Among the many cultural treasures within the Burke Museum collections is a full-size sailing outrigger canoe from the island of Chuuk in Micronesia. This canoe is not currently on display but will be part of the Ethnology exhibit of the new Burke opening 2019. The basis of our research was to understand and analyze how Chuukese knowledge about canoes was reflected in cultural aspects such as canoe design, songs, myths, and language. To deepen our understanding of the Chuukese canoe we researched cultural aspects through methods such as literature review, community interviews, and collections analysis. Our aim for our research was to give a greater understanding and contextualization in order to unlock the knowledge of the outrigger canoe from Chuuk within the Burke collection. Our hopes were that this research would give visibility to the Chuukese community as well as educate all Burke visitors and staff members.

The Marshall Islands are often recognized as the victims of US nuclear weapon testing, leaving a lot unsaid about who they are as a people. This dark past often times overshadows the resilience and ingenuity within the Marshallese culture. This research project is aimed to gain a better understanding of Marshallese culture through their canoes and navigation techniques. The way that they navigate and construct their vessels plays a large role in their lives; their voyages, their developed culture, language and livelihood. Our methods include interviewing Marshallese community members within Seattle, analyzing navigation articles, wave charts and using the Burke Museum collection database for information on Marshallese canoes. We anticipate that this project will result in the general public walking away knowing the strengths of the Marshallese and a better grasp of one of the cultures in Oceania that is often underrepresented. It is important to look into other cultures, especially those we do not know a lot about, because you can learn so much from them. We also anticipate making relationships with those we interview and by understanding the views and values of their culture. By the end we hope to have opened the door for future research in this realm to encourage people to explore this on their own and participate in clubs and organizations.

How is the representation of Yapese knowledge brought to the forefront of musuem spaces? How is Oceanic knowledge recognized as a way of life, through what Epeli Hau'Ofa draws from interconnectedness between community, family, and beyond the Western concept of Yapese outriggers being represented as: Just a boat? Our reserach dives into the history of the Yapese canoe, the spirituality behind its meaning, how it is constructed, and how the outrigger connects to resources and sustainability. Through interviews done with Yapaese youth and elder within the community, analyzing material culture, and participartory knolwedge through the emerison of Yapese dance, we were able to bring Yapese voice into the display that will be at the Burke Museum. We aimed to connect the modern knowledge we have today with the cultural context surrounding daily Yapese society. The importance behind bridging these two forms of knowledge is to expose and provide a deeper understanding to those who only have access to non-indigenous studies of the Yapese culture.

In Samoan culture the va’a alo, the word for canoe, represents Samoan culture and indigenous science. The relationship between the canoe and the people who continue to use them reflect Samoan mana (cultural spirit). To understand the meaning of the canoe, it is important to understand the complexity and interconnectivity between the va’a alo and the natural world as well as the activities of the people on and off the canoe. Much of the history and resources about the va’a alo that are accessible to students have been tainted by a colonial lens and we strive to counteract these practices and bring forward the beauty and relevance of indigenous knowledge connected to the va’a alo. Our research emphasizes the importance of how Samoan culture connects its people to the canoe. We examine the cultural significance of the canoe design and the role of each person on the canoe. To understand the Samoan canoe, we must also understand its people and cultural values as reflected in canoe practices. Our research methods include lived knowledge of ceremonies and spiritual beliefs as well as interviews with Samoan elders, analysis of mythology, tattoos, proverbs, siva samoa (dance), and published voyages. We are conducting this research to educate the Seattle public through the Burke Museum of the importance of indigenous canoes and their value in Samoan culture throughout history and still today. We hope our results will help current Samoan generations, and even non-Pacific Islanders, to keep in touch with their Samoan traditions and ancestors. Maintaining this indigenous knowledge for the future is also a prominent goal that we hope to pursue. We want to keep this Samoan and the traditions of the canoe alive.

The vaginal microbiome has a mutualistic relationship with the immune system and can have a major impact on health and immunity to diseases, specifically its role in prevention against STI’s and Bacterial Vaginosis (BV). BV has been found to be associated with the prevalence and incidence of multiple STI and HIV. We hypothesized that changes in bacterial composition would correspond to changes in inflammatory cell frequencies in the vagina and examined this using rhesus macaques (RM) treated with various antibiotic regimens.12 rhesus macaques were administered paromomycin (n=3), enroflaxin (n=3), clindamycin (n=3), or cephalexin (n=3). Vaginal biopsy samples were taken twice before antibiotics (ABX) and at 5 timepoints post-ABX. DNA was extracted according to standard protocol and bacterial 16s rDNA was amplified and quantified by PCR and sequenced using Illumina kits and the Illumina MiSeq platform to determine abundances of relative bacteria. Flow cytometry was performed on cells isolated from matched biopsies to assess inflammatory cell frequencies. For animals treated with cephalexin or paromcyin, we found that CD4+ T cells and CD8+ T cells spiked after treatment around day 14 and declined to normal levels by day 63. Additionally, we found that neutrophil abundances spiked between days 28-63. Animals treated with clindamycin increased CD4+ T cells and CD8+ T cell counts around day 28 through necropsy while neutrophil levels stayed constant. Those given enroflaxin spiked in CD4+ T cell and CD8+ T cell counts at day 14 then returned to baseline, while neutrophil levels spiked between day 14-63. We observed alterations in bacterial composition that was dependent on the ABX regimen given and observed associations between these changes and the immune cell changes we observed. Taken together, these data show that altering the vaginal microbiome results in changes in inflammatory cell frequencies that could have implications for STI risk.

Indoor Environment Quality (IEQ) is a vital topic to address in today’s studies as it presents a significant role to the overall well-being of professionals who work indoors. IEQ adheres to overall human reactions to cleanliness/dirtiness, surrounding temperatures, and other irritants that may exist. While studies of IEQ in office environment have been well documented, less is known about IEQ during construction of an interior renovation. There are numerous possibilities of exposure to contaminants and pollutants both during construction and renovation to workers and building occupants, whom become vulnerable to the dusts and odors from construction. Currently there are no enforceable indoor air quality (IAQ) standards targeted specifically for office environment, so it is vital to address these topics and increase awareness, advocate the practice of applying minimal toxic materials, and prevent health concerns. In order to promote productivity and bridge the gaps in awareness concerning IEQ and health in office buildings, this three-phase project at the University of Washington Tower (UW Tower) aimed to addressed and advocated the importance of providing satisfactory IEQ, sustainable renovated workspaces, and shared IAQ strategies that could be implemented during indoor construction and renovation projects. Overall, three phases were implemented in this project. Phase-One took place four weeks before retrofitting. Phase-Two occurred during the construction. Phase-Three occurred after moving to the retrofitted workspace. This project involved collecting and analyzing IEQ data as well as surveying employees at the UW Tower to assess their psychological state, regarding each individuals enjoyment, well-being, at their workspace before and after construction. Future investigations should be directed at understanding what types of construction practices should be used to reduce pollutants, airborne toxins to maintain satisfactory IEQ.

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

Parkinson's disease (PD) is degenerative disorder of the nervous system that primarily impairs motor function along with other cognitive functions due to a specific loss of striatal dopamine neurons. The most challenging aspect of treating PD is that there is no explicit cause or any definitive long-term treatment. Current therapies restore dopamine levels in brain to alleviate the symptoms of PD. In this study, our goal is to address and identify possible markers of PD by studying the action of dopamine using functional MRI (fMRI) data. Resting-state fMRI allows us to examine the patterns of neuronal firing in vivo. We performed fMRI in 26 PD patients (age = 68 +/- 8 years) before (OFF group) and after (ON group) administration of dopaminergic medication to understand which brain regions showed altered neuronal firing with dopamine therapy. We applied the Integrated Local Coherence (ILC) approach to study temporal coherence of neuronal fluctuations within regions. High ILC corresponds to coherent neuronal fluctuations or recruitment of larger number of neurons as baseline. Low ILC corresponds to reduced temporal coherence in neuronal fluctuations due to neurodegeneration. ILC was computed in the cortex and compared between the ON and OFF groups using a paired t-test. Significance was considered for a voxel-wise threshold of p=0.001 and a Family-Wise Error correction for multiple comparisons at p=0.05. ILC measures were higher bilaterally in the superior parietal lobe, angular gyrus, and precuneal regions in the OFF compared to ON group. These results support another study where increased temporal coherence was observed in the same regions in PD patients compared to healthy controls. These regions are also part of the PD-related disease pattern network involved in motor dysfunction. With this work we believe that administration of levodopa reduces the excessive recruitment of neuronal regions during rest in PD patients.

Traumatic brain injury (TBI) afflicts people of all ages, with older adults having the highest rates of TBI-related hospitalizations and deaths among all age groups. Many of the issues and complications that TBI patients face are mediated by the immune response. Aging is a complex process which results in a decline of the immune system due to the altering of cellular production, proliferation and function resulting in an overall decline of immunocompetence. Injury sets off a chain reaction of immune cellular responses, the cell of interest in this project is TH2 cells, which have been shown to play a role in chronic inflammation. The purpose of this study was to explore if the age of an individual influences the TH2 cellular response in relation to traumatic brain injury. The TH2 cells used in the study were collected from younger (aged 21-64) and older (aged 65+) adult participants at < 24hours following mild/moderate TBI and at 3 months post injury. TH2 cells were stimulated with phytohaemagglutinin (PHA) and anti-CD3 and then incubated overnight. They were then analyzed for IL-5 production using the ELISpot assay. The number of cells producing IL-5 were counted, in triplicate, and the mean was taken to determine cellular response when stressed. The results were compared to determine if there is a difference between cytokine release amongst younger and older adults who experience TBI. By having a better understanding of how TH2 cell function is affected by age, we are exploring if overall outcomes following traumatic brain injuries are related to differential immune responses. This knowledge can potentially assist in identifying strategies to improve clinical outcomes.

PEDOT:PSS is a conducting polymer that is very promising as the next generation materials for the transparent electrode. PEDOT:PSS-based organic electrochemical transistor (OECT) has been widely used for various sensing applications such as glucose, antigen, DNA, and pH sensing thanks to the much lower working voltages, typically less than 1 V, and known biocompatibility of a PEDOT:PSS. OECT comprises three electrodes (source, drain, and gate), a PEDOT:PSS channel between source and drain, and electrolyte solution of analytes. Electric current flows through the conductive PEDOT:PSS channel. However, upon the application of a positive gate voltage, cations from the electrolyte are injected into the channel, decreasing a conductivity of the PEDOT:PSS. Hence, electric current decreases as a gate voltage becomes more positive. In our previous work we examined the impact of double-in-plane gate electrode on the OECT performance and found it to have a much higher transconductance of 35 mS as compared to 13 mS of a single gate. Now we investigate if applying heat can further improve the device performances such as sensitivity and response time of the OECTs. To test this, we have integrated a micro heater made of ITO on top of the glass substrate then covered the heater with aninsulative layer on which all transistor electrodes are fabricated in the same plane. High conductivity PEDOT:PSS was used to create a channel between source and drain. Fisher brand pH meter calibration solution was used as the electrolyte with pH values of 4, 7 and, 10. A drop of electrolyte was placed just over the channel and the gate electrodes. Once fabrication has been completed the OECT’s are tested and characterized at various temperatures by resistively heated micro-heaters. This work is important as it will allow the development of highly sensitive portable OECT arrays for various chemical/biological sensing applications.

PEDOT:PSS is a conducting polymer that is very promising as the next-generation materials for the transparent electrode. An organic electrochemical transistor (OECT) can control the amount of current flow in a conductive channel through an electrochemical reaction in the PEDOT:PSS channel assisted by an applied electric potential at a gate electrode. PEDOT:PSS-based OECT devices are widely used for biological and chemical sensing applications due to their high sensitivity, low cost, flexibility and lower operating voltage, typically less than 1 V. In addition, OECT has shown improved sensing performance when the gate electrode is modified with biocompatible polymers, such as Nafion. Nafion can lead to a more highly selective OECT-based sensor. A key feature of OECT is that both ions and electrons are used as charge carriers. This is of particular interest and importance for chemical sensors. For example, by combining a proton-conducting electrolyte, a simple Nafion-based OECT humidity sensor can be implemented as Nafion changes its conductivity upon exposure to humidity. In previous work we examined the impact of a double-in-plane gate electrode on OECT performance and found it to have a much higher transconductance. Branching off from that, we now investigate the impact of Nafion on OECT performance. Particularly, we want to investigate whether OECT sensitivity depends on the presence of Nafion film. In order to determine that, we fabricate several devices in which all transistor electrodes are in the same plane. High conductivity PEDOT:PSS is combined with Nafion in order to create a channel between source and drain. Once fabrication is complete, we plan to test and characterize the OECT’s to determine whether OECT performance is optimized with Nafion film. This work is important as it will allow the development of highly sensitive portable OECT arrays for various chemical/biological sensing applications.

