For the first time we are able to non-invasively measure levels of a molecule that indicates the ageing and disease state of an individual. This molecule called nictotinamide adenine dinucleotide (NAD) and its other forms (NAD, NAD+, NADH) are related to aging and muscle function. High levels of the form NADH is found in individuals with disease and old age while high levels of NAD+ is found in active and younger individuals. Through exercise on elderly subjects we show that ageing effects on muscle can be reversed and levels of NAD+ and NADH can be restored to those found in adults. The form NAD+ is an index of mitochondrial capacity for making energy. With aging the oxidative capacity of the mitochondria declines, the amount of mitochondria declines and the levels of NAD+ declines. Through exercise training this effect can be reversed to yield higher muscle capacity in elderly. Our measurements were made on a 1.5 Tesla Magnet. We acquired Phosphorus spectra on the FDI (First Dorsal Interosseous) muscle and analyzed the data using software called jMRUI. From the Phosphorous spectra we are able to extract and analyze the NAD+ and NADH peaks.

The prevalence of HIV cases in the African born national population versus the African American or national population in general is notably high. In Washington state, there are approximately four times more HIV cases for the foreign born black male versus the African American black male along with about eleven times more HIV cases for the foreign born black female compared to the African American female counterpart. Stigma can impact medication adherence, quality of treatment and undiagnosed contributing mental disorders that, when treated, can improve one’s HIV status. However, little is known about how HIV stigma impacts the treatment and intervention outcomes for the African-born population. My lab as well as my individual role in this research project aims to analyze the nature of HIV stigma among this population, which will provide fundamentals of an intervention that is most ideal for African born population. We conducted semi-structured qualitative interviews with African born patients receiving treatment at Harborview Medical Center Madison HIV Clinic and those receiving social service at BABES YWCA network, and then I as the primary coder analyzed the data through ATLAS.ti, analytic software. Preliminary results indicate that stress due to community paranoia and disturbances due to family history of HIV are common obstacles faced by this population. These findings have important implications for focusing on treatment and other interventions for this understudied population.

HIV remains a serious health challenge particularly in developing countries. This can be attributed in part to the fact that many common diagnostic procedures in high-income countries are too expensive and technically complex to be practical in low-income countries. While there are several strategies for diagnosing HIV, one promising method is using the detection of the p24 antigen. The p24 antigen is a viral protein that can be detected within two weeks after HIV infection. This is useful because it allows for the detection of HIV infection sooner than the commonly used HIV antibody detection tests and rivals the more technologically complex nucleic acid detection methods. Our goal is to develop this test using a paper-based lateral flow membrane and a technique called immune complex dissociation (ICD) to reduce cost and increase sensitivity. The laboratory p24 antigen test was adapted into a paper format using the same reagents as the laboratory test. By comparing the results of the respective methods, we found that the paper test performed well compared to the laboratory test. This performance indicates that there is value in using the paper format and in exploring methods to increase the sensitivity of the assay. Test sensitivity can be compromised by the presence of antibodies that form complexes with the p24 antigen. These complexes reduce the amount of antigen that is free for detection. ICD restores this sensitivity by dissociating the antigen from these complexes. We tested the ICD process, to show that it is compatible with the paper format and improves sensitivity, by running parallel tests with and without ICD to demonstrate the efficacy of that procedure. The completion of this project will bring the paper-based assay one step closer to making a previously expensive, technology intensive, and operationally complicated test, accessible to those in low-resource settings.

We examined the impacts of fire on herbaceous community composition within the Abies lasiocarpa (subalpine fir) vegetation zone in the northern Cascade Range of Washington, USA. We used plant functional groups, classified based on growth form, to investigate how the ecological role and physiological niches of plants in burned and unburned subalpine parkland may differ, and how the pre-fire setting (closed forest, open forest, alpine woodland, krumholtz, alpine treeless vegetation) interacts with the severity of fire to affect the abundance of plant functional groups. We addressed these questions using field data collected in 2012, 17 years after the Butte Creek fire. We sampled 68 plots in the subalpine parkland ecotone, within or near the burn perimeter, in sites ranging from closed forest to treeless alpine vegetation (1800 m to 2250 m asl). We found significantly more cushion plants in unburned sites than burned sites. Sites that burned with high and very high severity had significantly more graminoids, herbaceous perennials, and tall shrubs. Likewise, closed forest and open forests had significantly more graminoids in burned than unburned areas. Although high intra-site variability and a lack of pre-fire data limit our inferences, our results support the hypothesis that fire influences the composition and function of herbaceous alpine and subalpine vegetation. Climate change may increase area burned and frequency of fire in high-elevation ecosystems, so our results serve as a starting point for future inquiry into the effects of fire on herbaceous vegetation in subalpine parkland.

Domestic violence, defined here as violent or aggressive behavior from one intimate partner to another, is one of the prime contributors of female homicides, known as femicide. Between 2005-2013, over 1042 women were reported murdered in Italy, increasing from 84 to 134 victims per year. My research analyzes women inequality in Italy by focusing on how domestic violence and femicide have been interpreted and portrayed to the Italian public. I pose the following question: In what ways have literature and media sources portrayed or helped raise awareness on women’s rights issues in Italy, specifically regarding domestic violence and femicide? This research is salient because most research focuses solely on developing countries, but when it comes to women’s rights, all countries including Italy are affected. In order to explore the relationship between intimate partner violence and femicide, I use synthesis and comparison of Michael Johnson’s Typology of Domestic Violence with other literature and social media. First, I analyze how literature and media sources portray domestic violence and femicide to the Italian public. Second, I compare my findings with Johnson’s interpretation of intimate partner violence. Third, I combine all said sources to formulate my own interpretation of domestic violence and femicide. Much of this research has been conducted in Italy and from Italian sources; therefore, most of the literature is translated into English. I hypothesize that cultural acceptance of gender inequality in Italy has contributed to domestic violence becoming a major factor in femicide. I anticipate that my research will help raise international awareness of femicide and domestic violence issues in Italy, and that the results will provide assistance in decreasing violence against women. I also seek to provide an alternate perspective of domestic violence, which I hope will lead to future research into the policy implications of my work.

Poliovirus (PV) remains endemic in three countries and is responsible for sporadic outbreaks in several others. Clinical surveillance for acute flaccid paralysis (AFP) is the gold standard for PV surveillance. However, as few as 1 in 100 to 1 in 1000 PV infections will develop AFP, particularly in well-vaccinated populations. Environmental surveillance of wastewater using a bag-mediated filtration system is currently being investigated to detect sub-clinical circulation of poliovirus. However, the filter samples will be collected remotely and evaluated centrally, which requires a shipping period. During this shipping period, bacterial and fungal growth may degrade PV on the filter surface. Inhibition of fungal and bacterial growth is necessary to ensure PV survival on filters during transit from field collection to the processing lab. Shipping on icepacks at 4°C is costly, thus finding an alternative is ideal. Preservative agents were investigated as an alternative to reduce microbial growth while not affecting PV recovery from its performance methods. Preservatives investigated included sodium azide, calcium propionate, o-phenylphenol, and sodium benzoate. Preservative solution or PBS control was pumped into the positively charged Virocap filter and eluted with beef extract, pH 9.50. After 1.5 hours, the eluate was pumped out, pH adjusted, and dosed with 10^2 PFU/mL PV1. Filters were run in duplicate and samples were plated on BGMK cells for enumeration by plaque assay. 0.0195% sodium azide eluate had a 64% recovery when compared to PV expressed in the PBS control eluate. 0.1% calcium propionate had a 102% recovery, 2% sodium benzoate had a 101% recovery, and 0.02% o-phenylphenol had a 111.1% recovery. Sodium azide is not recommended as a good preservative for PV due to low recovery, but 0.1% calcium propionate, 2% sodium benzoate, and 0.02% o-phenylphenol should be investigated further for PV preservation and recovery in wastewater over time.

Ocean acidification resulting from increased partial pressure of carbon dioxide (pCO₂) in seawater (due to increased atmospheric CO₂ levels) lowers seawater pH. Declining seawater pH dissolves shells and increases mortality of many shellfish. The risk of losing oysters is discouraging not only because of their influence on biodiversity, but also because of the economic importance to the shellfish industry. By studying the optimal growth conditions, the Friedman lab has been able to look at whether it would be feasible to grow Pacific oysters under present day or elevated pCO₂. To do this we raised groups of oysters in either high or low pCO2 levels and observed their mortality and overall growth. We have found that the oysters raised in the highest pCO₂ levels as well as those whose parents were raised in low pCO2 levels but were themselves raised in high levels had the highest mortality, while the oysters in the lower pCO₂ had lower mortality.

Cardiac arrest is a serious and often life-threatening event that can result in devastating outcomes. Targeted temperature management, or TTM, is a treatment utilized after cardiac arrest which improves patient outcomes. Determining the best treatment temperature and combination of sedative and paralytic medications, whose purpose is to slow the brain’s metabolism and maintain brain tissue oxygenation, will improve this beneficial treatment for future patients. The purpose of this study was to compare the time to ‘reawakening’, defined as the patient following commands, between post-cardiac arrest patients who received different combinations of paralytic and sedative medications and who were treated at 33°C or 36°C during TTM. Time to ‘reawakening’ after TTM is a critical factor in this patient population in terms of each patient's prognosis. The sub-aims of this study were to determine if time to ‘reawakening’ was influenced by: 1) cooling patients to the target temperature of only 36°C, and 2) the patient’s temperature when signs of shivering occurred during the TTM protocol. We were interested in studying these two aims because cooling patients to the target temperature of 36 degrees is expected to decrease the incidence of shivering and therefore less sedative and paralytic will be needed. Additionally, knowing what patient temperatures increase the incidence of shivering will better direct the dosing and timing of medications. Data for this study was retrieved through a retrospective chart review of 200 patients who received TTM treatment at Harborview Medical Center. Once we determine which treatment temperature and medication protocol results in the fastest reawakening and least amount of shivering, the results may influence future TTM protocols and could influence the care that future post-cardiac arrest patients receive. TTM could change in a way which ensures patients have the best possible outcomes after experiencing a traumatic event like cardiac arrest.

Vascular calcification greatly increases risk for heart disease, the leading cause of death in patients with diabetes and chronic kidney disease. Vascular calcification is an active process attributed to vascular smooth muscle cell (VSMC) mineralization. The sodium-dependent phosphate cotransporter, PiT-1, mediates VSMC calcification. The mechanisms by which PiT-1 causes calcification may include cellular matrix degradation, apoptosis, calcium phosphate vesicle release, and changes in gene expression. Of these mechanisms, my research focuses on the poorly understood signaling pathway by which PiT-1 induces VSMC calcification through up-regulating osteogenic (bone-forming) and chondrogenic (cartilage-forming) genes and down-regulating smooth muscle genes. These changes in gene expression make VSMCs more readily calcified in elevated phosphate. Recent literature suggests that VSMCs respond to elevated phosphate through PiT-1 with a novel cell signaling mechanism independent of phosphate uptake. My project concentrates on understanding the function of the PiT-1 protein's intracellular domain, which currently has no known function. I hypothesize that this section of PiT-1 is responsible for signaling in response to elevated phosphate, triggering a phosphorylation cascade that activates osteogenic transcription factors, such as Runx2, which initiate this osteogenic conversion. I am working toward integrating the gene for the intracellular domain of PiT-1 into the vascular smooth muscle cell genome to overexpress the truncated protein in cells. From my hypothesis that PiT-1 has a role in cell signaling, I predict that the overexpression of the intracellular domain of PiT-1 will reduce VSMC calcification by competing with the wild type PiT-1 protein for binding to proteins in the activation pathway, and inhibiting the signaling process. If my data support this hypothesis, I may engineer the intracellular domain of PiT-1 for therapeutic purposes.

Castilleja levisecta (CALE; golden paintbrush) is endemic to the Pacific Northwest prairies and is an endangered plant. Recovering this species requires an understanding of its seed production and dormancy. As a hemiparasite, CALE can acquire resources from host plants by forming connections with them. I am trying to find out whether host identity can affect the number of seeds per capsule by, for example, altering pollinator visitation. My research focused on the effects of two known hosts of CALE, Festuca roemeri and Eriophyllum lanatum. CALE were grown without a host or with one of these two hosts. Two pods were harvested from each of twelve CALE per host treatment, for a total of 72 capsules. Each pod was evaluated by counting the seeds inside and weighing the components of seed and chaff separately. With these data I determined fecundity and density of the seeds. To date my research indicates CALE may be benefited by Eriophyllum lanatum as these plants have greater fecundity than the no host treatment. Festuca roemeri had no major effect on CALE when compared to individuals grown without a host. This research indicates that hosts can affect reproduction by CALE, reinforcing the importance of considering host identity when recovering this species. Variation in seed dormancy among sites and/or years can affect the success of recovery efforts. I conducted germination testing on 8 accessions of CALE by putting seeds onto petri plates on moist filter paper, exposing them to cold moist stratification, and monitoring germination. I am interested in whether different populations of CALE may differ in their need for stratification. To date my research indicates population is important for how dormant CALE is and when CALE will germinate. The factors affecting dormancy and seed production in CALE are important for reintroduction and management of this endangered species.

