in the United States, were phased out during the 2000s. A 2017 study of women in California showed modest average annual percent increases in serum concentrations of PBDEs. Accordingly, the gut microbiome is increasingly recognized as the “second genome”, impacting crucial health-related factors like host xenobiotic biotransformation and energy homeostasis. Persistent dysbiosis may contribute to altered susceptibility of disease in adulthood. My goal for this study was to test the hypothesis that perinatal exposure to BDE-47, a common PBDE congener that can cross the placenta and enrich in breast milk, modifies the developmental trajectory of gut microbiota. Pregnant Wistar rats were orally exposed to BDE-47 (0.2mg/kg) from gestational day 8 to postnatal day (PND) 21. Fecal samples were collected from mothers at PND21 and male pups at PND65 and 120. I isolated Microbial DNA using 16S rDNA sequencing (n=5~9/group) and analyzed my data through QIIME. Perinatal BDE-47 exposure had minimal effect on the richness of gut microbiota in PND65 pups and mothers, but profoundly increased richness of gut microbiota in PND120 pups. In PND65 pups, only 4 taxa were persistently regulated by perinatal BDE-47 exposure. Interestingly, the effect of perinatal BDE-47 exposure was evident in PND120 pups, with an increase in 3 taxa in the Lactobacillales order and 11 taxa in the Clostridiales order. Targeted metabolomics has confirmed alterations of distinct microbial metabolites (short-chain fatty acids and secondary bile acids) corresponding to BDE-47-induced dysbiosis. In summary, the present study showed that perinatal BDE-47 exposure modified the developmental trajectory of the offspring’s microbiota, possibly producing delayed onset of diseases in adulthood.
 

 The city of Renton is a developing town located 12 miles south of Seattle. The city is undergoing growth and change and as a result, there are plots of land that are underutilized and dormant in the downtown civic core. The former Big 5 lot is a city owned parcel that is next to Piazza Park and Gateway Park. This is a space that welcomes you into Renton but is currently an empty gravel lot. This site has opportunity for revitalization that could ultimately improve the safety, perception, and activation of this entry way into Downtown Renton. How can civic engagement and design bridge the gaps in the city street? By doing a thorough site analysis, forming community relationships, and involving Renton communities in a design charrette, I hope to find an inclusive design that will incorporate ideas from the people who use this space and understand what they want in their neighborhood. By having this open design charrette, the community can have agency in the changes happening to their neighborhood by forming solutions for their space and connecting with neighbors they may otherwise have never met. This will build a strong foundation for the future developments to come in Downtown Renton.

Flow Cytometry is a quantitative data collection method which utilizes a laser and optics system to measure forward and side-scattering light from single cells in a heterogeneous solution, which when analyzed describe the structure and internal complexity of the cells in solution. Additionally, varying wavelengths of light emitted from the cytometer excite particular fluorescent dyes that can be conjugated to known antibodies, so that when cells contain the known antibody’s antigen, the dye color will be present. This allows for cell identification and/or protein expression to be determined and quantified within a heterogeneous mixture of cells. With the given technology, we optimized a flow cytometry panel for the use of analyzing immune responses to gene therapy treatments in canines. We stained extracellular and intracellular protein markers on canine peripheral blood mononuclear cells (PBMCs) with fluorescent dye conjugated antibodies thought to recognize canine antigens. This entailed staining the extracellular markers with conjugated antibodies, fixing and permeabilizing the cell, and doing the same to intracellular markers. Once this had been carried out, the cells were run through a flow cytometer to excite the dyes with varying wavelengths of light to highlight separate dye colors. Analysis of multicolored dye presence in cells post-excitement allowed for identification and quantification of cell types. We identified antibodies that recognize canine antigens and developed a multicolor panel identifying T helper cells, cytotoxic T cells, T regulatory cells, and B cells in canine samples. Once optimized, we used this panel to characterize immune responses in dogs following gene therapy. With a reliable canine cytometry panel, future canine immune responses, both broadly and in isolated muscular tissues, can be characterized.

Many illnesses such as influenza and the common cold present similar symptoms, which renders them difficult to diagnose without a formal molecular diagnostic test. Designing a diagnostic test that could be run in patients’ homes would address limitations of existing assays, but with the risk of patients attempting to self-treat without consulting healthcare professionals. As a result, this project has developed  a lateral flow assay (LFA), the same type of assay as an at-home pregnancy test, that is adapted to detect an infectious disease while blinding the end user from the result. Traditional LFAs indicate the presence or absence of a biomarker by capturing the biomarker with antibodies and labeling the capture event with colored nanoparticles; two lines indicate the presence of the biomarker and one line indicates its absence. We've proposed two methods of blinding the end user from the results. One is a system where two lines always appear in an LFA even in the absence of the biomarker, preventing the end user from interpreting the result. The color intensity of the two lines will be proportional to the amount of biomarker present; this relies on humans’ inability to reliably detect absolute color intensities to blind the assay results. Preliminary testing of an influenza LFA suggests that the proposed scheme successfully blinds immunoassays to the end user, but the limit of detection (LOD) is 20 times worse than traditional LFAs. The second method uses a randomized array of antibodies spotted on an LFA as a way to obfuscate the result but through imaging can later be interpreted. We've optimized the proposed schemes to improve the LOD, demonstrate that the assay can be quantified with a cell-phone, and enable quantitative detection of infectious disease biomarkers in the home with a blinded immunoassay.

Drepanosauromorpha is an extinct group of reptiles known from the Middle to Late Triassic (237–212 MA). The clade currently includes seven genera (Avicranium, Dolabrosaurus, Drepanosaurus, Hypuronector, Kyrgzsaurus, Megalancosaurus, and Vallesaurus) that are known from fossils collected in Europe (Italy, UK), North America (Arizona, New Mexico, New Jersey), and Asia (Kyrgyzstan). The first described drepanosauromorph, Drepanosaurus unguicaudatus, was based on a flattened holotype preserving most of a complete skeleton. Subsequently described drepanosauromorphs display the following diagnostic features: the length of the chevrons (ventral spines below the tail vertebrae) is substantially longer than corresponding tail neural spines, the cervical (neck) vertebrae are heterocoelous (saddle-shaped articular surface), the cervical ribs are absent as distinct ossifications, and the chevrons are fused to their respective centra. In recent years, both three-dimensionally preserved partial skeletons and isolated material of drepanosauromorphs have been found across both Europe and North America. These discoveries have helped shape our understanding of the biology and diversity of drepanosauromorphs. However, comparing isolated, three dimensionally preserved specimens to the more complete, yet two dimensionally preserved articulated specimens is difficult due to differences in preservation. Here, we describe a new drepanosauromorph species from the Chinle Formation in Petrified Forest National Park, Arizona based on the left second manual ungual (claw) . Some of the characteristics that distinguish this claw from those of most drepanosauromorphs is its size. It differs significantly from all known Drepanosaurus specimens (like the Italian holotype and the Hayden Quarry Drepanosaurus) because of the ventral placement of the cotyle (articulation surface), the height of the claw, the lack of compression along the pre-axial/post-axial plane, and a furrow along the midline. This new taxon not only highlights unsuspected morphological variation within Drepanosauromorpha, but also helps sheds light on the evolutionary history of smaller-bodied reptiles within Late Triassic ecosystems.

In 2009, the Department of Veterans Affairs (VA) integrated Store-and-Forward Teledermatology (SFT) to increase the dermatology care to patients with limited access. With this, patients are evaluated by their primary care provider (PCP) and referred to SFT for dermatology conditions. A technician on site takes images of the condition and send records to tele-dermatologist at a reading hub to evaluate and provide a differential diagnosis, treatment, and follow up. When skin biopsies are requested, Clinical Pathological Correlation (CPC) consultations are also requested. Dermatopathology reports are not standardized well and often require interpretation in context of other clinical information, including history, imaging, and microbiology studies to diagnose. Follow up imaging after an interval of treatment may be requested to confirm the diagnosis. The purpose of this quality improvement study is to assess adherence of PCPs to follow ups, determine whether failure to use means degraded clinical outcomes and interventions to improve outcomes. We conducted a retrospective review of 224 conditions addressed by teledermatology during the month of April 2018, on Veterans in the Pacific Northwest Network (VISN 20) where recommendations for either CPCs, re-imaging, or both were requested. We searched electronic medical records that requested follow-ups and determined a.) whether it occurred (if not, why); b.) timing it occurred; c.) affectability of treatment plans based on follow up findings; and d.) whether conditions were by intervention. Of 224 conditions reviewed, 161 requested CPC consultation, 63 requested reimaging, and 2 requested both. For CPC consultations, 90.06% patients had a re-consult, through CPC process or FTF and 9.4% of cases were lost in care. For reimaging consults, 73% of cases had reimaging or FTF re-consult while 27% of cases were lost in care. Data from this project will be used to improve follow up and quality of care Veterans receive through SFT.

Currently in Latin America, there are no nuclear weapons. In 1967, the Treaty of Tlatelolco was created and signed by Latin America and the Caribbean. This treaty prohibits the possession of nuclear weapons of any kind, making Latin America a non-nuclear weapon state. The research question I will be addressing is: Even though there are no nuclear weapons in Latin America, does nuclearism play a role in shaping its culture? As a native Spanish speaker, I am able to use my knowledge of the culture by using methods to analyze popular music, language and literature regarding nuclear weapons. I studied the lyrical and visual aspect of music to look for themes of the naturalization of nuclear weapons, as well as finding how language plays a role in its normalization. I analyzed literature in order to find commonality of nuclear cultures between nations that possess nuclear weapons and those that do not. My initial findings show that there is a strong presence of a nuclear culture existing in Latin America despite the fact that the region does not own nuclear weapons. Research also shows that nuclear culture is normalized through important themes such as gender and sexuality. Its normalization is often not obvious and is a part of daily life. These results were unexpected because I hypothesized for a nuclear culture to be nonexistent in a region that prohibits nuclear weapons. It is important to conduct further research on how nuclear weapons affect regions that are non-nuclear weapon states because it would create a broader understanding of the effects that nuclear weapons have on everyone and how it is a global issue that needs to be addressed. 

Emerging adulthood is a significant developmental period where individuals aged 18-25 years do not feel that they are adults, but on the path to becoming so. Individuals may describe their experiences within this life stage differently based on their racial identity. This research project asks: “How do young people of color in college describe their experiences of emerging adulthood compared to their white peers, and is this related to their mental health in different ways?” Within this study, I compare how students of color and white students view, experience, and navigate emerging adulthood and how this affects their mental health. Through interviews with young college students across racial groups at University of Washington (UW), I examine how they make sense of the stressors in their lives. Interview questions discuss significant areas of emerging adulthood, various social forces that could affect mental health, racial issues and socialization, and access to social support. I test the hypothesis that students of color describe their sources of stress as being more impacted by structural and institutional reasons, such as racism and xenophobia, while white students focus more on social and interpersonal reasons, such as families, relationships, and work. Emerging adulthood is a relatively new field of research and it is critical to understand how people of color experience this life stage. This research will contribute to current understandings and research of racial health disparities. It will also highlight areas for additional work addressing the significance and complexity of intersectionality within the emerging adulthood developmental period.

Autism Spectrum Disroder (ASD) occurs in one in every 59 children, yet the causal mechanisms remain widely unknown. Research is advancing through genetic testing as well through speculation of external environmental influences. Recent stuides have examined in greater depth gene by environment interactions and have found an impact on severity symptoms of ASD. This research follows the two-hit model of gene by enviornment effects and investigates the link of auoimmune disorders, specifically thyroid disfunction, Likely Gene Disrupting (LGD) mutations to genes related to ASD, and the relation to IQ and regression. Behavioral and cognitive data are collected using clinician-administered questionnaires and assessments. Those who carry an LGD mutation with exposure to maternal thyroid dysfunction lean towards a trend that show more severe behavioral phenotypes than those without an LGD mutation. These results spotlight the importance of gene by environment contributions in addition to mechanisms involved in the disorder. These findings may help improve future treatment and intervention for those with ASD. 

Theiler's murine encephalomyelitis virus (TMEV) is a positive-sense RNA Picornavirus used to model epilepsy, poliomyelitis and multiple sclerosis. Previous research has demonstrated a dependence of some Picornaviruses on host glutathione (GSH) in order to produce viable progeny. GSH depletion in host cells has resulted in unstable viral capsids, reducing viral fitness due to a lack of oxidative homeostasis. The objective of this study was to investigate the dependence of TMEV on GSH and determine the consequences of oxidative stress in the host cell due to the absence of GSH. Incubation of TMEV at denaturing temperatures with increasing doses of reduced GSH demonstrated that GSH stabilizes viral particles and 54% viral infectivity was retained with doses as low as 25mM GSH. Using L-Buthionine-sulfoximine (BSO) to deplete GSH in host cells, a 3-fold decrease in viral production was observed when compared with untreated cells. Interestingly, when GSH was restored in BSO treated cells using cell permeable GSH ethyl ester, TMEV viral production was partially restored and viral plaque formation was comparable in yield to an untreated viral infection. Virus production and viability were quantified using plaque assays on host cell monolayers. Next steps include monitoring viral genome production via RT-qPCR and quantifying GSH levels using fluorescence plate assays. RT-qPCR will be further utilized to examine other host stress pathways. This project will use TMEV to look at a host-virus relationship as it relates to an important host antioxidant system interacting with the capsid, assembly, and genome replication of the virus life cycle.

The transfer of carbon in and out of ecosystems is a complex process that is affected by many factors. The largest factor in carbon transfers is the photosynthesis and respiration rates of plants, which sequester and release carbon dioxide. Additionally, processes like soil leaching, sediment burial in lakes, downstream transport and even forest fires and animal migrations have an effect on the movement of carbon throughout ecosystems. In this study we ask the question: “How do physical and climatic conditions influence the concentration of carbon in small streams in the Pacific Northwest?” Our study site includes sixteen watersheds with areas that range from 500-2,500 acres in the northeastern portion of the Olympic National Forest. Using a GIS framework, we compiled satellite and LiDAR datasets of soil type, rainfall, slope, tree age and aspect and summarized these data for each of the sixteen watersheds. Our goal is to better understand which physical factors have the most influence on carbon transport in streams. By comparing our watershed-specific data to measurements of dissolved organic carbon and water quality characteristics in the streams, we identify correlations that can inform on the potential controls on carbon export in the rain-dominated catchments on the Olympic Peninsula.

Alzheimer’s disease (AD) is characterized as an irreversible, progressive brain disorder that gradually destroys memory and thinking skills, and eventually the ability to perform simple everyday tasks. Despite many decades of research focus on AD, the cause and mechanistic understanding of the progression remains enigmatic. Identification of amyloid beta plaques and hyperphosphorylated Tau in post-mortem analysis of brain biopsy is viewed as definitive for diagnosis of AD. Dr. Su-in Lee’s lab has developed a machine learning method that integrates brain tissue pathology metrics with gene expression analysis from the same patient samples. Their analysis identifies genes and pathways that are statistically-associated with the concordance of pathological AD phenotypes. Working with researchers in the Kaeberlein lab, we are using the nematode C. elegans to directly test the impact that these genes have on the progression of human tau-induced neuronal dysfunction and death. The Kaeberlein lab previously identified a subset of genes in complex I of the electron transport chain (ETC) that are highly correlated with human amyloid beta-induced paralysis. We are now extending that work by examining the relationship of these ETC genes in the lifespan and healthspan of human Tau-model nematodes. Our preliminary results suggest that reduction of Complex I activity increases the lifespan of human tau-models nematodes. We are conducting further studies to determine the replicability of these findings as well as disrupting ETC function with RNAi from other genes. Through directly testing nematode orthologs of human genes that are statistically-associated with AD neuropathology we will generate a better understanding of the cellular mechanisms that influence normative aging and Alzheimer’s disease.

During the Last Glacial Maximum (LGM), the Cordilleran Ice Sheet advanced into the northwestern United States and dammed the Clark Fork river in western Montana, forming Glacial Lake Missoula. The ice dam in the valley repeatedly broke, sending at least 100 massive outburst floods known as the Missoula Floods into eastern Washington where they incised deep canyons forming the Channeled Scabland. During the period of flooding, the Okanogan Lobe of the Cordilleran Ice Sheet crossed the Columbia Gorge onto the Waterville Plateau, diverting floodwaters away from the Columbia River into Grand Coulee, before blocking Grand Coulee itself. My research project examines the timing of glaciation of the Waterville Plateau and how it influenced the paths of the successive floods. To determine the timing of glaciation, my advisers and I studied glacially transported boulders that began to accumulate the cosmic ray produced isotope beryllium-10 (10Be) after they were exposed by ice sheet retreat. In the lab, we separated and dissolved quartz from our samples, purified beryllium, and then measured 10Be/⁹Be ratios using Accelerator Mass Spectrometry (AMS). From AMS measurements, we calculated the exposure ages of our samples. We expect the ages to fit within the established sequence of ice advance across the Columbia River, redirection of floodwaters down Grand Coulee, and eventual ice retreat to north of the Columbia River. Following this sequence, we expect our samples from the northern edge of the Waterville Plateau to be younger than the last floods down Grand Coulee (15,300 years) but older than samples from the Omak Plateau north of the Columbia Gorge (13,900 years). Along with dates from previous studies, the new exposure dates from this project explain how the Okanogan Lobe guided Missoula floodwaters and influenced landscape evolution in eastern Washington.

Progeroid syndrome is a group of genetic disorders characterized by accelerated aging. Molecular mechanisms of progeroid syndrome include abnormalities in genomic stability, nuclear structure, lipid and carbohydrate metabolisms as well as mitochondrial functions. Genomic instability is a major category of progeroid syndromes in humans. Prototypical example is the Werner syndrome caused by the mutations in the WRN gene which encodes a DNA helicase. Cells derived from progeroid syndrome patients generally exhibit phenotypes of accelerated cellular senescence with a very limited replicative lifespan. International Registry of Werner Syndrome recruits progeroid syndrome patients from all over the world for the genetic study. Among the subset of those patients, a recurrent disease mutation has been identified in the POLD1 gene. The POLD1 gene encodes a catalytic subunit of polymerase delta, a major replication polymerase which is also involved in translesion DNA synthesis. The POLD1 mutation is known to cause MDPL (mandibular hypoplasia, deafness, progeroid features, and lipodystrophy) syndrome. In our study, cellular model of MDPL syndrome was generated by expressing mutant POLD1 cDNA in human fibroblasts via lentiviral system. Consequences of the POLD1 mutation are determined by various assays including cell growth, accumulation of DNA damage and sensitivity to genotoxic agents. The eventual goal is to develop therapeutic approaches that ameliorate cellular disease phenotypes. We plan to test candidate therapeutic approaches using established POLD1 cell lines and assay methods. More recently, a mutation in the SMAD4 gene, was identified in one progeroid patient. SMAD4 gene encodes a crucial member of the cellular transduction pathway. The wildtype and mutant SMAD4 are being expressed in human fibroblasts to determine whether cells expressing mutant SMAD4 exhibit phenotypes of accelerated senescence. This project would provide us with an understanding of recently identified progeroid loci and likely sheds a light on the previously unknown mechanisms of normal aging and age-related disorders.

Humans hear sound through two main pathways: air conduction (AC) and bone conduction (BC). The AC pathway is dominant under normal listening conditions, but conductive hearing loss (e.g. outer/middle ear diseases) impairs one’s ability to hear by AC. BC hearing aids can improve hearing under such conditions. To determine the presence of a conductive hearing loss, BC hearing thresholds must be compared to AC thresholds. For populations that cannot respond reliably to behavioral audiometric testing (e.g. infants, elderly, individuals with cognitive impairments), clinicians instead record sound-evoked brainstem activity through the auditory brainstem response (ABR) test. While AC ABR test results are clinically reliable, BC ABR test results suffer from electrical artefacts generated by the BC transducer and variable ABR waveform morphology. Therefore, determining the presence of a conductive hearing loss by comparing AC and BC ABRs is often unreliable. This study aimed to (1) reduce the severity of electrical artefacts present in the early BC ABR waveform (Wave I/II) by shielding bone-vibrating transducers (Radioear B81) with MuMETAL and (2) improve the quality of the ABR signal by using ‘chirp’ stimuli (ascending frequency sweep) to enhance the summating amplitude of auditory neural responses. Ongoing measurements leverage three transducer types in total (shielded and unshielded BC, earphone AC) and three stimulus types (chirps, constant-frequency tone bursts, and broadband “clicks”) to evaluate main and combinatorial effects of the transducer and stimulus on BC ABR data quality. Early indications show that shielding the BC transducer does not materially change its frequency response. Therefore, any observed changes in the BC ABR waveform can be attributed to electrical shielding and/or stimulus modifications per se and not to unintended changes in transducer acoustic output. Data will inform efforts to improve the clinical reliability and utility of BC ABR measures for detection and treatment of conductive hearing loss.