Infective endocarditis (IE) is a life-threatening bacterial infection of heart valves. In comparison to treating other diseases, IE treatment is especially difficult to treat due to an increased resistance to conventional antimicrobial agents as well as a continuously high shear environment of the endocardium wall. Even after receiving prompt therapy, patients with streptococcal endocarditis often develop complications- including heart failure, progressive valve destruction, and stokes. Though the interactions between adhesive bacteria such as streptococci group of viridians (the major cause of IE) and platelets are known to facilitate bacterial vegetation in damaged heart valve, it is not well known how the bacteria bind through hitchhiker binding events (a specific interaction of platelets with streptococcus group viridans). Mainly, it is unclear whether bacteria bind to platelets and then to heart valves, or if the bacteria bind to platelets which are already found on inflamed heart valves.  To successfully characterize these spatial and temporal events, we used a parallel microfluidic device to develop a model. Specifically, we used our humanized in vitro model of infective endocarditis to understand the initial stages of the disease. We are demonstrating that the number of adherent bacteria can be measured after bacteria mixed with various blood components is washed through to the device, with sufficient accuracy to test hypotheses regarding the adhesion phase. Finally, we quantified the number of bacteria in vegetation after a growth phase following the adhesion phase. The findings from this design can potentially lead for the development of novel molecular therapeutic mechanisms. These will have implications not only for infective endocarditis, but also all other endovascular infections with a shear environment.

Antibiotic resistance, drug cytotoxicity, and lengthy treatment regimens are major barriers to ending the tuberculosis epidemic. Host-directed therapies (HDTs) that avoid direct targeting of Mycobacterium tuberculosis (Mtb) while enhancing macrophage clearance of the bacteria may overcome such challenges. Because host protein kinases (PKs) regulate multiple innate immune signaling pathways involved with Mtb clearance, we hypothesized that host PKs are HDT candidates. We investigated a group of ATP analogues with specific activity against parasite serine/threonine protein kinases called bumped kinase inhibitors (BKIs). BKIs inhibit few mammalian PKs, so they offer HDT potential while avoiding broad activity that could result in toxicity. To assess the effect of BKIs on Mtb growth within monocyte-derived macrophages (MDMs), MDMs from healthy donors were infected with a luminescent Mtb reporter strain (Mtb-lux) in the presence or absence of BKIs and daily luminescence readings were recorded. We found three BKIs that limit Mtb intracellular replication in MDMs at a final reaction concentration of 10-20 µM. Interestingly, none of these compounds inhibited Mtb-lux growth in 7H9 broth culture. To examine possible mechanisms, we measured the effect of the BKIs on pro-inflammatory cytokine release in MDMs in response to various stimuli including Toll-like receptor agonists, virulent Mtb, and the attenuated vaccine strain Mycobacterium bovis BCG. In response to all of these stimuli, the BKIs potently inhibited TNF secretion and moderately inhibited IL6 secretion by ELISA. In contrast, the mRNA expression level of antimicrobial peptide cathelicidin was maintained in the presence of the BKI tested. Since pro-inflammatory cytokine induction and cathelicidin expression are generally host-protective in early Mtb infection, it is unlikely that the effect of the BKIs on these pathways are responsible for inhibiting intracellular Mtb growth. We are currently evaluating the effect of BKI treatment on other antimicrobial pathways that restrict Mtb infection, including phagosomal uptake and autophagy.

Here we explore applications of multivariable calculus for studying three dimensional wave media in our environment. We employ regression based methods to derive analytic formulae for real wave. Using multivariable optimization methods, we derive the maxima, minima and saddle points of three dimensional functions. We use advanced data visualization methods to study the divergence and curl and illustrate how these can be used to study ocean waves- including their vorticity and circulation. The project provides hands on exploration of real world environmental science problems with advanced data visualization and shows how divergence and curl can be used to measure circulation and vorticity parameters of real wave media involving ocean waves. Real world manifestations of scalar and vector fields in our environment are also presented.

Monte Carlo simulations employ random probability distribution statistics to estimate areas and volumes. Here, we employ Monte Carlo simulations to estimate the numerical value of π. We inscribe a circle in a square board and throw N darts using random values for both x and y. The probability that the dart lies within the circle = area of circle/area of square. This relationship allows us to estimate π. We wrote EXCEL/JAVA code for this research. The accuracy of estimated π is improved as the number of darts N --> ∞. This research allows us to combine mathematics, computer programming and data visualization to estimate π. Important applications of Monte Carlo simulations to find areas and volumes of complex objects including rivers, landscapes and organisms which cannot be represented by analytic functions will be discussed.

Education on the current state of the food system can motivate individuals to create the food systems and generate demand for products they wish to see. With the idea that we are what we eat and how we consume, real food is the best medicine—for individual health, for society, and for the planet. The power of individual freedom does not mean anything goes, but rather informed, responsible choice that transcends to the global aggregate. Thus, respectful and healthy food systems begin with the individual, and have the potential to bring peace to communities and heal human relationships with land and each other, both locally and globally. Knowledge is power, and first starts with attention and awareness. Given the severe lack of transparency and multitude of socioenvironmental externalities within the industrialized food system, there is a need for adequate consumer education on practices and operations. Information on the consequences of these processes can influence attitudes to shift demand and create new vibrant systems. Here, the problem is the solution. To promote holistically healthy and nutritious systems, I created a disruptive advertisement campaign to highlight truths of the industrial system and its social and environmental externalities to inform consumers on cost and value of the products they are purchasing. This project juxtaposed the concepts of "farm to table" versus "firm to table," in additon to the applications of integrative sensory marketing tactics and culinary storytelling. Through the combination of art, music, poetry, and film, I sought to motivate people to think critically about the power of individual choice and what is behind a brand.

Duchenne muscular dystrophy (DMD) is an X-linked recessive genetic disorder, marked by progressive muscle degeneration due to the absence or impairment of the dystrophin protein. Our laboratory has been developing methods for gene therapy of DMD. The dystrophin gene is the largest known gene, which complicates gene therapy. We have shown that gene delivery vectors based on adeno-associated virus (AAV) can be used to deliver new genes body wide. However, AAV has a ~5 kb carrying capacity, so we have been developing miniaturized dystrophins. These smaller, highly functional dystrophins, which we named micro-dystrophin (µdys) were tested in a transgenic mdx^4cv  mouse model for DMD. Furthermore, we sought to develop a non-invasive method to evaluate treatment efficiency of µdys. In this project, the gait of mdx^4cv, wild type (WT) and transgenic mice were observed to deduce potential benefits of the µdys transgene. We hypothesized that µdys treatment will enable the gait of the transgenic mice to resemble that of WT animals as opposed to mdx^4cv. To test this, gait was assessed at three time points: 1.5, 3 and 6 months of age using the video-based Noldus CatWalk XT. Our results show that the length of a single stride of the transgenic mice hind paws increased over time compared to mdx^4cv. The normal walking pattern of mice consists of placing diagonal paws on the surface, one front and one hind from opposite sides. In the case of mdx^4cv, more paws were placed down for majority of the walk, as a compensatory mechanism for muscle weakness. The transgenic mice were found to walk with a diagonal pattern more frequently, like WT mice. Similarities in the gait of transgenic and WT mice help us conclude the µdys treatment was successfully able to mitigate the effects of DMD as seen by the gait analysis.

Kaposi’s sarcoma-associated herpesvirus (KSHV) is the etiological agent of Kaposi’s Sarcoma (KS), a highly vascularized tumor made up of cells of endothelial origin. KSHV establishes a predominantly latent infection in endothelial cells in culture and in the KS tumor. A previous study has shown that KSHV induction of the Warburg effect is required for the survival of latently infected endothelial cells. The Warburg effect, a common metabolic alteration in cancer cells, refers to an increase in glycolysis and a decrease in oxidative phosphorylation. The mechanism of Warburg induction by KSHV is currently unknown. I proposed to evaluate the role of endothelial cell specific hypoxia-induced factors (HIFs) on KSHV Warburg induction since HIFs have been implicated in Warburg induction in other types of cancer. I hypothesized that HIF2α mediates KSHV Warburg induction through expression of glycolytic genes. To test this, I constructed HIF2α knock-out cells using CRISPR/Cas9 gene editing. I then used RT-qPCR to measure glycolytic gene expression during KSHV infection of wild-type and HIF2α knock-out cells. I found that the transcript levels of certain glycolytic genes remained constant in KSHV-infected HIF2α knock-out cells as compared to KSHV-infected wild-type cells, showing that HIF2α is not responsible for glycolytic gene expression during KSHV infection. I am following up on the role of the KSHV latent gene KapA on the induction of glycolytic gene expression. KapA was previously found to interact with components of the Ras pathway. As the Ras pathway activates glycolytic genes through HIF1α, I hypothesize that exogenous expression of KapA will lead to increased glycolytic gene expression through increased expression of HIF1α. I will construct an endothelial cell line that overexpresses KapA using CRISPR/Cas9 system and then use RT-qPCR to evaluate glycolytic gene expression. These results will aid in the future efforts to develop antiviral drugs by targeting cellular metabolism.

Cystic Fibrosis (CF) is a genetic disorder that is characterized by recurrent pulmonary infections and a progressive decline in lung function caused by increased inflammation. While the host immune response can help fight these infections, an overzealous inflammatory response in the lungs may be harmful. Inflammation can be induced by multimeric proteins called inflammasomes, which catalyze the maturation of pro-inflammatory cytokines and pyroptosis. Our laboratory is interested in investigating genetic variants that alter the response of the NLRP3 inflammasome in human CF patients as a means of identifying potential targets for host-directed therapies. Preliminary data from the EPIC study has identified two genetic variants in CF children that is associated with colonization by P. aeruginosa, a common bacteria in the lung that can induce deleterious inflammation. We hypothesize that genetic variants in the NLRP3 inflammasome will increase the inflammatory response to bacterial infection and will lead to worsened pulmonary outcomes in patients with CF. First, we used CRISPR/Cas9 and gene editing techniques to knock out the NLRP3 gene in human cell lines. We then inserted NLRP3 genetic variants and stimulate the NLRP3 inflammasome using Pathogen associated molecular patterns such as Nigericin and ATP. The extent of inflammation was measured using ELISA (Enzyme Linked Immunosorbent Assay), and results were compared among NLRP3 genetic variants and wild type controls. The ultimate goal of this investigation is to learn how genetic variants are associated with the clinical outcomes of CF patients. Future studies can involve harnessing host-directed therapies to target specific inflammatory pathways in order to reduce harmful inflammation in CF. Finding the relationship between the NLRP3 inflammasome and CF is critical to generating an effective treatment for CF.

As one of the five leading causes of blindness, uveitis is the reoccurring inflammation of the uvea, demonstrating pathological changes in the eye. In recent years, optical coherence tomography (OCT) has been recognized as the leading, clinically accepted imaging modality for diagnosing major human optical diseases. Despite this, research on the clinical usage of OCT, primarily spectral domain OCT (SD-OCT) and swept source OCT (SS-OCT), for uveitis diagnosis remains sparse due to the lack of a quantitative-based set of parameters to assist with OCT image analysis. As a result, there is a need to develop an index of parameters that quantifies the microvasculature and structural changes associated with uveitis. To address this need, a novel five parameter quantitative-based metric consisting of distance of retinal detachment, retinal thickness, vessel area density, vessel diameter, and vessel perimeter was evaluated. Through layer segmentation of SD-OCT and SS-OCT scans, application of optical microangiography, and quantitative analysis of structural and microvasculature changes for healthy and uveitis cases, the clinical potential of SD-OCT and SS-OCT for diagnosing uveitis was evaluated. This project introduced a metric for evaluating changes associated with uveitis in a qualitative and quantitative manner to further understand the abnormalities that accompany the disease. Assessing the clinical efficacy of SD-OCT and SS-OCT for uveitis detection can provide insights on the most effective method for diagnosing this disease.

Antibiotic resistance is an intractable clinical challenge that disproportionally affects much of the world’s most impoverished populations. A critical driver of resistance stems from DNA mutations. Therefore, insights into how mutations arise in the genome is critical to understanding the development of antibiotic resistance. Our lab is currently identifying factors and environmental conditions that promote mutagenesis and bacterial evolution. Utilizing mutation rate analysis, we have identified factors and conditions that promote mutagenesis in divergent bacterial species. Additionally, using short-term evolution experiments, we have found that these factors promote the development of antibiotic resistance over time. This work provides novel mechanistic insights into mutagenesis and antibiotic resistance development in bacteria.