Levels of atmospheric carbon dioxide have been steadily increasing for decades, sparking the interest of many. In response, researchers have been studying the various components of the carbon cycle, including bodies of water as they act as both significant sinks and sources of carbon dioxide. This study examines the correlation between various water quality indicators and CO₂ flux within the Cedar-Sammamish watershed. At each site, CO₂ flux was measured and logged using an IRGA (Infrared Gas Analyzer) connected to a Plexiglas chamber dome floating on the surface of the water. Dissolved oxygen (DO) levels and pH were measured using Hach DO and pH meters, and water quality was measured using a field spectrometer.  Meteorological data and visual observations were also recorded.  Data was then analyzed for trends.  Preliminary data indicated a positive correlation between nitrate levels and carbon dioxide efflux.  Subsequent data has not necessarily followed this trend, indicating that other factors may be at work.  Understanding the various trends and possible predictors of CO₂ flux is important, as it will help create better models for global carbon cycling.

Deadly and leaving patients with little time to live, pancreatic cancer is the third largest cause of deaths due to cancer in the US. Early detection and research of the disease beyond current capabilities are crucial and could be achieved by imaging fully intact pancreatic tissue core biopsies (TCBs) in three-dimensions (3D). Hence, The Human Photonics Laboratory is developing a microfluidic device to process fully intact TCBs (L=0.5-2.0 cm, d=200-1200 µm) in an all-in-one approach. Simultaneously, the device transports the TCB towards a 3D imaging platform for the end goal of enhancing cancer diagnosis. To achieve this goal, each step must be fit and performed in the small device. Typically, microfluidic devices are microfabricated with rectangular cross-sectional channels and used with no larger than cells or cell slurries, but never TCBs. To prepare TCBs for a pathologist in a microfluidic device, transportation is done in curved, circular cross-sectioned channels (CCCs)—both of which have never been achieved before this project. The channels’ cross-sections are circular to produce an intuitive Poiseuille flow profile. TCBs require a smooth directional change due to larger length and diameter of a TCB. Therefore, curved channels are necessary for direction changes and an optimized device footprint. Traditional microfabrication methods are not practical due to the time and precision required for mircofabricatation of a smooth CCC. Therefore, a new simplified method to fabricate microfluidic devices was developed to allow for CCCs and transport availability for TCBs. This new method allows for microfluidic devices containing CCCs to be fabricated in less than one hour and can provide channels that curve in 3D. Transportation of TCBs through CCCs is demonstrated for planar and multi-dimensional direction changes. Minimized channel lengths required to successfully change a TCB’s direction by 90 and 180 degrees were determined to reduce the microfluidic device’s footprint.

Autism spectrum disorder (ASD) is a neurodevelopmental syndrome characterized by impairment in social interaction and restricted/repetitive behaviors. Perinatal complications, which occur at the time of birth, have been associated with the presence of ASD, including low birth weight, planned caesarian section, and umbilical cord problems. Though these complications and their link to autism have been heavily researched, the variability of perinatal complications has yet to be compared to the genetic diversity within ASD as a disorder. Due to recent advances in genome science, several dozen autism susceptibility genes have been identified that account for 10-20% of ASD cases. The goal of this study is to analyze both prevalence and type of birth complications in a large genotyped sample as a function of co-occurring genetic abnormalities. Using medical history data collected from a population of over 2000 genotyped families, we will determine the prevalence of perinatal complications within the presence or absence of genetic mutation. Autism severity will be examined as a function of presence of perinatal complications and presence of genetic mutations. Results from this study could serve as a starting point to further evaluate the potential shared etiology of autism and birth complications, as well as other potential genetic links among common co-occurring disorders such as gastrointestinal illnesses and epilepsy.

The First World War (1914-1918) introduced the world to the horrors of warfare on an industrial scale. But it also gave rise to the one of the most dynamic and active anti-war movements of the 20th century. This research explores the activities of the local Pacific Northwest anti-war movement during World War I. National resistance to the militarist and imperialist policies of the United States peaked during the war period, and the Seattle anti-war movement provides a fascinating case study of how socialists, anarchists, labor unions and pacifists organized a robust anti-war movement. Using a wide variety of contemporary local newspapers, letters, activist memoirs and labor union meeting minutes, this study weaves together the story of Seattle’s radical and pacifist organizations during the First World War. This study finds that despite aggressive persecution from the Federal government, conservative labor unions and pro-war business interests, the Seattle anti-war coalition continued to offer active and radical resistance to militarist policies up until the end of the war.

According to dual process models of alcohol use, both explicit (controlled/reflective) process and implicit (automatic/reflexive) cognitions are important predictors of alcohol-related problems. These models also suggest that there are certain types of people for whom implicit processes may be more influential – e.g., people who are more impulsive. Based on these theories, this study seeks to examine whether impulsivity influences the strength of the relationship between implicit drinking identity (cognitions about the self and drinking) and alcohol-related problems. 506 college students completed the Drinking Identity Implicit Association Test, the Impulsivity Subscale of the Substance Use Risks Profile Scale, and the Rutgers Alcohol Problem Index. As hypothesized, both impulsivity and drinking identity scores were significantly and positively correlated with alcohol-related problems. Moderation was also supported: drinking identity was more predictive of alcohol-related problems for those reporting higher impulsivity rather than lower impulsivity. These results are consistent with theories that suggest that implicit cognitions should be better predictors for individuals with higher levels of impulsivity. This suggests that targeting implicit drinking identity might be helpful in reducing alcohol-related problems, especially for those individuals with higher levels of impulsivity. In addition, targeting impulsivity may also help reduce alcohol-related problems.

Aphasia, a language disorder typically resulting from neurological damage such as a stroke, impacts an individual’s ability to use language, but is generally thought to leave broader cognitive skills intact. Some evidence, however, suggests that this may not be the case. In particular, Silkes (2010) asked participants with and without aphasia to complete a task that used language-based stimuli but did not require language processing. Surprisingly, most individuals with aphasia performed worse on this task than typical adults. It is possible that these findings reflect unexpected differences in broader aspects of cognitive processing, such as memory or attention. Therefore, to better understand these previous results, this study investigates differences between adults with and without aphasia in rapid perception of language vs. non-language stimuli on a computer screen. Participants include 11 typical adults and 5 individuals with aphasia seen over 1-2 two-hour sessions. Participants press computer keys to indicate whether a white rectangle, in each trial, is blank or contains linguistic or non-linguistic characters. The rectangles are masked, meaning that they are hidden among strings of letters and symbols. They are presented at various exposure durations on a computer screen, making them progressively more difficult to see as exposure duration decreases. Data collected reflect the shortest exposure duration at which participants reliably distinguish between filled and empty rectangles in each of three conditions (word, non-word, or non-linguistic filler). Comparing these thresholds between conditions lets us explore the relative role of language processing vs. other cognitive skills in this task, and how this may differ between adults with and without aphasia. If individuals with aphasia show different patterns of performance than typical adults, this will expand our understanding of the underlying processes that are impaired in aphasia. Ultimately, better understanding of these processes will lead to better treatment of this language disorder.

A major focus of breast cancer research has involved the catechol estrogen pathway. Estrogen DNA Adduct (EDA) is a novel biomarker that is hypothesized to play a role in initiating breast cancer. Pilot studies have shown elevated levels of EDA in women at high risk for breast cancer and with breast cancer. The overall purpose of this project was to determine whether the EDA biomarker has potential for clinical use for breast cancer prevention. The first step toward this goal was to examine the extent to which the biomarker varies over time in the same individual. The specific aim was to determine whether the variation between urine samples taken at two points in time is significantly different from samples taken at a single point in time. We utilized a convenience sample from the DEEM (Diet, Exercise and Estrogen Metabolites) study of 6 urine samples from 3 women at 2 separate clinic visits, conducted 3 months apart. Triple quadrupole mass spectrometry was used to process 37 estrogen metabolites in the urine samples. The fragmentation pattern of each metabolite was analyzed and compared to a panel of known estrogen metabolites in which the elution times were known. The correlation coefficient between the 2 clinical visits was 0.49. The results from this analysis indicate moderate correlation between 2 time points. We will await the results from the larger study to decide whether a one point in time urine collection is adequate for the overall project. The implications of the overall project are important because determining breast cancer risk from urine samples would be a sensitive and non-invasive method that could allow healthcare providers to better target the women that should receive careful monitoring, testing, and interventions.

Müller glia are the predominant glial cell types in the retina that play a critical role in development and neuronal support. In adult mammalian retinas Müller glia are mitotically quiescent. However in other organisms, such as zebrafish, the Müller glia re-enter the cell cycle, proliferate and differentiate into new neurons upon retinal damage to replace lost ones. The goal of this study was to promote Müller glial proliferation and regenerate neurons in the adult mammalian retina. p27 is a tumor suppressor and plays a role in controlling cell proliferation. To test if the loss of p27 promotes Müller glial proliferation in adult retinas, we have generated Müller glia-specific p27 knockout mouse. Using tamoxifen-inducible, CreER/lox system to control timing of p27 deletion in Müller glia our Western blot data shows that daily injections of tamoxifen for four days efficiently eliminated p27 expression in adult Müller glia. When p27 expression is lost, adult Müller glia appeared to proliferate. Our data suggest that p27 plays a role in keeping adult Müller glia from re-entering the cell cycle. The controlled re-differentiation of Müller glia and proliferation into new neurons could be used to cure diseases involving retinal damage or degeneration like macular degeneration.

Polymeric micelles are nanoscopic structures constructed with amphiphilic diblock copolymers constructed with hydrophobic and hydrophillic portions that spontaneously form micelles in solution. Small hydrophobic molecules, such as cancer drugs taxol and doxorubicin, can be encapsulated in the micelle, which effectively serves as a nanovehicle for drug delivery. Here, we will develop a diblock copolymer integrating polyurethane-based self-immolative polymers (SIPs). SIPs are polymers that sequentially disassemble into their building blocks once the disassembly process is initiated by a triggering event at the trigger head group. By using SIPs, the polymers that make up the micelle are designed to depolymerize which we hope to increase the efficacy of payload release and remove the ability for micelle reformation. For this project, the micelle and all parts of the system will be synthesized from the bottom-up; optimizing the molecular weight of the diblock for micelle formation, investigating the kinetics of depolymerization and thermal trigger activation, and examining the stability of the micelle.

Traumatic Brain Injury (TBI) is an issue that seriously affects people of all ages; older adults with TBI have the highest rates of hospitalization and death. Additionally the overall recovery is significantly poorer than a younger person with a similar TBI. With normal aging, there is a reduction in the number of white blood cells (WBCs). However, in certain chronic diseases with an inflammatory component that are more common with older age, such as diabetes, there may be an ongoing activation of available WBCs which could affect viability in response to injury. This investigation used data from an ongoing parent study of the immune response following TBI in order to examine the number of and viability of peripheral blood mononuclear cells (PBMCs) within 24 hours of TBI in both older and younger adults as well as non-injured controls (N=133). Older age was defined as 55 and older for the purposes of this study. Whole blood was collected and processed for plasma and WBCs from subjects using Ficoll technique (separation of blood components). Cells were manually counted and viability of cells was determined using the trypan blue method (type of stain to observe cells). Data analysis is underway. Descriptive statistics were performed along with ANOVA to assess for group differences in cell count and viability. Time from blood draw to processing will be used as a covariate. The results of this study will enable us to determine if lower cell counts or cell viability differ by age and injury status. This will provide support for or refute the hypothesis that the immune response following injury is different in older adults which could impact patient outcomes. By understanding this relationship, we can implement clinical changes to potentially help change the immune response and improve the outcomes older adults experience post injury.

Oxygen (O₂) is essential for aerobic organisms to complete development. However, genetic mechanisms exist to promote development and avoid damage under low oxygen conditions. Elucidating how these mechanisms regulate development is important for understanding diseases, such as ischemia and tumor formation, which have a hypoxic component. We are studying the hypoxic response in Caenorhabditis elegans, a genetically tractable organism that uses simple diffusion for gas exchange with the environment. Previous research has suggested that at 5000ppm O₂, loss-of-function mutations in either the transcription factor hif-1, or an AMP-activated protein kinase (AMPK) subunit aak-2, prematurely arrest development. Given that these two mutants have similar phenotypic responses in severe hypoxia, we hypothesized that aak-2 and hif-1 act in the same genetic pathway to coordinate developmental arrest in hypoxia. To test this, we pharmacologically activated AMPK and performed epistasis analysis with genetic mutations. We found that activating AMPK by treatment with Metformin in a hif-1 mutant was not sufficient to sustain reproductive activity in 5000 ppm O₂. We also generated a strain that constitutively expresses HIF-1 in an aak-2 mutant background and found no difference in developmental arrest from aak-2 mutant animals with wild-type HIF-1 activity. We conclude that aak-2 and hif-1 act in distinct genetic pathways to promote development in hypoxia. Our results suggest that C. elegans has multiple, redundant pathways that coordinate development in hypoxic conditions.

Nociception is the ability to detect noxious stimuli. Without nociceptors organisms would not be capable of sensing pain, a sensation that induces an avoidance response to minimize injury. Noxious stimuli, such as unusual thermal, chemical, and mechanical stimulation, are detected by groupings of peripheral neurons within the trigeminal ganglion and dorsal root ganglion. This is a screen that aims to identify zebrafish mutants that display abnormal nociceptive responses. We have developed a high throughput locomotive response screen, which we use to screen the third generation progeny of adult males, who have been treated with a mutagen. Following Mendelian genetics, we expect ¼ of the F3 generation to display a recessive phenotype. Any mutant nociceptive phenotype (i.e. decreased locomotive response to noxious heat or chemical stimuli) should be seen in this quarter of the population. Our preliminary data demonstrates that this screen is feasible. Upon identification of mutants we will characterize the observed phenotype by temperature and chemical based choice testing. We will use these mutants to identify genes involved in the regulation of stimulus detection and the development of nociceptive neuronal circuits. The long-term goal of this screen is to increase the understanding of nociception, which will aid in the search for new novel analgesics.