Ovarian cancer is the deadliest gynecological malignancy: nearly 70% of patients are diagnosed at late stage and 70% relapse. Cytoreductive surgery and chemotherapy are the standard of care, yet fewer than 50% of patients live 5 years past diagnosis. Innovative therapies are desperately needed. Immunotherapy using T cells engineered to express a T cell receptor (TCR) targeting proteins overexpressed in tumors is a promising strategy that limits tumor growth and has minimal toxicity. Mesothelin (Msln) is overexpressed in over 75% of ovarian cancer patients and has been identified as a promising cancer antigen because it contributes to the malignancy and invasiveness. Our group has shown that targeting Msln with engineered T cells (TCRMsln) in the mouse ID8 ovarian tumor model, which recapitulates essential aspects of the human disease, can prolong survival of mice with advanced disease. However, our data also show that immunosuppressive features in the tumor cause T cells to become dysfunctional and/or die. Fas ligand (FasL) is a transmembrane death-inducing protein present in ovarian tumors, and may be used by tumor cells to escape the immune response by inducing cell death of beneficial lymphocytes expressing the Fas receptor (Fas). We hypothesized that we could overcome this T cell evasion mechanism using immunomodulatory fusion proteins (IFP). We generated IFPs that combine the Fas extracellular binding domain to a co-stimulatory domain, CD28 or 4-1BB, instead of the standard death domain, to trigger T cell activation. T cells expressing an IFP had enhanced proliferation and persistence in ID8 tumors relative T cells lacking an IFP. Further, ID8 mice treated with TCRMsln T cells expressing an IFP had prolonged survival compared to mice treated with the TCRMsln T cells alone. Many solid tumors overexpress FasL, thus our findings have the potential to enhance engineered T cell therapy against other malignancies.

The Zea mays (maize) crop is essential to global agriculture and food security, and is also vital to the US economy. Like many crop plants, maize is often subjected to extreme environmental stresses, such as drought, extreme cold and high salinity, that negatively impact crop yield. Therefore, it is important to characterize the molecular (epigenetic) changes that occur to a gene under environmental stress conditions in order to manipulate these responses to improve crop yield under stress. We are interested in characterizing the epigenetic regulation of stress-responsive transcription factors under normal (control) and abiotic stress (drought) conditions in maize seedlings. Using bisulfite conversion of genomic DNA, we previously identified that the Zea mays basic transcription factor 3 (ZmBTF3) gene displays some variations in methylation patterns in parts of the gene promoter between the two treatments. To confirm these results, we used an alternative method: a methylation sensitive restriction digest technique, which uses methylation sensitive restriction enzymes (MSREs) that cut DNA molecules at precise locations and are sensitive to DNA methylation. Our results show some treatment (control vs. drought) and restriction enzyme (sequence/context) specific methylation patterns. Using these two independent techniques, we identify stress-responsive epigenetic variations (DNA methylation) in the promoter region of the ZmBTF3 gene, previously uncharacterized in maize. Ongoing research includes (i) characterizing the sequence contexts of these methylation patterns between the two treatments, (ii) determining if the observed DNA methylation changes correlate with transcription of the ZmBTF3 gene, and (iii) characterizing the drought response phenotype in maize plants with a mutation in the ZmBTF3 gene. This study will help us gain a better understanding of how the BTF3 gene in maize is regulated through epigenetic modifications.

The ability to respond to physical stress can be useful in gauging resilience to aging. Vaccine inoculation is an immune stress that triggers an easily quantifiable antibody response. This study was designed to identify antibody response patterns to a clinically relevant pneumococcal vaccine in mice, in order to show an association with resistance to age-related decline. Twenty C57BL/6 and twenty CB6F1 male mice in age groups of 8, 16, 24, and 32 months were inoculated with one subcutaneous dose of pneumococcal capsular antigen in adjuvant. Serum was collected 16 days later, diluted 1 to 625, and immunoglobulin G antibody levels were measured by an enzyme-linked immunosorbent assay (ELISA) using 410/490 optical density. All data points were standardized against serum from non-vaccinated mice. There was a clear differentiation between high and low antibody responders in both mouse strains, within the range of antibody levels following inoculation. Interestingly, the high antibody response pattern seen in mice at 8 months of age was also seen in a robust manner in mice at ages 16, 24, and 32 months, as opposed to their low-responding counterparts which actually showed decreasing antibody response patterns in an age-dependent manner. In general, C57BL/6 mice had a more vigorous antibody response than CB6F1 mice. These observations suggest that age impacts the effectiveness of a pneumococcal vaccine in conferring an adaptive immune response, and that certain individual mice can robustly respond regardless of age. This high response pattern can thus be very valuable in determining if a robust antibody response is a resilience factor capable of predicting resistance to age-related decline. The concept is clinically relevant since pneumococcal vaccine, for example Prevnar-13, is routinely used to protect elderly populations, and sera can be readily available to test robustness of antibody responses in relation to aging related parameters.     

Nearly 22 million HIV-positive people are receiving antiretroviral therapy in order to suppress their HIV infections. They need consistent viral load monitoring to track viral suppression and detect the possibility of viral rebound. Nucleic acid amplification tests (NAATs) are used to measure the viral load in a patient's blood. Traditional, laboratory-based NAATs require complex robotic systems to automate HIV RNA purification, amplification, and detection from blood. Since the majority of those living with HIV are located in low and middle income countries, there is a need for rapid viral load monitoring at the point of care (POC). We aim to provide accessible HIV viral load testing through low-cost, integrated POC NAAT devices. These proof-of-concept devices operate as a two-step assay to extract and detect nucliec acids in blood. An electrophoretic separation technique called isotachophoresis (ITP) separates HIV RNA from other components in a blood sample. An isothermal nucleic acid amplification assay amplifies the purified, concentrated nucleic acids in order to detect and quantify their presence. We present our development of a novel ITP system to remove potent contaminants from Proteinase K (PK) digested serum and extract highly pure nucleic acids automatically. Through computational modelling, a dual trailing electrolyte (TE) buffer system was designed to exploit the isoelectric point of PK for its removal, while simultaneously concentrating nucleic acids away from serum components. We demonstrate system control through comparison of experimental observations to model predictions by performing dual-TE ITP on pH paper. We also show that the dual-TE system improves upon previous limits of detection for DNA extraction and detection from complex samples. Our system processes 40 microliters of blood in 20 minutes using only simple buffers, a paper strip and an electric field - making it an ideal tool for use in a rapid NAAT for HIV viral load testing. 

Air pollution due to traffic causes many human health problems including neurological disorders. Recently, compelling evidence from the literature has demonstrated that gut microbiome is a newly discovered organ that critically regulates the neurodegenerative disorders including Alzheimer’s disease (AD) via remote-sensing mechanisms. One of the major classes of microbial metabolites are the secondary bile acids. My research focuses on the relationship between TRAP (Traffic-Related Air Pollution) and bacterial metabolism of bile acids that might have significant implications on human health. Male and female wild Type (WT) and transgenic (TG; over-expresses two human AD risk genes [mutant amyloid precursor protein and presenilin-1]) rats were exposed to TRAP or filtered air (FA) for different time points. I focused on rats up to 10 months old that were exposed to TRAP or FA for up to 9 months and from their intestinal contents I extracted bile acids, DNA and RNA to compare which factors might affect gene expression. Bacterial gene and taxa abundance were measured by quantitative PCR (qPCR) and statistically analyzed for significance. Two-way ANOVA analyses were conducted separately among male and female rats; only male rats showed significant changes by qPCR. Exposure to TRAP increased levels of Lactobacillus reuteri in WT males, but conversely decreased L. reuteri in TG males. By understanding different factors affecting bacterial metabolism of bile acids, we are exploring if this could possibly affect human health as well. This can potentially help clinicians and environmentalists to improve clinical outcomes and policies regarding traffic-related air pollution.

Wireless power transfer has many applications, from powering biomedical implants to wireless sensors. For more practical use, however, several challenges must be overcome, such as a lack of efficiency and power leakage to other nearby electronics. These issues become especially difficult to tackle with a moving receiver. To combat these problems, an array of magnetically coupled coils was designed. Previous work has shown the capabilities of this system when one coil of the array is supplied with power. In this work, I explore the possible benefits of having two coils in the array driven with power instead, studying the interaction between the different coils. By adjusting parameters such as the phase relationship between the two transmitters’ signals, we aim to optimize power delivery to specific targets and simultaneously minimize leakage to other areas. I tested different configurations of the system in a series of experiments and analyzed measured data to determine which setup is most favorable. Afterwards, I evaluated the efficiency of the configuration compared to the previous single-transmitter case. This provides better insight into how the coils in the array magnetically interact with one another, which will inform future design decisions. It can also eventually lead to better solutions for delivering high power to selected targets within a given space. This can create flexible, efficient, and safe wirelessly charged electronic implants for a variety of biomedical applications, enabling further research in the field and the development of novel solutions.

It is often assumed that terrestrial surface climate in the Arctic is largely controlled by the surface albedo. As the land surface becomes darker, it will absorb more solar energy. The extra absorbed energy is then released through longwave radiation and turbulent fluxes. If the total amount of latent heating is relatively constant, the extra absorbed radiation leads to warmer temperatures. The evaporative resistance of the land surface sets the difficultly for water to evaporate, and thus changes the partitioning between the turbulent fluxes of latent and sensible heat which could lead to a different surface temperature. These effects are known; however, it is unclear what the relative contribution of evaporative resistance and albedo are for the terrestrial surface climate. We used the albedo and evaporative resistance values derived from two common vegetation types, needleleaf evergreen trees and broadleaf deciduous trees, to simulate the climate response to a change in land surface albedo and evaporative resistance in factorial combinations. We find that changing the evaporative resistance between the two plant types has a large effect on the surface energy budget that is almost if not equivalent to changing albedo alone. Lower evaporative resistances lead to an increase of low clouds relative to higher resistance. As a result, less solar radiation reaches the surface when the evaporative resistance is lower. In contrast, the albedo controls how much of the incoming solar radiation gets absorbed. The reflection of light due to the difference in albedo is of the same magnitude as the loss of incident sunlight due to increased cloud cover under lower evaporative resistance. Our results demonstrate that realistic changes in evaporative resistance can have just as large of an impact on Arctic terrestrial surface climate as changes in surface albedo due to cloud feedbacks.

The North American Nanohertz Observatory for Gravitational Waves (NANOGrav) uses an array of galactic millisecond pulsars to search for low frequency gravitational waves. The stability of millisecond pulsars allows their pulse time of arrival (TOA) to be used as precise clocks. Gravitational waves will produce timing delays that are are correlated across pulsars. In order to detect such correlations in TOAs, we must also understand the noise processes in the pulsar signal. Noise model selection aims to produce custom noise descriptions for each pulsar. Using NANOGrav's search code enterprise a Markov Chain Monte Carlo (MCMC) algorithm is used to search for the most favored model. A hyper model framework is used to explore across a set of models, which have different red noise and dispersion measure (interstellar medium effect) processes. The posterior odds ratio is then represented by the relative amount of time the chain spends in a model. An iterative approach is taken, where one model selection analysis is used to inform the next set of models from which to choose. The resulting noise descriptions will aid in mitigating its effects within the pulsar signals, increasing chances of gravitational wave detection.

Recurring slope lineae (RSL) observed on Mars appear to be flows of liquid water because they seasonally propagate down sunny slopes in the spring and fade during the winter. Liquid water suggests the potential for life on Mars’ surface and has implications for future exploration; however, recent hypotheses contend that RSL form via dry sand avalanches. To test wet vs. dry flow hypotheses, we analyzed images and topographic data from Garni crater taken by the High Resolution Imaging Science Experiment (HiRISE) during the Martian summer and winter. Our results show that RSL size correlates with areas where we expect high windblown sand deposition, such as on the SE lee side of the crater, or in small gullies below large headwalls. Additionally, RSL do not appear on the wind-scoured NW side of the crater. These surface relationships indicate that RSL in Garni crater form via a dry process in which windblown sand is deposited by prevailing NE winds and seasonally avalanches down steep slopes. To further test our conclusions, we are examining additional confirmed RSL sites on Mars to see if they display the same behavior.

Methods to differentiate stem cells into cardiomyocytes have been well established. However, a limitation for the successful application of these cells for research and medicine has been their fetal-like phenotype with respect to cell size, contractility, calcium handling, metabolism, and electrophysiology. We sought to increase the maturity of human pluripotent stem cell derived cardiomyocytes (hPSC-CMs) through metabolic pathway regulation. We hypothesized that switching the main metabolic substrates from glucose to fatty acids, mimicking the switch from placental to breast milk nutrient consumption that occurs during development, will increase hPSC-CM maturation. RUES2 embryonic stem cells were differentiated into cardiomyocytes and then treated with base media with varying glucose and calcium concentrations and fatty acid supplementation. Using quantitative PCR to measure gene expression, we measured an inverse relationship between glucose levels and markers of cardiomyocyte maturation: increased expression of cardiac troponin I relative to skeletal troponin I isoforms (TNNI3:TNNI1), increased expression of metabolic (CPT1B, PPARGC1A) and electrical maturity markers (KCNJ2, RYR2). These maturation markers were not influenced with fatty acid supplementation but were enhanced upon the addition of thyroid hormone and dexamethasone. We further quantified nucleation and sarcomere spacing to assess structural features of maturation using confocal microscopy. To understand the mechanisms by which media nutrients and signaling molecules cause phenotypic changes we investigated the relationship between maturation and global epigenetic state. Western blot revealed increases in global acetylation levels, measured by histone H3 acetylation, linked to maturation signaling. These findings depict a direct relationship between glucose metabolism and the development of a mature phenotype in hPSC-CMs, mediated by epigenetic mechanisms.

Myocardial infarction (MI) is the leading cause of death globally. Methods to regenerate cardiac tissue after MI has focused on inducing proliferation in adult cardiomyocytes near infarcted tissue or injecting stem cell-derived cardiomyocytes with proliferative capacity into the infarcted tissue. However, optimal regeneration has not been achieved with these methods, as the mechanism behind adult cardiomyocyte proliferation is not well understood and proliferative stem cell-derived cardiomyocytes are phenotypically and functionally immature. Exploration of the mechanism of cardiomyocyte proliferation is therefore necessary to enable optimal regeneration of cardiac tissue and function and MI. We hypothesize that the sarcomere structure, the basic muscle unit of the cardiomyocyte, is the limiting factor in proliferation of cardiomyocytes. To investigate this hypothesis, we have performed a thorough characterization and comparison of stem cell-derived wild type cardiomyocytes (WTC-CMs) and troponin I double knock out cardiomyocytes (TNNIDKO-CMs) which have an incomplete sarcomere structure due to the lack of troponin I. After confirming TNNIDKO-CMs and WT-CMs only vary in their sarcomere structure, we developed a coculture platform to demonstrate the mechanical weakness of TNNIDKO-CMs sarcomere structure. We then performed proliferation assays utilizing multiple proliferation markers to observe if proliferation was higher in the TNNIDKO-CMs with the incomplete sarcomere structures. Preliminary results have shown that TNNIDKO-CMs are more proliferative than WTC-CMs, thus implicating that sarcomere structure plays a role in controlling cardiomyocyte proliferation. Successful characterization of TNNDKIO-CMs and their increased proliferative capacity will elucidate the sarcomere structure’s role in proliferation as well as develop a more comprehensive understanding of the underlying mechanism behind proliferation to help progress therapies for regeneration of cardiac tissue after MI.

The DAMIC experiment searches for dark matter particle interactions with silicon charged-coupling devices (CCDs). The expected signal are the nuclear recoils following the interaction between the external particles and the silicon nuclei of the CCD. These appear as groupings of pixels on the CCD images where the charge collects from the ionized silicon. Recently, it was proposed that the recoiling silicon nucleus could cause a secondary ionization signal a few pixels away. This is due to a three-body final state where a third particle, a photon, is emitted at the point of interaction. We investigated a series of images from a CCD that was exposed to a neutron source, which also produces nuclear recoils in the silicon. We looked for spatial correlations between events and found that there was an excess of correlated events within the energy range of the neutron source. This excess was found in the neutron data but was absent in the background data. Currently, we are looking at the energy and separation of the events in more detail to learn about their origin. If the observation of three-body final states is confirmed, DAMIC will have found a new way to search for dark matter.

Chlamydia trachomatis is a human urogenital pathogen and the leading cause of bacterial sexually transmitted infection worldwide.  A major aim of the Hybiske Lab is to develop a functional genetic understanding for Chlamydia. I am studying a set of newly generated C. trachomatis chimeric mutants that were generated from interspecies lateral gene transfer between C. trachomatis and the mouse adapted species C. muridarum. This series of recombinant strains contain a differing extent of genetic exchange surrounding the predicted inclusion membrane protein (Inc) CT147. CT147 is predicted to be secreted into the Chlamydia-containing vacuole (inclusion) membrane by type III secretion and subsequently mediate molecular interactions with host proteins. In cultured cells, strains lacking CT147 prematurely rupture inclusions at 24 hours post infection, in stark contrast to wildtype C. trachomatis or control recombinant strains that grow normally inside host cells and do not exhibit inclusion lysis at any stage of infection. We therefore hypothesized that the C. muridarum ortholog of CT147 is incompatible with the series of ~30 Inc proteins normally secreted by C. trachomatis, in such a way that inclusion integrity is not properly maintained during this strain’s developmental growth. I have used quantitative RT-PCR to evaluate transcript levels early and late in each strain’s life cycle to determine if the diversion in phenotypes is due to an alteration in the Inc’s promoter. I have expressed in trans CT147 in the chimeric strain lacking the Inc and analyze if CT147 can rescue the premature rupturing phenotype. Similarly, I expressed the C. muridarum ortholog TC0424 into wild type C. trachomatis to determine if the phenotype is dominant. Overall, we anticipate that a molecular and functional characterization of this novel Inc protein will reveal new insight into the mechanisms by which Chlamydia manipulate host cell function to facilitate their infection.

Euphausiids (krill) are zooplankton that play a large role in Puget Sound’s marine ecosystem. They are widespread and numerous and have been suggested to play a large role in energy cycling and food web dynamics. Vertical layering of species is not uncommon, and patterns can persist between years, suggesting a significance to the layering. During the day, euphausiids form deep layers in the water column with a thickness in the tens of meters where ecosystem dynamics may differ between the top and bottom of the layer. These layers can be detected by acoustic systems, but characteristics of individuals cannot be resolved. In this study, we used net tows to sample euphausiids at different relative depths within a layer. We recorded the length, sex, and species for statistical analysis to assess the homogeneity of the layer. Comparisons against other locations in Puget Sound will allow us to see if vertical structures are consistent or if other factors such as the presence of predatory fish can explain for differences. This project will provide insight on ecosystem dynamics and carbon cycling.

Over the last few decades, there has been increasing interest worldwide in nature preschool programs, which provide young children the freedom to explore, discover, and construct knowledge from their direct experience with the natural environment. This research project investigates how the presence of nature provides affordances that lead to important developmental outcomes. Using a naturalistic observational methodology, I collected over 700 short videos of preschool children (18 months – 6 years old) interacting with nature in a leading nature preschool program in Hong Kong. Analyses draw on interaction pattern theory, wherein an interaction pattern is understood to characterize essential forms of human-nature interaction, specified abstractly enough such that many different instances of the same pattern can be enacted. Results are revealing 38 keystone interaction patterns, such as Cohabiting with Wild Animals, Immersing One’s Body in Water, Splashing in Mud Puddle, Climbing High in Small tree, Gathering Nature Items, etc. Based on this interaction pattern analysis, I am then testing a core hypothesis: that children enact more relational behavior in more wild parts of the outside nature, and more domination behavior over nature in more domestic parts of outside nature. If this hypothesis is supported, it will provide data that speaks to how interaction with more wild forms of nature can help move our world away from its largely domination-oriented sensibilities (human domination over nature and over other people) to those that are more relational.

Methylmercury (MeHg) is a bioaccumulative neurotoxin, dangerous to human health even at trace levels. In inundated soils, MeHg is formed from inorganic mercury by mercury-methylating microorganisms; a process termed methylation. Demethylation, by contrast, converts MeHg into less-dangerous inorganic mercury, and also occurs via microbial activity throughout the aquatic soil profile. Rice grains can be contaminated with MeHg when grown in soils where methylation rates are high; human exposure to MeHg is thus a serious public health concern in places where rice cultivation, high rates of consumption, and soil mercury (Hg) contamination overlap. Our research aims to better understand the soil conditions that favor demethylation over methylation – this information can then be used to reduce rice grain contamination through agricultural practices or rice breeding programs. Specifically, our research focuses on the role of oxygenation and carbon root exudates on the net MeHg accumulation throughout the soil profile. Rice plants grow in flooded, oxygen-free (anoxic) soils, but their roots can leak oxygen (making the rice rhizosphere oxygenated in varying degrees), as well as carbon root exudates. Our project simulated both fully oxic and transiently-oxic (transition) zones, with two different levels of root exudates; we use isotopic tracers to assess respective methylation and demethylation rates in all four treatments in both the vegetated (rhizosphere) and non-vegetated (bulk) soil. Carbon root exudates have been collected from hydroponically-grown rice variety M-206, and can be applied to different soil zones via tubules. Oxygenation of the soil can be measured with mm-scale optode imagery, which allows delicate testing of various oxygen-introduction designs. My role in this interdisciplinary project has been to develop, scale-up, automate, and verify the accuracy and dependability of root-oxygenation and root-exudate introduction systems to be used in upcoming experiments.

In Zea mays (maize), MEDIATOR OF PARAMUTATION 1 (MOP1) is involved in paramutation and epigenetic regulation of gene expression. MOP1 in an RNA-dependent RNA polymerase that functions as part of the RNA-directed DNA methylation (RdDM) pathway, by producing double-stranded RNA molecules that are further processed into small interfering RNAs (siRNAs). These siRNAs are able to trigger DNA methylation which can decrease or silence gene expression. The MOP1-FLAG transgene was created by overexpressing the mop1 gene with the FLAG epitope tag. As a consequence of using agrobacterium-mediated transformation, the chromosomal location of the MOP1-FLAG transgene is unknown. To identify the sequences flanking the transgene, we used an adapter ligation-mediated PCR and cloning technique, as described by O’Malley. To do so, we first digested the MOP1-FLAG DNA with restriction enzymes designed to cut the DNA in specific locations along the genome. We then ligated adapters onto the DNA fragments. Through PCR using gene-specific and adapter-specific primers, we were then able to amplify the fragments that contain MOP1-FLAG and the surrounding genomic sequence, clone and then sequence them. We used the recovered flanking sequence to BLAST search the maize genome in order to identify the maize chromosome that the MOP1-FLAG transgene is on. Chromosomal mapping of the MOP1-FLAG transgene is useful to distinguish between the endogenous mop1 gene in ongoing complementation and chromatin immunoprecipitation (ChIP) experiments.