DNA origami nanotechnology has evolved rapidly since its conception eleven years ago. Both two-dimensional and three-dimensional nanostructures have been created with potential applications in targeted drug delivery, “smart” diagnostic technology, and the study of cell behavior. By annealing “staple” oligonucleotide strands to a single-stranded DNA scaffold we can effectively fold the DNA onto itself to build the nanostructures of interest. One of the primary physical limitations to what one can build is the scaffold. The most commonly used scaffold is derived from the bacteriophage M13mp18 and has a length of 7,249 nucleotides. Its length has previously been varied; however, an overlooked limitation is the secondary structure DNA naturally exhibits. These are sites in which the scaffold binds to itself, thus creating competition for staples to bind during folding reactions. To predict the impact that a designed sequence with little secondary structure could have, we analyzed the first 6,000 bases of the M13mp18 DNA sequence using NUPACK, a nucleic acid sequence analyzer, for their minimum free energy (MFE) at storage, manipulation, and maximum folding reaction temperature. Preliminary data shows M13mp18 exhibits less secondary structure at a high temperature (65°C) than at a low temperature (4°C) and increasing the concentration of divalent salts linearly increases the amount of secondary structure. Additionally, alternative, shorter sequences have been engineered and their secondary structure is being analyzed at varying conditions. To further determine the effects on yield and stability, structures will be folded using the designed sequence and the standard sequence as a scaffold. These will be compared through agarose gel electrophoresis and transmission electron microscopy. The results from this preliminary data could help us move us toward using a scaffold with decreased secondary structure present at folding temperatures which could potentially result in higher yields, shorter folding reactions, and increased stability.

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

Characterizing biological functions on a single molecule scale increases understanding of biological functions by providing information about the indiviual contributions which combine to create larger scale functions. Single molecule measurements are a crucial part of characterizing molecular interactions. Although atomic force microscopy (AFM) and magnetic tweezers are able to measure the response of single molecules to mechanical force, it is challenging to ensure single molecules are being measured. In this project, a precise DNA Origami structure was used to space molecules for single molecule force measurements. Base pair association between DNA nucleotides allowed specific nanostructures to be designed and fabricated. Molecules of interest self-assemble to specific sites of the structure. AFM was used for imaging and obtaining force measurements. This research investigates the strength of adhesion for double stranded DNA when subjected to different loading rates as a proof of concept. In the future, this structure will be used to determine force properties of diverse molecular interactions like platelet and bacterial adhesions.

Portland, Oregon takes the lead in the highest strip clubs per capita, however, strip clubs in Portland have gone unregulated, allowing for poor management and oversight of health and safety issues. When violence and exploitation occurs, exotic dancers have scarce resources to turn to due to the continued stigma of being a sex worker. Past research has explored limited issues related to exotic dancers, including drug use, sexually transmitted infections, and mental health problems, but few have questioned what safety measures are needed to protect women in this industry. This study aims to explore the exploitation and abuse that exotic dancers experience in order to improve the laws and regulations of strip clubs. Through this qualitative study, I will use semi-structured interviews in order to better understand experiences of interpersonal violence against exotic dancers including various forms of violence from clients, employees and law enforcement in Portland. Data will be analyzed using thematic analysis in order to establish working themes. The anticipated results of this study is that the interviewed participants will express various experiences of interpersonal violence and that there may be common variables to violence experienced in strip clubs such as race, age, structural safety features in clubs, and the availability of outside resources to report violence. It is also expected that violence perpetrated by clients and club managers will be among the highest reports by the participants. Lastly, it is hypothesized that women who have not experienced abuse and exploitation (or limited amounts) while at work will still fear experiencing it, which is still a cause for concern. This study provides a platform for exotic dancers’ voices to be heard, while also attempting to improve better working conditions of adult entertainment establishments.

A century of U.S. government-backed, anti-Asian discrimination culminated in the incarceration of Japanese Americans during World War II. Despite U.S. government insistence that anyone with up to 1/16th Japanese blood had to be incarcerated, the existence of white-looking children in concentration camps presented a segregation crisis. Race was segregation’s litmus test: if white was assumed loyal, Japanese was assumed disloyal. My paper uses original archival research to study attempts to reconcile this monoracial logic with the multiracial reality that exposed it - the U.S. government’s Mixed Marriage Policy (MMP). The MMP permitted some multiracial Japanese Americans to escape or avoid mass incarceration. My project argued that U.S. treatment of multiracial Japanese Americans rewarded the disavowal of Japanese identity with “integration” to project an image of liberal inclusion whilst allowing a reality of surveillance and segregation. When attempts to quantify racial mixtures became impossible, the MMP attempted to strip the trait of race from multiracial subjects in a policy of institutional “colorblindness” by evaluating loyalty on “objective” criteria alone. Individuals eligible for integration became symbols for the U.S. government to project an image of inclusive humanitarianism and racial tolerance in the post-war empire. However, these seemingly neutral criteria upheld U.S. imperial practices of racial segregation. The perceived disavowal of the racism behind incarceration sanitized the image of the U.S. government while quietly reproducing racial hierarchies through new domestic surveillance policies. Shifting segregation policies to subtler forms of institutional colorblindness strengthened the United States as an empire of white supremacy. Racism was at its most intractable and pervasive when acknowledging the existence of race became taboo. As the title “It Must be Odd to be a Minority” (Spanish translation) alludes, this research is significant to Asian American Studies because the current literature rarely address inter-sectional struggles with the greater community of color.

Diophantine equations are polynomial equations with integer coefficients. In 1970, Matiyasevich proved that an algorithm to decide whether a given Diophantine equation has a solution does not exist. We investigated some such equations including Pell and Thue equations, that have an infinite and finite number of solutions, respectively. Geometrically the solution set of Diophantine equations in 2 variables corresponds to plane curves, e.g. elliptic or hyperelliptic curves, and the number of rational solutions is related to the genus of the corresponding curve. We gathered statistics on the size of the solution sets in an attempt to address an important unsolved problem in arithmetic geometry, known as Uniformity Conjecture of Caporaso, Harris and Mazur. Our project involved an analysis of Python and C code, specifically through the CoCalc development platform, utilizing data from the L-functions and Modular Forms Database (LMFDB). Currently our results agree with the current known data on the sizes of solution sets, and we hope to extend our results to gather data on curves not currently in the LMFDB. This will serve as a testing ground for the Uniformity Conjecture.

Quantum Dots (nanoparticles with semiconductor properties) are currently produced from potentially toxic materials, and are expensive to prepare. Developing a less toxic, more renewable quantum dot has the potential for utilization in biosensors and bioimaging without the high cost or environmental pollution associated with current metal-based quantum dots. Methods for developing graphene quantum dots are being investigated by utilizing a sustainable carbon source. Specifically, the use of hydrogen peroxide as an oxidant in a hydrothermal reaction is being optimized in terms of reaction time, temperature, carbon:oxidant ratio, and oxidant concentration. Carbon sourced from research being conducted on campus allows for reduced cost and waste treatment while providing an alternative to metal-based quantum dots. Further work on the subject will include incorporating the quantum dots into handsheets (paper samples) to test fluorescence, which ultimately will be used as optical and photoelectric sensing materials due to their high stability and distinct long-term fluorescent properties. Additionally, there is potential to explore other oxidants and carbon sources that have minimal environmental impact.

The reduction of drug craving and subsequent relapse is central to the recovery process for individuals with substance use disorders. One of the goals of this project is to improve pharmacological treatment interventions for substance use disorders by better understanding how the neurotransmitter dopamine is involved in relapse. We investigated the relationship between drug craving and dopamine release in the nucleus accumbens core (NAC), an area of the brain that plays an integral role in reward-based learning and addiction, in male rats that have been trained to consume cocaine or alcohol. We tested the effects of L-DOPA, a chemical precursor to dopamine and a treatment that could reduce drug consumption, on craving and relapse-like behavior. Recent evidence from our lab suggests that decreased dopamine release in the NAC correlates with increased cocaine consumption in rats, and that L-DOPA administration attenuates drug intake. Preliminary data from our current project shows a similar effect of L-DOPA on alcohol or cocaine relapse. Our characterization of dopamine release in the NAC during both periods of drug abuse and withdrawal provides new insights for future studies and our use of innovative electrode implants for monitoring dopamine neurotransmission will pilot the technology for other drug self-administration studies. This will help to determine whether L-DOPA should be considered for treatment of cocaine and alcohol addiction in humans.

X-ray spectroscopic techniques utilize selective x-ray absorption or fluorescence to interrogate the element-specific properties of atoms in a sample of interest, such as oxidation state, ligand identities, and bond lengths. Until recently, x-ray spectroscopic techniques have been primarily limited to large-scale synchrotron facilities employing expensive commercial crystal analyzers. This leads to high barriers to access because of high competition for synchrotron beamtime and the large cost of acquiring optics not presently possessed by the facility. Over the past several years, the Seidler lab has pioneered solutions to both these problems. First, the development of lab-scale x-ray absorption and emission spectroscopy apparatus has enabled a wide range of studies without need for the synchrotron, and second, by designing an inexpensive method for manufacturing the necessary crystal analyzers. I focus here on the second issue, improving the availability and decreasing the cost of the crystal analyzers. Crystal analyzers are at the heart of high energy resolution x-ray spectrometers. They serve the same role as a prism or grating in visible-light spectrometers, that is, they disperse x-rays into their component energies. Our work using temporary vacuum forming of silicon wafers reduces the cost of such optics from $5000 - $10,000 to only a few hundred dollars. Furthermore, the use of vacuum together with modern computer-assisted machining gives the freedom to use either the traditional spherical shape or a superior customized toroidal form, specific to each study. These advances in instrumentation will dramatically speed up analysis of materials and permit feedback on synthesis procedures, battery performance, detection of hazardous chemicals, and catalyst activity.

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

This research focuses on the mathematics of gerrymandering. Gerrymandering refers to how political parties draw district boundaries to give them better odds at receiving a majority during congressional elections. Every 10 years district boundaries in the United States are redrawn for congressional elections by the current majority party. With such change in political cartography, redrawing district boundaries not only affects who wins but also the people who live within them. Given the loosely defined criteria for redistricting, we seek to quantify the process of redrawing district lines to determine when this partisan process becomes an act of manipulation and exclusion. We will be use The Metropolis Hastings (M.H.) Algorithm to produce a random walk that has a stationary distribution that will be the probability distribution of all possible districting plans for a given U.S state. By collecting congressional maps and election results, we implemented the M.H. algorithm in python to produce sample spaces for Washington State and Iowa. We will simulate local and federal redistricting requirements using self-defined parameters which measure: compactness of districts, population division, division of counties, and minority voter populations. We simulated election results with respect to our sample districts and compared the simulated outcomes with actual district maps and their election results. This study helps to determine if current redrawn maps legitimately reflect the people they purport to represent or if they are manipulations and subversions of our democratic process.

Although crystalline two-dimensional (2D) protein arrays are often found on the surface of archaea and bacteria where they form a protective S-layer, their potential in bionanotechnology applications remains unfulfilled. Progress in computation has recently allowed the (re)design of proteins for self-assembly into arbitrary structures. We are working with a rationally modified protein from S. typhimurium that can self-assemble into large (> 100 µm) and thin (~ 5 nm) hexagonal 2D arrays pierced by ~ 3 nm pores upon addition of divalent cations (e.g., Ca²⁺). The goal of our research is to test the ability of these arrays to organize gold nanoparticles (AuNPs) with desirable plasmonic characteristics. To this end, we stain protein arrays with the lipophilic fluorescent dye Nile Red, and analyze fluorescence microscopy images to quantify how the decoration of arrays with various concentrations of AuNPs affects the rate of photobleaching of the Nile Red fluorophore. Understanding how AuNPs bind to protein arrays could lead to further applications, such as templated growth of inorganic materials or co-assembly of enzymes and inorganic catalysts.

Antiretroviral therapy (ART) is the standard of care for treating human immunodeficiency virus (HIV) infection and suppresses virus levels but cannot eliminate latent HIV reservoirs. Latently infected cells are a barrier to HIV cure. “Shock and kill” is a strategy that uses latency-reversing agents (LRAs) to reactivate latently infected cells under suppressive ART, making the cells vulnerable for removal by host immune responses or other strategies. However, “shock and kill” fails in clinical studies due to the low potency and high toxicity of LRAs. Here we have developed a lipid-polymer nanoparticle platform that addresses “shock and kill” limitations by incorporating multiple LRAs to increase potency and to reduce toxicity by targeting HIV reservoirs in lymphatic tissues. We have shown that ~200nm nanoparticles sustain LRA release and induce latency reversal in a human T-cell line in vitro. To target lymph nodes, we have synthesized nanoparticles smaller than 100nm in diameter, which literature shows enhances lymph node targeting following subcutaneous injection. By adjusting the polymer and lipid concentrations as well as the organic to aqueous solvent ratio during formulation, we obtained an ultrasmall particle of ~100nm. Ex vivo organ imaging from mice subcutaneously administered these ultrasmall particles shows successful targeting to draining lymph nodes as well as other HIV reservoir locations, including the spleen and the gut-associated lymphatic tissue. The ultrasmall nanoparticles also show similar drug release and latency reversal properties as our previous formulations. The nanoparticle platform demonstrated here is able to target latent HIV reservoirs in multiple areas of the body, which is crucial for eliminating latent HIV reservoirs and achieving a cure.