Communication is prevalent and necessary in all social animals. It determines outcomes of competition for mates and food resources, and also allows for social organization. A wide range of communication strategies are used across the animal kingdom, but for primates - one of the most social groups in the animal kingdom -there are three main strategies for communication: auditory, visual, and olfactory. For my study, I focused on the question of how group size affects amount of communication within a group. I hypothesized that with larger group size comes a need for more direct communication, in order to maintain cohesion in a group with many individuals. Therefore, I predicted that a larger group would result in more complex vocalization usage in a primate which relies largely on vocalizations to communicate. Using the genus Eulemur as a study system, I investigated if vocalization complexity is related to social group size. Eulemur rubiventer and Eulemur rufifrons are an ideal system for this work, because they share similar habitats and predation risk, and are closely related, but differ in their social group size. I studied the species for a month in the primary forest of Ranomafana National Park, Madagascar, following and watching individual animals and continuously documenting their behaviors and vocalizations. I also used a microphone to record vocalizations to get better data on the different types of calls. I found that the species with larger groups (E. rufifrons) called 88% more often than the small grouped animals (E. rubiventer), and consistently used 4 more calls than the smaller grouped species. This preliminary evidence suggests that increased vocalization frequency and use of different calls are associated with higher sociality. I postulate that this increase in vocalization usage complexity is necessary to maintain cohesion in a large social group.

The brain effortlessly carries out the daunting task of visual perception by utilizing millions of neurons to process various aspects of the visual scene. The systematic arrangement of these cells across the primary visual cortex (V1) can be described by a set of superimposed maps that convey the orientation, scale, location and eye of origin of the image features that best excite the neurons. Current theory suggests these maps are arranged such that all combinations of stimulus parameters are covered equally and continuously in local regions across the visual cortex. This idea is appealing because it corresponds to the intuition that we should be able to see the features of a simple shape equally well at any rotation and at a variety of distances, and it is important because it places a constraint on the architecture of the cortex. To examine whether this constraint fits with other known anatomical and physiological measurements, we have conducted computer simulations to measure the evenness of coverage in large-scale, biologically plausible models of V1. We presented a large combination of visual stimuli to the model and computed a coverage metric, c', defined in the literature as the standard deviation divided by the mean of cortical activity across all stimuli. Taken together, c' and the associated map of neuronal activity in stimulus space reveal the coverage uniformity of map variable combinations. We found that our original models had a striking imbalance in activity across spatial scale, which counterintuitively arose from the assumption of a uniform change in neuronal receptive field (RF) size across the visual cortex. In these models, there were equal numbers of neurons with small and large RFs. Based on our observations, we are developing an improved model that uses a nonlinear distribution of RF sizes in an attempt to preserve uniform coverage.

Rumination has been linked to the onset and development of depression and anxiety. Rumination is a process of repetitive negative feelings and thoughts associated with an upsetting event or situation. In this study, I investigate whether rumination explains the relationship between different types of environmental adversity and symptoms of depression and anxiety in teens. Specifically, does rumination explain the association of trauma exposure, poverty, and race/ethnicity related with the onset of depression or anxiety? Data come from a sample of 168 adolescents recruited from the community in Boston and Cambridge, MA. To examine mediation I examined four sets of models testing the following relationships: 1) the association between each measure of environmental adversity and depression/anxiety, 2) the association between each measure of environmental adversity and rumination, 3) the association between rumination and depression/anxiety, and 4) a final model that included the adversity variables as well as rumination to see the attenuation in associations of adversity with depression and anxiety once rumination was added to the model. The findings suggest that, 1) child abuse was associated with elevations in depression and anxiety symptoms, and community violence was associated with depressive symptoms and marginally with anxiety symptoms; 2) child abuse was associated with higher engagement in rumination; higher income-to-needs ratio was also related to greater rumination; 3) higher degrees of rumination predicted both depression and anxiety symptoms; and 4) the association between child abuse and depressive symptoms was reduced by 24.5% after accounting for rumination, and the association between child abuse and anxiety symptoms was reduced by 39.8% after accounting for rumination. These findings fill the void in the literature regarding mechanisms linking different types of environmental stressors to the onset of depression and anxiety. This is important for development of interventions for preventing mental illness.

Endocrine disrupting compounds (EDCs) present in wastewater treatment plant (WWTP) effluents are a significant water quality issue. EDCs have been demonstrated to have adverse effects on aquatic life at extremely low concentrations. The synthetic estrogen, 17α-ethinylestradiol (EE2), is a particularly potent EDC of concern in WWTP effluents. Biological degradation is a critical mechanism for EDC removal in WWTPs. The goal of this research was to isolate and identify bacteria capable of degrading EE2 with an eventual goal of using the bacteria to improve WWTPs’ removal efficiencies. The experiments started with enrichments established in pH-buffered mineral salts media containing 1000 µg/L EE2 as the only added carbon and energy source, which were originally inoculated with activated sludge obtained from a local WWTP. Vitamin solutions were added to overcome loss of EE2 degradation abilities that were seen in earlier isolation attempts, and the new enrichments were monitored weekly for EE2 concentration using High-Performance Liquid Chromatograph with UV detection (HPLC-UV). Of the eight enrichments, three were found to degrade EE2 to below 200 µg/L within 54 days, as opposed to 120 days in the other enrichments. These were transferred to fresh media to reduce inactive bacteria concentrations through dilution and were monitored for degradation. Two of the three were transferred again after 78 days to fresh media and monitored for continued degradation. Transfer of the liquid cultures to solid media is currently underway to allow selection to single colony isolated cultures that can be assessed for their EE2 degradation abilities. This work is a promising advancement in the isolation of an EE2 degrader that will have a positive impact in bioaugmentation for the removal of EDCs from WWTP effluents.

The process of directing auditory attention was first analyzed by Colin Cherry in 1953 and classically dubbed “the cocktail party problem”, referring to how an individual is able to follow one conversation at a noisy gathering. In this project I will explore how eye-gaze position may direct auditory attention and thus affect detection thresholds of sounds in noise. Behavioral studies researching this issue have shown that it is easier to segregate a target sound when it comes from a different location than the masking noise, a phenomenon known as the masking level difference (MLD). This can be observed as the improvement in detection threshold of a tone in noise when they are separated versus when they are collocated. However, these past studies did not control for eye gaze. Recent electrophysiological studies have found that the inferior colliculus, a critical auditory midbrain nucleus, shows visual and oculomotor responses. The behavioral significance of these interactions to human listeners is not yet well understood, but suggests that the oculomotor system may be able to modulate auditory processing. My project focuses on eye-gaze and the MLD. I will test whether subjects have better detection thresholds when their eye-gaze is directed towards the location of the tone versus towards the location of the noise. The experiment is generally laid out in two blocks. During the first block of trials, the subject will have visual primers directing eye-gaze; in the second block, auditory primers that do not direct eye-gaze will be used. Control trials that give uninformative visual and auditory cues will also be tested. I have promising preliminary data shows that trials using informative auditory cues can improve thresholds over trials with uninformative auditory cues. However, the more noteworthy result this study looks for is the possibility of yet another improvement when eye-gaze is brought into play.

 I studied whether Chinook parr can tell the difference between full and half siblings based on their olfactory senses. 800 total parr were tested with four different female parents and the same male parent using a Y-maze device that allowed them to ‘choose’ the smell they preferred during the months of March and April 2014. The hypothesized results are that full siblings are recognized over half-siblings. If Chinook prefer their siblings over their non-siblings they are more likely to have a higher survival rate and lower predation rates because they will be less likely to be aggressive and cannibalistic, and more likely to school with these siblings

We researched how animals in Pacific Island legends vary from island to island, and the cultural significance of these animals. This research question directly relates to the readings we have done in Pacific Island Legends and Research is Ceremony. Pacific Island Legends has showed us a variety of stories from various areas of the pacific islands. Shawn Wilson’s book Research is Ceremony shows us the importance of using culture when teaching students. We used the methods of legend analysis, interviews, participant observation, and discourse analysis. We hypothesized that we will find patterns of animals used in the legends. Our research matters because legends are important for character building in children. Legends are important to bring to the classroom because they help people build relationships not just with people, but also with all of their surroundings.

In the San Juan Islands, drift macrophytes from shallow waters represent a significant spatial subsidy provided to the subtidal zone. This organic matter is a potential food source for deep dwelling herbivores like the red urchin Strongylocentrotus franciscanus. Little is known about how urchins capture and use drift material. A racetrack flume was used to examine the capture of drift macrophytes of various species and size by S. franciscanus. No species-specific selectivity was found, but urchins caught 100% of small macrophyte pieces. A significant decrease in capture efficiency was noted as drift algal size was increased, probably due to the urchins’ inability to fight current drag acting on pieces with larger surface area. This suggests that drift macrophytes could be the main food source for deep dwelling urchins where available, potentially explaining how herbivores subsist at dysphotic depths. 

As mobile touch screen devices become increasingly ubiquitous, they are also becoming more accessible to the visually impaired. Someone who is blind traditionally enters text on his or her phone by using a screen reader and the default keyboard layout. However, this method is slow and it is difficult to correct mistakes as one is typing. We developed Perkinput, a nonvisual text entry method that uses the 6-bit Braille character encoding. In Perkinput, instead of relying on the device’s voice over system to announce each letter that is pressed, this input is based solely on the Braille keyboard. The user simultaneously presses down with his or her fingers that correspond to the dots for the character in Braille he or she wanted to enter. Once entered, the text can be sent in a text message, an email, or simply copied to the clipboard for later use in other applications. Results have shown that the Perkinput method is more than twice as fast as using the default keyboard layout for the blind. I have implemented this method into an iOS application that is currently deployed on the iTunes Store. I have instrumented this application in order to gain insight into how people are using the program outside of a lab setting. This will help us improve Perkinput and make it more accessible to the blind community. Perkinput aims to make text entry easier and efficient for people who cannot look at their screen.

Arsenic (As) is a human toxin and carcinogen that can be ingested by drinking contaminated groundwater or by eating crops that are irrigated with contaminated water. In the past decade, studies have shown that arsenic contamination poses a threat to global public health. Despite the health risks, few countries regulate the arsenic content of food. With this research project, my mentor and I hope to obtain information that will be valuable for the formation of appropriate regulations about arsenic content in rice. We have chosen rice because it is a staple of the diet in Bangladesh, which is currently experiencing an epidemic of arsenic poisoning. Specifically, we are studying how the diffusion of dissolved oxygen into the root-zone of rice plants affects arsenic accumulation in rice grains. We have been able to visualize these concentrations in real time using two-dimensional optical oxygen sensors (optodes) placed on the root zone. We have also measured the concentration of arsenic in the rice grains. Oxygen oxidizes dissolved iron(II) into solid-phase iron (III), which can scavenge arsenic out of solution and reduce plant exposure to arsenic. Twelve rice plants were studied, half grown in ambient temperatures and half in elevated temperatures to simulate a warmer climate. We chose to grow half the plants in elevated temperatures because many of the world’s rice producing regions are projected to experience warmer climates in the futures. Our data have provided valuable information about how dissolved oxygen concentrations near the roots of rice plants change temporally and spatially. Additionally, we've found that when grown in elevated soil temperatures, rice plants grow larger and have proportionately larger root systems. These larger plants require more water, and thus pull more arsenic from the soil porewater toward their root system, which ultimately results in greater uptake of arsenic and accumulation of arsenic in plant tissues.

The lab I am involved with investigates the molecular events of neuromodulation, a form of neuronal chemical signaling that determines behavior, emotions, learning and memory. Neuromodulators are carried and released by dense core vesicles, a type of cellular vesicle which little is known about. Dr. Ailion's lab has performed genetic screens for C. elegans mutants that have altered dense core vesicle secretion and has isolated many unique mutants. During my time in Dr. Ailion's lab I focused on genetically mapping two of these mutants which were given the names yak90 and yak91. With yak90, I used a well-established mapping method where my mutant strain was crossed to marker strains which contained alleles causing obvious deformities on each chromosome. Generations later, I examined their offspring and was able to pinpoint one mutant phenotype that was not segregating according to Mendelian ratios, indicating linkage to chromosome IV. When a candidate gene was found near the linkage site, I did a complementation test and confirmed that yak90 contains a mutation in an already characterized gene, unc-31. With yak91, a new method was tested using a marker strain that contains alleles for multiple fluorescent tags instead of body deformities. This was necessary because yak91's mutation causes it to be "egl", or distended with mature eggs, and it was difficult to tell it apart from one of the marker phenotypes. The cross with the new strain was a success and after examining the progeny, linkage was found on chromosome IV. Another complementation test was performed, and yak91 was found to contain a mutation in ric-8. Total loss-of-function mutations in ric-8 are lethal so yak91 must contain a splice site or point mutation that significantly alters the function of the protein product. Both genes I identified play important roles in neuromodulation. 