Bacteria can colonize many types of surfaces if those areas have the necessities for survival; these surfaces can act as a shared point of contact for the potential spread of diseases. A prime example lies on the handles of the immensely popular ride share bicycles in Seattle. By swabbing from the handles of bikes in different public locations across Seattle, we can assess the bacterial load. We examined the extent of bacterial colonization on bike handles at light rail stations, dog parks and different neighborhoods at different times of the day. This analysis highlights the level of risk these shared contact points pose with a focus on what conditions are conducive to high bacterial loads. 

Water is the substance that exists everywhere in our lives ranging from drinking water to the blood in the body. It is well known that there are 3 phases of water: gas, liquid and solid. Yet, in Dr. Gerald Pollack’s lab, we conduct researches on the Exclusion Zone (EZ) water, which we term as the ‘Fourth Phase of Water.’ Dr. Pollack’s lab centers largely on the identification of EZ water and many applications in nature and technology. Among the natural applications, since EZ water fills out cells, and they cannot function without enough EZ water, the lab emphasizes on the role of EZ water in human health, including cell biology. Dr. Pollack’s lab conducts the research that is uncovering the nature’s hidden secret and the tremendous potential of EZ water to be applied to different bioengineering products. I am currently conducting a project on how Wi-Fi impacts EZ water as an external source of disturbances. Humans are exposed to Wi-Fi signals constantly in our everyday lives. As human body cells are filled with EZ water, we predict the Wi-Fi signals could alter our bodily functions through changes in EZ water properties such as amount of EZ water. As EZ water can be built around hydrophilic substances, Nafion tube, hydrophilic tube is used to build EZ water, and then I can measure the amount of EZ water by measuring the length of EZ water built around the tube in 2D picture. For this project, we compare the difference in the amount of EZ water built with and without presence of Wi-Fi. We currently have preliminary results that Wi-Fi decreases amount of EZ water. As a further step in the future, I hope to research on different bioengineering fields to reduce the effect of Wi-Fi on EZ water for further health care.

Hearing loss is often due to the absence or degeneration of hair cells in the cochlea, thus it is important to understand the transcriptional control mechanisms specifying the prosensory cells that generate hair cells and support cells. Early B-Cell Factor1 (Ebf1) is a transcription factor that was brought to our attention from motif enrichment in replicated ATAC-seq peaks detected in prosensory cells and non-prosensory cells. We observed that in the open chromatin regions and dynamic regions during the development of prosensory cells showed greater enrichment of Ebf motifs. This suggested that Ebf1 could be acting as a pioneer factor. To determine whether Ebf1 influences cochlear development, we generated a Sox2CreER: Ebf1 fl/fl allele by crossing Sox2-CreER mice and Ebf1-floxed mice. Administration of tamoxifen to mice orally leads to Cre-mediating deletion of Ebf1 DNA binding domain and formation of the recombinant Ebf1-GFP fusion protein. To determine whether the Ebf1 knockout is successful we will compare Ebf1 expression between the Ebf1 knockout and wildtype through qRT-PCR. We will also compare the localization of Ebf1-GFP fusion protein in the Ebf1 knockout and wildtype. To determine whether Ebf1 affects cochlear differentiation, we will immunolabel for Sox2, Egfp, and Myo7a, this allows us to determine the presence of support cells (anti-Sox2), hair cells (anti-Myo7a) and the Ebf1 reporter (anti-Egfp) and compare support cell and hair cell counts between the Ebf1 knockout and wildtype. If the comparison shows a decrease or increase in support cell and hair cell counts in the Ebf1 knockout compared to the wildtype or the lack of support cells or hair cells in the Ebf1 knockout, then it suggests that Ebf1 is necessary for cochlear differentiation.

Drug addiction is a neuropsychiatric disease characterized by compulsive and uncontrolled drug use. Rodent self-administration models can represent certain aspects of substance abuse in humans. Studies have shown drug use and drug-associated cues increase dopamine transmission. Data from the Paul Phillip’s Lab demonstrated rats that escalated in their cocaine intake had a decrement in dopamine release to cues in the nucleus accumbens. Administration of Levodopa (L-DOPA), the molecular precursor to dopamine, decreased cocaine consumption to pre-escalated levels. However, we have not yet confirmed whether the impact of drug-associated stimuli and its dopamine-mediated aspects can be generalized to opioid use. Thus, the current study investigates if increased dopaminergic signaling via L-DOPA decreases consumption of fentanyl, a highly potent synthetic opioid. We tested L-DOPA’s effect in two separate behavioral assays. The first assay is a two-bottle choice paradigm in which the animal is given 3-hour access to liquid fentanyl (50μg/mL) and water. Additionally, animals were trained to self-administer fentanyl, in which rats were required to nose poke for liquid drug delivery. Preliminary data shows intraperitoneal injection of L-DOPA significantly decreases overall fentanyl consumption in both two-bottle choice (p<0.05) and in the instrumental task (p<0.05). These data imply that dopamine release is regulating opioid consumption. A second aim of the current work is to characterize drug-taking patterns in animals self-administering fentanyl orally. Permitting animals to extended access to drugs of abuse is known to induce escalation of drug intake. Utilizing this paradigm we provide six hours of liquid fentanyl access and examine intake patterns of individual animals across sessions. Future studies will utilize electrochemical detection techniques to examine subsecond changes in dopaminergic signaling during oral self-administration. Overall, this work provides evidence that dopaminergic signaling regulates fentanyl consumption and treatment with L-DOPA can stabilize and reduce drug intake.

Domoic acid (DA), a common marine neurotoxin found in marine organisms such as shellfish and finfish, is gaining public attention with increasing outbreaks in the USA, Australia, China, and some countries in Europe. Most DA outbreaks are observed along coastal regions, increasing the risk of exposure by seafood consumption. However, little is known about the effects of low level prenatal exposure of DA. To address this growing public health issue, we administered behavioral and cognitive tests on 27 Macaca fascicularis infants prenatally exposed to 0, 0.075, and 0.15 mg/kg/day of DA. Their cognitive capacities were analyzed based on their speed of learning new tests using the Wisconsin General Testing Apparatus (WGTA). The WGTA requires testers to present stimuli to the infant and, depending on the response, reward the infant for a correct response. I was one of several testers that worked with the infants during testing sessions 5 days per week. I also worked with the investigators and data analysis team to analyze the results of the WGTA tests. Results from early cognitive tests of object and spatial discrimination did not indicate a statistically significant detrimental effect of DA on these basic learning tasks. This suggests that DA does not have an impact on basic discrimination learning in the early stages of life (< 1 year). However, due to the potential for delayed toxicity of DA, more complex learning and memory tests are being administered as the infants mature. The results of this study will provide insights into future research and influence policies being implemented regarding seafood consumption and food safety.

Seasonal dark streaks on Mars known as Recurring Slope Lineae (RSL) propagate down steep, warm slopes and appear to be liquid water flows. However, the mechanism behind RSL formation is controversial, and both dry granular flow and percolating water hypotheses have been proposed. To determine if water is responsible for RSL formation, I investigated similar dark streaks generated by percolating water in the McMurdo Dry Valleys (MDV) of Antarctica, an extremely cold and dry Mars analog site. The goal of this research is to identify the source of water to the MDV streaks, and to compare the MDV streaks to Martian RSL. I characterized the MDV streaks by (1) analyzing a ~30-day time-lapse video of the streaks collected on site, (2) investigating the drainage hydrology, and (3) comparing hundreds of satellite images of the streaks from 2003-2017. My results show that the MDV streaks are very different from Martian RSL, which indicates that water is not involved in RSL formation. Unlike Martian RSL, I found that MDV streaks propagate downslope at much slower rates compared to Martian RSL, and do not grow and retreat seasonally. Furthermore, MDV streaks have distinctive patterns not apparent in Martian RSLs, and rapidly darken/lighten in response to relative humidity changes. Finally, MDV streaks form in response to extremely warm summer temperatures, conditions which are unlikely to prevail on Mars. These results are important for understanding how and if liquid water occurs on Mars’ surface.

Rhabdomyosarcoma (RMS) is the most common pediatric soft tissue sarcoma. The survival outcomes are poor for patients with relapsed and metastatic disease. Embryonal RMS (ERMS), a major subtype of RMS, is driven by genetic mutations in the RAS pathway. Cancer stem cells (CSCs) drive the process of self-renewal to recapitulate the heterogeneity of the cancer and are thought to be responsible for cancer relapse due to their resistance to conventional chemotherapy. In ERMS cells, a population of CSCs has been identified and is believed to play a critical role in tumor relapse and metastasis. A previous screen of all known human kinases identified candidates that played a role in regulating self-renewal of ERMS CSCs. I have prioritized two most promising candidates, ERN1 and MAPK10, for further characterization. I hypothesize that these kinases regulate the self-renewal capacity of CSCs but do not affect growth of non-CSC tumor cells. Using the gene-editing tool, CRISPR (Clustered Regulatory Interspaced Short Palindromic Repeats)/Cas9, I knocked out ERN1 and MAPK10 in ERMS cells and assessed their role in regulating ERMS CSC cell growth and self-renewal. To assess whether the effects of gene disruption are specific to the changes in the CSC population in vitro and in vivo, I used an ERMS CSC reporter cell line that specifically expresses Green Fluorescent Protein (GFP) in CSCs. The ERMS CSC reporter cell lines harboring ERN1 or MAPK10 gene disruption are subjected to self-renewal assays in cultured ERMS cells in vitro and ERMS xenograft model in vivo. My findings will provide new insights into the biological mechanism underlying as well as new potential targets against relapse and metastasis of ERMS.

 Esophageal adenocarcinoma (EAC) has received considerable attention recently due to a three-fold increase in occurrence affecting 20,000 people each year in the US with <20% patients surviving 5 years past diagnosis. Thus, there is an urgent need to advance our understanding of EAC’s molecular pathology and to use this understanding in improving our ability to prevent and manage EAC. Gene mutations and epigenetic alterations drive the formation of a pre-malignant condition called Barretts’ esophagus (BE), which can then progress to EAC. Epigenetic modifications of numerous genes, in the form of DNA hypermethylation with subsequent gene silencing, have been demonstrated to occur frequently in BE and have been postulated as a driving force for EAC formation. In prior studies, we discovered a novel methylated gene, TUSC1, with silenced expression in primary EAC tissue samples and cancer cell lines (Yu et al., Gut 2018). This study aims to investigate the biological consequence of TUSC1 loss in EAC cell lines by utilizing CRISPR-Cas9 gene editing technology. We hypothesize that TUSC1 is a novel tumor suppressor gene in EAC. To test this hypothesis, we will be generating TUSC1 knock-out (KO) EAC cells by introducing TUSC1-silencing guide-RNA into EAC cell culture. We will be assessing the extent of TUSC1 KO at the gene expression and protein level by conducting quantitative real-time PCR and Western blotting, comparing the KO cells to the control cells. We will also use PCR-based sequencing to verify the DNA alteration introduced by CRISPR in single-cell colonies. Successful completion of these experiments will lead to the next stage of phenotypic assays, in which we will investigate whether loss of TUSC1 in EAC cells would promote oncogenic behaviors of cancer cells. The proposed studies would demonstrate the biological function of TUSC1 in EAC and illustrate the molecular mechanisms of DNA-methylation driving EAC tumorigenesis.

Non-coding regions account for approximately 98% of the genome and play a significant role in regulating and maintaining levels of gene expression via transcriptional and translational control mechanisms. Our lab focuses on the functional characterization of non-coding regulatory regions in the human retina and identifying mutations within these elements that contribute to inherited retinal diseases. In pursuit of this long-term goal, my aim is to establish an in vitro model to dissect non-coding regulatory elements in the human retina. Retinal organoid cultures are a promising new system for studying the development of the human eye, however it is currently unknown if organoids recapitulate all of the features of the adult human retina. Based on similarities of cell types and gene expression, we hypothesized that retinal organoids recapitulate some non-coding regulatory features of the normal human retina. To identify both shared and specific non-coding regulatory elements, I profiled the epigenetic landscape of developing human retinal organoids using a genome-wide sequencing approach (ATAC-Seq) to quantify chromatin accessibility - a feature of non-coding regulatory elements. I then used bioinformatics techniques such as genome track assembly, peak calling, and gene ontology to compare my organoid dataset to adult human retina data we previously generated and to a published dataset on the developing human retina. We found distinct sets of non-coding regulatory elements that were shared between retinal organoids and the human retina, as well as elements that were unique to each system. These comparative data have yielded additional insight on which non-coding elements may influence retinal disease phenotypes. Furthermore, these data will potentially give us a clearer understanding of the epigenetic landscape of the developing and adult retina in a context that will drive progress towards regenerating damaged photoreceptor cells in the future.

The most effective semiconductors used as absorber layers for solar cells have concerns regarding high capital expenditure (CapEx) for new manufacturing facilities, earth abundance, toxicity, or cost-volatility of the materials. Solution processing is a low cost, low temperature development method leading to lower CapEx. The exploration of new photovoltaic materials seeks to develop an earth abundant, non toxic semiconductor via solution processing with efficiencies comparable to materials like silicon or CdTe. Bismuth rudorffites (chemical formula A_aBi_bX_a+3b) are an interesting category of new materials, proven to be solution processable, to have high absorption, and to be capable of cell efficiencies over 4%. My project seeks to optimize the thin-film morphology and the open circuit voltage (V_oc) of bismuth rudorffite layers, both of which are crucial to achieving high efficiencies. A good morphology will be phase-pure and densely packed, with large grains. By determining the effects of each parameter of the thin-film deposition process (spin-coating, in our case) through Scanning-Electron Microscope imaging and X-Ray Diffractometry, I have determined an optimized deposition procedure leading to good morphology. The utilization of Absolute Intensity Photoluminescence techniques (AIPL) allows for prediction of the V_oc to a high degree of precision without building an entire solar cell, instead only measuring the absorber layer. By illuminating the absorber and detecting the re-emitted light, models can determine the density of "radiative recombinations" of electrons and holes, which correspond to electrons that would be capable of generating a voltage and providing electrical power. By using this method and by building an understanding of rudorffite crystal growth, I have attempted to reduce "non-radiative recombinations," increasing the PL and hence increasing the capacity for high V_oc in rudorffite cells. Here is presented current data, results, and recommended experiments necessary for rudorffites to be a successful photovoltaic material.

Chimeric antigen receptor (CAR) T-cell therapy is the latest treatment option available for those suffering from certain forms of cancer such as lymphoma and leukemia. These engineered cells are able to recognize specific proteins found in tumors, and subsequently induce CAR-T cell proliferation, cytokine secretion, and lysis of the cancerous cells. Despite its promise, a percentage of patients who receive this treatment develop a range of neurotoxic symptoms. My research project tests the hypothesis that endothelial activation of vascular tissue in the brain, which would allow for increased permeability of immune cells through the blood-brain barrier, is contributing to the development of these clinical symptoms. Using a technique called immunohistochemistry, I used the antibodies claudin-5 and cd31 to fluorescently label tight-junction proteins and adhesion molecules of endothelial cells from brain tissue harvested from a developed mouse model. This mouse model received CAR-T cell injections and underwent behavioral testing to confirm the presence of neurotoxicity symptoms. I then used microscopy skills to visualize the labeling of the endothelial cells and proteins. If my hypothesis is correct, I expect to see a quantifiable decrease in the number of cerebral tight-junction proteins connecting endothelial cells along the blood-brain barrier, as compared to negative control tissue that received no CAR-T cell injections. In order to make these comparisons, I will use a software program such as Image-Pro Premier software (Media Cybernetics) to help me quantify the positive fluorescence labeling of endothelial cell proteins and adhesion molecules in both the control and experimental tissue. Tissue with less tight-junction proteins and adhesion molecules would permit the influx of foreign particles into the CNS. Understanding the cause of CAR T-cell related neurotoxicity will be first step in promoting prevention and increasing the effectiveness of this new cancer immunotherapy.

Cranial elaboration, in the form of domes, horns, and bony bosses, has evolved multiple times in vertebrate history, including in non-mammalian synapsids, the extinct ancestors of mammals. The lack of similarly thickened skulls in living animals has meant that very little can be inferred about how these features developed or why they evolved. Here we use comparative bone histology to describe the microanatomy of Oudenodon, a 255-million-year-old synapsid with distinctive nasal bosses. We compared thin-sections from the thickened portions of Oudenodon to the non-thickened skull of its relative, Diictodon, in order to better understand how cranial elaboration developed in synapsids. We took thin sections from the thick nasal bosses as well as non-thickened regions of Oudenodon to capture changes in tissue microstructure. Then, we compared these thin-sections to similar regions of the skull in Diictodon, which lacks cranial elaboration. In the bone tissue of both Oudenodon and Diictodon, we observed a cancellous, spongey interior sandwiched between two layers of compact cortical bone. This pattern of bone is typical in many modern skulls but the thickness of the cancellous region in Oudenodon is strikingly thicker, even in regions away from the boss. We hypothesize that increased cranial thickness in Oudenodon is due to this middle expansion of spongey, cancellous tissue. As a result of the increased bone thickness, sutures in Oudenodon are deep, wide, and convoluted when compared to the relatively simple interdigitated sutures in Diictodon. These and other histologic comparisons with distantly related taxa allow us to interpret the growth and construction of cranial elaboration in synapsids, adding to our understanding of how these thickened skulls evolved. Future work can also explore the possible soft tissue covering of these bosses and domes, which may have been used for intraspecific display or combat. 

The focus of this research is on Spanish heritage language (HL) and second language (L2) learners. An HL learner is a student who comes from a house where Spanish is spoken, but still; needs Spanish classes to master certain aspects of his/her first language. Sometimes English is also spoken at home: e.g., one parent speaks Spanish and the other English, or the student speaks Spanish with his/her parents but English with his/her siblings. On the other hand, an L2 learner is a student who is learning Spanish in a classroom setting. His/her first language may be English or any language other than Spanish. Between these two groups of students, there are important differences when it comes to learning Spanish, for example, L2 students are more knowledgeable about Spanish grammar rules and academic vocabulary. On the other hand, HL students have more fluency and much more knowledge about the culture. The focus of this research is on how the interaction between an HL and an L2 learner in a classroom impacts learning for both students. My role in this research is to transcribe the audio-recorded conversations between two L2 students and to compare these conversations with those between the same L2 students and an HL learner. I will analyze how the students collaborate and how they work to find the solution to any challenge they face that is associated with vocabulary, grammar or orthography. I hypothesize that pairing an L2 and an HL student will generate more interaction since each student offers different sources of knowledge. Pairing an L2 student with an HL student creates a diversity of ideas that I expect to increase learning. This analysis will help us to better understand how to create a more efficient learning environment, for both HL and L2 students, within mixed classrooms.

With the discovery of radioactive materials, many institutions have conducted numerous radiation experiments in order to further understand the effects of radiation and radioactive contamination on human bodies and their environments. While doing so, there has been a great amount of unequal health disparities among the different communities involved. Institutions, like the University of Washington, while held in high regard, have participated in experiments that have affected the livelihood of many people. To this day, common knowledge of the University of Washington’s participation is still obscured. There are many institutions in the United States that are like UW and are known for their extensive and groundbreaking research; with the funding and power they hold, people often don’t question their research or their ethical approach to conducting it. From our research, we obtained a greater understanding of what occurred throughout the experiments - thus our goal is to bring attention to the actions of the University of Washington researchers’, C. Alvin Paulsen’s and Lauren R. Donaldson’s, unethical research practices in the Marshall Islands and UW Walla Walla Prison Radiation Experiments. Our methods include analyzation of interviews with Tom Carpenter - the Executive Director of Hanford Challenge, discourse analysis, reviews of relevant literature and interpretations of visual elements. Because the research of C. Alvin Paulsen and Lauren R. Donaldson is locked away in UW’s Special Collections Library, we were unable to analyze their research directly. We anticipate that this project will ensue more curiosity and lead to the general public learning more about the University of Washington’s participation in human radiation experiments.

It is an evitable instinct to develop snap judgements of people as we encounter them in passing; therefore, our experiment attempted to replicate this quick encounter and asked the question of whether one’s gender and race impacted how they perceive others’ friendliness. Our sample consisted of 35 males (27.1%) and 89 females (66.7%). 82 of our participants were Caucasian (63%), 25 Asian-American (19%), 4 African American (.03%), 1 Hawaiian (.007%), 20 Latino American (15%), 14 who identified as mixed race (10%); all an average age of 23 years (SD = 2.6). Participants were shown 8 photographs of White and Latino men and women smiling for 5 seconds each. They then had to rate the friendliness of each photo within 15 seconds of viewing. Our findings suggest that the intersectionality of race and gender play a role in how individuals perceive men and white men. Implications of these findings suggest that a holistic view of a person’s identity will give a better indication of how they might view those who do and do not look like them.