ImageJ allows users to create plugins that work with other imported packages and the ImageJ libraries. Using the ImageJ API (application program interface) and the macros recorder built into ImageJ, each image analysis performed within the Lee laboratory at the Department of Radiology was programmed into individual plugins by both Vineeth Narajala and Selina Liu, to be used by research scientists. Before writing each data analysis plugin, the standard operating procedure (SOP) of image analysis created by the Lee lab was practiced manually by both the programmers so we understood the process researchers perform on each data set. After understanding the SOP, we commented a simple outline in Java to start writing the plugin code. After the code was outlined with comments, Selina wrote algorithms for portions of the analysis that required numeric patterns and searched through the ImageJ API to manipulate the image using built-in commands. Methods were created to perform calculations, scale the images, and close extra images that were generated during the analysis. These methods helped generate the final image map used for measurements by the researchers. Plugins were tested for usage and updated when a researcher required other procedures that were not specified in the SOP. We also created a python program in Python 2.7 to automate the data analysis of the dataset. The program can also plot rudimentary graphs of the analyzed results. The python program used pandas to analyze the data and matplotlibs to create the graphs. Overall, each plugin and the automation program save researchers hours of time from importing, calculating, and archiving the images when following a single SOP. The research scientists typically used Microsoft Excel to analyze the data after the images were created and regions of interest were identified. This method was very time consuming and could not be scaled to different input sizes.

Standard medical practice does not consider a lateral leaning uterus to be medically relevant. However, many indigenous cultures globally have used uterine abdominal massage to correct a “displaced” uterus to enhance fertility. A leaning uterus could theoretically interfere with ovarian function. Additionally, Research indicates that the circulatory functions, the autonomic innervations of the uterus, and pelvic vein incompetence may negatively affect ovarian function, and fertilization. This study examines a population of 30 U.S. fertility patients undergoing ovarian stimulation for an In Vitro Fertilization (IVF) procedure (an assisted reproductive medical technique used to assist with the conception of a child). We will identify differences in the quantity, and size of follicles that are produced by the ovaries of patients with a leaning uterus. At the beginning of a patient’s IVF cycle, researchers will palpate the lower abdomen to determine the position of the uterus. After the patient completes their series of gonadotropins, prescribed hormones used to stimulate follicular growth in the ovaries, physicians will record the number, size, and location of each follicle observed. We predict that a laterally leaning uterus reduces follicle number and size. If our results identify a correlation between uterine displacement and follicle development, then additional research should explore potential causes. A positive correlation would also suggest that complementary treatment options for a laterally leaning uterus should be investigated.

Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder involving impairments in social communication and repetitive and restrictive behaviors. Children with ASD are oftentimes diagnosed with cognitive impairment, specifically below average intelligence scores and atypical brain function in relation to early developmental regression. In order to analyze neural activity, Electroencephalogram (EEG) is used to monitor brain activation during certain tasks. EEG is a non-invasive tool that uses scalp electrodes to record neural activity frequency. EEG is divided into frequency bands, including the Alpha band frequency (neural activity between 6 and 12 Hz), which is present during the relaxed awake state of individuals and thought to be related to functional inhibition. Previous EEG studies consistently detected abnormalities in resting state alpha among individuals with ASD when compared to neurotypical counterparts. Findings suggested that reduced resting state alpha power was exhibited in brain regions involved in sensorimotor skills and higher-order cognitive functioning. Although many studies compare the difference between ASD group and neurotypical group, more research is needed to study the alpha power patterns within the ASD group. This study aims to compare EEG peak alpha power and average alpha power between high functioning (NVIQ>100) and low functioning children with ASD. 100 participants (50 males and 50 females) aged 6-18 participated in the study. All participants met criteria for autism diagnosis on a clinician administered standard interaction, and completed the DAS-II, which measures verbal and non-verbal cognitive abilities. Participants watched calm screensaver like videos while high density EEG was collected. We hypothesize that the children with ASD and lower functioning will have reduced average alpha power and reduced peak alpha frequency when compared to higher functioning children with ASD. The results of this study will provide insight into of differences within children with ASD.

Carnivorous plants live in low nutrient environments and consume insects for heterotrophic nutrients. While previous research has typically focused on how pitcher plants capture prey, there is a lack of research concerning how pitcher plants attract pollinators. Scent is an important component of insect attraction, and this study explored whether pollinated and unpollinated plants produce different scents. This information will help us better understand the mechanism of pollination in carnivorous plants. We hypothesized that unpollinated plants will give off a different scent than the pollinated plants in order to attract more pollinators. The plants used for this experiment are the Sarracenia flava (yellow pitcher plant) which is endemic to the southeastern United States. We created two treatment groups consisting of pollinated and unpollinated plants inside a climate-controlled growth chamber at 25°C. Plants were watered from the base with unfertilized water. Scents were collected for 24 hours using Porapak Q adsorbent matrix and analyzed using a Gas Chromatograph Mass Spectrometer to identify the compounds. We anticipate that our results will further our understanding of how plants and insects interact. Future studies and analyses will focus on insect behavioral responses to plant scents, and on how insect antennae respond to each scent component.

Autism spectrum disorder (ASD) is one of the fastest growing childhood disorders, becoming a major public health concern. Studies have shown that children with ASD are more likely to be exposed to perinatal complications than typically developing (TD) children. Sex differences have also been shown to affect ASD diagnoses. However, variables that affect severity of ASD are still understudied. Understanding factors that impact ASD severity may assist in establishing methods to identify ASD outcomes, and target children at high risk for worse outcomes with treatment. The study aims to investigate IQ differences in children with ASD on variables including birth weight, gestational age, sex, and birth order. 150 children (75 males and 75 females) aged 6 to 18 years with a confirmed diagnosis of Autism participated in the study. Autism diagnoses of the participants were confirmed via ADOS-2, a clinician-child measure that scores on child’s social, repetitive behaviors and communication skills. Parents completed a self-reported demographic questionnaire about family demographics, and the Autism Center of Excellence subject medical history form, a medical interview with information on pregnancy complications and child medical history. All subjects completed the DAS-II evaluation tool that measures the cognitive abilities (IQ) of children on verbal and non-verbal domains. We hypothesize that children with lower IQ levels (full scale IQ<80) will have lower average birth weight, average smaller gestational ages and a higher number of pregnancy related complications. We also expect that given the higher rate of ASD incidence in boys, within the ASD group, there will be a main effect of sex with more males (n=75) having higher rate of pregnancy complications than females (n=75). Results will help establish a better understanding of other prenatal variables that may be correlated to later severities of ASD, and provide support for treatment targeted at prenatal risk.

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

Zika virus has become a major epidemic around the world due to the serious birth defects that it can cause; this has led to an increase in research regarding Zika and how to diagnose the disease. Diagnostic tests require a specific sample type to be tested for the presence of a virus, and because it has been shown that Zika viral levels are more consistent and reliable in whole blood compared to plasma or serum, whole blood is the more efficient sample type. Current strategies for diagnosing Zika fall short because there is limited data on how the virus presents itself in the body, and many of these strategies utilize expensive and time-consuming methods that are not feasible in low-resource settings where Zika is more prevalent. Therefore, there is a need for a low-cost and instrument-free process that can effectively purify Zika virus RNA from whole blood in order to allow for detection of the viral RNA. This project dealt with optimization of an existing lab protocol that required laboratory equipment and resulted in low efficiency. The aim was to develop a robust, high-efficiency, instrument-free RNA purification protocol for whole blood samples. The method of RNA purification consisted of a lysis and binding buffer, followed by RNA purification using silica beads embedded in paper to extract pure RNA from the sample. qRT-PCR was then used to quantify the resulting RNA. So far, the paper-based extraction method recovers approximately 20% of the initial target RNA; however, there are still some techniques that will be employed in the future to help improve this recovery rate. The goal of this project is to increase RNA purification efficiency and to provide an alternative mechanism to purify nucleic acids that can be used in a Zika virus diagnostic test.

The removal of contaminants from aqueous media is a challenge faced in many engineering systems. In particular, fermentation processes during biofuel production is hampered by a variety of toxic compounds present in hemicellulosic hydrolysates. Adsorption is an efficient and economic method of reduction in the amounts of phenolic compounds, acetic acid, aromatic compounds, furfural and hydroxymethylfurfural normally found in hemicellulosic hydrolysates. Activated carbon is currently the most widely used adsorbent. However, its poor reusability and its limited capacity to uptake larger molecules due to size exclusion effects necessitate the investigation into alternative materials. Carbon nanomaterials exhibit high specific surface area and open pore structure, making them very compelling for hydrolysate detoxification. To overcome the tendency of carbon nanomaterials to aggregate, which greatly reduces the number of sites available for adsorption, we developed mesoporous, nitrogen-doped, reduced graphene oxide aerogels with an open three-dimensional network. Graphene oxide was first prepared from renewable carbon sources and reduced by hydrothermal treatment to form hydrogels, which were then freeze-dried in tert-butanol to form aerogel sorbents. By adjusting the different synthesis parameters (i.e. temperature, pH, chemical dosages…), we were able to finely control the pore structure and chemical composition of the nitrogen-doped graphene aerogels, as measured by nitrogen physisorption and elemental analysis. Results revealed superior adsorption properties than activated carbon for the hydrolysate detoxification, which improved fermentation yields.

Excessive and unchecked deforestation can create a cascade of extinctions. A field-deployable DNA screening tool that can be used by non-scientists will prevent illicit timber shipments from reaching a commercial market by flagging products sourced from endangered species. The DNA screening tool transports reagents and samples using the anisotropic ratchet conveyor (ARC), a portable digital microfluidic system. The screening tool recognizes the DNA barcode using species specific primers and DNA amplification indicates the identification of a species. Isothermal amplification methods are easier to integrate into the portable DNA screening tool and there is currently no isothermal amplification method for timber DNA. The loop-mediated isothermal amplification (LAMP) method was designed for integration in a portable identification system since this method has the ability to perform rapid amplification and is robust to inhibitors. The species for which amplification was performed were eastern white pine (Pinus strobus), Spanish cedar (Cedrela odorata), and white oak (Quercus alba). The first step was to identify the genetic target for amplification and design LAMP primers for this sequence. The genes selected were rbcL and matK since these chloroplast genes diverge between species and are conserved within tree species. LAMP uses six primers: the backward inner primer(BIP), forward inner primer(FIP), the forward loop primer(FL), backward loop primer(BL), forward primer(FP), and backward primer(BP). Species specific LAMP primers were designed. The primers were validated on synthetic oligos. Extraction of DNA is challenging because the DNA is trapped in between thick cell walls. Timber DNA amplification is challenging because inhibitors, include polysaccharides and phenols, bind or degrade DNA polymerase, and prevent amplification. Extraction and purification methods were investigated to provide amplifiable DNA. Isothermal amplification was performed on the ARCs. The portable DNA identification system will identify timber species for conservation biology.

The majority of urinary tract infections are caused by E. coli bacteria. E. coli infections are strengthened due to E. coli’s ability to bind to mannosylated cells. A receptor protein on E. coli, FimH, has two domains: a regulatory pillin domain and a lectin domain (LD). In the presence of a force, the pillin domain detaches from the LD allowing the LD to go from its low to high affinity state. The naturally occuring mannose sugars on Horseradish Peroxidase (HRP) are known to bind the LD of FimH. The mannose binding pocket is suspected to open transiently, even when bound to mannose sugars. Based on the interaction of HRP with FimH, HRP may not regularly dissociate during these episodes, but we suspect that free mannose can induce the dissociation of HRP from FimH in these moments. To determine if mannose can improve HRP dissociation from LD, we are using an assay similar to a competitive Enzyme Linked Immunosorbent Assay. We expect to see a decrease in HRP bound to LD in the presence of free mannose compared to the absence. Ultimately this experiment provides an explanation of mannose monomers as an inhibitor for longer chains of mannose binding and a premise for a larger study on alternatives to E. coli antibodies that can competitively inhibit FimH from binding mannosylated cells.

Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder characterized by marked impairments in social skills, communication, and behavioral aspects of typical development. Research has shown that individuals with ASD often present with psychiatric comorbidities such as Depression, Anxiety, Obsessive Compulsive Disorder, Attention Deficit Hyperactivity Disorder and Bipolar Disorder. Comorbidities can have a broad and significant impact on a child’s health and wellbeing and such conditions are significantly more prevalent in those with autism than in the general population. This study aims to explore the relationship between psychiatric comorbidities and autism severity in children with ASD. 100 children (males=50, females=50) aged 6-18 participated in the study. All participants met the Autism diagnostic criteria on the ADOS-2, a child-clinician interaction measure that measures child’s social, repetitive behaviors and communication skills. Parents completed the Autism Center of Excellence subject medical history form, with information on child medical history. Problem behaviors and low IQ scores in children with ASD may be the symptom of underlying psychiatric comorbidities instead of the autism itself. Due to this, treatment of comorbid medical conditions may result in dramatic improvements in the quality of life of both children with autism and their caregivers. In this study, we expect that children with a higher rate of psychiatric comorbidities will score higher ADOS calibrated severity scores with a higher rate of autism symptoms and will score lower on IQ measures. Results will help establish a better recognition of comorbid medical conditions as critically important issues to address in treatment approaches.
 

The electrochemical growth of single-crystalline germanium (Ge) nanowires has been previously demonstrated in an aqueous solution for use in complementary metal oxide semiconductor (CMOS) technologies. The motivation for growing these nanowires using electrodeposition is to improve the purity of germanium nanowires relative to traditional synthetic methods. However, nanomaterial growth has been shown to be highly sensitive to both oxygen and water and can lead to impurities, surface layers or morphology changes. . We have grown germanium nanowires in anhydrous organic solution in a nitrogen blanketed electrochemical cell. We have then compared the morphology and material properties of the wires grown in aqueous solution to the wires grown in organic solution to determine the effects of water and oxygen on the wire growth. Improving nanomaterial growth will help in having more efficient computers and cell phones by improving semiconductors.

Religious rhetoric has been a common tool in politics for the majority of American history, from Thomas Jefferson being “unfit to lead a Christian Nation” to Ronald Reagan’s “City Upon a Hill”. Although the Constitution declares the government to be secular, members of Congress, to varying degrees, regularly invoke religious imagery and rhetoric in the public communications. This study seeks to understand why. I examine congressional religious rhetoric using a unique data source of congressional webpages from the massive .GOV collection of the Internet Archive Project. I hypothesize that members' personal beliefs and electoral strategies help to explain differences in website content. I measure the personal religiosity of members using a carefully constructed scale of involvement in their religious communities. I measure district religiosity using information about district-level church attendance and prayer frequency from the Cooperative Congressional Election Survey. Finally, I draw from established religion lexicons to measure religious emphasis in congressional website content. I find positive, statistically significant support for both hypotheses. This work sheds light on politicians in particular members of congress are actively seeking to brand themselves through the internet for political purposes.

Research Family is a group of Pacific Islander students who research a variety of topics including healthcare, education, and representation. In Spring 2017, Research Family explored connections between the movie Moana and the living cultures of Oceania, which many students are part of. In a video produced by the Burke Museum, they shared cultural knowledge within the Oceanic objects in the museum collections and how they are featured in Moana. Methods used includes analysis of material culture and film, and interviews with Pacific Islander community members. Material culture and film analaysis compared cultural objects in the Burke collections and those in scenes from Moana. Results were used to develop a video used in the Burke's educational programs. This project has been valuable in giving voice to Islander students in sharing their own perspectives and ancestral stories. For the symposium, a Research Family member will present this research so that knowledge within Pacific Islander communities and the Burke can continue to be made more accessible.

Peripheral neuropathies involve the destruction of peripheral nerves, which leads to impairment of the neuromuscular junction (NMJ). This is the area where the nerve transmits information to muscle. NMJ breakdown will cause this synapse to degrade, generating symptoms such as reduced muscle contraction, respiration, and movement. The problem is that current efforts to develop treatments against peripheral neuropathies are severely dampened by having a lack of human-based models of synapses. Therefore, there is a need for a non-invasive method to explore and characterize synaptic function for future treatments. This research study offers a novel system to investigate the differences in neuromuscular junctions between healthy and disease states by utilizing induced pluripotent stem cells (iPSCs) to derive an in vitro NMJ. Procedures involving the differentiation of healthy-state iPSCs into motor neurons have been optimized. The iPSC cultures were matured until day 45 after induction towards a neural ectoderm lineage, and were analyzed using immunocytochemistry, imaging, patch-clamp electrophysiology, and flow cytometry. Differentiated neurons stained positive for neuronal marker p75, Islet-1 and choline acetyl-transferase (ChAT). Electrophysiology data showed neurons were capable of high degrees of repetitive firing sequences, while flow cytometry showed neuronal purity in culture was roughly around 97%. Human skeletal muscle myoblasts have also been differentiated into myotubes-the precursors for muscle tissue-and imaged for acetylcholine receptor clusters. The culture medium was supplemented with various additives in order to determine which medium promoted greatest acetylcholine receptor (AChR) cluster density and size. It was found that AChR clusters are more prominent and enlarged when the muscle cells are cultured with Agrin supplement. Ongoing studies are looking at combining these cell types into a novel contractility assay in order to investigate NMJ function in vitro. The establishment of this system will enable more effective applications for novel therapeutics and disease progression studies.

Modern disease research utilizes two-dimensional (2D) stem-cell tissue culture models, simplified 3D engineered tissues, and animal organisms to study microenvironments and human physiology. However, in vitro platforms often oversimplify the physical tissue niche and animal models do not always accurately represent the function of human tissues. For instance, 2D tissue platforms used to study cardiac biology are limited because they cannot accurately recapitulate the pumping motion of the human heart which is responsible for the circulation or blood. Furthermore, animal models have an under-representative cardiovascular physiology making them inadequate systems for studying human cardiac biometrics. As such, we propose to develop a 3D tissue culture system that can accurately mimic the hierarchical organization of different human tissues. Using our novel flexible cell-sheet stacking technique, we can precisely stack layers of organized cell-sheets to create 3D laminar tissues. Then, these organized laminar tissues can be manipulated by the flexible scaffold into complex 3D tissue shapes using custom-made molds. For example, the human heart is helically aligned cardiac tissue throughout its structure that allows for the generation of intraluminal pressure during ventricular contraction. Inspired by the intricate architecture of human myocardium, this project aims to analyze how varying degrees of cell orientation can influence intraluminal pressure generating function. To account for the hollow and conical nature of the human heart architecture, we have designed a model for casting closed 3D hydrogel scaffolds with a hollow lumen that allows for intraluminal pressure measurements. The proposed model will allow for the determination of the optimal angle of cell alignment that produces the greatest intraluminal contraction. We will validate this platform using a contractile mouse skeletal muscle cell type. This approach can be adapted to model the organization of any contractile muscle tissue and be used to study the function and microstructure of human tissues.

Current drug testing methods are unable to accurately predict and study the effects of drugs on human myocardial tissue. These methods are unable to accurately mimic the physiology and maturity of native cardiac tissue, and as a result, the tissues are unable to react to cardiotoxic drugs the same way that native cardiac tissue. Therefore, there is a need for physiologically accurate and mature tissue constructs in order to test clinical drugs for effectiveness, cardiotoxicity, and arrhythmic effects. To fulfill this need, we will use an electroconductive bioink containing decellularized extracellular matrix (dECM) from porcine cardiac tissue, reduced graphene oxide (rGO), and incorporated human induced-pluripotent stem cell (hiPSC)-derived cardiomyocytes to develop a more physiologically accurate cardiac tissue construct. This will result in more adequate cell maturation, and therefore, more accurate preclinical drug screening. The success of this project would lead to the development of high throughput production of biomimetic cardiac tissue models for use in accurate drug screening, along with improving the understanding of cardiac maturation.

Stem-cell derived engineered cardiac tissues are a promising avenue for the research of heart disease, enabling disease-specific modelling and drug screening. However, their validity as a model hinges on the similarity to native cardiac tissue, both in super- and sub-cellular structure and organization. When cultured on nanopattern substrates, myocytes orient the sarcomeres along a similar axis, allowing for greater force production and higher similarity to native cardiac tissue, though the evidence of the finer details are obscured by the diffraction limit of light. Super-resolution microscopy has opened the door to the analysis of diffraction-limited biological structures, and one such recently developed super-resolution technique, Expansion Microscopy (ExM), has made this analysis more accessible. By embedding the fluorophores from an immunostained sample into an expandable hydrogel, sub-diffraction details are physically enlarged and made measurable on standard fluorescence microscopy equipment. In this work, expansion microscopy was performed on engineered cardiac tissue to evaluate the effect of the nanopattern substrate on sub-sarcomeric structure and organization. As expected, it was found that the sarcomeres were more aligned within the cardiomyocytes, and the length between the z-lines were increased when cells were cultured on the nanopattern substrate as compared to the flat substrate. In addition, the width of the Z-disks were significantly different in nanopattern cultured cardiomyocytes as compared to myocytes cultured on flat substrate. The transverse tubules, responsible for a unified action potential, were larger in diameter and better localized with the Z-line, and the myosin heads were closely localized with the actin filament. When examined with super-resolution microscopy, the engineered cardiac tissues display sub-sarcomeric organization that allows for greater and more efficient force production, further demonstrating the efficacy of nanopattern substrates in cardiac cell differentiation and maturation. Though ExM needs further validation, it has proved a powerful sample-side tool for probing diffraction limited features.

Originating from an outbreak in Brazil, with an estimated 440,000-1,300,000 Zika cases in 2015, Zika virus infection (ZIKV)  has made its way into the United States. The objective of this study was to examine the changes in the gastrointestinal microbiota after ZIKV infection and investigate how this contributes to microbial translocation, immune activation and inflammation in the periphery and CNS. Eight pigtail macaques (PTM) and eight rhesus macaques (RM) were infected with a Brazilian isolate of ZIKV. DNA extractions were carried out from PTM rectal swabs and were used to analyze microbial shifts through 16S rRNA analysis. Production of short chain fatty acids (SCFAs) in the gut were measured by GC-MS. Expression of microbial translocation markers (LBP) were analyzed by ELISA in PTMs. Inflammation and immune activation were determined from neopterin production and kynurenine:tryptophan ratio (KTR) in the plasma and CSF of both species by tandem LC-MS/MS. We found that ZIKV infection results in microbial dysbiosis in the rectum of PTMs, including loss of beneficial Firmicutes phyla and an increase in opportunistic pathogen associated bacteria such as Proteobacteria and Spirochaetes. A significant decrease was seen in total SCFA production in PTMs 7 days post-inoculation (dpi) (p=0.0125). Plasma LBP was significantly increased 3 dpi in PTMs (p=0.0305). A statistical increase in neopterin and the KTR was detected in plasma and CSF of both species 7 dpi (all p values <0.0001). Moreover, the loss of Firmicutes Solobacterium in the male PTM after ZIKV infection was negatively associated with microbial translocation (p<0.0001, LBP) and inflammation (p=0.0374, KTR). These data indicate that microbial dysbiosis after ZIKV infection is associated with microbial translocation and inflammation, which may underlie the localized inflammation and immune activation occurring in the CNS during ZIKV infection and provide possible evidence for a mechanism on how CNS inflammation occurs in ZIKV infection.

Human immunodeficiency virus (HIV) infects over one million women annually. Pre-exposure prophylaxis (PrEP) drugs are developed to prevent HIV acquisition and have yielded varying results in women. Despite adherence, recent evidence suggests biological factors, such as the vaginal microbiome, contributes to its variability. Such drugs are tenofovir (TFV), tenofovir alafenamide (TAF), tenofovir disoproxil fumarate (TDF), and dapivirine (DPV) and their efficacy in HIV prevention are vital to public health. There is recent evidence demonstrating vaginal dysbiosis is associated with an increased risk of HIV transmission by bacterial metabolism, altering PrEP pharmacokinetics (PK). Vaginal dysbiosis occurs when the dominant Lactobacillus is replaced with a more diverse anaerobic community, including Gardnerella. To investigate the impact of the vaginal microbiome on PrEP PK, I incubated target Jurkat cells, with various PrEP drugs in the presence of Lactobacillus and Gardnerella vaginalis. Lactobacillus spp. represents the healthy commensal species, while G. vaginalis represents dysbiosis. Abiotic and drug free samples were used as negative controls. Using Liquid Chromatography-tandem Mass Spectrometry, I measured residual PrEP drugs, bacteria mediated metabolites, and pharmacodynamically active metabolites representing target cell uptake at different time points. In the presence of G. vaginalis, we saw a significant decrease in extracellular TFV (p<0.0001) and DPV (p<0.001) when compared to Lactobacillus and abiotic controls. We saw a milder effect with TDF (p=0.004) and TAF (p=0.03), most likely due to the pro-drug formulation. When comparing bacterial metabolites, we observed an increase in the presence of G. vaginalis for TFV (p=0.0001), but not in abiotic and Lactobacillus samples. Similarly, we saw a decrease in pharmacodynamically active metabolites in the presence of G. vaginalis for TFV (p=0.0004) and DPV (p<0.0001) and an increase in abiotic and Lactobacillus samples. By improving the health of the vaginal microbial communities, we can improve the adherence of PrEP drugs and improve HIV prevention.