 The development of drugs is essential for human health. Approximately 40-60% of all currently prescribed drugs target a specific type of membrane protein called a G-protein coupled receptor (GPCR). In the human body, the binding of a neurotransmitter or hormones to a GPCR transmits signals across the membrane to bring about an intracellular response, which ultimately permits cells to communicate with each other and regulate body physiology. The Hague lab studies the molecular mechanism of drugs targeting GPCRs. Currently, we are investigating an important structural portion of certain GPCRs called the PDZ binding motif, which is a site for protein-protein interactions. My role in the lab focuses on the somatostatin (SST) receptor subfamily, which regulates the endocrine system and neurotransmission by inhibiting the release of secondary hormones produced in the gastrointestinal tract and pituitary gland. A drug that targets SST receptors is octreotide. This drug inhibits growth hormone and insulin release, and is FDA approved for the treatment of growth-hormone producing tumors and GI tract disorders. Interestingly, all five SST GPCRs contain this PDZ-binding motif, and my research examined the importance of this motif using a variety of biochemistry techniques that quantified the expression, localization, signaling, and protein-protein interaction network. I created SST receptor mutants lacking the PDZ-binding motif using polymerase chain reaction and then transfected the SST mutants into human cells. These novel clones were subjected to plasma membrane assays, confocal microscopy, and mass spectrometry analysis. I found that removing the PDZ-binding motif had minor impact on overall receptor function, but more studies are necessary to determine the role of the PDZ-binding motif for SST receptor function. Our ultimate goal is to identify novel PDZ-interacting proteins for GPCRs, and then disrupt or enhance this interaction with novel small molecules to treat disease.

Sulfate-reducing bacteria are widespread and live in many environments. Some sulfate reducers are capable of growing in a mutualistic relationship with methanogens. In nature, diverse sulfate-reducing bacteria have repeatedly evolved into obligate mutualists. We want to study how this evolution occurred by using a model system for evolution in the lab between a sulfate reducer, Desulfovibrio vulgaris, and a methanogen, Methanococcus maripaludis. After allowing these two organisms to evolve for 1000 generations in an environment that forces their cooperation, 12 out of 22 D. vulgaris populations lost the ability to reduce sulfate (sulfate-minus genotypes). We want to test whether the ratio of sulfate-minus relative to sulfate-plus (a genotype still able to grow on sulfate) genotypes in coculture affects the fitness benefit of the sulfate-minus genotypes. To do this, a sulfate-minus and plus D. vulgaris were placed together and their relative abundance in coculture was tracked over time. The experiment will tell us if some genotypes have the ability to take over when they are rare. To track these changes, we are using a method called FREQ-Seq. FREQ-Seq is an inexpensive way of analyzing the frequency of certain genes or other DNA sequences in a mixed population over time. We can use this method to understand how these populations of D. vulgaris evolved. I originally predicted there would be a higher sulfate-minus to plus ratio at the end of the competition compared to the initial ratio. D. vulgaris is an interesting model organism for studying the evolution of obligate sulfate-reducer/methanogen mutualisms because it can live either alone as a sulfate-reducer or together with other organisms in a syntrophic relationship. The data we collected can help us better understand the mechanisms of natural selection that cause sulfate reducing populations to become obligate mutualists.

Medical imaging is a non-invasive process to acquire visual data of the internal aspect of a body, with the purpose of performing clinical analysis. Medical ultrasonography is a medical imaging technique that utilizes ultrasound waves to produce an image of muscle, tendons, and many internal organs. The use of this technology as a screening tool has greatly improved the diagnostic and early detection of cancer and disease, allowing treatments to start at an earlier stage of disease development. However, it has also increased the risks of false positives and unnecessary biopsies that can outweigh the screening benefits. As a result, additional screenings are often performed to reduce the percentage of false positives. This is an expensive process that can further increase when different doctors order different ultrasound screenings. This research responds to a request from Philips Healthcare. Philips seeks to improve the design of ultrasound imaging systems and the current use of their ultrasound imaging systems in patient diagnostic procedures. In order to do so, my research involves creating a database to store, manage, and classify the data from patients and doctors from the UW department of radiology. Using this database, I will perform a statistical analysis of the diagnostic data to find the utilization of specific features and modes on the system, and to determine the relationship between the number of false positives and false negatives and potential linkages to settings or image quality. The expected results from this research include a prototype of instructions and recommendations for the use of ultrasound imaging systems, based on the statistical analysis of the data, generalized to apply to other Philips customers currently using Philips Ultrasound machines, and a set of recommendations for the design and availability of specific data in future Philips Ultrasound machines.

This research traces the origins of electron density fluctuations in the HIT-SI experiment. HIT-SI is a magnetic confinement experiment that uses two helicity injectors to initialize and sustain current in the confinement region. Densities of 1-10e19 m^-3 with density fluctuations related to the injector frequency are measured with an FIR interferometer. After spheromak formation, injector currents flow in the direction of toroidal current in the confinement volume. Peaks in the density fluctuations are seen when the injector current passes through the beam path of the interferometer. These observations are consistent with particle motion in the direction of injector current as expected by anti-dynamo action in this region. Furthermore, we have observed fluctuations that indicate that the injector current displaces the confined current. Calculating the toroidal current centroid from surface magnetic probe measurements as a function of time provides further testing of this model. Understanding density fluctuations allows a more complete description of the physics of current drive in HIT-SI.

Landscape immersion, commonly accepted as best practice for zoo exhibit design, often fails to provide meaningful moments between visitor and animal that can trigger an empathetic connection. With many zoos seeking to further their conservation mission, exhibits must push the boundaries of immersion design and provide opportunities for cognitive and affective stimulation for visitors. Exhibits that provide visitors with both an intellectual and an emotional connection to the animal increase the desire to learn more about the species and its habitat and, in turn, foster a reverence for the natural world that can lead to a more environmentally conscious shift in behavior. In analyzing research on conservation psychology and visitor motivations, I found zoos create and support a social context surrounding the interaction with nature. Offering multiple ways for visitors to engage simultaneously with each other and the exhibit improves the social quality of the visit, increases connection to the animals, and concern for their wellbeing. In conversations with designers and curators, I found animal wellbeing, visitor experience, and animal husbandry are essential components to exhibit design. Each offer opportunities that enable an empathetic connection that can increase desire to care for animals at the zoo, and as a consequence, for the species and the broader ecosystem in which those animals live. Finally, I visited three case studies that demonstrate a progressive immersive design approach: the Woodland Park Zoo Humboldt Penguin exhibit, the Arizona Desert Museum Desert Loop Trail, and the Bronx Zoo Madagascar! exhibit. I found that these exhibits contained cultural and ecological narratives that highlighted impacts people have on those particular ecosystems. The immersive nature and compelling narrative of these exhibits prompts individuals to reconsider their role in environmental problems and conservation action, and see themselves as part of the solution.

Endophilin is an essential protein for membrane dynamics. It harbors a BAR (Bin–Amphiphysin–Rvs) domain, which acts as a basic modual for shaping membranes. Deletion of Endophilin impairs endocytosis, which leads to defects in cellular signaling. Despite the importance, how Endophilin is regulated remains elusive. Here, we propose that the bending activity of the Endophilin BAR domain is modulated by phosphorylation. We will use biophyiscal/biochemical approaches to investigate Endophilin-membrane interactions. Our result will provide new insights into molecular mechanisms for controling membrane dynamics. We use liposomes as an in vitro model. We follow the kinetics of Endophilin-membrane interactions using fluorescent probes. We identify key residues for Endophilin-membrane binding using site-directed mutagenesis. We believe this research will help us understand the mechanism for shaping cellular membranes, in particular, how Endophilin BAR domain bends membranes.

 Snailfishes of the genus Careproctus are known to deposit egg masses inside the gill cavity of lithodid crabs. Identification of the species responsible has been inconclusive due to the difficulty associated with identifying snailfish eggs or larvae to species. DNA samples were collected from egg masses found in crabs both in the commercial golden king crab (Lithoides aequispinus) fishery and during survey work conducted by the Alaska Fishery Science Center. Egg masses were found in both golden king crabs and scarlet king crabs (L. couesi). Cytochrome Oxidase I (COI) was amplified from egg mass samples and sequenced. Comparison of COI sequences from eggs with COI sequences from positively identified adult vouchers yielded identification of 75 egg masses to species: 38, 29, 7, and 1 egg masses were identified as Careproctus rastrinus, C. colletti, C. furcellus, and C. simus, respectively. Egg masses were determined to contain eggs from only one species. These results are the first positive identification of the snailfish species responsible for laying egg masses in crabs. Identification of species involved may be useful in further attempts to classify the nature of this relationship between snailfishes and crabs.

Proteins that share similar 3D structures, or folds, can be grouped together into fold families, and evidence suggests that there may be common folding mechanisms that exist within these fold families. Finding these common folding mechanisms will shed light on the way in which folding is determined among proteins, which is a major question in biochemistry. Here I investigate the dynamics and unfolding pathways of 18 members selected from the sixth most populated fold family, the SH3-like barrel domain. The SH3-like barrel fold is an all-beta fold, constructed of beta strands only. Using molecular dynamic simulations at high temperatures, the unfolding pathways, including the characterization of transition states, can be studied for each of these proteins. A broad analysis of native and non-native contacts and secondary structure content will allow common folding patterns to be determined across the fold family. It is anticipated that a hierarchical loss of contacts between the beta-strand of the fold, with those between the turns being maintained longer will be observed. Here I report an initial analysis of the unfolding of these 18 members of the SH3-like barrel fold family and present the observed commonalities, as well as variances across the pathways.

 The purpose of this study is to determine structure-solvent property relationships in organic photovoltaic polymers, with the overarching goal of increasing the efficiency of organic solar cells (OPVs). OPVs are of great interest due to their flexibility, low environmental impact, and modest cost. Additionally, OPVs can be dissolved in organic solvents and printed using roll-to-roll, high-throughput processing – a feature that lends them a large advantage in the photovoltaic industry. Unfortunately, OPVs fall short within the realm of efficiency; the ~10% efficiency of OPVs can hardly rival the ~40% efficiency of inorganic photovoltaic technology. Improving the efficiency of OPVs is an important obstacle in producing low-area, economically viable solar cells. This project aims to use computational models to study the role of organic solvents in mediating the self-assembly of polythiophenes, a commonly studied class of OPV polymers. These models are generated in GROMACS, a program that uses an empirical potential energy function for the polymer, solvent, and polymer-solvent interactions to predict the molecule’s time-dependent behavior with classical molecular dynamics. In particular, these simulations can predict how physical properties such as the free energy of the polymers change as the torsional angles between monomers are varied throughout the simulation. Moreover, changes in the preferred conformations of the polymer are primarily signified by the lowest free-energy states. If we do discover changes in the preferred conformations of the polymer, simulations can be used to test whether these changes are predominantly due to the solvent or the structure of the polymer. This yields information about the equilibrium and self-assembly of the polymer, which can eventually improve the efficiency of OPVs by allowing more control over the polymer nanostructure during high throughput manufacturing processes such as roll-to-roll printing.

Understanding how the brain processes information using neural circuits remains a challenging task. For example, although neurons in the mammalian visual cortex are known to be specialized for processing particular visual features, such as motion, color or depth, little progress has been made on elucidating the underlying circuit diagrams. To address this problem, we have developed a system with a Java-based user interface that can apply optimization strategies to rapidly test competing models against large amounts of neurophysiological data, parallelizing the computational load across a cluster of workstations, to uncover plausible circuit models. In order to demonstrate the effectiveness of this system, we are applying it to understand the function of motion-sensitive neurons in the primate visual cortex. These neurons are direction selective (DS), meaning that they respond well to a visual stimulus moving in one direction but not in others. Previous studies demonstrated that this response also changes with stimulus speed: as the visual world moves faster, the neurons appear to operate on a shorter timescale. Current mathematical models for DS neurons, which are based on filters that change position linearly with time, predict the response to some stimuli but do not account for the ability of the neuronal response to adapt to changes in speed. We hypothesize that a model using a filter that changes position nonlinearly with time will better explain the experimental data. To discover this filter, we are building several candidate models and will apply our optimization system to test their performance against our own experimental data. We will test these nonlinear filter models against an alternative that uses multiple linear filters, each tuned for a different velocity. If our approach can improve upon current models for DS neurons, it may offer neuroscientists a powerful tool for revealing neural circuits that underlie visual perception.

‘Aigarchaeota’ is a candidate phylum of Archaea known only by 16S rRNA gene fragments from cultivation-independent microbial surveys and a single composite genome from Candidatus ‘Caldiarchaeum subterraneum’, an inhabitant of a subterranean gold mine in Japan. Gene sequences reported in various publications were found almost exclusively in geothermal settings, but a comprehensive assessment has not yet been performed. The purpose of this study was: (i) to rigorously define the phylum; (ii) to gain insight into the phylogenetic and potential taxonomic structure of the phylum; (iii) to assess the distribution of ‘Aigarchaeota’; and (iv) to design ‘Aigarchaeota’-specific 16S rRNA gene primers. Public databases were mined for 16S rRNA gene sequences related to known ‘Aigarchaeota’ and a combination of approaches were used to rigorously define the phylogenetic boundaries of the phylum and compile a neighbor-joining and maximum likelihood phylogenetic tree. Primer template gene sequences were aligned in ClustalW in order to locate regions that are suitable for targeting genus-level groups. ‘Aigarchaeota’-specific primers for the polymerase chain reaction (PCR) amplification of 16S rRNA genes were designed using sequence alignments and reviewed using the Ribosomal Database Project Probe Match tool. The analyses supported the proposed relationship between ‘Aigarchaeota’, Thaumarchaeota, Crenarchaeota, and Korarchaeota in the so-called ‘TACK’ superphylum, and identified ~300 16S rRNA genes and gene fragments affiliated with ‘Aigarchaeota’, including those recovered from terrestrial geothermal systems on several continents and marine geothermal and subsurface samples. ‘Aigarchaeota’ belonged to at least three family- to order-level groups and at least 13 genus-level groups which are represented in the resulting phylogenetic tree. All genus-level groups were recovered from geographically distant locations, suggesting a global distribution. The primers will be used to determine the presence and abundance of ‘Aigarchaeota’ in a wide variety of samples from terrestrial geothermal systems in the U.S. and Asia using quantitative real-time PCR.