The interactions between pollinators and plants have a strong correlation to the fitness and reproductive success of both parties involved. These interactions are responsible for most of plant reproduction by seeds and they also drive evolutionary diversification of both plant and pollinator species. Wind turbulence plays an important role in navigation by smell, which is important for many pollinators while locating flowers. Climate change may alter wind patterns, which in turn may affect the ability of pollinators to locate flowers. The goal for this project was to determine the effect of wind on pollinator success. We determined the visitation rate of pollinators at Oenothera pallida flowers in the field by analyzing infrared camera videos recorded last summer at a field site in Grant County WA. Next we ran a multiple linear regression to determine the effects of wind speed, temperature, humidity, and ozone levels on floral visitation rates. Pollinators of Oenothera pallida include the hawkmoths Hyles lineata and Manduca sp., various bee species including Andrenids, Apids, Lassioglossum sp. and Megachilids, Bembix wasps, and various flies. Wind speed is the strongest variable that affects pollinator visitation at different times of day, which implies that changing wind patterns significantly impact plant-pollinator interactions.

Human pathogenic viruses are responsible for nearly all recent pandemic diseases. We set out to search for viral protein sequences that could be important for tissue tropism. To achieve this goal, human pathogenic viruses were classified according to the tissue they infect (pulmonary, gastrointestinal, etc.) — irrespective of whether they were enveloped or non-enveloped RNA or DNA viruses. Next, we developed a customized amino acid sequence alignment program to speed up protein-sequence comparisons and alignments in each viral category. We identified the conserved seven amino acid motif, VAIVLGG, in both Old World and New World alphaviruses. Our further analysis localized the VAIVLGG consensus sequence on the adherence spikes of the chikungunya virus (CHIKV), a well-known mosquito-borne arthrogenic member of the Old World alphaviruses which caused a recent chikungunya fever outbreak in Florida. Our further search revealed that this sequence is located within the viral region involved in its binding to the newly-discovered human CHIKV receptor. In light of the fact that several ongoing clinical trials are aimed at developing vaccines against CHIKV, it is tempting to entertain the idea that our identified VAIVLGG consensus sequence might potentially be used to serve as a single-antigen for producing a pan-vaccine effective not only against CHIKV but also the following alphaviruses: Onyong-nyong, Semiliki Forest, Ross River, Mayaro, VEEV, WEEV, EEEV, and Sindbis.

The kinetochore plays a key role in aligning chromosomes during mitosis and helps ensure proper separation of duplicated DNA molecules into daughter cells. Some proteins that associate with the kinetochore regulate attachment to microtubules by destabilizing weak attachments and stabilizing strong attachments. In the model organism Saccharomyces cerevisiae, the Ipl1 kinase and Stu2 protein have similar effects on regulating tension on the kinetochore. Since Ipl1 is a kinase, and Stu2 is phosphorylated, we believe Stu2 function may be regulated by Ipl1. To test if Stu2 function is dependent on phosphorylation by Ipl1, we mutated possible Ipl1 phosphorylation sites and observed its effects on Stu2 function. Four Ipl1 target consensus sites within the Stu2 protein were selected for this study. We used site-directed mutagenesis techniques to alter these potential Ipl1 phosphorylation sites on Stu2 by mutating serine codons to alanine codons. We successfully constructed S40A and S430A/S593A mutations in Stu2 using the megaprimer whole plasmid (MEGAWHOP) cloning technique. We then introduced the mutated version of stu2 into yeast and conducted phenotype tests to determine if inactivating these putative phosphorylation sites affected its function. Our initial results indicated that phosphorylation at sites S430 and S593 may not be required for proper Stu2 function. We suggest that further testing of Ipl1 phosphorylation sites could reveal possible mutations that lead to malfunction of Stu2 that then affect the kinetochores ability to release improper attachments to microtubules. This would give insight into how signaling between kinetochore proteins can help to ensure proper chromosome segregation and avoid aneuploidy.

Field research is an important way to understand complex ecosystems and the roles of individual wildlife species within these systems. As climate change and other human factors continue to affect our global patterns, studies must be conducted to assess the health of current populations and predict future trends. Many studies involve direct or indirect contact with the focal animals, which may impact the fitness of study animals despite efforts of researchers to minimize cost. Long-tailed Jaegers (Stercorarius longicaudus) in Denali National Park, Alaska were captured and fitted with satellite-linked GPS trackers to study migratory routes. The birds were tagged by other researchers while on their summer nesting grounds caring for eggs or recently hatched chicks. This disturbance has potential to affect the nesting success of the jaeger which is thought to already be in decline in the area. A long-term study of the nesting success of jaegers and other shore birds in DNP is being conducted to assess the suggested decline in these species. What impact did radio tagging nesting jaegers have on nesting behavior and success? I collected behavioral data in the field during a four-week period in July of 2018. With a UW grad student, I directly observed 2 breeding pairs of jaegers that had been tagged and 3 that had not. We observed the birds from over 150 meters away, recording parental feedings, chick protection, and vigilance. Preliminary analysis suggests that the two subsets of jaeger behaved differently during chick fledging. This could have impacted the way chicks were raised and the nesting success rate of tagged parents. Further analysis into the feeding rates and protective behavior is underway to determine the complete impact of radio tags on the population.

Sleep problems are prominent in adolescence and most commonly include short sleep duration, poor sleep quality, and insomnia symptoms. These problems are even more pronounced in youth with headache, with research finding that poor sleep contributes to increased headaches and disability. It is important to screen for insomnia in order to accurately diagnose and treat this disorder. However, there is currently no brief, adolescent-focused measure of insomnia that would allow for a high level of accuracy in screening and diagnosis that is relevant for youth with headache. A recently developed screening tool, the Adolescent Insomnia Questionnaire (AIQ), appears to be a valid measure of insomnia in adolescents with chronic pain, diagnosed sleep problems, and in the general community. This study aims to extend validation of the AIQ to children and adolescents with headache from clinical and community settings. 169 adolescents (ages 12-18) were enrolled and completed the AIQ and the Adolescent Sleep Wake Scale (ASWS), a measure of sleep quality, to determine the validity of the AIQ as an insomnia screening tool for youth with headache. Reliability, or internal consistency, of the items in the questionnaire was tested by computing Cronbach’s Alpha. The correlation between the AIQ and ASWS was high (0.736), indicating high validity of the AIQ as an insomnia screening tool for youth with headache. Cronbach’s Alpha was 0.892, which indicates high internal consistency of the AIQ. Based on these results, the AIQ appears to be a valid and reliable tool in the screening and diagnosis of insomnia in adolescents with chronic headache. Further research should continue to focus on insomnia screening within specific adolescent populations at high risk for insomnia, and the development of effective treatments tailored to these populations.

In recent decades, increased nitrogen (N) pollution in coastal aquatic ecosystems caused by increasing agricultural and urban activities has led to extensive habitat degradation and loss, change in the structure of aquatic food webs, and higher frequency of hypoxia. Nitrogen is ubiquitous in the biosphere, entering coastal environments through multiple pathways including ground- and surface waters, plus atmospheric deposition. The fate of much of the N entering coastal environments is not well established. In particular, the magnitude of N consumed at coastal margins, versus exported to downstream estuaries is poorly constrained. It is widely recognized that inland wetlands are important N sinks, as they are sites of fixation of reduced N to inert dinitrogen gas, however the role of coastal wetlands as N sinks is more difficult to establish due to the dynamic nature of these tidal environments. Here, to better understand the role of coastal wetlands in the global N cycle, we established a high-resolution budget of nitrate (the most abundant form of reduced N) from 9/12/2017 to 10/12/2017 at First Mallard Slough within the Suisun Marsh complex, a brackish tidal marsh in the San Francisco Bay Estuary. We modelled nitrate concentrations at 15-minute intervals using a submersible ultraviolet nitrate analyzer (SUNA), and matched these estimates with simultaneous hydrodynamic measurements of water flux. Data were synthesized in Python to establish 15-minute resolution estimates of nitrate mass exchange, showing that the wetland exported a net total of 2.54 Mg of N as NO₃^2- over the complete measurement period, or 84.6 kg N per day. Contrary to other studies showing wetlands are important nitrate sinks, our result revealed that the Suisun Wetland complex was an important N exporter to the San Francisco Bay Estuary, at least over the period measured here. Longer-term observations are needed to confirm this pattern at a complete annual scale.

Oral swab analysis (OSA) is a possible alternative sample type for tuberculosis diagnostics. It has been observed that tongue swabs contain greater amounts of Mycobacterium tuberculosis DNA than cheek swabs (p<0.0001) from tuberculosis patients. After determining that oral microbiota follows this same pattern, several factors including time-of-day swabbed and health status were analyzed to understand factors affecting the amount of bacteria on the tongue. This project aims to optimize the oral swab sampling methods in order to facilitate more sensitive diagnostic tests, using universal bacterial 16s rDNA as a proxy for Mtb DNA. Previously tested samples from South Africa were further analyzed to investigate amount of oral microbiota by day collected, HIV status, health status, and other demographic factors. To evaluate whether collecting multiple swabs per sample yielded more universal bacterial DNA, tongue swabs were taken from healthy volunteers in Seattle. Each subject provided a 1-swab sample and a 3-swab sample, which was then extracted and analyzed by a previously optimized universal bacterial PCR. Additionally, tongue scrapers are being assessed as an alternative to oral swabs. Swabs collected early in the morning had more bacterial DNA than swabs collected later (p<0.03). 3-swab samples yielded an average of 2-fold greater amounts of bacterial DNA than 1-swab samples. Bacterial biomass correlated with M. tuberculosis signal in most comparisons. Bacterial biomass may serve as a useful proxy when developing better oral swab sampling strategies for TB diagnosis.

Nanopore sequencing is a “third-generation” sequencing approach in which a constant electric voltage is applied across a nanoscale pore and the changes in the ionic current flow through the pore are measured as single molecules such as RNA or DNA pass through it. It is our goal to expand and adapt this sensing technology to enable single-molecule proteomics. Specifically, being able to characterize protein post-translational modifications at the single-molecule level is important for quantifying protein complexity and understanding how different protein mod-forms contribute to cellular processes such as differentiation and the progression of disease states like cancer. In this project, we modified a model protein to contain a protein kinase A phosphorylation motif with the purpose of demonstrating the ability to discriminate the modified protein from the unmodified with the Oxford Nanopore MinION, a high-throughput nanopore sequencing device. We hypothesize that the observed ionic current pattern will change upon phosphorylation and enable direct quantification of modified peptides. Ultimately, these analyses will inform us of the general ionic current signature that phosphorylated residues generate, which can then be added to our growing library of nanopore signal signatures that are informative of protein sequence and structure at the single-molecule level.

Food contamination outbreaks have become increasingly prevalent in the United States. Food processing companies often do not have sufficient resources to accurately monitor pathogenic bacteria and biofilms on their food preparation surfaces. Unfortunately, consumers assume that the food is safe because it is packaged and ‘screened’ but invisible bacterial contamination may be present. This creates an opportunity to improve methods for detecting pathogenic bacteria in food handling and processing environments. BioVizia provides an alternative solution for detecting pathogenic bacteria on food processing surfaces that is efficient yet effective. We have developed a device that uses an LED to excite a fluorescent dye. Fluorescein is an FDA approved dye that exhibits pH dependent spectral properties. When viable pathogenic bacteria metabolize sugar, they produce acidic byproducts. Therefore an optical system using fluorescein as a pH disclosing agent may provide sufficient sensitivity for detecting bacterial contamination. Our optical system records the fluorescein emission spectra which contains two overlapping, pH dependent spectral features. The fractional amount of the two contributing bands are calculated using a spectral unmixing algorithm. A calibration with standardized pH buffers yields a linear relationship between pH and the fractional amount of each band. This noncontact optical pH measurement method has been successfully employed in an in vivo dental study to measure the pH drop produced by dental plaque following a sucrose rinse. We seek to demonstrate that BioVizia can make the detection of pathogenic bacteria and biofilms on food preparation surfaces fast and quantitative.

Sarcopenia, or age-related of loss of muscle mass and function, is associated with a decline in quality of life for elderly populations and few effective treatment options. Sarcopenia is linked to mitochondrial dysfunction and elevated mitochondrial oxidant production. We are investigating the role of mitochondrial oxidative stress in sarcopenia using a mitochondrial targeted therapeutic and a mouse model of accelerated sarcopenia. SS-31 is a mitochondrial targeted peptide that associates with cardiolipin, decreases oxidant production, and increases ATP production. Superoxide dismutase 1 knockout (SOD1KO) mice lack superoxide dismutase 1 (an enzyme that converts the oxidant superoxide into hydrogen peroxide and molecular oxygen) resulting in an accelerated sarcopenia phenotype. We are testing whether treatment with SS-31 preserves muscle function in the SOD1KO mice. We hypothesize that improving mitochondrial function with SS-31 treatment will delay the decline in muscle function in the SOD1KO mice. To test this, we are administering SS-31 to SOD1KO mice through surgically-inserted osmotic pumps for 8 weeks between 3 and 5 months of age (the published timeframe for the onset of skeletal muscle decline in SOD1KO mice) and performing in vivo muscle function measurements of the gastrocnemius before pump insertion and monthly after pump insertion for 3 months. We compare muscle functional measurements with histological and biochemical analyses of mouse tissue samples upon euthanasia and determine skeletal muscle fiber type, metabolite and protein concentrations, and muscle fiber respiration and oxidant production. We expect SOD1KO mice with SS-31 to have a lower rate of decline in muscle force production and increased fatigue resistance over time, higher max ATP production, and decreased oxidative stress. The effect of SS-31 on muscle function, mitochondrial quality, and redox homeostasis has exciting potential as a translational therapeutic treatment for human sarcopenia.

Understanding how adolescents explain gratitude in peer interactions uncovers how they view their identities and social worlds during a time when they are transitioning to the responsibilities of adulthood. Earlier studies define “gratitude” as a state of appreciation, and have shown that adolescent feelings of gratitude correlate with increased well-being, academic performance, and prosocial behavior. Furthermore, our previous findings suggest adolescents have differing rationale for why they feel grateful in situations when they either enact or receive calming, angering, avenging, and reconciling intervention from their peers. The goal of this study was to ask: 1) How do adolescents explain feelings of gratitude they feel following intervention in victimization events? 2) How do rationales for feelings of gratitude vary between actor and recipient of a peer intervention? 3) How does gratitude differ when adolescents calm, amplify, avenge, or reconcile a previously victimized peer? We qualitatively coded explanations provided by 265 adolescents for emotions in each condition. Our findings showed actors felt more gratitude when calming their peers, and recipients felt more gratitude after reconciliation. Peer gratitude was predicted to be more strongly linked to a desire for security when the subject was the recipient (e.g. “I was grateful she looked out for me”), and more strongly linked to a desire to display competence when the subject was the actor (e.g. “I was grateful she took my advice”). We carried out quantitative analyses using repeated measures analysis of variance and Epistemic Network Analysis. The findings from this study contribute to understanding peer relationships, which could help educators navigate student actions that de-escalate conflicts and promote well-being in student social environments.

Epithelial-mesenchymal transition (EMT) refers to a biologic process that allows a polarized epithelial cell, which normally functions in the basement membrane of a cell, to undergo biochemical changes that makes it express as a mesenchymal cell phenotype. This mesenchymal phenotype allows the cell to have enhanced migratory capacity, invasiveness, elevated resistance to apoptosis, and increased production of extracellular matrix (ECM) elements. The process of EMT is considered completed once the underlying basement membrane breaks down, and the mesenchymal cell becomes migratory. Another component that proves EMT is the loss of e-cadherin. E-cadherin refers to cell-to-cell adhesion and the degradation of e-cadherin levels are a hallmark of EMT happening. There are three distinct types of EMTs; I will be focusing on type II EMT. Type II EMTs are associated with inflammation/wound repair but usually stops once inflammation subsides. However, in the context of organ fibrosis, type II EMTs can continue to over-respond to a persisting inflammation and can lead to organ death. In my experiment, I hypothesize that in HEK 293 human cells, SNAP -Δ1-91 alpha-1D adrenergic receptors undergo type II EMT. SNAP -Δ1-91 alpha-1D adrenergic receptors are a truncation of the extracellular portion of the receptor. Certain receptors undergo this truncation to increase its expression. It is shown that in SNAP – Full Length alpha-1D adrenergic receptors  (wild type receptors) do not undergo EMT. I will be able to observe the process of type II EMT through imaging the breakdown of the cell membrane in SNAP- Δ1-91 alpha-1D adrenergic receptors and the measuring of e-cadherin levels. The purpose of this research would be to potentially influence future therapeutic interventions that target wild type receptors to induce would repair. 

Business intelligence (BI) utilizes data analytics to strategize decision-making for businesses to improve performance and sustain competitive advantage. Our goal in this research is applying machine learning and data science to predict customer purchase behaviors in order to illuminate the value of BI. We collected and compiled 3 million daily transaction-level data from a popular online grocery in 2017. The dataset details items purchased and items reordered for each transaction, as well as the time when the customer last ordered. We proposed multiple predictive models where key variables are determined through a feature selection. The estimation of our models enabled us to predict when a customer makes their next purchase, to suggest complementary products for customers, and to calculate the probability of an item being reordered. These results provide important managerial insights into improving the key performance indicators (KPI) of the online grocery business. Our BI research framework is applicable to other businesses with large volume of customer transaction data, where machine learning and data science is useful to identify growth opportunities and prescribe competitive strategies for the business.

Ribonucleotides are essential components of the cell: they are the building blocks of RNA and DNA, key signaling molecules, and metabolic intermediates. Maintaining proper ribonucleotide balance is critical for cell survival. An essential, highly-conserved enzyme that regulates purine biosynthesis is IMP dehydrogenase (IMPDH), which catalyzes the first committed step in the production of GTP. In humans, there are two IMPDH isoforms: IMPDH1 is present in low quantities in most cells, and IMPDH2 is upregulated during proliferation. Both IMPDH isoforms form higher order structures in cells and assemble into filaments and bundles of filaments in vitro. Nine point mutations in IMPDH1 have been discovered that cause retinal degeneration and ultimately blindness in humans. Our current findings show that these point mutations in IMPDH differentially impact the protein’s ability to assemble into filaments in vitro. We hypothesize that the ability of IMPDH to polymerize will affect the protein’s activity because of the interplay between protein structure and substrate binding. We use negative stain electron microscopy to first characterize the polymerization behavior of IMPDH in the presence of different ligands: the substrates IMP & NAD+, as well as allosteric effectors ATP and GTP that promote polymerization. In addition, we employ kinetics assays that vary levels of substrate and GTP to quantitatively assess enzyme activity by measuring NADH output. Characterizing each mutant’s behavior will be the first step to understanding the molecular mechanisms that cause retinal disease in IMPDH. In a future study, we can use cryo electron microscopy to solve the structures of mutant protein.

Chester Morse Lake is the primary reservoir of drinking water for the greater Seattle area, provides hydroelectricity via a thirty-megawatt power plant, and releases fresh water downstream to prevent sea water from infiltrating into Lake Washington. The reservoir is filled by snow and rainwater that falls within the relatively small Cedar River Municipal Watershed. A healthy snowpack accumulated during winter is necessary to maintain proper water levels of the reservoir.  Even during a year with average precipitation, the lake can only provide Seattle with enough water for one water cycle year. This study aims to determine how snowline rise, related to gobal temperature increase, would impact the water budget of Chester Morse Lake—and in turn how those changes would impact Seattle's water needs. The lake's water budget is calculated by first analyzing historical data from snow courses and automated snow telemetry sites within the Cedar River Municipal Watershed. Average snow water equivalent values at varying elevations are applied to a digital elevation model of the watershed in order to calculate the volume of water stored within the snowpack at differing elevations. This allows us to determine how much snow bound water is lost within the watershed with incremental steps of snowline rise. Since melting snowpack sustains the lake level during Washington's drier months, this study can help quantify how much snowline rise the Cedar River Municipal Watershed can experience while still maintaining the working state of Chester Morse Lake.

Methanol is a common pollutant in freshwater ecosystems due to its widespread use in industrial operations, fuel, antifreeze, paints, and insecticides, and being a result of the burning of garbage. As a bioindicator species, Daphnia magna health indicates changes in aquatic ecosystem health. They are an important part of the food web, eating algae, and as a food source to insects and fish. No previous studies have examined the effects of the pollutant methanol on Daphnia heart function and mortality. This experiment examined the effects of varying methanol concentrations on heart function and mortality of Daphnia magna. It was hypothesized that methanol significantly affects the heart and mortality rate of Daphnia. Fifteen experimental biospheres were used in each trial, with three jars for each of the five concentrations. The biospheres were filled with deionized water and methanol in concentrations of 0 ppm (control), 822.6 ppm, 1644.5 ppm, 3289.0 ppm, 7119 ppm. In a second trial, the concentrations were 0 ppm, 822.6 ppm, 1644.5 ppm, 205.7 ppm, and 411.3 ppm. Heart and mortality rates were observed and recorded for each trial over 4-8 days. For each jar, videos were recorded for 15 seconds each and heart rate was counted, and mortality counted every other day. Based on the survival and heart rate differences, it was concluded that as methanol concentrations increase, the heart rate of Daphnia varied but didn’t respond linearly to concentration levels. Additionally, higher concentrations of methanol negatively affect survivability, although the initial control groups had somewhat high death rates. This study highlights the negative impact of methanol pollution on Daphnia because a negative impact on Daphnia affects the whole freshwater ecosystem. Indeed, in Lake Washington, Daphnia represent a major source of nutrients for juvenile Sockeye Salmon, making Daphnia indispensable for their growth.