Human immunodeficiency virus (HIV) infections are often paired with microbial translocation within the gastrointestinal tract (GI). In-vivo studies show that HIV-associated microbial translocation results from multiple immunopathological events occurring at the GI mucosa: early, detrimental, severe CD4(+) depletion in mucosal regions, mucosal immune hyperactivation and inflammation, and intestinal epithelium damage. Previous human studies have shown anti-inflammatory effects of cannabis, along with slowed GI tract disease progression. This project aims to further understand HIV infection and its response to patients’ cannabis use. We hypothesize the anti-inflammatory effects of cannabis should decrease the microbial translocation within HIV+ individuals. Using stool from HIV+ and HIV- patients, DNA and short chain fatty acid (SCFA) extractions were performed. The DNA was extracted using Power Fecal DNA extraction kits. In order to understand microbial community and how it relates to SCFA production, the extracted genomic DNA was PCR-amplified and will be sequenced with an Illumina MISEQ. SCFA extraction was done with ethyl acetate. We analyzed the samples using gas chromatography-mass spectrometry, and it showed HIV+ patients had a decrease in acetic (p=0.0057), propionic (p=0.0325), butyric (p=0.0007), iso-butyric (p=0.0039), and valeric acid (p=0.0133). When compared with HIV- patients, there’s an overall decrease in total SCFA (p=0.0012). These results demonstrate the detrimental effects HIV infection has on SCFA production, which can lead to a decrease in available energy for colon cells and disrupt gut microbial community health. However, amongst HIV+ with cannabis use, we saw an increase in acetic (p=0.0173), propionic (p=0.0087), butyric (p=0.0173), iso-butyric (p=0.0043), and total SCFA (p=0.0057). The HIV+ patients that used cannabis saw improvement in microbial community health, which is a promising sign that cannabis assists with the recovery of antiretroviral treatment.

In mammals, daily rhythms of physiology and behavior are synchronized to a 24-hour light-dark (LD) cycle via input to the suprachiasmatic nucleus (SCN), the master circadian clock. Disruptions to the circadian system are associated with neurological and psychiatric disorders, including mood disorders like depression. These disorders are associated with symptoms such as sexual dysfunction and anhedonia, the inability to experience pleasure from activities that are typically enjoyable. Previous work has shown that rats exposed to a 22-hour LD cycle, which leads to desynchrony between neuronal oscillators in the SCN and mimics an internally desynchronized state, display behaviors indicative of these symptoms. Jet lag is a common challenge to the circadian system and, in rats, causes desynchrony between SCN neuronal oscillators. We hypothesized that desynchrony induced by jet lag could also lead to depressive symptoms. We measured sexual behavior before and after a 6-hour phase shift, simulating jet lag. Male rats were placed in an arena with a receptive female and sexual activity was quantified. We also performed a saccharin preference test where males had continuous access to water and saccharin solution. The volume drank from each bottle was measured daily; anhedonia is evident as a decrease in the preference for saccharin solution. Locomotor activity was recorded using infrared detectors, to associate behavior with the amount of time it took for males to re-entrain to the new LD cycle. Six-hour advances and delays of the LD cycle were not associated with behavioral manifestations of depression. This work, combined with previous work, provides greater insight into the consequences of circadian disruption and suggests that mental health consequences depend on the specific type of circadian misalignment. Whereas steady state misalignment induced by exposure to 22-hour LD cycles is associated with a depressive phenotype, the transient misalignment induced by jet lag is not.

The North Korean nuclear crisis is severe, with North Korea having developed missiles potentially armed with nuclear weapons that can reach the continental US. However, the international response has mainly been ineffective in stopping North Korea. Additionally, South Korea’s new attitude going towards negotiation with North Korea is an important game-changer. Through this research, I plan to explore the questions of why the international sanctions have been ineffective, how South Korea’s changing attitude can influence this issue, and what can be done to solve this issue completely. For this research, I have collected information from many sources both from the US and in Korea, including books, journals, and newspapers. Some of my findings are that there are loopholes to the sanctions, especially China not enforcing the sanctions and trading key goods with North Korea, especially oil. Additionally, the Moon Jae-In administration’s new strategy towards the issue, going more towards negotiation, may be catastrophic and must stop immediately. To solve this issue, South Korea must stop doing peace talks with North Korea, as such talks were catastrophic during the past, and stay on the same page with the US to motivate China from not trading with North Korea, especially oil which is crucial to its survival, as North Korea cannot produce its own oil. This may be enough to force North Korea to denuclearize. A better solution is to assassinate the dictator of North Korea, Kim Jong Un, which will lead to disorder in North Korea as Kim Jong Un does not have a successor currently, and South Korea and the US can use this opportunity to destroy the weapons of mass destruction in North Korea. This research is crucial for maintaining the peace and security not only in the East Asia region, but also for the entire world.

Every nation state has its foundational stories and Afghanistan is no exception. Classical historiography and national myth contend that the Durrani Empire, founded in 1747 by Ahmad Shah Durrani, marked the beginning of the modern Afghan nation-state. As the fledgling polity subsumed all of present-day Afghanistan and Pakistan in addition to parts of Iran and the Central Asian republics, it found itself the object of ‘The Great Game’ in which the expanding Russian and British empires sought to control the region. I assert that, while it is certain that 'The Great Game' and Ahmad Shah influenced the growth of Afghan nationalism, traditional historiography fails to account for the deliberate, ruler-driven work that went into the Afghan centralization project. Rather than playing pieces propelled through their early centuries on a vast geopolitical Great Game board, the Shahs of the Durrani Empire and the Emirs of the Emirate of Afghanistan determinedly enacted policies furthering their goals and visions for the state. Concurrently, British India, governed by the Council of India, sought to shape the Afghan state to suit its own needs vis-a-vis Russia and Persia. I also maintain that while the early stages of the nation building project were a response to the political and military needs of Ahmad Shah, the relative power of each state shaped the later phases. The Durrani Empire initially had a military advantage, but later British territorial annexations in India facilitated power projection further into Central Asia, thereby imposing their image of Afghanistan over its local population. I argue fundamentally that Afghan national identity was shaped through a shifting relationship with Britain as a consequence of successful as well as abortive policy decisions from both parties which, when combined with the framework established by early Durrani rulers, coalesced to give form to Afghan nationalism.

Rather than assuming the transhistorical existence of Kurdish nationalism, this paper identifies and explains the material motivations behind the formation of the short-lived Mahabad Republic in 1946. I argue both the tribal chiefs and urban elites of Kurdish society felt compelled to break from Tehran as they, along with the rest of Kurdish society, became more connected to a wider economy than ever before. Previous political movements within Kurdish society against unjust treatment from the Iranian central government had been led by the tribal chiefs whose hegemony over the rural areas had made them powerful forces to be reckoned with. In 1946, with the tribal chiefs undermined by anti-tribal policy from Tehran, and the urban population and wealth in Kurdish society growing at a rapid rate, the Mahabad separatist movement emerged as the first Kurdish rebellion to be directed and inspired by the urban elite. Yet the success of the movement still necessitated the cooperation of the landholding tribal elite, as they provided the military organization crucial for victory. Both groups, who held the bulk of power within Kurdish Iran, were motivated by adverse treatment associated with the Iranian state, including manifest corruption, cultural oppression, and economic recession. In that context, I argue, the landholding tribal chiefs and the emergent urban elite forged a secession movement away from Iran to establish the first successful Kurdish ethno-state.

Before the Battle of Lepanto on October 7, 1571, the Republic of Venice’s relations with the Ottoman Empire were tumultuous and tentative. As the most powerful Mediterranean maritime force in the 16th century, it was Venice’s mission to protect Christendom from Ottoman Islamic armies. To fight this maritime crusade Venice employed privateers and corsairs, individuals who, in exchange for payments, supplied their own vessels to police the waters of the Eastern Mediterranean in search of Ottoman vessels. Since Venice relied on trade for basic provisions, Venetian authorities approached naval aggression as a necessary defensive measure. Venice’s lack of self-sustainability meant that protecting its imperial holdings was critical to the longevity of the city itself. As Venice won the Battle of Lepanto, destroying the Ottoman fleet, Venetians regained their sense of naval supremacy. Although Venice lost the larger Ottoman-Venetian war, as in the three previous was, the Battle of Lepanto marked a pivotal moment in Mediterranean history, driving Venetians to recapture some of what they had lost and to rebuild their once vast merchant empire. Confident in their naval prowess, Venice’s merchant galleys spread far and wide across the Eastern Mediterranean to forge new trade relations with the Ottoman Empire. Through these relations, Venice portrayed themselves as the gateway to the East by supplying themselves and Western Europe with exotic goods. I argue that The Battle of Lepanto ushered in a new era of economic expansionism grounded in a Venetian sense of naval superiority that allowed Venice to end its reliance on privateering and corsairing to protect its empire.

Polymer based fullerenes are used as photovoltaics in solar panels. Fullerene C60 molecules have icosahedral based structures resembling geodesic domes. Fullerenes have convex polyhedral shapes which obey Euler’s topological rules. Their novel structures involve Golden ratios. Here we use vector calculus methods to calculate bond lengths and bond angles and provide estimates for the volume and surface area of the molecule. The calculated average bond length (1.4320 Å), edge length (2.4252 Å), bond angle (116o) are in good agreement with reported experiments. The estimated fullerene molecularvolume is 788 Å3 and surface area is 426 Å2. To understand the critical effect of dimensionality on volume, we have studied the volume of a hypersphere in n-dimensions. The project provides hands on exploration of real world problems and data visualization.

Photovoltaic (PV) electricity generation has become much cheaper in recent years and as a result is becoming a larger percentage of total energy production. However, growth is limited due to the high capital expenditure (CAPEX) required to build new PV factories with current technologies. Solution processing techniques (spray coating, roll-to-roll, etc.) to deposit thin-film absorber materials such as CuIn(S,Se)₂ and Cu(In,Ga)(S,Se)₂ represent a much lower CAPEX alternative to current PV processes. Using simple metal chloride precursor salts dissolved in polar aprotic solvents, our group has shown solar power conversion efficiencies of 13.4%, which is a world-record for solution processed CIS. Understanding the complexation chemistry of precursor salts in solution is essential to making stable solutions which produce homogeneous absorber layers after thermal annealing. Using solubility experiments and calorimetry to examine interactions between the precursors in anhydrous dimethylformamide (DMF), we were able to infer participating molecules and stoichiometry of the complexes formed in solution between the metal chlorides, thiourea, and solvent molecules. We have also made CIS absorbers under various thermal annealing conditions, and studied the resulting changes in 1) elemental composition profiles using glow-discharge optical emission spectroscopy (GDOES) and energy-dispersive X-ray spectroscopy (EDX) and 2) film morphology using scanning electron microscopy (SEM). These results represent steps forward in improving solution processing techniques for low CAPEX solar cell manufacturing which will increase the prevalence of renewable energy to combat global warming.

Silica nanoparticles are extensively used in semi-conductor industry as abrasives in various polishing steps. It is important to be able to conduct rapid, robust surface area measurements of the dispersion that do not require dilution and drying. The focus of this research is to explore nuclear magnetic resonance (NMR) technique as a means for determining surface area of silica nanoparticles and its sensitivity to temperature and trace level contamination. NMR is a technique that can be used for determining the surface area of silica particles in dilute and concentrated solutions. After application of large magnetic field, water protons in the vicinity of nanoparticles relax faster than protons in the bulk liquid. Thus, the average relaxation rate of the sample is proportional to the particle loading, particle surface area, and a proportionality constant, specific surface relaxivity, that is unique for different materials. Silica nanoparticles of sub 100 nm size are studied. Specific surface relaxivities for the materials are found and the effect of various contaminants active in NMR are studied. The lowest limits of detection for possible industrial contaminants are obtained. The interaction of surfactants with silica particle surface are studied using NMR technique. The gelation process of silica nanoparticles and its relationship with relaxation time is investigated by time-resolved dynamic light scattering (DLS) and NMR. Only recently has NMR become available as a bench-top instrument targeting widespread adoption for process control and monitoring. This study advances the knowledge on the various ways this relatively new technique can be applied to the characterization of sub-100 nm silica particles, what is useful for semi-conductor industry and nanoparticle slurry manufacturers.