Age-related cardiac pathologies are currently endemic in most developed nations and account for a large number of premature deaths and huge medical expenditures. Although lifestyle-associated risk factors have frequently been correlated with risk of cardiac impairment, it is also clear that aging impairs heart function even in the absence of these risk factors. Caloric restriction (CR) is known to extend lifespan and offset age-related impairment in diastolic function in murine models. Rapamycin is a CR mimetic that also extends lifespan (when given throughout life) and is protective in models of cardiac hypertrophy and failure. However, the potential role of Rapamycin for treatment of impaired heart function in aging has not been established. To determine the effect of short-term Rapamycin treatment on cardiac aging, we monitored cardiac function in 25 months old C57BL6/CR mice fed for 10 weeks with a control diet or a diet containing 14ppm encapsulated Rapamycin. Analysis by tissue dropper imaging showed improvement in diastolic function in the treatment group as early as 4 weeks. Normalized heart weights were also lower in the treatment group compared to old control mice, suggesting that short-term sub-acute Rapamycin treatment can reverse cardiac aging and regress age-related cardiac hypertrophy. Proteomic analysis showed increased stability (half-life) of the cardiac global proteome, increased abundance of mitochondrial proteins, and decreased oxidative damage of proteins in the treatment group. Further analysis revealed metabolic remodeling in the glycolytic and TCA pathways that improve energy metabolism and cardiac function in 10 weeks Rapamycin treated mice. Data from murine models offer potent approaches that may be replicable in humans and may prove effective in management of cardiac and perhaps other age-related ailments. In this project, we both assist in preparing the control and treatment diets, mice handling, imaging preparation, tissues harvesting, data analysis, and experimental design for future experiments.

This study examines the effects of administering hydrogen sulfide (H2S) to ancient plant species to examine the organisms’ response to the stress. While sulfur is an essential macronutrient required by several organisms for growth and productivity, there are many toxic variants of the element that have detrimental effects and produce physiological stress. It is speculated that the accumulation of H2S, a lethal gas, may have existed as a major contributing factor in past mass extinction events, where the environment was fairly anoxic with fluctuating temperatures. The potential of this toxic variant to exist as an environmental stressor suggests that certain organisms may have adapted to survive these periods of mass extinctions. It is hypothesized that due to the abundant presence of hydrogen sulfide in the past, ancient land plants may have an adaptive advantage that allowed them to survive and thrive. In the study, species of bryophytes, specifically Hypnum and Dicranum are exposed to specific concentrations of aqueous H2S over a 7 day period and measured for their photosynthetic capacity at timed intervals using a FluorCam. Studying the effects of this toxic gas on ancient plants is imperative to our understanding of sulfur’s varying biological roles, and provides insight on the evolutionary phenotypic variations amongst plants and stress responses in order to survive mass extinctions. Current results indicate that bryophytes are able to tolerate significant quantities of the toxic substance and show resilience through increased photosynthetic capacity over a period of exposure, indicating a genetic and phenotypic legacy response. The results also imply that H2S may have the potential to act as a plant regulator due to its diffusive properties and influence in minute quantities.

Solar power is an increasingly significant resource as we look to move from fossil fuels to a cheap and sustainable source of energy. Solar cells can be manufactured using organic semiconductors by using cheap roll-to-roll printing techniques, however, the efficiency of such organic photovoltaic (OPV) devices is currently too low for cost-effective implementation. These devices utilize a built-in electric field, resulting from the difference in potential energy between the device’s electrodes, to collect photogenerated charges at the electrodes as current. Fine-tuning of the electrode energy levels also dictates the amount of voltage that can be generated by the device. As a result, the ability to chemically alter the electrode energy levels can greatly influence the overall power output of the solar cell. Phosphonic acid self-assembled monolayers (SAMs) are molecules that can be chemically attached to a variety of electrode interfaces and have been shown to alter the energy levels of certain electrodes. I am investigating the effect that attaching SAMs to the zinc oxide surface of an OPV electrode will have on both the built-in voltage and power conversion efficiency of an OPV cell. In order to test the hypothesis that the SAMs can affect OPV performance, I have fabricated solar cells with SAMs in order to compare them with solar cells without SAMs. Experiments that measure the built-in voltage of the device and investigate the lifetime of photogenerated charges will help to clarify the specific role that the SAMs play in affecting OPV device performance. If this hypothesis is correct, we have the potential to achieve higher power conversion efficiency than what is currently reported in these devices and this may lead to a greater emphasis towards understanding the role of interfaces in developing sustainable solar technology.

Cochlear implants are electronic devices surgically implanted into the inner ear to restore hearing in those with severe or profound hearing loss. A signal processing strategy in the device’s computer interprets the input sound and sends information to the nerves of the inner ear. Mandarin Chinese, spoken by 900 million people, is a tonal language that consists of four tones, each conveying different meaning. Unfortunately, cochlear implant users who speak Mandarin have difficulty perceiving tonal changes in speech with current signal processing strategies. Improving tone perception in Mandarin-speaking cochlear implant users is an ongoing topic of signal processing research. However, if English speakers’ Mandarin tone identification can be used to evaluate signal processing strategies, a pilot study could begin with English-speaking cochlear implant users, who are easier to recruit in the US. The purpose of this study is to test the validity of using native English speakers to evaluate Mandarin tone perception with novel processing strategies. Using a Mandarin tone perception test, we evaluated the ability of English-speaking subjects to categorize spoken tones into the four Mandarin tones – rising, falling, flat, or falling then rising. Ten normal-hearing English speakers were able to correctly identify tones, on average, 88% of the time and three subjects with cochlear implants achieved 61% correct identification on average. Two processing strategies were evaluated on the normal hearing listeners using acoustic simulations of cochlear implant signal processing: CIS, a common clinically-used program, and HSSE, a novel program developed at UW. HSSE was shown to significantly improve perception of tones in normal hearing subjects (p<0.001). These results suggest the possibility of evaluating novel sound processing strategies for tonal languages using English-speaking cochlear implant listeners as test subjects.

 The development of new medications is critical for treating disease and extending life. Approximately 40-60% of drugs target a specific type of membrane protein termed G-Protein Coupled Receptors (GPCRs), which permit cells to communicate with each other (by binding neurotransmitters) and regulate body physiology. The Hague lab studies the molecular mechanism of drugs targeting these receptors. Specifically, they examine a small, yet important structural portion of the receptor - the PDZ binding motif - which acts a protein-protein interaction site. Interestingly, of the ~800 different GPCRs in the body, 30 have this PDZ binding motif, including those activated by the neurotransmitter 5-hydroxytryptamine (5-HT), which is commonly known as serotonin. Serotonin regulates many key CNS processes including mood, sleep, and appetite. Current 5-HT medications that are on the market are used to treat depression, generalized anxiety disorder, and social phobia. Two common antidepressants that affect serotonin GPCRs are Selective Serotonin Reuptake Inhibitors, or SSRIs, and Monoamine Oxidase Inhibitors, or MAOIs. My goal was to examine the necessity of the PDZ binding motif for 5-HT serotonin receptor function in human cells. To do this, HEK293 cells expressing the wild-type 5HT receptor (WT) or mutated 5-HT receptor missing the PDZ binding motif (ΔPDZ) were subjected to diagnostic assays including: microscopy, protein biochemical analysis, proteomics, and cellular signaling. In summary, the data suggest the PDZ-binding motif is not essential for 5-HT serotonin receptor function in HEK293 cells, although further experiments are necessary to solidify this conclusion.

Imidacloprid (IMI) may be a viable alternative to carbaryl for controlling burrowing shrimp (Neotropea californiensis) that destabilize sediments resulting in poor survival and low yields of the commercially harvested Pacific oyster (Crassostrea gigas). Previous laboratory tests indicate the shrimp are overtly affected (immobile, cannot burrow) when exposed to IMI in sediment pore water, but are not killed. These results contrast sharply with observed efficacy in the field, i.e. mortality 72-96 h post application and subsequent reductions in burrow counts. Understanding the factors governing efficacy in the field may improve control. We exposed 11 adult female shrimp that had burrowed within 30 cm of native sandy sediment to each of four concentrations of IMI (Nuprid® 2F) for 96 h: 6, 30, and 150 ppb active ingredient. We compared the response of these shrimp to that of 10 negative controls. Surface water (10 cm) was exchanged with clean seawater (salinity=30 ppt) 6 h post dose and then twice daily simulating tidal exchanges. Behavior and water quality were monitored once daily. All shrimp in the IMI exposures were overtly affected and mortality was dose dependent: 0 ppb (0%), 6 ppb (9%), 30 ppb (27%) and 150 ppb (82%). The LC50 was 51 ppb (95% CI=24-146 ppb). Mortality at 150 ppb occurred 30-54 h post dose; mortality at lower concentrations occurred between 54-78 h. Shrimp that survived the highest doses were closest to the surface when immobilized where dissolved oxygen (DO, % saturation) was greatest. Immobilized shrimp were unable to maintain their burrows, the burrows subsequently collapsed, separating them from the DO within the surface water, resulting in asphyxiation. Results suggest the shrimp can tolerate very low dissolved oxygen within sediment without IMI, but their sensitivity to IMI increases due to factors associated with their impaired ability to maintain burrow integrity and circulate water.

Language models characterize the probability of a sequence of words for use in a variety of natural language processing applications, including automatic speech recognition. Web text is a key source of data for developing the language models used in such systems because of its sheer volume, and the fact that much of it is freely available to the public. However, web text varies broadly in genre, depending on purpose, audience, formality, and other characteristics. For example, the difference between the formal exposition of a Wikipedia article and the informal banter between two Twitter users. When using web text to train language models for conversational speech recognition in particular, it is important to find text that resembles that speaking style. When training a language model using various web text sources, we use a measure of worth called perplexity. By selecting web text that matches the conversational style of speech, the language model perplexity improves, which generally leads to higher accuracy speech recognition. I work on selecting text taken from Twitter. This involves research on what kinds of Twitter searches will result in tweets containing useful text, as well as how to identify Twitter users who post useful text.

Diverse lines of evidence indicate that humans have come to dominate many environmental and climate systems across the globe, prompting some researchers to declare the present part of a new geologic age known as the “Anthropocene.” Since plants form the base of many biological ecosystems (including those to which people belong) and agriculture alone covers approximately forty percent of land surface, studying how humans appropriate Earth’s plant production allows us to explore one of the most significant ways people have come to dominate Earth systems. Previous work has mapped the global distribution of plant growth supporting humans but failed to fully link this production to specific populations. To understand these connections, we begin by tracing global agricultural and forest production through a simplified representation of the global economy (containing about sixty million economic flows). To do this, we use global economic data collected by the Global Trade Analysis Project, enabling us to connect fields and forests with the often distant human populations whose lives they eventually support. Our model accounts for indirect plant consumption (for example, factory products require plant consumption by laborers) as well as plant materials people consume directly. Mapping these results and transforming them through Geographic Information Systems (software which can visually and computationally manipulate the results in diverse ways) allows us to describe major intersecting processes of globalization linking distant peoples and lands. For us to respond effectively to the increased human domination of Earth systems, improving our understanding of these socioecological relationships will be critical.

Mutualistic Relationships are critical for the stability of ecosystems but their mechanisms are poorly understood. Local adaptation is an indication of how specialized the organisms are to their mutualistic partner. Most experiments that study locally adapted species focus on host-parasite and trophic interactions, however, we focus on two species, Desulfovibrio vulgaris and Methanococcus maripaludis, existing in a mutualistic relationship. We used 6 independently evolved populations. The individual species in the co-evolved populations were separated and paired with a partner from a different evolved population to see if they grew faster with the partner they evolved with. We tested for local adaptation by frequently measuring the optical density of the cocultures. The OD measurements were used to calculate growth curves. The growth curves were compared to determine if the co-cultures were locally adapted. Our results indicated that neither species was locally adapted.