The equivalence principle maintains that all mass is equally affected by gravity and is fundamental to our understanding of gravitational physics. Torsion balance experiments at the University of Washington have tested the equivalence principle at the 10^-13 level. Torsion balances are susceptible to systematic uncertainty caused by changing gravitational gradients formed in the environment, e.g. rainfall saturation in nearby hills. If changing gravitational gradients could be continuously monitored, then the full torsion balance sensitivity (differential accelerations below 10^-15m/s²) could be reached. The goal of this project is to measure and correct for gravitational gradients. Simultaneously monitoring gravity gradients and testing the equivalence principle requires the construction of a concentric torsional gradiometer. Such an instrument has never been built before, requiring unique geometrical design constraints. Several functional prototypes have been constructed along with a complimentary data acquisition system. Improved equivalence principle limits will further constrain the unification of gravity with the standard model of particle physics.

STUDIO is a peer mentoring program that focuses on connecting University of Washington (UW) undergraduate student mentors with low income, immigrant and refugee youth through Science, Technology, Engineering and Mathematics( STEM). The program is a partnership with the Neighborhood House community center in the High Point Neighborhood of West Seattle. Neighborhood House provides the facilities and is the gathering place for UW mentors and youth mentees on a weekly basis. As STUDIO is offered as an undergraduate course (EDUC 421), the mentors visit Neighborhood House once a week and then attend a weekly seminar class on campus as well. The program began as a research study that focuses on promoting youth interest in STEM. However, over the past few years it has made progress in undergraduate STEM learning research as well. As a lead mentor within the STUDIO program, I have an opportunity to participate in research aspect as well as cultivate mentorship with youth, and supporting other mentors. In this study, I explore how relationships between youth and mentors develop in STUDIO. I am doing this through analysis of documentation of STEM and non-STEM activities, written reflections of mentors and interviews. They are analyzed for types of relationships that mentors develop through this program as well as themes and patterns of development. The goal is to better understand how a mentorship program that focuses on bridging the gap of educational inequity for youth lends possibility for undergraduate learning through relationships building.

The environment in which a molecule resides can drastically affect both its reactivity and its spectroscopic properties. These effects can be clearly seen in phenomena such as solvochromism or increased reactivity in a protein active site. The most accurate models that can capture these effects are purely quantum mechanical, but they also have a steep computational scaling cost that prohibits their use on large molecular systems. In order to circumvent this, less expensive models, such as molecular mechanics, can be used for the environment while maintaining the accurate model for the system of interest. In recent years, development of polarizable molecular mechanics has enhanced the accuracy of this technique for time-independent systems, but a gap still exists for time-dependent systems. In particular, the frequency dependence of polarizability has yet to be addressed. This research uses frequency dependent polarizabilities to parameterize a novel molecular mechanics scheme. Specifically, a machine learning model is trained to predict the best locations to place isotropic polarizabilities in order to recover the molecular, frequency-dependent polarizability.

If Timothy Egan, author of The Good Rain, or any other local were to describe the Pacific Northwest in words it would only take three, "drip, drip, drip". Rain is a common visitor to the mountains and valleys of the Pacific Northwest region, created millions of years ago by glacial melt. This system of weather which both keeps the forests evergreen, the skin moisturized, and air clean... and it is also something that defines the culture of this area. Other cultures like Japan or Denmark have chosen to design for their climates in order to live in better harmony with their climate. The Japanese design for their climate by creating atmospheric rain gardens and use materials that change over time with the weather. They challenge the idea of negative associations with rain by creating a more harmonious relationship. Denmark ranks consistently among the happiest nations on the planet, yet they have some of the harshest winters. What is their approach? The Danish term, "Hygge" refers to a feeling of coziness and happiness. Instead of dreading the winter, Danes accept it by coming together with their community around hearths, lighting candles, and eating comfort food. Our region too has a symbiotic relationship with our weather. This research shows how rain is beautiful and experienced by every sense in the Pacific Northwest... sight, smell, sound, touch, and taste. By designing for the climate by engaging the senses we can create calming aesthetics, improved mental heatlh, and a stronger community. This project will show the ways in which this region we call home is atmospheric, beautiful, and unique. Rain is not just a pattern of weather; Egan shows that rain is an essential element woven deep within this region's history. In fact, rain is still formative here, a part of the regional DNA. 

In recent years, researchers have dedicated much effort to overcoming the ~250 nm spatial resolution limit of light in order to reveal biological details that have been obscured by diffraction. A new form of super-resolution microscopy called expansion microscopy (ExM) relies on physically expanding a fixed specimen in a swellable hydrogel polymer and offers a simple, inexpensive approach to achieving ~70 nm resolution with conventional confocal microscopy. A critical and understudied step in this process is the homogenization of the embedded sample by proteolytic enzymes, enabling artifact-free expansion. However, in large and complex samples like Drosophila, enzymatic digestion is time-consuming and sensitive to experimental parameters such as fixation, hydrogel composition, and tissue type. To overcome the limitations of enzymatic digestion, I have explored parameter space for rapid peptide cleavage using air-tight stainless-steel vessels to achieve high temperatures and pressures not typically accessible in the lab. Additionally, a small-molecule digestion agent, dimethoxyiodobenzene, was tested in order to provide site-specific peptide cleavage and enhance tissue homogenization. The modified digestion process was first validated using standard immunofluorescent microtubules in cell culture. Next, Drosophila tissue was treated using thermal digestion to confirm the applicability of this technique in robust, difficult-to-expand tissues. This improved ExM protocol holds the potential to increase sample throughput, reduce expansion-related sample distortions, and extend ExM to be applicable to a wide range of previously incompatible tissues types, enabling pathologists to better analyze and assess diseases in human tissues.

The Bonneville Landslide dam, also known as the Bridge of the Gods, blocked the Columbia River about 550 years ago at the site of the modern Bonneville Dam, on the Washington-Oregon border. According to Klickitat lore, the Bridge of the Gods was created by the chief of all gods to join the lands north and south of the river. The dam’s failure, thought to be a result of the violent dispute between the chief’s sons, led to an outburst flood that drowned a forest and carved the Cascade Rapids. Sedimentary deposits from this dam break flood have been observed downstream, but the flood behavior and inundation pattern remains unknown. In this study, we created a paleo-digital elevation model (DEM) of the Columbia Valley Gorge landscape before the flood, which will serve as the basemap for numerical models of the flood. The paleo-DEM combines three data sets: 1) topographic data derived from the 1868 and 1901 U.S. Coast and Geodetic Survey historic topographic survey maps and bathymetric depth values from hydrographic sheets; 2) bathymetry of the Lower Columbia River with removed modern structures in Portland, validated by tide records from 1853 to 1876; and 3) bathymetry upstream from the Bonneville Dam, merged with adjacent topography and derived from NOAA data. In ArcGIS, we filled in data holes and modern channels and subtracted modern structures in an attempt to accurately represent the paleo-environment. Because the Columbia estuary is heavily influenced by tides, we used historic tide observations to create a low and high tide paleo-DEM to make preliminary analyses of how the tide might have influenced this flood. Once we know the paleo-topography of the Columbia Gorge, Portland basin, and Columbia Estuary, we can begin to numerically model this flood and explore its geomorphic impact.

Developing treatments for complex disease is hindered by a variety of obstacles including clearance by the reticuloendothelial system, degradative proteases of blood and tissue microenvironments, and overall limited tissue penetration. Nanoparticles hold potential as drug delivery platforms for overcoming these problems, where they can be used to encapsulate and protect enzyme therapeutics and improve delivery to specific organs of the body. Using poly(lactic-co-glycolic acid) (PLGA) polymeric nanoparticles with a poly(ethylene glycol) (PEG) coating and catalase as a model enzyme, we compared two methods of nanoparticle formulations for enzyme encapsulation: nanoprecipitation and double emulsion. We tested the effects of F127 (Pluronic F127), P80 (polysorbate 80), and PVA (poly(vinyl alcohol)) surfactants on the size, polydispersity index (PdI), zeta potential, and enzymatic activity of nanoparticles formulated via nanoprecipitation. We determined PVA to be the ideal surfactant with the greatest enzyme loading for nanoprecipitation (~3.6%), similar to the activity obtained from double emulsion (~3.7%). For double emulsion, we determined similarly that PVA worked the best out of the surfactants tested. However, the nanoprecipitation method provided little to no enzyme protection in the presence of a protease with complete deactivation within 4 hours, while double emulsion nanoparticles extended activity through 24 hours (~6.6% of original activity). We further optimized the double emulsion method by altering the sonication times, determining that a sonication time of 15 seconds yielded particles with an activity of ~3.5% while maintaining similar size, zeta potential, and PdI. We also found that sonication conditions significantly affected enzyme deactivation. With a modified bicinchoninic acid assay, we measured total protein concentration within the particles, allowing us to calculate enzyme percent deactivation from formulation processes. Altogether, our work shows that enzyme-loaded nanoparticles made via the double emulsion method achieve high encapsulation and protection of enzymatic cargo for drug delivery.

As the global burden of neurological diseases continues to grow each year, there exists a need for drug delivery vehicles that can overcome barriers specific to the brain. The heterogeneous brain extracellular matrix (ECM) is an understudied barrier to effective therapeutic delivery, particularly in the presence of disease states. We utilize a novel multiple particle tracking (MPT) approach to characterize microstructural changes in perineuronal nets (PNNs), a key structural mediator of plasticity, in the developing brain. Our overarching goal is to develop a combined approach of MPT, statistical analysis using Python-based software packages, immunohistochemistry (IHC), and mRNA expression profiles to monitor changes in PNN structure and function through development and in the presence of neuroinflammation and oxidative stress processes. For this, we cultured 300 μm-thick organotypic whole hemisphere (OWH) brain slices prepared from postnatal day 35 (P35) rats. We treated slices with 100 ng/mL lipopolysaccharide (LPS, induced-inflammation model) or 100mM glutamate (MSG, induced-excitotoxicity model) for 3 h, removed the toxin and fixed slices at 1 h, 6 h, and 24 h after toxin removal. Fixed slices were stained using Wisteria floribunda agglutinin (WFA) and PNN counts were quantified using the ImageJ software package. In LPS and MSG-treated slices, 100-nm particles were added to live slices stained with WFA and MPT was performed in WFA+ regions, followed by statistical analysis of individual nanoparticle trajectories. From the IHC imaging and PNN count quantification, we observed differences in the number and morphology of PNNs present in the MSG and LPS models when compared to healthy controls. Characterizing structural changes in PNNs in living tissue furthers our understanding of the impact of neuroinflammation and oxidative stress on neuronal plasticity, and the subsequent impact on progression of neuropsychiatric diseases.

The rocks that comprise the San Juan Islands were transported thousands of kilometers along the coast of North America, and then stacked together during 50 million years of subduction off the coast of northern Washington. Unravelling the origins of these rock packages is critical to understanding the tectonic history of the Pacific Northwest. Pillow basalts (pillow shaped structures formed during submarine eruption of basaltic lava) at two locations on Lopez Island are examples of two unrelated units. While the basalt units are only 2 km apart and similar in texture and mineralogy, they differ in age and possibly magmatic origin. The radiogenic isotopic compositions of Nd, Sr and Pb in magmas provide information on their source. Since Earth’s mantle has a heterogeneous isotopic composition, it is possible to infer the volcanic setting in which the basalts formed. Little chemical and no isotopic data exist for these rocks. We analyze the Sm-Nd, Rb-Sr, and U-Pb isotopic systems of samples from both pillow basalt exposures, and compare the measured isotopic ratios to known variations in magmatic sources. During microscopic examination of the sample mineralogy, we identified strong metamorphic alteration to the pillows, which would alter their chemical composition. To obtain the original isotopic composition of the samples we developed a procedure to remove altered minerals and added elements using successively stronger acid leaches. We are testing this on subsamples of a single “pillow” with different extents of alteration to test if we can obtain original compositions. With these ratios we can determine the volcanic setting of these units and gain a better understanding of complex structural geology of Lopez Island. If we can see through alteration to original isotopic compositions, it will open a new way to investigate the origin of the complex geologic history of the San Juan Islands.

Retinal diseases tend to effect specific neuron subtypes, ranging from age-related macular degeneration, which is caused by the deterioration of photoreceptors near the central portion of the retina (macula), to glaucoma, which identifies abnormally high intraocular pressure resulting in the death of ganglion cells. Unfortunately, adult mammals are not able to regenerate retinal neurons. Conversely, zebrafish, frogs, and various amphibians are able to completely regenerate their retinal neurons in many different animal models of damage, and restore retinal structure and visual function. The source of regeneration stems from the resident Müller glia cells, which normally provide neuronal support and span all three retinal layers. A critical gene for the initiation of transforming Müller glia into neurons was found to be Ascl1. This led our lab to hypothesize that the introduction and upregulation of Ascl1 in mammalian Müller glia might stimulate them to become retinal neurons after damage, as occurs in these other regenerating species. Indeed, after introducing Ascl1 into the Müller glia of mice, we found newly regenerated retinal interneurons (bipolar cells) that successfully integrated into the retinal circuitry and functionally responded to light stimulus. In addition to Ascl1, we have identified another transcription factor, that when introduced in combination with Ascl1, stimulates the generation of a different retinal interneuron (amacrine cells). Ectopic expression of a proneural transcription factor to stimulate retinal regeneration provides a potential therapeutic intervention for treating blinding diseases, that even now, have few modest treatment options. In contrast to prosthetic devices and stem cell-based therapies, neuronal regeneration via viral injections is advantageous in regards to host tolerance and reducing the invasiveness of a given treatment, since the patient’s own Müller glia are the source cell of the new neurons; and therefore, immunosuppression would likely not be required.

Exosomes are 40-50nm extracellular vesicles released by all cell types, and are involved in a variety of cellular mechanisms including modulation of immune response and cancer microenvironment. Exosomes embed proteins, lipids, and nucleic acids from the parent cells and circulate in abundance in human serum. Recently, exosomes have been shown to have potential application as cancer biomarkers with potentially increased sensitivity and specificity compared to traditional protein or nucleic acid markers. In cancer patients, exosomes are also shed in real time, allowing potential applications in directing therapy, monitoring treatment response, and surveying recurrent disease. Using a known tumor marker, carcinoembryonic antigen (CEA), we examined the role of CEA-specific exosomes as a colorectal cancer biomarker. To establish the methodology, we used CEA-secreting colorectal cancer cell lines LOVO and HT29. We compared exosome isolation methodologies and established an ultracentrifugation-based technique to maximize both purity and yield. Through this methodology, we isolated exosomes from cell-free media and demonstrated that CEA co-localizes with coxasackie-adenovirus receptor (CAR), a senescence-related marker of interest in our laboratory. This finding suggests that tumor-derived exosomes could be used to quantitatively define certain cellular events. We then used archival and fresh patient samples to examine whether the CEA-exosomes could be applied in disease monitoring in patients with metastatic colorectal cancers receiving chemotherapy. Efforts are ongoing to define whether CEA-specific exosomes are tumor specific, and whether exosome conjugate protein and nucleic acid can be further used as novel biomarkers in selective clinical situations.

Computer vision models are used to help analyze biomedical images for diagnosis and treatment through looking for differences between images by a comparison to a template image. For instance, optical coherence tomography (OCT) is used to diagnose and treat retinal issues. When looking at the brain, injury, cellular uptake and characteristic features vary across regions, therefore images are often segmented into established brain regions to determine how the brain is impacted in a particular study. Current models fail to work in segmenting brain regions because each brain has variation in local microstructure, making it difficult to compare one brain to another. Furthermore, when brains are sliced, the exact location within the brain can be difficult to pinpoint, particularly in regard to depth, because the regions vary slice to slice. Therefore, my research addresses the increasing need for a method of analysis to align and compare images from brain regions across slices from a single brain, and from brain to brain. Using scikit-image analysis tools, I extracted information from cell images and videos of nanoparticles obtained in brain slices and determined trends within various regions. My program extracted cell density, shape, and death, then analyzed the uptake of nanoparticles to determine where a small segment of an image is most likely located within the brain. Iterating over the entire image generated a rough map of the regions within the brain which is refined using mapping descriptions detailed in literature. This research resulted in a systematic program that uses image analysis tools to extract features of defined brain regions. This program allows for quick, accurate and consistent analysis of regional differences of cellular features, nanoparticle distribution, toxicity, and other important measures.

Fetal Alcohol Spectrum Disorders (FASD) encompass medical conditions resulting from prenatal alcohol exposure (PAE), including brain-based central nervous system deficits and physical impairments. Previously, FASD conditions that did not meet Fetal Alcohol Syndrome (FAS) diagnostic criteria were diagnosed as having Fetal Alcohol Effects (FAE). Beginning in 1974, Ann Streissguth, Ph.D. and colleagues at UW led multiple studies on FAS and FAE. The primary investigation was conducted from 1992 to 1996 among over 400 diagnosed individuals age three to 51 years old, with the purpose of examining types and magnitudes of secondary disabilities, i.e., problems not present at birth but occurring across the lifespan as a consequence of PAE. In a study recently funded by NIH, UW researchers are recruiting prior study participants to ascertain current physical health, mental health, and functional status. During online searches for former subjects, researchers discovered that many with FAS or FAE were deceased. Among 438 diagnosed subjects, 23 (5.25%) were deceased (mean age at death 36.8 years), compared to one of 60 (1.67%) control subjects (age 35 years). Death certificates have been obtained for 18 individuals. Causes of death among the diagnosed included physical health conditions: heart-related (27.8%), cancer (16.7%), kidney-related (5.6%), liver-related (5.6%), diabetes (5.6%); and conditions related to mental health: alcohol and/or drug abuse (16.7%), accidents (11.1%), suicide (5.6%), and violence (5.6%). Cause of death for the control was cancer. These data indicate a three-fold greater proportion of deaths among FAS/FAE diagnosed individuals compared to controls in this study population. Death certificate information suggests a high proportion of FAS/FAE deaths were related to physical and mental health conditions known to be associated with PAE. Our findings speak to the importance of preventing PAE, early diagnosis among the exposed, and medical and social interventions to reduce risk factors associated with FASD.

Mosquitoes primarily navigate using their olfactory system, and can use this system to form “memories” that influence their choice in hosts. When a mosquito encounters an odor, information is sent through the antennal lobes in the brain to the mushroom bodies, which are structures responsible for learning and memory consolidation. This odor-learning pathway is mediated by neurotransmitters like dopamine and serotonin. Recent research has shown that the mosquito Culex quinquefasciatus has extremely low levels of dopamine in the antennal lobes compared to other species, and is unable to learn to avoid odors associated with a negative response. This led us to predict that dopamine is essential for aversive learning in mosquitoes. We hypothesized that Cx. quinquefasciatus differed from other mosquitoes in learning ability because they were previously tested in the light and they are the most nocturnal of the originally tested species. To test this hypothesis, we conditioned the mosquitoes in the absence of light in an aversive learning paradigm to measure how frequently they chose to avoid the conditioned odor. An inability to learn regardless of light condition would indicate that the role of dopamine as a neuromodulator in the antennal lobes evolved partly to allow diurnal mosquitoes to avoid defensive hosts. Next, specific neurotransmitters in the antennal lobe were mapped using confocal microscopy, revealing their concentrations which may explain behavioral differences from other mosquitoes. Most mosquito species show some plasticity in host selection, which can lead to the transmission of animal diseases, like West Nile Virus, to humans. Mosquitoes are the world’s deadliest disease vector, killing over 700,000 people globally each year, so understanding how and why this adaptation occurs can help us understand the framework that underlies the spread of mosquito borne diseases and bring us one step closer to solving this global issue.

 RNA-directed DNA methylation (RdDM) is an epigenetic pathway that induces transcriptional gene silencing through DNA methylation of target genes. The Zea mays (maize) RMR1 protein has an important role in the RdDM pathway as it functions to assist the process of making double stranded RNAs, required for progression of the pathway. Abscisic acid (ABA) is a plant hormone that accumulates under abiotic stress, and can inhibit seed germination. We determine if the RMR1 protein is involved in epigenetic regulation under abiotic stress by measuring maize phenotype and identifying transcriptional changes in ABA treated (vs. control) rmr1-1 mutants. To determine the effect of the rmr1-1 mutation on maize phenotype, we are measuring shoot length, primary root length and additional roots in maize germinating seeds from a segregating family. The genotype of the individual seeds is determined by amplifying the region of the rmr1 gene that includes the point mutation (C to T) that is on the 4th exon of the gene, followed by Sanger sequencing. The genotype is then associated with the measured phenotype. We are also interested in determining if ABA-induced transcriptional factors are differently expressed in rmr1 mutant compared to wildtype under ABA, and this will be measured by quantitative reverse transcription and PRC(qRT-PCR). This research is in progress and results will be presented. Maize and other crop plants are often negatively affected by abiotic stress, therefore, understanding how epigenetic pathways are involved in these responses is important to agricultural productivity.

The population of multiracial and multicultural individuals in the United States has steadily risen, but little to no public spaces have been designed to represent them and express their identities. Individuals in this group can find themselves feeling isolated from spaces because they feel like “imposters” or that they have to choose only one part of their identity to belong. How can we create public spaces that encourage people to express all parts of their multiracial or multicultural identity in a way that is inclusive, educational, and encourages cultural exchange? Through research of existing methods and practices, this project addresses how public spaces can be created to include multiracial and multicultural individuals. I provide methods and practices in the four categories of cultural exchange, cultural education, safety and inclusion, and expression. These methods are compiled into a set of guidelines and best practices to guide designers through the creation of multiracial and multicultural spaces. Since white public spaces have created the standards, these guidelines fill a gap in non-white spaces and spaces where multiracial and multicultural individuals can find belonging in. As a product created for designers, these guidelines bring the multiracial and multicultural identities into conversations and processes that they would not normally be a part of. This project reflects my own desire to see my multiracial and multicultural identity and others like me reflected in public spaces and serves as an example of why spaces like this are important and why representation matters.