Posttranslational modification with the small protein ubiquitin (Ub) is an essential process in various regulatory pathways of eukaryotes, such as protein degradation, DNA repair, and the cell cycle. Misregulation of ubiquitylation has been associated with diseases such as cancer and neurodegenerative disorders. Ubiquitylation is accomplished by an enzymatic cascade that involves a family of ~40 ubiquitin conjugating enzymes (E2), which form thioester intermediates with Ub, called E2~Ub conjugates. In most ubiquitylation reactions, it is the E2 that covalently attaches Ub to substrate proteins. While the overwhelming majority of E2s ubiquitylate the ε-amino group of substrates’ lysine residues, important exceptions have recently been discovered. For example, Ube2W has been identified as the only human E2 that exclusively ubiquitylates the α-amino group of substrates’ unstructured N-termini. Knockout of Ube2W in mice leads to severe developmental abnormalities, suggesting its importance for early postnatal survival. Little is known about the molecular mechanism of Ube2W’s unusual specificity and structural insights to the catalytically-relevant species, the Ube2W~Ub conjugate, are lacking. Here, I report the formation and purification of the first stable Ube2W~Ub conjugate mimic. Using a combination of biochemical techniques and nuclear magnetic resonance (NMR), I characterized atomic-level changes within the Ube2W~Ub conjugate during substrate recognition and catalysis. This investigation will expand our mechanistic understanding of E2s and establish insights to a biochemically fascinating and biologically relevant enzyme.

Cells, making up every living organism on earth, are extremely complicated biological machines. Much research has been done on how cells function, including how proteins made by cells work together to create biochemical pathways necessary for growth. Recently, computational simulations of biological processes have become possible, such as in the field of systems biology, which takes a holistic view of an organism to elucidate function. Previous research has constructed an accurate "whole-cell" model of E. Coli metabolic function. But, understanding metabolic behavior is still a challenge, especially from external perturbations in the environment or an internal alteration in the form of an insertion of an extra protein. This research uses an E. Coli whole-cell model—containing carbon-dependent metabolic pathways in E. coli— to study how perturbations will affect the pathway. External changes in the resources available to the cell or an internal change to the cell’s components are simulated. In response, specific changes to the metabolic behavior of proteins will be made. These changes are made using optimization algorithms, which minimize the output of a growth “cost” function, which maximizes the growth rate of the cell. This represents the effect of evolution over time for the cell to reach an optimal level of growth. The “Tellurium” software package, using the Python programming language and created by the Sauro lab, was used for this experiment, and a collection of scripts that can be used in Tellurium were made to generalize the reproduction of this process to any model, and to visualize the results. This research can give greater insight to how cellular metabolic processes as a whole behave, and can give scientists working with in vivo experiments better predictions of the consequences of perturbations, externally or internally, on a cell.

Chemically induced dimerization (CID) systems, which are systems that involve the dimerization of two proteins only in the presence of a specific molecule, have shown a great potential in studying and controlling cellular signaling pathways. However, current methods for identifying CID systems for any given target based on small molecule-protein interactions remains a challenge in the area of protein design. Our research team proposes a general approach for identifying new CID systems for which may have clinical and therapeutic applications. To do this, we aim to create nanobody-based CID binders. Using a technique known as “Trinucleotide-Directed Mutagenesis,” our team has been able to create a diverse nanobody library of over 109. Phage display allows us to screen this library for specific nanobodies that can bind with high specificity and affinity to a specific molecule. Currently, we are using cannabidiol (CBD) as a target molecule. After performing several rounds of selection, in order to validate our system’s specificity and selectivity, we use ELISA assay tests as well as Bio-Layer Interferometry to measure the binding affinity and binding rate of our system. In order to ensure the specificity of our CID system we tested it against, tetrahydrocannabinol (THC), a structural homolog. To date, we have successfully found three different nanobodies that can bind with high affinity and specificity to our small molecule of choice. As we move into phase two of our project, we are currently working on identifying the second nanobody in order to form a complete CID system. Designed CID systems will not only provide personalized choices for patients showing different drug responses, but also serve as orthogonal chemical control of different cell subpopulations and cell behaviors to improve therapeutic efficacy and safety.

The decriminalization of abortion has been a contentious issue in many countries throughout the world. Not only does the issue evoke religious debate, but a country's abortion laws also highlight the relationship between the state and women's bodies. The courts can have a considerable impact even in sensitive issues in society. Governments that have an independent judiciary as well as international courts in particular can provide a means for institutional change to occur. The purpose of this study is to understand the role that international courts' judicial policymaking plays in nations with restrictive abortion laws by examining the interactions between international courts and the domestic legal system. More specifically, the focus is on the case of Ireland due to its restrictive abortion laws and its increasingly independent judiciary as well as the fact that it is embedded in numerous international legal systems, such as the European Court of Human Rights (ECtHR). The HUDOC ECtHR Database, the Curia European Court of Justice Database, the Supreme Court of Ireland Judgement Database, as well as the Irish Statute Book were utilized in order to compare both domestic and international judicial rulings to Irish policy changes. Through examining the progression of the decriminalization of abortion in Ireland, the study concludes that international courts are in a unique position to provide incentive for countries to clarify ambiguity in their abortion policy and to institute domestic services. Although the focus is Ireland specifically, the study provides a general framework for the examination of international courts’ impact on other member states and contributes a more nuanced understanding of international courts' role in policymaking.

Oncolytic adenoviruses such as serotype 5 adenoviruses (Ad5) selectively infect and destroy cancer cells and are widely used in preclinical and clinical trials for gene therapy. However, Ad5 has many downsides including preexisting anti-Ad5 immunity in humans, and the Ad5 receptor (CAR) is known to be down regulated in many aggressive tumors. Species B adenoviruses which use a different receptor than CAR are an alternative which shows great promise. These vectors avoid the immune response against Ad5 and show different cell tropism. Our lab has identified desmoglein2 (DSG2) as the main receptor for a group of species B adenoviruses, including Ad3. DSG2 is an epithelial junction protein and is highly expressed in malignant tumors. During Ad3 infection, binding of Ad3 fiber to DSG2 triggers the transient opening of these intercellular junctions and thus supports the lateral spread of the progeny virus. Our lab has recently developed an Ad3 fiber knob mutant (Y250F) which has an enhanced affinity to DSG2. We have shown that an increased affinity is correlated with a stronger ability to open these junctions. In this study, we developed an Ad3 based oncolytic vector containing fibers with enhanced affinity to DSG2 (> 400x higher than wild type Ad3.) We developed this vector using PCR site-directed mutagenesis and cloning the recombinant gene in E. coli. By inserting our gene into a Ad3 plasmid it allowed us to transfect the plasmid into human embryonic kidney cells (HEK 293 cells) and to amplify and recover the mutant oncolytic virus. We are working on in vitro experiments and in vivo tumor xenograft models to test our hypothesis that the oncolytic virus with an enhanced affinity to DSG2 will be translated to a significant improvement to the spreading of progeny virus, and thus a significant improvement to the effectiveness of oncolytic virotherapy.

Nuclear fusion power is one of the best candidates for the next generation of energy. It has many desirable properties such as producing more energy than fossil fuels per kilogram of fuel, zero carbon emission, and producing no long-lived radioactive waste. Therefore, nuclear fusion power is worth pursuing and it has been studied for decades. One of the critical issues in nuclear fusion research is the impurity contamination. The impurities released from plasma-facing components through various plasma-wall interactions can lead to dilution of the fusion fuel. Therefore, it is very important to study impurity content and behavior. The impurity level is an important parameter in the research of magnetically confined plasma and can be quantified by the ion effective charge, Z_eff. Ion effective charge can be derived from bremsstrahlung emissivity from the visible spectrum radiation of plasma. The objective of this project is to set up a calibrated system that yields high precision in measuring bremsstrahlung emissivity. It is important to absolutely calibrate the system because impreciseness of bremsstrahlung emissivity measurements gives the inaccurate values of Z_eff. In our calibration, a Stabilized Halogen Light Source (SHLS), integrating sphere, and a photodiode are used. We collimate the light from SHLS and send it to the integrating sphere through fiber optics. The light in the integrating sphere is captured by a photodiode and a telescope and is transferred to current and voltage signal respectively. Our goal is to get the correct calibration factor that will give us correct values of bremsstrahlung emissivity measurements.

Wintertime air pollutant emission trends are poorly understood in comparison to emission trends in the summer mostly due to a lack of available and analyzed data on precursor air pollutants in the wintertime. This creates uncertainty in current atmospheric chemistry models. “WINTER 2015” was an aircraft research campaign launched in February 2015 that was executed to measure pollutant concentrations in addition to other data. All of which were relevant to the transportation, distribution, and chemical kinetics of pollutants and aerosols across the northeastern United States. The colder temperatures as well as lack of available sunlight have significant effects on chemical kinetics in the atmosphere. In particular, during the daytime, nitrogen oxides tend to produce ozone (O₃), a criteria pollutant regulated by the U.S. EPA, but nitrogen oxides destroy ozone at night. Longer nights, and lower sunlight during the day may mean that nitrogen oxides net destroy ozone for much of the winter. Current air quality models do not accurately simulate the nighttime chemistry of nitrogen oxides. I am examining the wintertime relationship between nitrogen oxides and O₃ using data taken in the WINTER 2015 campaign to gain insights into the extent to which wintertime nitrogen oxide emissions produce or destroy ozone. This information will then improve atmospheric chemistry models that are used to forecast air quality in various regions. It is expected that in the wintertime, the amount of reactive nitrogen oxide is limited relative to hydrocarbons. This nitrogen limited regime would mean that reactive nitrogen oxides have a greater role in the destruction of ozone, than the production of ozone.

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

Aerosol particles, solid or liquid particles suspended in the air, can affect Earth’s climate by scattering and absorbing sunlight. PM_2.5, particles less than 2.5 micrometers in diameter, are largely responsible for degraded visibility and easily traverse respiratory system pathways causing adverse health effects in humans. Often, a majority of PM_2.5 is composed of organic matter formed through photo-chemical reactions of hundreds of volatile organic compounds (VOC). This process depends on nitrogen oxide radical (NO_X = NO + NO₂) concentrations in the atmosphere, now predominantly contributed by anthropogenic emissions. NO_X and VOC react to produce organic nitrates, thought to be significant contributors to PM_2.5, but for which measurements are generally lacking. My project involves developing a concrete assessment of the role of organic nitrates as contributors to PM_2.5. I am developing an analytical method to thermally desorb organic nitrates from atmospheric particles collected on filters and promptly decompose them into nitrogen dioxide (NO₂). The resulting NO₂ is measured with a Cavity Attenuated Phase Shift (CAPS) spectroscopy instrument. I am establishing whether there is a direct correlation between the concentration of organic nitrates in PM_2.5 and desorbed NO₂. The goal is to quantify organic nitrates without individually measuring each of the likely hundreds present in the ambient atmosphere. Moreover, the thermal desorption process provides information on the physical properties of organic nitrates, such as effective saturation vapor pressure, needed for air quality computer models to accurately simulate their contribution to PM_2.5. As a result, I will help develop a better understanding of how natural and anthropogenic emissions affect the composition of the atmosphere by allowing assessments of how PM_2.5 levels have changed in response to NO_X emission reductions by the Clean Air Act.

Familial Platelet Disorder with Predisposition for Acute Myeloid Leukemia (FPD/AML) is an autosomal dominant human disorder caused by germline, heterozygous mutations in RUNX1. RUNX1 is a master regulator of hematopoiesis and has specific roles in megakaryocyte maturation and the production of platelets. Monoalellic mutations in RUNX1 result in haploinsufficiency of RUNX1 protein, leading to thrombocytopenia and impaired platelet function before leukemic transformation later in life. RUNX1 is controlled through direct positive auto-activation and its half-life is tightly regulated through ubiquitin-mediated proteasomal degradation. Tightly regulated auto-regulatory circuits are known to have capacity as centers for epigenetic cellular memory. Cellular memory effect offers the opportunity to transiently manipulate steady state product levels and observe maintenance that continues the newly attained levels.The goal of this work is to determine if the positive feedback loop controlling RUNX1 expression has capacity for epigenetic cellular memory that is responsive to transient RUNX1 overexpression. We hypothesize that increasing the presence of endogenous RUNX1 in RUNX1-deficient cells will correct megakaryocyte maturation and platelet formation. To initially determine if an increase in the half-life of RUNX1 will correct megakaryopoiesis, a series of ubiquitylnation and proteasome inhibitors were administered to HEK 293t cells for 6hr, 12hr, and 24hr periods to determine their effect of RUNX1 production and stability, showing increases in RUNX1 expression at RNA and protein levels. iPSC's derived from FPD/AML patients will be ultimately differentiated and analyzed via flow cytometry to observe the inhibitors' effects on platelet production. Anticipated results from this work hope to confirm a dose-dependant response in the epigenetic programming of RUNX1 that could illuminate novel therapies for individuals with FPD/AML.