Cochlear implants (CI) are neural prostheses that provide individuals with profound hearing loss the ability to hear through artificial electrical stimulation to the inner ear. Despite the relative success of cochlear implants in providing speech in quiet settings, listening to complex signals such as music or speech in background noise is still difficult. Spectral resolution, the ability to extract frequency information from a signal, is important for interpreting complex signals, and this ability is impaired in CI users. In this study we compared two measures of spectral resolution: a pitch discrimination task and vowel identification. An individual’s ability to identify vowels depends on how well they can distinguish characteristic concentrations of energy at specific frequencies. Pitch discrimination is the ability to perceive small directional changes of sound frequencies between two pitches, and like vowel identification, relies heavily on one’s ability to discern frequency information. In this study we tested the pitch discrimination ability of CI users through the Clinical Assessment of Music Perception (CAMP) test (Kang et al., 2009), where participants were presented two tones 1-12 semitones apart and asked to identify the higher of the two. We then compared performance on the pitch perception test to the CI users’ scores on a vowel identification test, which included a closed set of ten vowel stimuli presented by a male or female speaker. Since spectral resolution is integral to both tasks, we expect to find that CI users with low scores on vowel identification also perform poorly on the pitch discrimination task. By understanding pitch and vowel perception we might inform the development of new signal processing that can optimize the transmission of music to cochlear implant listeners.

Tuberculosis is the second-leading cause of death due to a single pathogen, Mycobacterium tuberculosis (Mtb), with an estimated two billion people currently infected. Drug-resistant strains have emerged that are unmanageable even with combination drug therapies. Therefore, the development of novel drugs aimed at previously untargeted biochemical pathways in Mtb is of utmost importance. Among potential candidates is a newly identified proteasomal degradation pathway termed pupylation. In this system, proteins in Mtb damaged by the reactive oxygen and nitrogen species of the host’s immune response are tagged with the small prokaryotic ubiquitin-like protein (Pup) and shuttled to the 20S proteasome for degradation. Pup-mediated degradation allows Mtb to recycle key cellular components and remain virulent. Our interest is to study the two key enzymes required for pupylation: the proteasome accessory factor A (PafA) and the deamidase of Pup (Dop), which is also involved in the reverse pathway known as depupylation where Pup is removed from the substrate. Our interest is to characterize the mechanisms and substrate scopes of both Dop and PafA to facilitate the design of novel inhibitors. We synthesized and employed a model fluorescent probe that mimics the site of pupylation on a target protein to study the rates of the pupylation and depupylation enzymatic reactions. Since the Pup-probe conjugate is a substrate for Dop we also studied depupylation. We anticipated Dop to be the faster enzyme since it had fewer substrates to bind than PafA and our studies have revealed that Dop is much faster. Though the purpose of depupylation is currently unclear, our investigation has determined the relative kinetics of these opposing enzymatic pathways. The quicker kinetics of depupylation indicates pupylation of proteins also serves as a post-translational regulator rather than existing exclusively for degradative purposes.

Developed in the mid-1990s, the Implicit Association Test (IAT) has been used in psychological experiments to measure the strength of a person’s automatic associations between concepts and attributes. IAT measures are shown to predict people’s behavior more accurately than do parallel self-report measures in socially sensitive domains such as race and age attitudes. The Brief IAT (BIAT) uses a similar procedure to the standard IAT, but with simplified instructions and different task structures. Unlike the standard version, the BIAT instructs subjects to respond in each trial with a “focal” key to only two of four categories (focal categories) that they are told to focus on and with a “nonfocal” key to the other two categories (nonfocal categories). The present research examines whether the BIAT has the ability to identify whether categories are associated with positive or negative valence (positive or negative attributes of a person, object, or event). It also seeks to compare the BIAT’s association strengths with those obtained from the standard IAT. One hundred voluntary undergraduate students from the University of Washington completed two BIATs that differed only in the identity of one of their categories. The same subjects were also administered two parallel standard IATs with the same categories. D scores, an effect-size measure, were calculated using data from the BIATs and standard IATs to estimate the strengths of association between pairs of categories. Through their task structures, the BIATs are expected to identify more precisely than the standard IATs can the valence association of each category. Each BIAT’s association strengths are also expected to approximate those obtained from the corresponding standard IAT. The significance of this research lies in its potential to support the development of more valid and useful IAT methods for determining a person’s unconscious attitudes toward individual objects and concepts.

Disfluent speech has typically been regarded as noise in spoken language processing: aspects of speech that should be ignored in order to automatically detect and understand the intended meaning of spoken language. However, it has also been suggested that disfluencies provide information about a speaker's cognitive processes and efforts to manage the discussion. Most work on disfluencies has investigated very controlled scenarios or conversational speech. In our work, we are studying high-stakes debates, including Supreme Court oral arguments and congressional hearings on the financial crisis, in addition to informal conversations among strangers and family members. By studying disfluent speech in both high and low stress situations, we can better understand the impact of stress on disfluency rates. We use text alignment techniques to understand the relationship between the perceived mistakes and correction. We subdivide and partition disfluencies into categories by classifying inserted, deleted, and substituted words according to their semantic similarity; thus, making correlations between social context and disfluency rate more evident in addition to providing a better interpretation of speaker opinions. Preliminary results show that lawyers have a tendency to model their speech patterns off of the justices they are speaking to, but not vice versa. That is, lawyers tend to be more disfluent when the justices are speaking disfluently, which indicates that disfluent speech reflects social context. Thus, we hope to develop ways to automatically detect and understand deeper meaning in spoken language, such as defensiveness and strength of opinions, through our study of disfluent speech.

Children’s oral narratives can give clinical insight into their language abilities. Often, clinicians use narrative performance as a screening tool for diagnosis of language impairment. Hoffman (2009) found that finding a proportion of utterances that contain semantic or syntactic errors ([RESTRICTED] utterances) is an efficient and effective tool for differentiating between narratives produced by children with typical development and those with specific language impairment (SLI). Using a group of 48 age-matched pairs of 8-10 year old children, Hoffman (2009) found that this tool differentiated between the groups. Post-hoc analysis found that this tool accurately identified those with SLI when using a diagnostic criterion of 14% and higher proportion of [RESTRICTED] utterances, correctly classifying 85% of her sample. Confirmation of these findings is necessary if this tool is to be developed for clinical use. This investigation attempts to replicate Hoffman’s 2009 findings with an existing set of narratives elicited using similar methods. Narratives from 16 age-matched pairs of 8-9 year old children, half with known language impairment identified by an interdisciplinary team assessment, half from children with typical development, will be segmented and coded using methods described in Hoffman 2009. The two independent coders will be blind to diagnosis, age and gender. Proportion of [RESTRICTED] utterances will be calculated for each transcript. We hypothesize that the groups will differ in the proportion of [RESTRICTED] utterances and that Hoffman’s 2009 diagnostic criterion will accurately identify children with and without language impairment. We anticipate reliable results that are similar to Hoffman’s (2009), within a reasonable margin, given the small group size. Replication would indicate that this method has the potential to be an efficient and effective clinical screening tool that warrants further development. Future research would need to confirm generalizability with larger, randomized groups

Barth Syndrome is a rare X-linked genetic disorder that can cause cardiac myopathy, muscle weakness, fatigue, immune dysfunction, and childhood mortality. Like many such diseases, Barth Syndrome is the product of a mutation encoding for a single protein, Tafazzin, a phospholipid-lysophospholipidtransacylase found primarily in cardiac and skeletal muscle, where it plays an integral role in modifying cardiolipin, a component of the mitochondria, or energy production organelles of the body. When Tafazzin, and consequently the modified form of cardiolipin are absent, the function of the mitochondrialelectron transport chain, the primary pathway by which the body converts food into useable energy, is reduced. We hope to rescue defective cardiolipin modification through Tafazzin protein therapy and learn more about tafazzin structure and function. To this end we used X-Ray Crystallography to obtain a three-dimensional electron density map corresponding to the diffraction pattern of the protein, based on the distance and angle between each atom. The determination of structural properties illuminated binding sites and chemical interactions in both functional and mutant Tafazzin. This was supplemented by the synthesis of enzymatically active and stable human and mouse Tafazzin using E. coli (BL21(DE3)pLysS). Overexpression of Tafazzin results in relatively pure inclusion bodies which we we isolated through protein metal affinity chromatography. We produced several protein coding variants of Tafazzin in order to study the enzymatic activity of different mutants. Understanding of structure-activity relationships in Tafazzin will direct future work in Barth Syndrome treatment by facilitating  in vivo studies of Tafazzin protein delivery.

Proton-coupled electron transfer (PCET) occurs in a variety of oxidation/reduction reactions. This thermodynamically-coupled transfer of an electron (e–) and a proton (H⁺) is important for many reactions, including catalysis and energy generation, and may occur through different mechanisms. Zinc oxide (ZnO) nanoparticles are useful for studying factors that influence the rates of PCET reactions in at metal-oxide surfaces. The ZnO nanoparticles used in this research have been well characterized and, as a colloidal solution, can be treated as molecule-like reactants in experiments. The ZnO nanoparticles described in these experiments are capped with dodecylamine (DDA), and then dispersed into air-free toluene, an aprotic solvent. The use of an aprotic solvent is important to ensure that the e–/H⁺ are transferred from the nanoparticle. When these nanoparticle solutions are irradiated with above-bandgap radiation, an electron is excited into the conduction band. This leaves a hole in the valence band that, from previously demonstrated research, is immediately quenched by EtOH left over from synthesis; EtOH provides both an electron and a proton, keeping the nanoparticle neutral. When the reduced and protonated ZnO nanoparticles are reacted with 2,4,6-tri-tert-butylphenoxyl (^tBu₃ArO·), an electron and a proton are transferred from the reduced ZnO nanoparticle to the ^tBu₃ArO·, yielding the corresponding phenol, ^tBu₃ArOH. The kinetics of this reaction are monitored using laser flash photolysis. The rates of PCET are affected by the reduction potentials and the pKa of the reactants. The reduction potentials of the nanoparticles may be tuned by changing the particle size. Initial results also show the concentration of the capping group affects the rate of PCET. We are investigating how these factors, reduction potential and capping group concentration, influence the rate of PCET from reduced and protonated ZnO nanoparticles.

Proteins perform a vast array of functions within all living organisms. These functions are heavily dependent on the protein’s 3-D structure. Cellular stress can result in the loss of protein structure and can lead to a wide variety of problems, one being the formation of insoluble protein aggregates. Aggregates can inhibit proper protein function, disrupt cellular homeostasis, and are implicated in many diseases. There exists a family of proteins, known as the Small Heat Shock Proteins (sHSPs), which are thought to combat aggregate formation. They interact with misfolded and aggregate-prone proteins (clients) to delay the formation of insoluble aggregates. How sHSPs delay aggregation is not well understood. I seek to characterize interactions between sHSPs and their clients. A binding interaction between the sHSP αB crystallin and the model client Δ131Δ (a mutant of staphylococcal nuclease) has previously been characterized by NMR. My goal is to confirm this interaction and look for additional interactions between these two proteins through chemical cross-linking. Chemical cross-linking is a process that links two proteins that interact. One can use this method to detect which surfaces of proteins are involved in a protein-protein interaction. The chemical cross-linker I am using is incorporated as an unnatural amino acid (p-benzoyl-L-phenylalanine, or BpA) into the sHSP αB crystallin. Upon exposure to UV light, BpA can covalently cross-link to another protein if it comes into close contact with it. This approach can allow us to explore how sHSPs interact with the client Δ131Δ. By gaining an understanding of this specific sHSP-client interaction, I hope to provide insight into general mechanisms of how sHSPs interact with clients, a process that plays a critical role in cellular health.

Older adults who participate in regular physical activity have better emotional health, as well as reduced mortality and morbidity, compared to older adults who do not participate. Mall walking programs are an existing form of low-cost physical activity for older adults that provide level walking surfaces, security, and other amenities like benches and restrooms. Although some mall walking programs have existed for decades, there is scant evidence supporting this easily accessible form of regular physical activity for older adults. The purpose of this study is to identify and describe actual and perceived costs of existing programs in mall and non-mall locations, such as arenas. As part of a larger study, structured interviews have taken place at ten mall and five non-mall locations in five different states. Mall managers, mall walker program leaders, and program participants have been interviewed over a six-week period. All interviews have been transcribed and coded for anonymity. Cost-related themes from the transcripts have been extracted and added to those identified from an already completed literature review. The data set is being analyzed using the Strauss and Corbin model of grounded theory to identify themes and categories with the intent of developing cost-structure models that reflect successful programs. Themes identified include shared program costs between the site and a hospital, regular blood-pressure testing, and retail stores offering discounted coffee for participants. By identifying best fiscal practices and cost-related variations that encourage the diversity of participants, future efforts may be directed at developing a cost calculator to help programs identify and track their costs. This component may help in establishing low or neutral-cost programs and therefore increase the accessibility of physical exercise to a wider range of older adults. 

The development of simple and affordable diagnostics is critical to the diagnosis, monitoring, and management of disease. Nucleic acid amplification has become the gold standard for many diagnostic applications due to its high sensitivity, specificity, and low limit of detection. Fluorescent dyes typically detect the success of amplification, but require expensive optical equipment including lasers and filters. A cheap and visually distinctive method for detecting nucleic acid amplification will simplify and lower the cost of molecular diagnostics. This research project aims to develop a simple colorimetric reaction for detection of loop-mediated isothermal amplification (LAMP) reactions. LAMP produces large amounts of pyrophosphate by-product during amplification. Pyrophosphate complexes many metals and can displace dyes bound to metals in solution to create color changes. Our goal is to identify a set of chemicals consisting of colored dye and metal ions that will present an unambiguous color change denoting success (or lack thereof) of amplification. Using knowledge of metal-ligand formation constants, we have determined a group of metal-dye complexes that may be viable candidates for detection and are currently testing them in the laboratory. One example is indigo carmine dye. In the presence of pyrophosphate, the dye stays blue (a positive test), while the lack of pyrophosphate will turn the dye clear (a negative test). We are in the process of fully understanding the chemistry of this reaction and further optimizing the process to improve its viability. Exploration of other metal-dye complexes, as well as continuing investigation of the literature, will be conducted to improve the present results. This colorimetric reaction has the potential to simplify and lower the cost of DNA detection.