Insect pollination is crucial to agriculture and conservation, but little is known about the ecology and evolution of floral scent, which is one of the strategies that plants use to attract pollinators. Flowers that rely on insect pollinators have floral scent compositions that attract certain types of pollinators more than others. Oenothera pallida is a plant which is pollinated by both daytime and nighttime pollinators, so examining its floral volatiles gives us an idea of what attracts the different pollinators to this flower. My research examines how floral scent emissions from Oenothera palllida differ between the day and nighttime, and how these differences in floral scent emission affect the attractiveness of the flowers to different pollinators. I extracted the floral scent from Oenothera pallida that is grown in the lab. I used Porapak traps to sample volatiles from each plant for six-hour periods in the evening and in the morning, which allowed me to see the change in composition depending on the time of day. I analyzed the floral scent samples using gas chromatography - mass spectrometry (GCMS). Then I created artificial scent blends in mineral oil that reflected the scent compositions of daytime and nighttime floral scent emissions. I exposed the hawkmoths and honeybees to the different scent compositions in a wind tunnel and observed the different responses of the two species. Finally, I determined what proportion of the moths or bees were able to locate the scent source by counting the number of individuals that flew upwind and landed on the artificial flower. 

One of the most important goals in human biology research right now is finding a cure for cancer, particularly for those tumors which cannot be easily removed or treated, such as gliomas and glioblastomas in the brain. By analyzing receptors that usually aid the brain, we can determine if they are crucially used against us when tumors develop. Tropomyosin receptor kinase B (TrkB), encoded by the NTRK2 gene, is known for critical roles in neuronal survival, differentiation, and molecular properties associated with memory. Is it possible that forms of this essential receptor become harmful in the context of tumors? In order to test this, a variant of TrkB was tested in vivo, in mice, and overexpressed in tandem with cancer-inducing growth factors, to see if tumor growth would increase in aggressiveness and in vitro, in neurospheres to observe size and proliferation. In both cases, tumors did increase in all ways hypothesized, but the results of these experiments have shown to go beyond the initial scope of the brain. Even though the receptor typically works within the central nervous system (CNS), when coupled with the loss of tumor suppressors in mice, effects extended beyond the CNS, causing tumors in the liver, spleen, kidney, soft tissue and blood. This finding proves that a TrkB variant may be a key factor in tumor growths throughout the whole body. Moving forward, using a short hairpin designed to knock out the TrkB variant, the absence of the receptor in tumor growth will be analyzed, and if there are consequences, this could spell out further contributions to our knowledge of cancer treatment and suppression.

Carbon dioxide concentrations have been on the rise since preindustrial times due to anthropogenic emissions. Understanding how past climates have responded to changes in the atmosphere is important to understand how our current climate will react to changes in our present-day atmosphere. Soil carbonates record the temperature at the time of their formation in their stable isotopic composition (called clumped isotope geochemistry). Ancient soil carbonates can record the temperature and allow us to better understand paleoclimates. Understanding what time of year soil carbonates form allows us to better interpret the temperature being recorded. The timing of changes in soil moisture is likely one of the most important environmental factors to consider. We test whether soil carbonates form during soil drying events using soil moisture and temperature data measured remotely by a satellite called Soil Moisture Active Passive (SMAP). This satellite has been gathering near-surface soil moisture data globally since 2015 at 35-65 km resolution. We compare the air temperature of the month with the greatest net negative soil moisture content month (determined from the satellite data) to the measured growth temperature of soil carbonates (estimated through geochemistry). We first compare the month of drying of three locales in North America, then extend the analysis globally to all locations for which soil carbonate clumped isotope data exist. Preliminary results suggest that the temperature of the month with the most drying agrees with formation temperature we estimated from clumped isotope geochemistry within one degree for a site in Nebraska and within seven degrees for a site in Wyoming. These results suggest that soil drying promotes soil carbonate formation in some environments. By using soil carbonates to explain past climates, we will improve temperature change estimates, which will help improve climate models for the future.

There are countless times in the past where people have attempted to expose systematic injustices committed by the U.S. government. Despite the fact that Hanford was a critical site in producing plutonium for the atomic bombs dropped during World War II, the contamination and subsequent health disparities remain shrouded in mystery and present dangers to future generations. In this project, we explore how the Hanford facility and the release of radioactive waste impacted the culture and daily activities related to diet, health, and faith of indigenous peoples in Washington State, as well as efforts by the government and native tribes that have been made in regards to cleaning Hanford and protecting tribal lands. By comparing interviews of Native Americans affected by the Manhattan Project, their oral histories, literature, public speeches, and using website discourse analysis of governmental sites, we made several important observations. Through our research, we found that among the devastating results of the Hanford contamination, the most common theme was the upheaval and marginalization of indigenous culture and the resulting inability of Natives to take part in community building activities such as wild game hunting, fishing, spiritual ceremonies, and trade with neighboring tribes. Not only did contamination tarnish relationships that local natives had with each other and the land, but there was and remains a strong correlation between subsequent cancer-related health disparities and bioaccumulation in natural resources. Nuclear radiation resulting from the Manhattan Project is not an issue of the past; its effects are far-reaching and will continue to mutate the physical and cultural conditions of the Native American tribes who lived in the area, relied on its resources, and were biologically affected by the processes involved at Hanford.

Proteins are essential to life, but many structural methods fail to capture the dynamic nature of proteins. This means researchers are left with an incomplete view of how protein function and structure relate. The Stoll lab uses electron paramagnetic resonance (EPR) to study the dynamic structure of proteins. The project I am working on is investigating the way in which the measurement conditions in EPR affect the determined protein structure. We use maltose binding protein (MBP) as a model system, since its structure has been previously well-characterized. My primary role has been to create new mutants for site-directed spin labeling, in which a radical spin label is attached to the protein. This radical is measured by placing the sample in a magnetic field and results in a probability distribution of distances. Common spin labels used in EPR, however, have many rotatable bonds, andd can cause uncertainty in the extracted distance distribution. Our project is investigating the contribution of spin labels to the EPR experiment. I use polymerase chain reaction to create new mutants of MBP by swapping a native residue with a cysteine residue in the mutants. Each mutant has one or two amino acids replaced with a cysteine. After mutating the DNA, I then transform the mutant DNA into wild type cells to grow the mutant protein and purify the protein. The spin label forms a disulfide bond with the cysteine residue in the mutant, providing an unpaired electron for measurement. By using various commonly used spin labels on many different site pairs in MBP, we hope to develop a model in which the contribution of spin labels to the probability distribution of distances is accounted for. This will ensure more accurate results in determining protein structure and will aid in structural characterization of many proteins.

Transcranial magnetic stimulation (TMS) of the visual cortex can induce phosphenes - highly transient, generally formless lighted areas at the periphery of the visual field - of stimulated test subjects while they look at a small visual target. Non-diagnostic ultrasound, applied to the visual cortex, can also induce phosphenes, studied while test subjects had their eyes closed during stimulation. Here, we sought to study potential visual alteration of a visual target during application of diagnostic ultrasound to the anatomical location where TMS induced phosphenes in the periphery of that visual target. First we used TMS, guided by anatomical landmarks, to stimulate the visual cortex and generate phosphenes in the periphery of a visual target. Next, we applied diagnostic ultrasound over 21 trials for 15 seconds per trial to a test subject while they looked at a white cross with a beginning baseline and a mix of random sham and treatment diagnostic ultrasound exposures. 10/11 test subjects observed TMS-induced phosphenes. Diagnostic ultrasound stimulation of the visual cortex induced visual effects in 7/10 test subjects, with no effects in 3/10 test subjects. The likelihood of the 7/10 test subjects to observe a visual effect increased as the experiment progressed, increasingly so as ultrasound exposure increased. Diagnostic ultrasound, delivered transcranially to healthy test subjects, altered the perception of a visual target and generated a lasting effect on their visual perception. This observation of a prolonged effect on visual cortex is consistent with recent work on stimulation by diagnostic ultrasound of the human motor cortex as well as earlier work on stimulation of the human amygdala. These results suggest diagnostic ultrasound may one-day find rapid application to humans for a variety of purposes, and also raises questions about the advisability of applying diagnostic ultrasound to the human brain without medical justification.

By their second birthday, toddlers help others. Moreover, infants as young as 9 months of age can detect others’ needs. Yet it is unclear if early helping behavior is based on and motivated by an underlying assessment of others’ needs, or motivated by other factors, like the desire to socially interact or affiliate with others. Here, we investigate whether toddlers utilize an experimenter’s needs when helping. We presented N=24, 24-month-old toddlers with two helping tasks: a puzzle and hunger-or-thirst task. In the puzzle task, toddlers watched an actor fail to complete a puzzle due to a missing puzzle-piece. Toddlers then had the opportunity to help the actor by either bringing her a puzzle-piece that fit the puzzle (need-fulfilling) or a puzzle-piece that did not fit the puzzle (not need fulfilling). Overall, toddlers were more likely to help with the puzzle-piece that fulfilled the actor’s need than the puzzle-piece that did not fulfill the actor’s need, p=.008. In the hunger-or-thirst task, the actor told toddlers that she was either hungry or thirsty. Toddlers could help the actor by giving her one of three different items: (a) cereal, (b) water, or (c) a shoe. Here, toddlers brought the needed item (e.g. cereal if she was hungry) at chance, p=.11. However, toddlers were more likely to bring the needed or the thematically related item (e.g. water if she was hungry) significantly more than chance, p<.001. Our findings provide initial evidence that 24-month-old toddlers are motivated to help based on others’ concrete needs: toddlers brought the needed puzzle-piece. However, toddlers have a harder time helping appropriately when the actor’s need is internal and therefore more abstract; hence, the equal likeliness to help with the needed and related item during the hunger-or-thirst task.

The Arab American population is severely understudied despite their recent but also historic presence in the United States. This underrepresentation in research signifies a void that translates to a lack of understanding towards Arab American culture. This qualitative study was conducted to make clearer the correlation between gender norms in the Arab American community and the acculturation of Arab American young adults into mainstream American society. Eight 30-45 minute interviews were conducted in a semi-structured form with Arab American young adults aged 18-24 years. It was hypothesized that Arab American women were more likely to separate, whereas Arab American men were more likely to integrate into American society. The results are discussed through the comparison of the gendered experiences of the participants against the framework of acculturation. This study identifies central questions and issues that are posed for the acculturation of Arab American young adults, and directions for future research.

Rats produce ultrasonic vocalizations (USVs) in a range from 20-kHz to 95-kHz that vary in frequency and shape across social and motivational contexts and can correspond to the affective state of the animal. To assess these USVs accurately and efficiently, our lab created DeepSqueak, a novel machine learning software package that expedites the detection and analysis of rat USVs by using neural networks to differentiate them from noise. DeepSqueak also allows for automatic and unbiased classification of USVs into discrete categories using call parameters such as shape, frequency and duration. Prior to this unbiased categorization method, identified 14 subjective categories in 50-kHz rat vocalizations that could be manually identified by a trained experimenter. These categories have received some limited study, but the excessive labor and time needed for manual classification restricted broad adoption. We aim to use neural networks to quickly and automatically classify USVs into these categories to promote broad adoption and better our understanding of the relationship between USVs and behavior. The process of training our neural network to differentiate between vocalizations was approached in two ways. Audio files were converted to sonograms through DeepSqueak and manually labeled. Thousands of these labeled calls were then inputted as training data for the neural network. This method allowed the network to learn using a large set of labeled vocalization data. The second method is based around the manual selection of an optimal call for each subtype using DeepSqueak's "call clusters" function; the neural network was then trained around how closely vocalizations matched the optimal calls. We now plan to compare DeepSqueak's automated calls and clustering to manual scoring in order to develop the best possible system that reliably categorizes USVs, thus allowing for more specific analyses of USV categories and behavior.

Development of technology, including artificial intelligence, has been controversial due to the potential negative effects. Many believe it is an auspicious industry and that technology will eventually replace the work of the human labor force. In this research project, our team analyzed the effects of technology in the labor market on the labor force within the next few decades. To accomplish our goal, we developed a model that can interpret the correlations between various factors. Specifically, this research analyzed data, including the employment rate, unemployment rate, number of occupation categories, and involvement rate of technology from varied industries. In addition, the Bureau of Labor statistics database was primarily used to regress the model. We expected to see a decrease in low-skilled occupations, such as cashier, in a short run. These types of occupations will be replace by IoT or artificial intelligence. High-skilled occupations, such as lawyer and surgeons, will still be demanded and irreplaceable in a short run, but would eventually be displaced in the long run. A shift would occur from low to high skilled occupations, due to factors such as social demand, working efficiency, and wage polarization. The employment rate goes down during the short run since more jobs are replaced by artificial intelligences and robotics. However, in a long run, more occupations will be created which will recuperate the fall in employment rate occurred during the short run. This research is very crucial and necessary because of the rapid growth of technology and its immense impact on the human labor force market. This research could ultimately provide information for governments and policy makers regarding potential growth sectors in the economy due to technological changes. Also, future generation can be more aware of this technological change, so that they can choose majors with accurately reflecting future employment trends.

When bacteria experience high salinity environments, such as the brines of sea ice, they take up compatible solutes to protect against osmotic stress. Examples of compatible solutes include amino acids, betaines, and other organic molecules that accumulate in the cells, balancing the osmotic difference between cytosol and external environment without impacting intracellular functions. I am exploring the mutualism of sea-ice bacteria and diatoms (an algal source of compatible solutes for bacteria), and the effects of salinity shifts on this dynamic. I have determined specific growth rates for five strains of bacteria at different combinations of temperature (–3°C to 1°C) and salinity (17 – 55 ppt) that mimic sea-ice conditions. Four strains derive from a collection of Antarctic bacteria found growing mutualistically in diatom cultures: 1) strain Fc1, most closely related (by16S rRNA gene sequence analysis) to Marinobacter psychrophilus strain i20041; 2) Fc4, closest relative Pseudoalteromonas arctica strain A 37-1-2; 3) Nl1, closest relative Glaciecola pallidula strain DSM 14239; and 4) Tr1, closest relative Colwellia rossensis strain S51-W. The fifth was isolated from Arctic sediments but has since been found in sea ice: Colwelia psychrerythraea strain 34H These strains were tested in a defined medium, composed of glucose, vitamins, and a nitrogen source (GVaN), and a complex medium, Marine Broth 2216. Those subjected to higher salinities could be tested at subzero temperatures due to the lowering of freezing point by the salts. During the incubations optical density and cell counts were determined and used for calculations. After determining permissive growth conditions from calculated growth rates, strains will be selected for experiments using specific compatible solutes and/or diatom exudates.

As of now, mRNA vaccines have been deemed as a potent replacement for current vaccine models against infectious diseases for their improvements in B-cell and T-cell immune responses. Usually, when soluble, subunit antigens are delivered, they are scattered and randomly bind to B-cell receptors, often loosely. However, with a nanoparticle carrier for antigens, there would be more effective crosslinking with B-cell surface immunoglobins as there is a higher density of structurally ordered antigen arrays presented by the nanoparticle. As a result, the B-cell creates a stronger immune response. Additionally, the multivalent particles also favors the creation of long-lasting immunity against a given virus. My team and I are currently developing a self-assembling protein platform using dn5A and dn5B protein components as a carrier for an mRNA vaccine against the flu. My project mainly focused on optimizing the co-secretion of the two particles by exploring different models and combinations of both. This is important as the translated cage not only has to be able to self-assemble but also be capable of doing so without producing excess protein in order achieve its purpose. To do so, I investigated 12 different constructs of dn5A and dn5B through transfections and analysis with western blots and electron microscopy. We used the data collected to improve the dn5A/dn5b protein platform utilized alongside flu mRNA vaccines, helping them better achieve potency. Overall, if effective, the new vaccination model can be utilized for other infectious diseases, including HIV and meningococcus.

Prostate cancer, the second most common cancer in American men, has a relatively low fatality rate – only around 2% of men will actually die of the disease. Prostate cancer has many treatment options. Each of these treatments comes with varying and oftentimes severe symptoms, so choosing a treatment plan is often based on patient preference. Since treatment is based heavily on patient’s values, it is important that patients are well informed about various treatments and related side-effects. This study aims to reveal how a patient’s socioeconomic background influences their decision making processes, with particular focus on how they receive information related to prostate cancer treatments. We review articles and studies from the past 10 years to determine how they address ethics in prostate cancer decision-making. The three framework topics used are: 1) how healthcare providers influence the decision-making process with their ethics and values, 2) how the socioeconomic and cultural factors of a patient informs their decision-making in prostate cancer treatment, and 3) how patients receive information and whether that information is reliable and accurate. In this literature review we find that patients are presented treatment options differently based on their education levels, race, and socioeconomic background, which has potential ethical implications. As this review progresses, we expect to organize these studies to inform how to best provide information to patients of varying cultural backgrounds. We aim to clarify future areas of study towards arriving at ethical consensus in decision-making in prostate cancer. Since decision-making in prostate cancer is a cost-benefit analysis, usually a trade-off between quantity and quality of life, studying how to best involve patients of varying backgrounds in the decision-making process is crucial to treating the disease.

Dandy Walker malformation (DWM) is the most common human cerebellar malformation, affecting 1 in every 3000 live births. DWM is an imaging diagnosis that is characterized by three features: cerebellar vermis hypoplasia, an enlarged posterior fossa, and an enlarged fourth ventricle. Although recent advances in neuroimaging have improved diagnosis of DWM, virtually nothing is known about the cellular and histological defects that lead to DWM. One major reason is that little human specific data is available describing the histology of normal and abnormal human fetal cerebellar development. Currently, there is limited published fetal pathology of DWM. There is no comparative analysis available and most studies are confounded by lack of molecular confirmations of diagnoses. We have carried out the first comprehensive histo-pathological analysis of human DWM. Such histo-pathological analysis, that I specifically was responsible for completing, included measuring the length and cell density of certain regions of the developing cerebellum in the 36 DWM cases, such as the external granule layer and the rhombic lip. Our results indicate a significant reduction in size and area of neuronal progenitor zones in the developing human cerebellum. We also observe aberrations in the developmental trajectories of specific cell types like Purkinje cells, and progenitor zones like the rhombic lip. Through our analysis of the human fetal DW cerebellum, we begin to directly address the developmental pathology of human DWM beyond that of the mouse models that share similar pathology. We believe our studies will fundamentally improve our view and understanding of the biology of the human cerebellar development and give us insights on the developmental pathogenesis of DWM.

Neonatal mammalian heart tissues possess regenerative capabilities after injuries like myocardial infarctions that are mostly lost in adult mammalian tissues but conserved through adulthood in other vertebrates like zebrafish. Previous studies have shown that regeneration in ventricular cardiomyocytes (CM) occurs through de-differentiation and proliferation, but the underlying mechanisms that cause cardiomyocytes to enter the primed cell-cycle are unknown. Here we show that amino acid and metabolite levels in injured cardiomyocytes result in a primed state for regenerating cells. In chemically ablated zebrafish, it is shown that the amino acid profile activates the mTOR pathway to drive regeneration. Amino acid activation of mTOR is a result of high glutamine and leucine levels post-injury and in early heart regeneration in adult zebrafish, which is lost in adut mammals. Inhibition of the Wnt/β-catenin signaling pathway upstream of mTOR shows down regulation of mTORC1, showing that mTOR is necessary for CM proliferation in regenerating heart tissue. How Wnt signaling gets activated upon injury is unknown, and this study aims to understand the pathways upstream of Wnt signaling for activation. It is known that scarring needs to occur before regeneration occurs in heart tissue. This study also investigates why macrophages are essential for scar formation in ablated heart tissue and its underlying mechanisms. Further, single cell RNA sequencing one-week post injury is used to determine cell fates of the heart tissue. Cardiac cell types like CMs, endocardial and epicardial cells, and bulbus arteriosus (BA) cells were activated post-injury, with epicaridal cells promoting CM regeneration and BA cells activating signaling pathways during heart regeneration. This study demonstrates the signaling and metabolic pathways that activate cardiomyocyte regeneration in zebrafish hearts.

Asymmetric cell division (ACD), a process that generates daughter cells with different cell fates and sizes, is a fundamental mechanism for generating cellular diversity during development. We use Drosophila melanogaster neural stem cells, or neuroblasts, to study ACD. Neuroblasts provide an ideal model for ACD since they are intrinsically polarized and divide with physical as well as molecular asymmetry, resulting in a self-renewed stem cell and a smaller ganglion mother cell (GMC). Kinesins, plus-end-directed motor proteins, have previously been implicated in asymmetric cell division and spindle dynamics. However, the specific kinesins that influence ACD and the mechanism by which they do so remains unknown. Elucidating the function of kinesins in cell division will help establish a more holistic view of cell development. To learn the role that kinesins play in asymmetric cell division, we performed an RNAi knockdown-based live-cell imaging screen of most kinesins in Drosophila. We found that knocking down the Drosophila kinesin genes Klp3A, Klp10A, Klp59C, Klp67A, Klp68D, CG14535, cos, or ncd causes the mitotic spindle to bend during metaphase and anaphase. We hypothesize that this phenotype is due to the spindle being so large that it buckles under the pressure of the cell as it divides. We are currently investigating this hypothesis by imaging knockout mutants to confirm this phenotype and tagging each kinesin with GFP to study how these proteins are localized during typical ACD.