The acrosome is a sperm-specific organelle required for the fertilization of the ovum in most animals. However, the molecules required for its formation during development are largely unknown. Toward identifying the function of candidate proteins, we are testing a system known as deGradFP in Drosophila melanogaster which targets fluorescently-tagged fusion proteins for degradation. This system depends on the ubiquitin-tagged proteasomal degradation pathway. Currently, we are testing whether this system works at different stages of spermatogenesis by targeting Yellow Fluorescent Protein (YFP) tagged Rabs, a small GTPase required for vesicular trafficking. Our preliminary results suggest successful targeting of the YFP-tagged Rab6. We are currently testing additional YFP-tagged Rabs, as well as sperm-specific proteins. The results should reveal whether the proteasomal pathway is working in all stages of spermatogenesis and aid in the understanding of proteins required in the acrosome biosynthesis pathway. Overall, our findings will expand our knowledge of sperm formation and function.

Diabetes is increasingly prevalent in the world, and there are currently over 29 million people in the United States with diabetes. Type 1 diabetic patients depend on insulin injections to maintain their blood insulin within a certain level so that their cells are getting enough sugar for energy production. Type 2 diabetic patients mostly rely on diet treatments and combinations of insulin and other drug treatments to avoid hyperglycemia. Moreover, type 2 diabetes often leads to different complications such as cardiovascular disease, blindness, and kidney failure. The goal of our study is to investigate insulin effects on the activation of macrophages, which are immune cells with important roles in inflammation. Since a pro-inflammatory state of macrophages can enhance insulin resistance and lead to cardiovascular diseases, it is crucial to understand if insulin changes the macrophage activation states that can cause off target effects leading to other medical complications. The experiments for this project are performed using RAW 264.7 cells, an immortal cell line derived from mouse macrophages. A dose experiment of insulin stimulation was performed to test if phosphorylated STAT1 (pro-inflammatory or M1) and phosphorylated STAT6 (anti-inflammatory or M2) were detected via western blot. Additional experiments determined the intensity of the macrophage response by measuring downstream signaling proteins (PI3K or IRS2) via immunoprecipitation and western blot. Also, RNA extraction and qPCR were performed to see if the gene transcription of macrophage polarization is activated by the above transcription factors. For example,  TNFα and IFNγ were measured for M1 polarization and IL-4 and IL-10 were measured for M2 polarization. Finally, NF-κB, another transcription factor was measured to determine if phosphorylation occurred, which should lead to M1 gene transcription. Together, these experiments revealed whether insulin affects key pro-inflammatory and anti-inflammatory signaling pathways in macrophages.

Diagnostic tests in mental health can often lead to inconclusive diagnoses, or diagnoses that take months to come to. The focus of this study is to identify neuropsychiatric conditions earlier and more accurately using voice analysis. Our study tested the ability of a speech analysis software to determine whether a patient suffers from a given mental illness, since mental illness can affect speech patterns. For example, one standard tested against in depression is a slower speaking rate. This study examined the relationship between voice as an indicator of those illnesses by analyzing short, random speech samples from patients with a diagnosed psychological or neurological condition. Our large team of interns was divided into several partnerships that focused on collecting samples of one specific disease. These samples were then analyzed for speech markers related to that condition by initially extracting audio, linguistic, and prosodic features and then using various statistical tools, mainly in python, to build predictive models using these features. These samples, along with controls from unafflicted patients, were then cross-referenced against an objective scale rating of the given condition, such as the PHQ-9 questionnaire for depression. The degree of correlation revealed by this analysis was used to determine if specific voice features were predictive of illness. We hope to make this software accessible to individual practitioners in a mobile application, with the potential to allow an individual practitioner to identify mental and neurological conditions much sooner, more accurately, and less invasively, allowing for earlier and more effective treatment.

Development of traditional anti-cancer drug has suffered from low success rate to difficulties in engineering approaches and clinical trials. Since metastasis is the major cause of cancer death, the current trend has been shifting towards a combined therapy of traditional cancer drugs and anti-migratory therapy. Cell migration assays provide straightforward visual and efficient quantitative analysis on cell migration distance and pattern. To implement these assays, one of common approach is to apply an elastomer block and create a cell-free area into which adjacent cells can migrate without damaging the cells. Our lab’s current cell exclusion migration assay is limited by uncontrolled barrier block adhesion to the substrate surface and to the well wall due to hand cutting and placement of the block. Therefore, to improve the usability and reproducibility, an accurate migration assay is developed to integrate an approach of controlling the geometry of the barrier block and confining the cell seeding area against cell penetration under the block. Our proposed barrier block fabrication utilizes laser-cut acrylic molds, which produce barrier blocks consistently in the same geometry. The block-placement device is optimized by designing a row of handles, which allows for placement of multiple blocks into the multi-well tissue culture plate at once and adjusts their positioning and adhesion precisely. Block-controlled migration is validated using a multi-well cell migration assay with respect to its ability to consistently confine cell seeding area and efficiency of use. The success of this method enables a more efficient method of anti-migratory drug screening and in vitro migration pattern analysis.

Over 70 million people are infected by HIV and 79 million of Americans by HPV every year. Even in developed countries, these particular sexually transmitted diseases (STDs) grow at an unyieldingly steady rate. In the Chiu Group, we address this increase in infection by working on the development of a fully automated microfluidic instrument to help improve early diagnosis of HIV and HPV. While many diagnostic techniques already exist, our goal is to advance state-of-the art approaches in novel microfluidic technologies, primarily concerning the reduction of cost to run clinical samples, shortening the time required to analyze samples, and enhancing the reliability of results. We are developing our automated microfluidic instrument in two phases. The first is a preparative step in which we create high-quality microfluidic chips that help digitize thousands of nanoliter droplets in a static array of wells. In the following experimental step, we amplify target HIV/HPV sequences in these nanodroplets from patient samples through polymerase chain reaction (dPCR) and the static array format provides a direct readout through changes in fluorescence of the sample droplets.The successful implementation of the instrument together with the microfluidic chip will maintain a high level of accuracy and sensitivity as well as observe a large decrease in cost and time for diagnostics. Among the conventional diagnostic instruments available today, our development will offer a faster, cheaper, and more accessible way to diagnose HIV and HPV, and ultimately slow the rate of STD cases throughout the world.

Prevalence of youth with Type-2 Diabetes (T2D) is increasing. Youth with T2D are at risk for cardiovascular disease and are advised to take on lifestyle change behaviors to improve outcomes, such as exercise, improving diet, and managing stress. The process of goal setting includes determining what needs to be accomplished and creating a plan to achieve this result. Goal setting has been found to help create healthy habits that can aid in the management of disease. While previous work outlines the importance of goal setting in T2D, little is known about the goals set by youth with T2D and whether they influence one’s health. For this study, we sought to examine the content of goals amongst youth with T2D and to examine whether the type of goal is associated with glycemic control. One hundred and seven youth with Type-2 Diabetes completed a clinical intake survey during their clinic visit at Seattle Children’s Hospital in 2017. The goals were categorized into altering blood sugar and blood glucose intake (N=27, 25.32%), changing eating habits (N=20, 18.69%), insulin management (N=15, 14.02%), improving or decreasing exercise (N=12, 11.21%) and decreasing highs or lows through exercise (N=5, 4.67%). Our next step (currently in progress), is to examine the association of these goal categories with A1C to better understand whether the type of goal relates to concurrent glycemic control. We anticipate that those with higher A1C may choose goals related to exercise and eating habits more than those who have lower A1C and are in good control. These results will inform future interventions to use goals within this population to provide tailored education to improve outcomes in youth with T2D.

Ca²⁺, or Calcium ions, are very important signaling molecules that are essential to normal eyesight. A light-sensitive layer in the eyes, called the retina, contain photoreceptors which require proper concentrations of Ca²⁺ for correct function. Mitochondria in the retina may help store Ca²⁺. To transport Ca²⁺, the mitochondria rely on Mitochondrial Calcium Uniporter proteins (MCU) and Mitochondrial Calcium Uptake 1 regulators (Micu1). This study hypothesizes that the Micu1 to MCU ratio influences the levels of Ca²⁺ in the photoreceptors and that an abnormal Micu1 to MCU ratio may compromise photoreceptor health. To analyze the Micu1 to MCU ratio, quantitative polymerase chain reactions (qPCR) are conducted. Retina cells are compared to other cell types, such as brain and heart cells, to determine the ratio of Micu1 to MCU relative to other tissue types. qPCR is also used to determine the Micu1 to MCU ratio in cells designed to express Micu1 or MCU abnormally. Current results suggest that the retina and brain express higher amounts of Micu1 than the heart, but the retina expresses the least MCU. It is hypothesized that most of the MCU channels in the retina are regulated by Micu1. On the other hand, heart tissue has more MCU and less Micu1, suggesting that the MCU channels are not regulated to the same extent. This makes sense because the retina and brain both contain large amounts of neurons, while the heart largely contains muscle. Therefore, different cell types with different functions express unique Micu1 to MCU ratios. Cells which are designed to express Micu1 or MCU abnormally have different ratios that may be insightful in addressing visual disorders. Further work may include manipulating the Micu1 to MCU ratio and observing the consequent effects on the photoreceptors.

First-generation college students (FGs; students whose parents have not completed college) often experience more difficulties transitioning into college compared to continuing-generation college students (CGs; students with at least one parent who has completed college). We hypothesize that some of these difficulties stem from the different cultural roles and expectations among interdependent FG families compared to independent CG families. In two studies, we examined cultural models of family (i.e., patterns of ideas and practices implicit in the family context) among FGs and CGs. In Study 1, we documented the prevailing ideas and concepts that FGs and CGs (N=518) associated with family by coding open-ended free-association responses. Both FGs and CGs associated the idea of family with affection, support, immediate family members and personal development. Although not statistically significantly different, FGs tended to associate family more with biological lineage, negative emotions, extended family members, and interdependence. In Study 2, we used a close-ended design to further investigate the patterns that emerged in Study 1. For instance, we anticipated that while both FGs and CGs would associate the family with support, FGs would be more likely to think more of emotional support while CGs would be more likely to think of instrumental support (e.g., financial assistance, career advice). Socioeconomic status is largely invisible and often overlooked in the college setting. By understanding more about FGs’ conceptions of families and their relationships to college, we hope to find ways to help FGs balance their roles as family members and college students and thus ease their transition to college. 

Nanowires have shown significant promise as high-capacity, conversion-type lithium-ion battery negative electrodes. Investigating the local properties of these materials during cycling has primarily been done via in-situ transmission electron microscopy or synchrotron-based techniques. Both techniques require highly specialized equipment that is not readily available. Atomic force microscope (AFM)-based measurements of electronic and ionic transport offer another alternative. However, analyzing these electrode materials via AFM has proven difficult due to the large surface variations in Z-height and the flexibility of the wires, which can trap and damage AFM tips. Therefore, sample preparation becomes critical. In this study we screened a variety of preparation methods including epoxies and resins and from those results, determined successful methods to prepare and ultramicrotome samples to create thin slices of electrode that can support analysis via AFM. These images allow for the elucidation of surface characteristics to support future surface functionalization and show that AFM can be applied to the imaging of these types of electrode materials to obtain nanoscale properties. A stronger understanding of local properties in these materials is critical to future developments that are highly anisotropic and require nanostructures.

Chalcopyrite copper iron sulfide (CuFeS2) nanocrystals have gained recent interest due to their metal-like optical response, despite their complete lack of free charge carriers. These novel optical characteristics make CuFeS2 an intriguing material for a variety of applications, including photovoltaics and photothermal applications. Unfortunately, synthesis of high quality CuFeS2 nanoparticles is difficult due to the difference in the reactivity of the two cations, often resulting in binary or polydisperse nanocrystals. To gain better control over nanocrystal morphology, we synthesized CuFeS2 nanocrystals via a hot injection method and studied the effect of the cation precursor ratio on the resulting properties of the nanocrystals. Transmission electron microscopy, X-ray diffraction, and UV-vis-NIR spectroscopy were used to analyze the nanocrystal composition, morphology, and optical characteristics. Based on the characterization data, a 1:2 molar ratio of copper to iron precursor was optimal for producing high quality, monodisperse CuFeS2 nanocrystals. These developments in morphological control will aid in future studies of quasi-static resonances in these materials.