Acute viral respiratory infections are responsible for much of the infectious disease in the world. Of the known respiratory viruses, influenza is probably the most dangerous. In addition to the relative lack of knowledge on how influenza produces systemic symptoms, little is known about how it affects the central nervous system (CNS) and subsequent recovery outcomes. Following an acute viral infection, the body undergoes a state of acute stress response (APR). APR is a complex array of physiological responses that leads to changes in behavior and body temperature, anorexia, immobility, sleepiness, and malaise. Anecdotal and personal experience suggests that sleep becomes more prolonged while one is battling influenza infection. Following an infection, cytokines and other inflammatory regulators affect sleep and body temperature caused by influenza. Cytokines are signaling molecules that are generally involved in the immune response following trauma or infection. IL1β, a focus of this study, is a particular cytokine that has been extensively studied for its involvement in physiological sleep regulation in normal healthy organisms and in those subjected to an immune challenge. IL1β alters the sleep profile post-infection by enhancing non-eye rapid movement sleep (NREMS). Such increase in NREM sleep has been demonstrated to increase the probability of survival due to microbial challenge in rabbits. I will focus on the involvement of IL1β and its receptor (ILR1) in influenza-induced NREMS APR responses. A transgenic mouse strain that selectively expresses IL1β receptors on neuronal cells in the brain will be used for this study. I hypothesize that ILR1 on neuronal cells in the brain is necessary for the virus-induced APR following an infection. Whether more sleep (specifically NREMS) promotes, as enhanced by IL1β, and less sleep impairs, recovery from infection remains to be determined.

Substance use in adolescence is a serious societal problem that results in a variety of severe negative consequences for youth. There is a growing body of research that examines substance use, consequences, and psychological dysregulation, but little that examines all three variables together. In order to understand reasons for why adolescent substance users continue to use despite negative consequences, the current study examined the relationship between substance use, consequences, and psychological dysregulation, with psychological dysregulation as a potential mediator between substance use and consequences. The participants were 123 adolescent substance users. Participants completed assessments to measure criteria such as substance-use quantity, substance-use related consequences, and psychological dysregulation, which was further broken down into affective dysregulation, behavioral dysregulation, and cognitive dysregulation. Alcohol-quantity at intake was found to be a significant predictor of consequences, with psychological dysregulation as a significant mediator in the relationship. Marijuana-quantity at intake was not found to be a significant predictor of consequences, but when psychological dysregulation was added as a second predictor variable, it was found to significantly predict consequences. Additionally, alcohol-quantity at intake was significantly correlated with behavioral dysregulation through the aspects of impulsivity, inattention, hyperactivity, and aggression; affective dysregulation through the aspects of emotional reactivity and irritability; and cognitive dyregulation through the aspect of cognitive flexibility. These findings suggest that psychological dysregulation influences how substance users perceive their consequences, and that substance users are more likely to experience psychological dysregulation as a result of use. The results of this study indicate that psychological dysregulation plays an important role in why substance users continue to use despite consequences, and reveals one potential mechanism through which substance users interpret their consequences. Through further investigation, these findings have important societal implications and provide a basis to alter the methodology and theory behind the treatment of substance use disorders.

Climate change is a crucial factor that affects plant physiology, population dynamics and geographic ranges. Little is known about the effects of changing climate on conifer morphology, whether their key morphological structures have the ability to change in response to environmental differences and what the impact of these changes mean for future ecological population dynamics. Are morphological and physiological traits locally adapted within a species or do they acclimatize to specific environmental conditions? Two studies were conducted to test 1) whether morphological structures of conifers differ between source populations when transplanted across an elevation gradient and 2) whether photosynthetic levels under a light treatment differ between source populations. Tsuga mertensiana seedlings from three study sites, varying from high to low elevation on Mt. Rainier, were each transplanted across and beyond the species' elevation range. For the first study, measurements of shoot to root ratio, specific leaf area (SLA) (m²/g) and leaf mass vs. stem mass were calculated. We expect our results to show that as elevation increases, SLA and shoot to root ratio decrease, however overall values are smaller for trees at higher elevation. This indicates that within a single species, trees from distinctive ecotypes are inherently different morphologically, even though all seedlings have the ability to acclimate to changes in elevation. The second study manipulates light as a single variable and addresses whether the driving force of morphological and physiological characteristics are due to light levels at different elevations or whether T. mertensiana seedlings at different ecotypes are genetically different physiologically.

Marine debris is a prevalent form of environmental pollution in which man-made products are released into oceans and waterways. Debris objects pose a variety of concerns, including entanglement and ingestion by wildlife, toxicity, and introduction of invasive species (biofouling). The Coastal Observation and Seabird Survey Team (COASST), a citizen science program at UW, is currently developing a marine debris monitoring protocol. The protocol calls for field surveys documenting basic site characteristics and attributes of debris objects. Seventeen attributes were chosen as indicators of potential harm to wildlife (e.g. loop presence and bite marks), invasive species threat (biofouling), and debris movement patterns in the ocean (e.g. size, material). Our team analyzed images from a database of over 5,000 marine debris photos collected by COASST at over 200 beach sites in the Pacific Northwest and Alaska. We utilized an iterative approach with two students independently assigning attribute states (e.g. color: black, bite marks: yes) to debris objects from 900 randomly selected photos. We compared results to understand likely sources of human error. Initially, we found that color, malleability, geometric shape, material, intactness, and weathering were attributes that posed the greatest challenges – where surveyor disagreement (error rates) exceeded 15%, with some approaching 50%. After three rounds of result analysis and attribute definition refinement only 5 of the 17 attributes had error rates exceeding 15% (range 16-30%), reducing the likely error volunteers will make. The resultant standardized attribute definitions and state assignment protocol will provide a means of collecting reliable (i.e. low error) baseline abundance and distribution marine debris data as well as risk assessment based on specific attributes of use for further research, conservation endeavors, and resource management.

 Breast cancer is the most common type of cancer in women, and 40,996 women died of cancer in 2010. I am working with Dr. Keryn Reding from the School of Nursing on examining estrogen DNA adducts (EDA) for their clinical utility as a biomarker for breast cancer. EDA is formed when estrone or estrodial are oxidized to form quinones. These compounds then attach to DNA, causing mutations that lead to cancerous cell growth. The EDA are then excised and released into the blood stream and excreted through urine. I will analyze urine samples in a triple quadrupole mass spectrometer in order to see if the ratio of EDA to parent estrogens is higher in women with breast cancer than women who did not develop breast cancer. My analysis will investigate the inter-variability of EDA in premenopausal and postmenopausal women to see if this biomarker can be accurate and reliable for women of all ages. We expect results to show that premenopausal women will have less EDA due to their younger age and lower risk of developing breast cancer. By May when I present at the URP, I will have results from the mass spectrometer and I will use the McNemar's test for statistical significance. We are investigating a hypothesis that a high EDA ratio will be associated with breast cancer risk, and thus the EDA ratio may have clinical applications for breast cancer prevention and screening. Because it is a non-invasive method of measuring the risk of developing breast cancer, it could be an ideal complement to current screening approaches, such as mammograms or biopsies.

Biomarkers capable of diagnosing and tracking the progression of Parkinson’s disease (PD) are urgently needed. Saliva has been explored as an alternative to a more traditional sample source such as cerebral spinal fluid (CSF), which involves painful and invasive collection processes, and blood. Indeed, PD patients typically have dysfunction of salivary production, indicating that the disease involves this organ system. In order to increase sample availability, many protocols use cotton or plastic to stimulate saliva production. However, this raises the question of how these materials affect salivary protein composition, specifically in regards to proteins of interest as biomarkers. In order to explore these effects I incubated various materials potentially capable of stimulating increased saliva production in saliva samples and measured the concentration of alpha-synuclein (α-syn), a protein believed to be important in PD pathogenesis and a possible biomarker, and total protein. By comparing the concentrations of α-syn, total protein, and the α-syn:total protein ratio between the various material groups and control (no material) groups I am able to determine whether the materials increased, decreased, or had no effect on protein concentration. It was hypothesized that all tested materials would decrease both α-syn and total protein concentrations by some degree due to protein attraction to the materials. The results of this study contribute to a clearer basis for salivary biomarker studies involving induction techniques, facilitating collection techniques in a clinical setting, particularly in older patients with decreased saliva production.

The United States spends 16% of its GDP on Healthcare, but it still has the most, inefficient, and fragmented system of care in the world. This project strives to assess the current health care system’s shortcomings, and at the same time, show the effectiveness of the health care reform, which is the original version of Obama’s Affordable Care Act that Massachusetts (MA) enacted in 2006. By addressing the government’s core regulation, the “three legged stools” of reform in MA respectively, the three policies and their effectiveness will also be analyzed at both the state level and comparing the state and the nation as a whole, since the system of ACA resembles MA’s reform closely. By comparing various properties of MA to the U.S. as a whole, such as comparing population’s income distribution, proportion of people with different levels of education background, health care expenditure from various income individual or families, poverty rate, etc., we can see whether the national application of health care reform will be successful as it is in Massachusetts. The result is that the prediction of expanding the MA health care reform national wide may not lead to as impressive changes as MA’s due to vastly different variables. Also since it is now mandatory for people to be covered by health insurance, the government may put itself into a position of long-term deficit by paying premiums for the “poor”, which will end up with higher budget deficit. Though “three legged stools” effectively implemented at the state’s level, it conceals more potential risk and obstacles in the States with a much larger scale, and may end up with less effective result with much more diverse populations.

Macrophage have roles in promoting and resolving inflammatory responses in the lung, and they do this in part by their ability to polarize into M1 or M2 cells depending on environmental signals. Lipopolysaccharide (LPS), a microbial initiator of inflammation, activates macrophages to the M1 polarized state, which drives the inflammatory response. M2 cells, which can be induced by cytokines IL4 and IL13, are involved in promoting wound repair responses and are considered reparative cells. Macrophages maintain their plasticity, and in vivo, pulmonary macrophages switch from M1 to M2 states during pneumonia resolution. In this project, we sought to determine the functional consequences of this macrophage repolarization using an in vitro model. We hypothesized that repolarization of LPS-treated macrophages (M1 cells) to M2 cells would alter their responsiveness to further LPS challenge. We cultured bone-marrow derived macrophages from mice. We exposed the macrophages sequentially to LPS, IL4 and IL13 or media alone, and then rechallenged with LPS. We harvested cells for RNA for analysis of gene expression of M1 and M2 markers using qRT-PCR. We found that repolarization of macrophages toward M2 states potentiated the immunoparalysis seen in LPS-treated macrophages. These results suggest that M2 cells may dampen macrophage inflammatory gene expression to promote resolution of inflammation but may also contribute to increased susceptibility to recurrent infection.

Growing evidence indicates rapid and sensitive diagnostics for infectious disease can alleviate the healthcare burden. Laboratory diagnostics are quality-oriented and highly sensitive, but they require professional training, high cost, and extensive time. Most importantly, they are not accessible in low-resource settings. Recently, research has been focused on transforming laboratory diagnostic into a “lab-on-a-chip” format, which could allow on-site screening for infectious disease with micro-scaled sample volume. These microfluidic devices are typically portable and disposable but still require a pump-based instrument to control fluid movement and timing. In addition, challenges also remain on how to dry and rehydrate the reagents on the device. Here we propose a solution by replacing the pumps with wicking as the driving force, and adding programmed wicking to automate assay steps. We print nanopatterns on the channel celling and/or floor to locally modulate the capillary flow rate, and we will also utilize dry reagents to minimize the user steps. The microfluidic channel and nanopatterns are fabricated by low-cost PDMS molding. The outcome will be a quantitative understanding of the tunability of the flow rate modulated by nanopatterns, and this knowledge can be applied to achieve sequential delivery.

Three weeks into the Rwandan Genocide, the United States State Department Spokesman, Christine Shelley said that acts of genocide were occurring in Rwanda. When asked how many acts it takes to make it a genocide, she denied the question, saying that it was irrelevant. There is a plethora of synonyms for the term "genocide" and I seek to find to what extent this idea has evolved conceptually and why. The international community will not become involved in other country's affairs unless the crisis is defined as genocide, and so there is importance in understanding the concept. This research will allow a greater understanding of what “genocide” entails, and when the international community must take action. I expect there to be a correlation between the development of human rights theory and the emergence of a broad range of words to characterize genocide. This link will be sought through observance of instances of mass atrocities and how they were characterized at the time. The term “genocide” did not come into use until the 1940’s, but there were genocide-like events since before this. These atrocities were labelled differently at the time, and so I will look into these definitions and how it could possibly be renamed today. Definitions provided in major treaties and documents will be considered. I will apply the changing labels for different atrocities to the evolution of human rights theory by considering the major human rights ideas at the time. I anticipate that as multiple crises ensued, human rights theory developed from the ancient religious views through the conception of natural law to the modern expression of human rights. As this theory developed, new terms emerged, conceptualizing the different catastrophes. Ultimately, human rights abuses led to a shift in human rights theory, prompting it to create new vocabulary for genocide.