For many Somali refugees in Italy, the journey from Somalia to Italian land is fueled by an overwhelming desire to seek better opportunities in education, employment, health, and lifestyle. As a country previously known for its luxurious beach resorts and affectionately named “the nation of poets,” Somalia has since dramatically shifted to a land inflicted with ongoing violence, terror, and instability. In this research, we will be exposing how the legacy of Italian colonial power has led to numerous detrimental effects on both the people and the government in Somalia. Furthermore, we will be investigating the ongoing refugee crisis in Somalia, focusing specifically on political and colonial history. Using an ethnographic approach, our research project provides insight into the harsh realities that face Somali refugee immigrant populations in Italy. Over the course of six weeks in Rome, Italy, our team has engaged in qualitative research methods in which we collected personal testimonies from current Somali refugees living in Rome through observations, interviews, and daily interactions. The results of our research will uncover the role Italy has had on the ongoing humanitarian crisis affecting the Somali diaspora.

Manipulating airflow over aerodynamic surfaces with plasma, compressed air jets and textured surfaces has become an area of intense aeronautical research and international competition in the last few years. Electrohydrodynamic (EHD) thrusters or plasma actuators have been demonstrated as remarkable devices for separation control and lift enhancement. The application of EHD thrusters to an aerial vehicle can drastically reduce the power consumption, weight and response time of mechanical controls. The focus of the present work is to determine the performance of a full-scale aircraft wing with an integrated corona discharge driven EHD thruster numerically. The numerical model is carried out by coupling the interactions between fluid mechanics and electrostatics. The study has been conducted on an augmented NACA 0012 airfoil with trailing edge flaps at a Reynolds number of 160,000 (10m/s). The EHD induced jet delays separation while lengthening and flattening the separation region. Preliminary results show that the actuator has increased the moment on the airfoil by 50% which helps in better maneuverability. The numerical results are compared with the experimental wind tunnel results. These findings can favor a strong design of a new generation energy-efficient aircrafts

Tin-doped indium oxide (ITO) is a n-type semiconducting material that have been widely used in solar cells, smart windows, and transistors. This material conducts electricity due to excess free charge carriers which charge-compensate the tin dopants. We are working to develop new chemical treatment methods to build optoelectronic devices from ITO nanocrystals. Colloidal nanocrystals are well-suited for solution-processing and low-temperature deposition techniques. These routes can be ideal for fabrication of thin-film electronics, especially on flexible substrates; however, increasing electronic communication between nanocrystals require post-deposition treatments. Few low-temperature methods to create conductive films from oxide nanocrystals have yet been reported. We seek to increase the conductivity of ITO nanocrystal films with ligand-exchange procedures to decrease the distance between each nanocrystal, then chemically crosslinking them. We synthesized ITO nanocrystals, then resuspended in solvents at high concentrations for film deposition. We first modify the surface of our nanocrystals by replacing the native long nonpolar ligands with short polar ligands. The modified crystals were deposited by spin-coating onto glass substrates and a variety of solvents/conditions were tested to optimize uniformity and thickness. Four-point probe measurements resulted in sheet resistance (R_s) ranging from 1 MΩ/square (ligand exchanged nanocrystals) to 2 TΩ/square (untreated nanocrystals). Profilometer measurements probed film thickness that can be used to calculate our films' bulk resistivity. Next, we used zinc and aluminum compounds as chemical solders to build bridges between nanocrystals to increase the material’s conductivity. R_s drops to ~0.15 MΩ/square with aluminum bridges and ~0.10 MΩ/square with zinc bridges. We plan on using other undoped metal oxides with this same scheme and apply them to thin-film field effect transistors (FET) to investigate how these treatments improve FET performance. We are also working on using similar techniques with SnO₂ nanocrystal films for application as electron-transport layers in perovskite solar cells.

Every year 26,000 pounds of human waste left by Mt. Everest climbers is disposed in pits near Gorak Shep (elevation 16,942ft.), a village close to Everest Base Camp in Nepal. The Mount Everest Biogas Project (MEBP) is working to build an anaerobic digester (AD) adapted to the extreme conditions of Mount Everest to treat this waste. All project materials must be carried by foot, including the biologic seed for starting the reactors. Thus, identification of a near-by seed is a critical step in the project’s success. Archaeal microbial community from five anaerobic digesters in Nepal were profiled. House-hold digesters and a mid-sized municipal digester in Katmandu were compared. The goal was to determine if methanogenic populations critical for establishing anaerobic digestion were similar among the potential seeds. Between 65,511 and 94,602 archaeal sequences were recovered from each sample. The sequences clustered into 580 operational taxonomic units (OTU). Species richness and Shannon-Weaver diversity indices ranged from 238-320 and 2.38-3.03, respectively. Significantly lower proportions of Methanosaeta, an important genus of acetoclastic methanogens, were detected in the municipal AD sample than in household AD samples (31% and 43%, respectively; t-test p=0.05). Conversely, the other known genus of acetoclastic methanogens, Methanosarcina, represented < 0.2% in all samples. Methanogen populations (phylum Euryarchaeota) dominated all samples (73 to 97%). However, household AD samples contained a significantly higher proportion (21% versus 3%, t-test p=0.007) of poorly characterized archaeal phylum with unknown function in anaerobic digesters. Principle Component Analysis (PCA) revealed that 2 of 3 household AD were similar. Thus, while all systems contained the Methanosaeta and other methanogenic species desired for startup of the MEBP AD, continued study of anaerobic digester is needed to understand how microbial communities evolve in response to the extreme temperatures of Mount Everest to assess the prolonged sustainability of the system.

Astrocytes are a type of glial cells in the central nervous system, play a critical role in protecting neuronal signaling by regulating brain homeostasis, synaptic plasticity and transmission, and blood brain barrier functioning in central nervous system. Accumulating evidence has indicated that abnormal behaviors of astrocytic functions, including astrodegeneration and astrogliosis, are implicated as the primary factors contributing to a number of chronic neurodegenerative diseases such as Alzheimer’s disease (AD) and Parkinson’s disease (PD). Kir4.1 is an inwardly rectifying K+ channel expressed on the projections of astrocytes, which serve important roles in the neuroprotective function of astrocytes, such as maintaining K+ homeostasis and regulating extracellular glutamate. Abnormal expression of Kir4.1 has been reported in certain neurodegenerative diseases, including Amyotrophic lateral sclerosis (ALS) and Huntington’s disease (HD), suggesting a vital role in the development of pathophysiology. However, the association between the molecular mechanism and expression of Kir4.1 and the underlying pathogenesis of AD and PD has been largely uninvestigated. In this study, we have had the critical opportunity to access human post-mortem brain tissue, provided by the University of Washington Alzheimer’s Disease Research Center, and conducted confocal microscopy studies. Through a quantitative immunofluorescense staining approach, we expect to demonstrate a distinct expression pattern of Kir4.1 in various brain regions of AD and PD post-mortem tissues when compared to control subjects. Determining the role this protein has in neurodegeneration may provide new insight into the development of therapeutic targets to ameliorate the progression of AD and PD.

Electronic movement can be modeled using the Schrodinger equation. For many-electron systems, however, these equations are not algebraically solvable, which is why this research uses direct numerical integration of Schrodinger’s equation to model time dependent electronic characteristics of molecules. The choice of numerical integration scheme can drastically change the outcomes of the simulation – even causing qualitative changes in molecular behavior. First, an advanced numerical integration technique (4th order Magnus propagator) has been implemented in the ChronusQuantum software package. Next, the effects on molecular behavior of choosing this integration scheme over preexisting schemes are evaluated. The implemented integration algorithms can be used to model the elementary steps of chemical reactions, as well as analyzing the effects of light on electron movement. The research provides meaningful information about the impacts of different implementations of algorithms along with analyzing the simulated behavior of electrons.

The sensory mechanisms by which organisms orient towards potential food prior to initiating movement are well-researched. However, behavioral mechanisms in stimulus-poor environments which determine foraging through seemingly stochastic movement variability or random-walk models remain poorly understood. Existing literature describe analyses of a variety of single-organism emergent movement patterns but do not appear to offer comparative analysis between single- and multi-individual environments nor within degrees of resource availability. We introduce a new analysis of observed fluctuations in spontaneous movement by Caenorhabditis elegans exposed to diverse conditions of competition and resource abundance. We describe a sequence of experiments which quantify the movement patterns of C. elegans through video imaging pattern recognition codified by run-length-time and turn-angle-time in comparison to recursively updating algorithmic position estimation. We expect to observe movement patterned on optimized explore-exploit strategies—such as simple random walk or Lévy flight—with frequency of implementation influenced by both population and resource density.

Depression is a neuropsychiatric disorder with a high rate of recurrence and increased mortality. One in six people experience depression at some point in their life, and the disease burden was over $200 billion in 2013. While little is known about the underlying neurobiological processes, the presence of inflammation in the central nervous system has been observed in those suffering from depression. This inflammation, mediated by microglial activation, astrocytosis, and pro-inflammatory cytokine production is involved in the progression of this disease. Past research has focused on the response of microglia in adults, but there are limited studies on the developmental features. Therefore, using a Sprague-Dawley rat model of lipopolysaccharide (LPS)-induced inflammation, this study aimed to understand the progression of the inflammatory response in the development of depressive-like behavior. We determined a suitable dosing scheme to induce inflammation while minimizing mortality to be an intraperitoneal injection (i.p.) of 0.05 mg/kg LPS on postnatal day (P) 7 and 0.1 mg/kg LPS on P9, P11, and P13. Control animals were injected with saline. The presence of inflammatory response was evaluated at P14, P21, and P35. This study showed that rats exposed perinatally to LPS had an increased number of microglia in the hippocampus as well as a hyper-ramified microglial phenotype in comparison to control animals. Similarly, rats treated with LPS showed decreased expression of anti-inflammatory TGF-β and increased expression of pro-inflammatory cytokines TNF-α and IL-6. LPS treated rats also tended to display more anxiety-related behavior including avoiding the open arms of an elevated-plus maze. These results support that LPS exposure in rats can be used as a model to study the effects of inflammation in the developing brain of rats displaying depressive behavior.

A protein's function is dependent on its structure, which is made up of amino acids. Proline, (an amino acid) is known to cause the kinks and turns in protein structures. However, little is known about the influence of pH on the isomeric preference of proline-attached dipeptides. For this experiment, the isomeric preference of methionine-proline was measured in 10% solutions for pH levels of 7 and 11, the pH of the human body falls between the range of 6 and 9. At pH 11, NMR-90 spectra showed that the cis- isometric form was preferred at a rate of 14% more than the trans- isometric form, measured by the alpha hydrogen. At neutral pH of 7 trans- isomers are preferred 36% more than the cis- form measured by the alpha hydrogen and 73% more measured by the delta hydrogen. In conclusion, this experiment supports the hypothesis that proline-attached dipeptides’ isomerization is pH dependent and is more likely to be in cis- form when in high pH in comparison to a neutral pH. The purpose of this experiment is to determine if pH levels can change the structure of a protien, with further research exploring if the change of structure changes the function. This is important to determine if medications containing amino acids can have an optimal or range of pH.

Over the past several summers, Washington state has faced high levels of wildfire smoke exposure. Significant research has indicated that wildfire smoke is a public health hazard. Public health professionals require evidence-based communication and intervention methods for use in exposed communities. It is valuable for researchers to understand current practice-based risk communication and management challenges to inform their research strategy and priorities. In response, the University of Washington's School of Public Health faculty and students convened a wildfire smoke risk communication symposium on October 30th, 2018, to foster academic-practice partnerships among regional stakeholders, identify existing risk reduction and communication challenges, and identify research needs. We conducted pre and post symposium surveys to collect information on participants’ goals, demographic characteristics, and symposium satisfaction. Descriptive statistics were calculated and displayed on graphs and tables. The registration survey identified the most common participant goals for the symposium which were to learn about lessons learned from public health practitioners related to wildfire smoke and to identify collaboration opportunities. Participants had a variety of roles related to risk communication and research. The evaluation survey revealed that over half of participants reported knowledge increases on wildfire risk communication, the future of wildfires in the Pacific Northwest, and practice-based responses to wildfire smoke. Over three-quarters of participants reported developing new connections that could lead to new collaborations in the future. Our findings suggest that there is an interest in working collaboratively to improve risk communication during wildfire events to address knowledge gaps and challenges impacted communities may face. We recommend engaging stakeholders and participants to identify the best communication methods and work with multidisciplinary partnerships that will be crucial to prepare for future wildfire seasons.

The application of quantum dots (QDs) is increasing in optical manufacture (solar cells), biological and chemical devices (cancer research). Exposure to QDs can potentially lead to a variety of adverse health effects especially for children and pregnant women. The goal of this study is to determine the toxicity of CdSe/ZnS QDs on brain development of both sexes using in vitro techniques. To determine sex-specific response, we used human neural progenitor cells (hNPC) lines derived from male (NSC-H14) and female (hNP1). An in-vitro model was established using an adverse outcome pathway (AOP) framework. We plated cells in proliferation or differentiation media for treatment to assess the morphology and biochemistry response in cells. Two QDs, differing in their surface chemical properties: carboxyl functional group – ITK and polyethylene glycol (PEG) without reactive functional group (Qtracker) were assessed. Cadmium chloride (Cd) was also tested to determine whether the toxicity of QDs is associated with ion release. The NSC-H14 and hNP1 cells were exposed to QDs of concentration from 0, 2.5, 5, 10, 20 and 40 nM on days in vitro (DIV) 0. After 24 hours, we evaluated the number of cells remaining (cell viability) with an LDH assay at each dose treatment. The results showed that exposures to ITK QDs demonstrated significant dose-dependent decreases in viability of both cell lines during the proliferative stage. Male (NSC-H14) cells were more responsive than female (hNP1) cells to the cytotoxicity of ITK. We did not observe significant dose response for Qtracker and Cd at the same dose range as ITK, either in proliferation nor differentiation stages of both male and female cell lines. Our results indicate that the coating on quantum dots may play a significant role in the exposure and toxicity of the cells, suggesting potential strategies to reduce the adverse health effects of quantum dots.

The concept of a laboratory often conjures up an image of an isolated and sterile room tucked away in the core of a building, inherently creating a physical and social barrier between the sciences and humanities. For centuries, this view was largely appropriate as many laboratories were designed in this way for privacy and security. However, 20th century research laboratories have begun to challenge this notion as an architectural building typology. As laboratories began to populate cities and academic institutions, especially after WWII, it became increasingly important to consider the perception of these spaces and their impacts on the built environment and the expanding scientific research workforce. I will be analyzing laboratory design guides and recommendations from both architects and scientists as well as examining a selection of laboratories with notable architectural qualities, focusing on key changes and trends in lab design. The literature and architecture help demonstrate the evolution of the laboratory. Rapidly changing digital technologies and methods of experimentation have led to a more collaborative research environment and a more business-oriented mindset. In addition, scientific research companies have redirected focus to the scientists to maximize efficiency and profitability and have placed greater emphasis on the physical building and the image it conveys. Sustainability has also become a key issue as laboratories are increasingly evaluated by their impacts on human and ecological well-being, resulting in a shift towards occupant-based design. Through these factors as well as a growing knowledge of the physical work environment and its link to human health, I will establish the importance of the qualitative role of architecture in creating positive and healthful impacts on its users and the environment in a traditionally utilitarian building typology.

Despite their sophisticated visual system, convergent and comparable in complexity to that of vertebrates, Octopus rubescens is largely nocturnal and forages mostly at night. Without visual information, their primary means of gathering information from the environment is through the sophisticated chemotactile sensory system within their arms. Octopuses blinded from lesions to their optic nerves have been observed relying on chemotactile perception of their environment with their arms fully extended to maximize their sensory range. Such behavioral profiles optimizing the acquisition of one sensory modality in the absence of another would be critical for navigating and monitoring changes within their environment. Our intention is to characterize how Octopus rubescens modifies its chemotactile range after an acclimation period of either light or darkness, simulating a natural 24 hour light cycle, and then a rapid change to the opposite lighting condition. Using 3d tracking cameras we will be able to quantify the change in the range of arm extension and overall posture that accompanies locomotion during light and dark conditions.

BiI₃ is a nontoxic and relatively abundant material with a bandgap of ~1.8eV that displays promising photovoltaic properties. However, BiI₃ solar cells have not reached efficiencies of greater than 1%. One of the major problems is the existence of deep defects in the materials which serve as trap states and increase non-radiative recombination. Here, defect engineering by both isoelectronic and non-isoelectronic doping of BiI₃ is studied to reduce the concentration of deep defects and increase the concentration of free charge carriers, aiming to improve the photovoltaic properties of BiI₃ solar cells. To evaluate the effect of dopants on defect passivation in BiI₃ films, photoluminescence and photoconductivity measurement are applied to determine quasi-fermi level splitting (QFLS) and carrier diffusion lengths, respectively. Additionally, dark photoconductivity measurements are used to determine carrier concentration. Preliminary results have shown an increase in QFLS under an iodine rich environment, though not significantly enough to drastically impact BiI₃ solar cell performance. There is much room for further exploration of dopants and their effect on BiI₃. With every dopant tested we learn more about the properties of BiI₃. This work will deepen our understanding of optoelectronic physics and defect chemistry of BiI₃ solar cell materials, optimize the quality of BiI₃ thin films, and increase the efficiency of BiI₃ solar cells.

Alzheimer’s disease (AD) is a neurodegenerative illness affecting millions of individuals in the United States and represents the leading cause of dementia worldwide. AD is pathologically defined by abnormal accumulation of interneuronal plaques composed of amyloid beta protein and intraneuronal tangles composed of tau protein. The focus of our current research involves understanding how tau protein homeostasis is restored using the model organism C. elegans. One process by which protein homeostasis is modulated is through the endoplasmic reticulum unfolded protein response (UPRER), which is composed of three signaling branches. Initially, the UPRER acts to restore normal protein folding, but if restoration is impossible, it triggers apoptosis. Our lab became interested in this signaling pathway after we identified the UPRER master transcription factor XBP-1s as a modifier of tau pathology (tauopathy). Specifically, XBP-1s overexpression protects against tauopathy in our C. elegans model. Previous RNA sequencing (RNAseq) analysis identified several downstream target genes upregulated with XBP-1s overexpression in our pathological tau C. elegans model. To follow up, I am working on understanding the molecular basis of XBP-1s-mediated tauopathy suppression by generating C. elegans models containing target genes of interest. Assessment of the effect on tauopathy phenotypes includes behavioral analysis by performing a liquid thrashing assay and tau protein analysis via the Western blot technique. Using the microinjection technique, I have generated a transgenic C. elegans model overexpressing hsp-4, an upregulated XBP-1s target gene identified by RNAseq that potentially modulates tauopathy. We are currently determining whether overexpression of hsp-4 can ameliorate tauopathy similar to XBP-1s overexpression. Gaining further information about the role of these XBP-1s target genes in tauopathy using the model organism C. elegans is valuable for future translational studies in mammals, along with being integral to research for neuroprotective therapies for neurodegenerative diseases such as AD.

When seeking to better understand specific bedrock river erosional processes due to flooding, numerical modeling can help answer many questions, specifically the extent to which floods contribute to setting the landscape. The eastern Himalaya experiences multiple flooding events of different magnitude: annual monsoon floods (10³m³/s) and centennial outburst floods (10⁵ m³/s). This region also experienced at least two ancient megafloods during the Holocene (10⁶ m³/s). Previous studies of flooding in the region have assessed the potential geomorphic role of the outburst floods and megafloods; however, the relative geomorphic impact of annual monsoon flooding remains unknown. To fully understand the relative erosive power of these eastern Himalayan floods, it is necessary to compare the hydraulics of outburst dam-break floods to the hydraulics of seasonal monsoon flow. To do this, we use the program GeoClaw to numerically simulate monsoon flood flow in this region. GeoClaw, which uses the 2D shallow water equations, has accurately been used to model outburst flooding events, including the centennial outburst floods and the ancient megafloods. By modifying the program to simulate constant monsoon discharge, we can analyze patterns of flow velocity and depth (GeoClaw outputs) to understand the spatial pattern of shear stress during monsoon floods. We expect to find that monsoon flow will yield lower magnitudes of shear stress and more homogeneous patterns of potential erosion compared to those observed for the outburst floods and megafloods. Understanding these erosional spatial patterns will help us better recognize the relative contributions of various magnitude floods and the extent to which each can set the landscape.

In the United States, the use of nuclear weapons is often associated with an era of scientific discovery which led to the security of the nation; yet there is another side to the nuclear era, one characterized by loss and irreversible consequences that is often overshadowed. One manner in which individuals connect to nuclear culture is through nuclear tourism: tourism centered around visiting sites associated with the nuclear age ranging from museums, to nuclear storage facilities, and even cities. I found myself intrigued with people’s obsession towards this dark area and wondered what laid beyond the tourism itself and how tourism affects society’s perceptions of nuclear weapons. I aimed to discover what side of the nuclear arms argument is being portrayed, and the potential implications, through analyzing the structure and advertising behind prominent tourist locations in the United States and Japan. After critically evaluating five nuclear tourism locations, it is clear that nuclear culture was largely portrayed with a sense of nationalistic pride which concurrently creates misconceptions about the use of nuclear weapons, numbing society to the humanity and suffering behind the machines. However, there were a few locations that painted the nuclear era in a different light; one that is truthful to the mass destruction and loss created by the nuclear era, sparking conversations that can lead to positive change. Overall, while nuclear tourism allows individuals to explore nuclear issues that face the world today, we must look beyond the technological contributions of the nuclear era and remember the humans whose lives were forever harmed as a result of using these weapons. It is critical to have avenues, such as tourism, to share knowledge about nuclearization that not only generate awareness but also work towards a world where nuclear weapons are simply a thing of the past.

Polymorphisms in the gene, FKBP5, and its resulting protein, FKBP51, are associated with stress-related disorders. Although FKBP51 inhibitors may have antidepressant-like effects, the relevant brain regions mediating this effect are still unknown. We found that FKBP51 expression is elevated in serotonin neurons of the mouse dorsal raphe nucleus (DRN) after stress, so we tested whether FKBP51 inhibition in the DRN by the novel FKBP51 antagonist, SAFit2, has antidepressant-like effects. First, we implanted guide cannulas into the DRN of wildtype mice stereotaxically, then we habituated the mice to 2.5% sucrose-containing bottles in their home cages overnight. On the following two days, the mice were stressed through repeated forced swims after receiving either SAFit2 (n=8) or a vehicle (n=7) to the DRN via the cannulas, prior to each swim session. That evening, the mice underwent a sucrose preference test to assess motivation by quantifying sucrose versus water preference using lickometers. On the next day, the mice were tested in a three-chambered social interaction test, where one chamber contained a wired cup enclosing another mouse of the same sex and the other chamber had an empty wired cup. Our results show that the SAFit2 and vehicle mice had the same immobility time during the forced swim stress, signifying that SAFit2 did not interfere with our immediate stressor. The SAFit2 mice demonstrated an increased preference for sucrose after stress compared to the vehicle mice, indicating greater motivation to consume a pleasurable liquid. However, there was no significant difference in the time spent interacting with the same sex during the social interaction test. This suggests that SAFit2 may have blocked stress-induced anhedonia by inhibiting FKBP51 activity in serotonergic neurons, as measured by the sucrose preference test. Further studies of FKBP51 inhibition in the DRN can lead to potential therapeutic treatments of neuropsychiatric disorders.

A DNA screening tool is being developed to allow rapid DNA testing in the field to identify endangered species of timber and wildlife. This work describes the design and testing of a chip holder and a gasket to improve the performance of this tool in the field with the consideration of usability, manufacturability and functional constraints. The chip holder is composed of a cradle with a hinge, two glass chips and one gasket. This chipset contains all reagents required to perform a DNA amplification test and features microfabricated heaters with electrical contacts to drive this reaction. Prototypes for chip holders with different hinge thickness and designs were fabricated in polypropylene using a Lulzbot Taz-6 3D printer with an Aerostruder tool head. The hinges were tested manually to ensure that the design parameters provided a stable joint. Gaskets were created by pouring Smooth-On Liquid Silicone Oomoo 25 into 3D printed molds. Silicone gaskets and chips undergo thermal testing on hot plate at 95 °C for 25 minutes to test if adhesion changes. Leakage testing for the gaskets is done through placing 0.2 g of water between gasket and chip and pressure are added between the chips to check water loss. We found the optimal material for gasket under DNA testing condition is Liquid Silicone Oomoo 25, and the best adhesive for the gasket and glass chip is silicone based adhesive GE Silicone II. Future work would be finding a more efficient method to produce the gasket, apply adhesives and adhere the gasket and glass chip. For the chip holder, the next step would be choosing the manufacturer, and select the specific polypropylene for mass production.

 Adults use many forms of information when deciding how to act in any situation. We are investigating the types of information infants use when determining how to act in a novel reaching task. We are looking at costs (how far they must reach; Study 1) and the social value of the object they are acting toward (Study 2). In Study 1 (ongoing), we tested 6-month-olds (n=25) and 9-month-olds (n=14). Infants completed a warm-up task to measure their maximum reach. During test trials, they were presented toys at 3 different distances: one inch away (Easy condition), one inch past maximum reach (Hard condition), and 27 inches away (Impossible condition; Figure 1). Infants reached more in the easy (93.2%) than the hard (72.6%, β=-1.90, p<0.0001) and impossible conditions (19.3%; β=-5.45, p<0.0001; Figure 2A). Infants also reached more in the hard than the impossible condition (β=-3.5, p<0.0001; Figure 2A). A within-subjects one-way ANOVA revealed a main effect of condition on infants' latency to reach F(2,73)=127, p<0.0001. The average latency increased from easy (2.61+/-2.05seconds), through hard (4.93+/-3.21seconds), to impossible (9.29+/-1.13seconds; Figure 2B). This indicates that infants are less likely to reach for objects when costs are high. In Study 2 an actor will manipulate one toy to be exciting (“I love this toy!”) and one toy to be boring (“Eh”), 3 times, 10 seconds each. We hypothesize that if infants use social value in their decision-making process, they will persist more when reaching for the exciting toy, particularly in the hard condition when reaching is costly. Even though infants engage in less complex decisions than adults, we are able to see evidence of decision-making processes in infants’ actions, supporting the idea that humans’ ability to perform these processes may emerge during early infancy.

Larval tadpoles of the frog Xenopus tropicalis exhibit a natural ability to regenerate multiple tissue types in response to injury. Unlike tadpoles, humans are incapable of regenerating a majority of their major organs and tissues following traumatic injury, often resulting in an irreversible loss of function of the affected tissues. While both non-regenerative and regenerative organisms undergo a period of wound healing in response to injury, the former then undergo scarring, whereas regenerative systems forgo scarring and ultimately regenerate the lost or damaged tissue. After tail amputation, reactivation of the cell cycle in the remaining tissue is required to promote cell proliferation in order to create the cells that will populate the regenerated tail. However, the molecular mechanisms that enable naturally occurring regeneration are not entirely understood. In order to better understand how wound healing promotes regeneration in tadpoles, I used immunofluorescent microscopy of Phospho-histone 3 (PH3) to assess the mitotic activity of Xenopus tropicalis tails during early regeneration. Over the first two hours post tail amputation, image analysis of PH3-positive cells shows that the amount and localization of mitotic activity varies greatly in the remaining tail tissue. Specifically, tissues adjacent to the amputation site transiently experience a dramatic decrease in mitotic activity beginning at 45 minutes post amputation (mpa), followed by the return of mitotic activity to these areas after 75mpa. I hypothesize that cell cycle inhibition during this 30 minute window is an important point of regulation during the regenerative process and may be a critical component of setting up a regenerative response to traumatic injury. Identifying mechanisms that enable regeneration will be critical for the development of clinical therapies that promote regeneration in humans

The University of Washington (UW) has a rich history around diversification and over the past 50 years anti-affirmative educational policies have reconfigured what “achieving diversity” looks like beyond admission statistics. Effective support is critical for the underrepresented minority (URM) student who gets into the UW and faces many disadvantages that make it difficult to succeed. The UW Educational Opportunity Program (EOP) Scholars Academy was created in 1968 to facilitate the metamorphosis (transformation) of low-income, first-generation URM students into independent and successful scholars. However, what is not publicly known is why the EOP Scholars Academy support program is effective and in what ways. This study explores how the EOP’s process of curating the student metamorphosis experience impacts 1) students’ academic outcomes and 2) their sense of belonging. The chosen field of perspective in this study is Organizational Communication (OC), looking at the interaction between parts of an organization (UW’s EOP and students) and the resulting behavior as seen through student actions. Some OC concepts used in exploring students’ responses to EOP affiliation include performance, social support, motivation, sense-making, diversity, and identity. Pre-existing data of two EOP-affiliated student-groups (~165 in EOP-1 and ~165 in EOP-3) include longitudinal grade point average, retention, major acceptance, and campus resource engagement metrics over the 2015-2016 school year. The data was statistically analyzed and compared across the two EOP-affiliated student groups, where EOP-3 consists of conditionally admitted Scholars Academy students and EOP-1 consists of non-conditionally admitted students. It is hoped these findings will assist in informing improved diversification policies, program changes, and future research on URM support programs within similar public selective universities.

The Moses Prairie Project is an effort to restore and enhance culturally important plant species on the Quinault Indian Nation Reservation through the traditional land management practice of controlled burns. Moses Prairie was selected because it was the only wetland fully owned by the tribe, unlike the other various prairies that are on allotted acreage. The prairie is a fen which makes it a biodiversity hotspot that supports both plant and game species if managed well and is not encroached by the surrounding temperate rainforest. In September of 2015, the prairie was burned for the first time in 150 years. I witnessed the complex difficulties and successes that come with collaboration across different agencies, cultures, and peoples. It brought up questions of what it meant for conservationists to do a cultural resource restoration project for tribes on the Olympic Peninsula, in the Pacific Northwest, and the rest of the United States and beyond. There are more contexts that bring to light why this project conserving both culture and the environment. I analyzed the data from the vegetation monitoring project on Moses Prairie, researched Quinault natural and cultural histories, looked at the kind of laws and systemic barriers that for tribes doing natural resource management, suggested future considerations such as climate change, and made recomendations on how to do more holistic and interdisciplinary natural resource management and ecological restoration. The goal of this report is to analyze the way restoration on reservations is shaped by the historical climates and natural events, tribal culture and resource management, and the past and present colonization and capitalization of the landscape. The aim is for scientists in my position to consider the many influences of the way a landscape is formed and the considerations we must keep in mind going forward with climate change and the continual erasure of the tribes. I also hope to provide a resource for the tribe to be able to reference either for their own knowledge or for people they hire or work with.

Growing reliance on antibiotics in livestock production, commercial agriculture, and human healthcare has created evolutionary pressures on bacteria. These pressures have given rise to a new threat to public health, drug-resistant microbes. In addition, antibiotics eliminate all microbes, including the beneficial ones, and are not advisable for long-term use. Recent advances in the understanding of bacterial virulence via quorum-sensing (QS) has presented the scientific community with a promising new approach for alleviating the ongoing overuse of broad-spectrum antibiotics. Quorum-sensing is a form of coordinated gene expression mediated through detection of specific population density. Bacteria use QS as a way to regulate behaviors including biofilm formation, virulence, and motility. Quorum-sensing inhibition (QSI), is the ability to prevent QS and is used by organisms across kingdoms. This prevalence suggests that disrupting prokaryotic communication is either a common defense tactic against infection or acts as a competitive advantage in resource acquisition. Fungi, a kingdom in direct competition with prokaryotes are prime candidates for broadening our understanding of the mechanisms behind quorum-sensing. With its abundance of endemic fungi, the Puget Sound region provides a unique opportunity to screen species for QSI compounds. In this study, fungi representing diverse ecological niches were collected from local forests around the Puget Sound and isolated on potato dextrose agar plates. To screen fungal isolates we used C. violaceum, a bacterium that forms purple colonies when able to quorum-sense and changes to white when a QSI is present. Our results suggest fungi are an underexploited and unexplored source of novel bioactive molecules that could provide a method to inhibit virulent effects of bacteria without damaging an organism’s microbiome.

Amyotrophic Lateral Sclerosis (ALS) is a neurodegenerative disease that results in progressive degeneration of upper and lower motor neurons, leading to muscle weakness, paralysis and death. Currently, ALS affects 15,000 Americans in the U.S., who have an average life expectancy of three to five years at the time of diagnosis. There are only two FDA-approved medications for ALS treatment, which minimally slow but do not reverse the progression of the disease. Understanding the genetic causes of ALS can help us to identify more effective treatments, therefore we seek to identify pathogenic variants and investigate how they contribute to the death of motor neurons. We previously showed that a tandem repeat in an intron of the gene WD-repeat-containing protein 7 (WDR7) may be involved in ALS. To better characterize this repeat, we PCR-amplified the repeat region and quantified repeat size in 500 ALS samples, including those from sporadic cases and those with known pathogenic variants. These repeat sizes were compared to approximately 500 Parkinson disease samples, 100 Primary Lateral Sclerosis samples, and 500 control samples from the Coriell Cell Repository, to verify whether expansion of this repeat was specific to ALS. Furthermore, to determine if repeat blocks were enhanced in certain subsets of patients, the lengths of the intronic repeats in genomes of ALS patients were profiled and compared with de-identified phenotypic information. To resolve the exact sequence of repeat in ALS samples, a subset of patient DNA samples and controls were sequenced using single molecule real-time (SMRT) sequencing. Together, these findings help us gain insight into the disease and guide us to develop a better treatment.

The damascene process is an additive manufacturing technique commonly used in the nanofabrication industry to produce semiconductor devices. This process utilizes deposition and patterning of successive layers to produce interconnected copper patterns separated by interlayer dielectric. The goal of this project was to implement the damascene process to develop and refine methods at the Washington Nanofabrication Facility (WNF) for manufacturing multi-layer devices. For our purposes, we constructed an integrated passive device (IPD) that contains capacitors, resistors, and inductors. We utilized basic nanofabrication tools in our damascene process including deposition, photolithography, etching, electroplating, metrology, and polishing tools. In fabricating this method at the WNF, our main objective was to produce a highly repeatable device with structural integrity. The main challenges accompanied with this involved generating a successful etch on all three layers of the IPD and optimizing polishing conditions. Cross sections of the final product were analyzed in order to demonstrate that the layout expected from the process was achieved. The procedure we developed can be applied to future multi-layer damascene processes at the WNF. Multi-layer devices are significant in the semiconductor industry as they allow for high packing density and an increased variety of circuit configurations in a compact device.

The 6He experiment located at the North Physics Lab aims to reach sensitivity 10 ^-3 or better in searching for beyond standard model tensor currents that violates chirality. The Fierz interference coefficient (little b) is linearly depended on tensor couplings and can be experimentally extracted by precisely measuring the 6He beta decay spectrum. The technique of cyclotron radiation emission spectroscopy from Project 8 (A neutrino experiment located at the UW Physics building) will be used to reconstruct 6He beta spectrum by measuring the cyclotron radiation frequency of the decayed electrons. Each piece of the energy spectrum will be measured separately by varying the magnetic field strength. Since the total number of 6He atoms entering the decay volume can vary over time, each part of the spectrum needs to be normalized to the same scale before combination. This requires a monitoring system that counts the total number of 6He atoms over each data taking period. As part of the effort to prepare for the upcoming 6He experimental run, this project is to develop this monitoring system so that it maintains its stability at the level of 10 ^-3 . The test was done on three experimental setups including a pair of gas counter plus silicon detector, a pair of scintillators and a single silicon detector under vacuum. Of the three setups, the single silicon detector reached desired stability on the most recent experimental run although more validations are needed. A successful setup of the monitoring system will help the experiment to reach desired sensitivity with spectrum normalization. And the detection of tensor currents implies the existence of symmetry breaking with chirality in beyond standard model theories.

This work describes an inexpensive and accurate gesture control implementation designed for an industrial setting. Sensing hand movements and being able to remotely operate devices without use of a tangible control can be useful, particularly in manufacturing applications where other methods of communication may not be available. One gesture recognition method is to use a camera or set of cameras to capture the motions of the user. However, this method imposes line-of-sight workspace constraints and is sensitive to environmental factors, such as consistent lighting conditions. My approach is to use an instrumented glove that detects the amount of bend in specific joints and sends those positions to a central processor that is programmed to recognize control gestures. Similar glove controllers are available but are either not well suited to an industrial setting because the sensors are vulnerable to metal dust and debris, or are not accurate enough to identify commands quickly and consistently. My version has custom sensors exactly fitted to this application and aims to have all sensors sealed and self contained to protect against contamination. This system is able to capture high resolution movement from the wearer and either save that data for machine training or send it immediately to be acted on. Going forward, onboard capabilities such as local gesture recognition will be added, as well as allowing the user to add custom gestures suited to their particular application.

The construction of the Hanford Nuclear Site was to aid the production of the atom bomb for the United States in World War II. This led to an era of secrecy, especially for the Hanford workers. A whistleblower is someone that brings about safety concerns about nuclear production to the public, but only with the risk of losing their job. Recent trends have shown that there are major consequences to whistleblowing, as many in the past who whistleblowed lost their jobs. However, whistleblowing is crucial to sustain the safety and health of many workers. Our purpose is to identify the motivations of these workers for either speaking out against the program or staying silent. Through analyzing interviews, literature and discourse, we hypothesize that whistleblowers at Hanford spoke out when they felt their moral obligations outweighed any monetary or social gain. Because the government heavily suppressed the voices of workers, we wish to better understand how society fosters environments where people are comfortable to speak out as opposed to promoting an environment of secrecy.

A series of ultraviolet exposure tests were conducted on a high-oil content, paraffin-based wax binder used in an operational U.S. Thoroughbred horse racetrack to simulate multi-year outside exposure. This type of hydrocarbon binder is commonly used in synthetic granular composites used in North American Thoroughbred horse racetracks and other equine sports surfaces. The function of the binder is to hold together the sand, polymer fiber, and rubber particles that constitute the surface. Previous research on this binder extracted yearly from the same racetrack over a six-year pear period, during which the track was not altered compositionally, showed that environmental oxidation increases over time. This degradation can potentially affect the mechanical performance of the overall surface which may impact the safety of both horse and jockey/rider. The goal of this work is to demonstrate how accelerated aging, in a short period of time, can mimic multi-year exposure using an UV-A equipped oven, and test results from fourier transform infrared spectroscopy (FTIR), gas chromatography (GC-FID), and differential scanning calorimetry (DSC).

The majority of research concerning the effect of intranasal oxytocin (inOT) on social cognition have used tasks that explicitly ask participants to focus on social information, such as identifying the emotion of face stimuli or interacting with other participants. As such, the variety of contexts from which data are derived are limited and have not examined the impact of inOT during tasks in which social information is available but not explicitly assessed by the participant. Here, we measured inOT’s effects on face processing with a novel task that does not require participants to explicitly assess social information, but instead relies on the uncanny valley effect. The uncanny valley describes how people tend to rate objects more favorably as they become more human-like until an object is nearly, but not completely human, at which point eeriness or repulsion is evoked. Participants viewed images of faces with varying degrees of human likeness and provided eeriness ratings while reaction time and eye-tracking data were collected. The results revealed that while inOT affected neither the magnitude of eeriness ratings nor eye movement patterns, inOT did decrease reaction times for providing eeriness ratings with the largest effect being for stimuli rated as being intermediately eerie. Thus, our results indicate that oxytocin can modulate the processing of social information in contexts other than explicit emotion recognition or social interaction tasks.

Merkel cell carcinoma (MCC) is a rare and aggressive cutaneous malignancy with a high propensity for recurrence and distant metastasis. Individuals with chronic immunosuppression have both a higher predilection towards developing MCC and tend to have a more aggressive disease course. Chronic lymphocytic leukemia (CLL) is among the most common types of immunosuppression associated with MCC. Immune-checkpoint inhibitors (such as anti-PD1 or anti PD-L1 therapies recently approved for cancer treatment) are associated with improved disease-specific survival and are often used to treat patients with progressive, metastatic MCC. However, the effectiveness and side-effect profile associated with treating metastatic MCC in CLL patients with immunotherapy is not well categorized. This study seeks to understand the risk-benefit profile of immunotherapy in this setting, and a possible combined role for radiation in the treatment of CLL patients. Data was abstracted from a Seattle-based prospective registry of 1,439 MCC patients in which 9 patients were identified to have had CLL and been treated with immunotherapy. Patients were assessed for side effects of immunotherapy, progression of disease and survival status. Six patients had side effects from immunotherapy with 5 of the patients having side effects that resulted in termination of treatment. The average number of doses of immunotherapy received before termination was 3. Eight patients had progressive disease after the initiation of immunotherapy, 4 of whom have died of progressive MCC. No patients have had a complete and ongoing response to immunotherapy. These findings suggest that despite the efficacy of immunotherapy in immune-competent MCC patients, this approach may be less effective in CLL patients than immunocompetent patients. In additional, the side effect profile seemed to be more frequent in CLL-MCC patients. Neutron radiation and combination therapy are discussed as potential treatment options. Further investigation into treatment options for MCC patients with immunosuppression, such as CLL, is needed.

With the rise of social media numerous nationally publicized incidents of large groups of people harassing a private party over the internet have taken place. A review of current research points to several possible causes. One body of research suggests certain patterns in neural activity which could be encouraging individuals to harass total strangers online - a phenomena which may be partially to blame. These patterns may be anthropological artifacts evolved to protect humans in primitive tribal groups which provide neurological rewards for actors who punish detrimental behavior in bad actors. These reward structures are now manifesting in the online environment due to its unique low-risk nearly anonymous nature and/or lack of tangible repercussions that would normally inhibit this behavior. Other researchers suggest these attacks may be a form of virtue signaling to let peers know the harasser is not like the perceived bad actor. (e.g. harassing a perceived racist signals to others that one is not racist). The issue is so new there is no strong scientific agreement in the psychological community as to what is really taking place, or in some cases even what terminology applies. Research in this topic may lead to better understanding of human machine interaction, and cyber-psychology.

Barcoding of physical objects with molecular tags holds an advantage over traditional paper or electronic barcodes in that they are discreet, durable, and difficult to falsify. Here, we developed a DNA tagging system that labels objects to verify their authenticity and trace their origin. We chose DNA as our tagging medium due to its information storage capacity and chemical stability, allowing us to generate a wide variety of unique barcode sequences that can be read by Oxford Nanopore’s MinION sequencing device. The MinION contains an array of thousands of nanopore sensors that are capable of sequencing single strands of DNA. The nanopore sequencing process creates distinct disruptions in the ionic current through the sensors that are indicative of the DNA sequence. However, the DNA basecalling software that processes the raw ionic current is computationally expensive, making it impractical when our goal is to quickly “scan” and identify a tagged sample. Because of this, we designed our barcode sequences to generate unique current patterns that are identified using a simple classification algorithm as opposed to arduous basecalling. So far, we have synthesized and classified a set of 96 barcodes that can be indiscriminately combined to create multi-bit tags. In a given tag, each bit is defined by the presence or absence of a particular barcode, and in practice, we have assembled and read up to 16-bits. We have also explored increasing bit capacity by independently varying barcode lengths, which adds another dimension to the barcode space. We also tested the durability of our barcodes by drying them onto filter paper and sequencing them 24 hours later, proving that our barcodes could survive in a dehydrated state. Future experiments will aim to lengthen this duration and expose the barcodes to different environments, in order to better simulate intended tagging conditions.