Soil moisture is a variable that is difficult to quantify due to its large spatial heterogeneity, its lack of extensive ground-based measurement networks, and its strong dependence on many meteorological and biological factors. However, records of soil moisture are essential for developing more accurate climate models and providing constraints on processes controlling plant productivity and heat fluxes. My research aims to further develop these records by determining whether maximum temperatures can be related to the amount of soil moisture in a particular region. Previous studies have shown that plant transpiration accounts for more than 80% of evapotranspiration, the sum of evaporation and plant transpiration from the Earth's land and ocean surface to the atmosphere. We hypothesize that the variability of maximum temperatures in vegetated regions is determined by the amount of soil water available there. By analyzing latent heat, temperature, and soil moisture data collected from various flux measurement towers around the United States, we found that days with relatively low latent heat flux values occurring at high maximum temperatures have statistically drier soils compared to days where high latent heat flux values occur at high maximum temperatures. This relationship seems consistent only when the site under analysis is located in a wet environment that is rarely water limited.

The world’s future energy needs will almost certainly require extensive use of renewable sources of energy. Organic photovoltaics are a particularly lucrative source of energy due to their cheap materials and ease of production compared to inorganic solar cells. However, organic photovoltaics (OPVs) currently suffer several drawbacks: they have an efficiency of, at most, around 10% and they are unstable – they may begin to degrade within five to seven years. This project aims to alleviate these defects by gaining a greater understanding of the chemical interaction between interfaces within the solar cell. This project is a comprehensive study of the interactions between phenyl-C₆₁-butyric acid methyl ester (PCBM) and calcium. PCBM is an extensively researched molecule which acts as an electron acceptor in OPV devices. PCBM is typically paired with an electron donor such as poly-(3-hexylthiophene) in a working device, and calcium has energetic properties which allow for very good electron transfer at the cathode of such a device. We use adsorption micro-calorimetry under ultra-high vacuum conditions to study the reaction at the interface between calcium and PCBM, and surface analytical techniques to determine growth modes and chemical binding of calcium and PCBM. These experiments will elucidate the mechanisms of interface formation of this understudied but important OPV system.

Proteins are functionally dependent on their 3-D structure. Many proteins share similar structural folds arising from either convergent evolution or a common ancestor. Understanding a protein’s folding pathway is a fundamental problem of biochemistry. The Daggett Lab created the Consensus Domain Dictionary to categorize common 3-D protein folds, termed fold families, based on various arrangements of secondary protein structure. Evidence suggests there may be common mechanisms in the folding and unfolding of members of a fold family. Here, we look for such characteristic mechanisms within 14 members of the Ubiquitin-like family, the 8th most commonly found protein fold. These proteins have a common core structure with sequence identities ranging from approximately 25% to 85%. Using Molecular Dynamics simulations to model the proteins denaturing at 498K, we compare transition states in the unfolding pathway, various atom-atom contact data, and the alpha-helical content amongst protein fold family members to analytically determine the existence of family-specific folding mechanisms. We anticipate that the early pathway will revolve around helix-turn-helix rotations or splays, sequential alpha-helical melting, and spatial separation of the four main beta sheets.

It is known that exercise improves cancer survival, however, there is an unknown molecular link between physical activity and cancer occurrence. The purpose of this study was to determine the feasibility of studying biologic mechanisms related to exercise and cancer survival in the LIVESTRONG YMCA program. Eligible subjects were males and females who were diagnosed with prostate or breast cancer in the last three years, between 35-80 years of age, willing to provide urine samples at four time points, and enrollment in the 12-week LIVESTRONG YMCA program. Through a partnership with the University of Washington (UW) Mass Spectrometry Center and the UW Office of Nursing Research, two specific biomarkers were analyzed from the urine specimens. One of these markers is Estrogen DNA Adduct (EDA), an estrogen metabolite that binds to DNA and creates an increased potential of DNA mutation and cancer development. The other is 8-OH-dG, a biomarker related to oxidation. To determine the feasibility, we administered questionnaires to better determine patient satisfaction and calculate the percentage of participation and retention. One questionnaire surveyed the acceptability of our biospecimen collection procedures to participants, anticipated acceptability of additional biospecimen collection (blood and tissue samples) for future projects, and willingness to have a DEXA scan (for compensation). In order to determine the feasibility of conducting the study on a larger scale, we evaluated the percentage of participants enrolled out of those recruited, percentage of participants who provided urine samples out of those enrolled, and the percentage of participants who completed the program. Continuing to invest in our therapeutic, diagnostic and genetic understanding of cancer means that in the future, patients will have options based on scientific evidence.

The Farnsworth-type IEC reactor was once considered to behave as a point source of neutrons with reference to the spherical central accelerating grid. This was assumed because the deuteron-deuteron fusion reaction is inherently spherically symmetric (isotropic), and current theory suggested that the vast majority of fusion events were occurring in the deepest region of the potential well (the accelerating grid, which is also the geometric center of the reactor). However, anecdotal evidence has suggested that isotropy may not be empirically accurate. Our main objective was to conclusively test the assumption by measuring deviations from uniformity in the neutron flux. To measure this we used three different types of detector: CR39 plastic, BTI bubble detectors and He-3 dosimeters. We exposed the CR39 slides to fast neutrons (2.45 MeV) at a fluence of 10^6 n/cm^2, and they indicated apparent anisotropy (p-value of .0035) with higher flux at the front and rear of the machine. The BTI bubble detectors and He-3 tubes also corroborated a higher neutron density at those sites. We then hypothesized that beam loading on the front and rear conflats by the plasma "jets" emanating from the central cathode could be responsible. Measurements with paired He-3 tubes after blocking the jets with quartz glass showed the apparent anisotropy reduced by 38% on average (p << .001). This quantitative confirmation of anisotropy, and the significant (but not sole) role that beam-target fusion plays therein, represents an important shift in the understanding of the Farnsworth-type reactor, which could have important implications in plasma physics and the development of fusion energy.

Internet resources provide an abundance of information about diabetes, mostly without any quality control. Providing resources to patients can be challenging for student and new graduate nurses due to the vast amount of potential websites. We were seeking new ways on how student and new graduate nurses can assess the value of patient websites focused on diabetes. The aims of this study were: 1) to identify the most frequently accessed diabetes websites by (N=142) undergraduate nursing students; 2) to evaluate the data based on quality criteria to see which websites provided the most complete information, and 3) to make website recommendations for patients with diabetes in regards to disease recognition, treatment, safety, and lifestyle choices. This secondary quantitative analysis was conducted with de-identified data from a class assignment at the UW School of Nursing. Websites were accessed a total of (N=399) times. Each website was evaluated for 12 categories with a quality score of 0-9 for each category. A score of 0-3 meant minimal, 4-6 moderate, and 7-9 meant complete information for that category. For each category we took the mean score of all individuals who evaluated that website to determine its strength. After identifying duplicates, a total of (N=53) websites were identified. Based on the highest quality scores, the top 10 websites were four governmental, four non-governmental and two commercial. Of these, the most complete website was diabetes.org with a mean rating of 89.3 out of a possible score of 108. The next two contenders were kidshealth.org and niddk.nih.gov with mean scores of 77.1 and 74.9 respectively. Educating nursing students and new graduates about the value of safety and quality of information on the web will enable them to better inform patients and families. More research is needed if this type of education makes a difference in patient outcomes.

Spontaneous neural activity (SA) during brain development has been implicated in processes ranging from regulation of gene expression to development of neural networks that ready organisms for post-natal life. Though SA is a well-known phenomenon, the mechanisms and developmental processes mediating its behavior are not well understood. This research aims to elucidate some of these processes. Preliminary findings have focused on defining dopamine’s (DA) and serotonin’s (5-HT) role in spontaneous activity in the developing mouse brainstem. It has been shown using transgenic mice expressing markers for proteins that interact with DA or 5-HT that SA propagates through regions containing these markers. I am now expanding this work by performing calcium imaging and confocal microscopy along with whole cell patch clamp in these transgenic mice to characterize SA in regions where the markers are highly concentrated. In addition, I have been working with a colleague from the Phillip’s lab, using voltammetry to try and record the extracellular release of DA. These experiments will establish whether 5-HT cells act as drivers for SA and if such activity can trigger DA release. The implications of this research are multifaceted. Primarily, it will expand on the anatomy and physiology of the developing dopaminergic and serotonergic pathways in the mouse brain. Second, its findings may shed light on pathogenesis of certain disorders involving these pathways by contributing to the understanding of how SA mediates their development.

Low resource clinicians face several challenges in diagnosing disease at the point of care. One of the way diseases can be diagnosed is by DNA amplification, but first amplifiable DNA must be released from the cell. Staphylococcus Epidermidis is a bacterium that is very difficult to lyse. I examined three methods of S. Epidermidis cell lysis that are feasible to use in low resource settings by measuring the amount of amplifiable DNA recovered from the lysed cells. The three methods used were: a Bead Beating machine, the Omnilyse, and a boiling water bath. A bead beater is a mechanical method of lysing cells requiring electricity. An Omnilyse is a battery operated portable machine with glass beads to lyse the cells. The boiling water bath used was a beaker on a hot plate. All of these methods have comparable cost per samples value, and can be operated with relatively simple training. I used three to five intervals of time during which the S. Epidermidis cells underwent the different lysis techniques: 30, 60, 90, 120, and 360 seconds. I found the Omnilyse outperformed the bead beater and hot bath. It was 31.23 percent more efficient at extracting amplifiable DNA, making it the best of the options tested for point of care diagnosis. Future expansion of experiments could include testing the lysis methods with different bacteria to determine if the efficiency of recovery of amplifiable DNA is comparable to S. Epidermidis' efficiency.

Effective security mechanisms are essential to the widespread deployment of pervasive systems (i.e. desktops, cell phones, etc.). Much of the research focus on security in pervasive computing has revolved around distributed trust management; managing the data obtained from interactions with external sources to computationally determine their reliability. While such mechanisms are effective in specific environments, there is no generic framework for deploying and extending these mechanisms over a variety of pervasive systems. We present the design and implementation of a novel framework called Distributed Trust Toolkit (DTT), for implementing and evaluating trust mechanisms in pervasive systems. The DTT facilitates the extension and adaptation of trust mechanisms by breaking down these mechanisms into interchangeable components, allowing users to select specific features of their mechanism that they would like to use for a particular system. Furthermore, the DTT provides a set of tools and interfaces to ease implementation of trust mechanisms and facilitate their execution on a variety of platforms and networks. In addition to the adaptability and extensibility provided by this design, we demonstrate through simulation that use of DTT improves utilization of resources and enhances performance of existing trust mechanisms in pervasive systems. We are currently developing an implementation of the DTT that can be easily deployed in pervasive environments, specifically for the Android platform.

The ubiquity of computing devices such as smartphones and wearable devices has given users access to technology at all times. However, user interactions with these devices are often cumbersome. Interacting with these computing devices is of increasing importance and minimizing their negative cognitive effects is critical to usage of these devices in order to allow users to focus on the task they are trying to accomplish, not the technologies they are using to accomplish them. I evaluated how people currently interact with computing devices such as the smartphone, wearable devices, and computers, and how these technologies try to solve computing inputs in order to minimize the negative cognitive effects of user interactions. I achieved this by identifying how users interact with computing devices and how those interactions translate to actions and outputs. I also used literature reviews to understand how people currently interact with computing devices and examined current research on cognitive impacts of human-device interactions. Analyzing how users of these existing devices interact with them informed interaction design decisions for the second part of my study. Using insights gained from this research, I designed and prototyped a wearable technology (WT) that extends the input capability of computing devices to simplify user interactions. The aim of the WT is to provide an easy and intuitive way to send instructions to a device. It uses Bluetooth to communicate with devices and transmit input and outputs between the user and their devices. Computing has become increasingly mobile. It serves as a way to augment life without the confines of space such as with the desktop computer. My research will help to elevate the mobility of computing and inform how we interact with computing devices as they become more ubiquitous.

In addition to having massive environmental and public health impacts, the livestock sector of the farming industry raises important ethical questions about the humane treatment of workers and animals. One response to the industrialized animal food system has been a push to eat ethically sourced meat from family farms. In theory, this allows the consumer to trace back their food to the source, interact with the people handling their food, and support a more humane treatment of animals. Eating locally sourced meat is a part of the larger “local food movement”, or campaign to eat foods from within 400 miles. However, there has been backlash against the local food movement, with critics arguing that the movement itself has its own set of problems. This study aimed to achieve two goals. First, I critically examined the local meat movement to determine whether or not I believed “local” food was a viable solution to the problems that exist within industrial agriculture. Second, I aimed to raise public awareness about family-farmed meat and the broader local food movement. To accomplish this task, I conducted interviews and reviewed the current literature about food issues. I interviewed chefs from local restaurants that serve family-farmed meat to gain a better understanding of their motivations. I also read primary literature, magazine articles, newspaper articles, and books related to the local food movement. I concluded that the local food movement, in addition to “local meat”, offers many benefits that industrial agriculture does not. However, as pointed out by many critics, the movement does not fully address the wide array of environmental, economic, and ethical concerns within the agriculture industry. To summarize my conclusions and raise awareness about the subject, I created a booklet about local food. The problems in the food industry will not be solved overnight and the first step is to generate an educated public that is willing to make necessary changes.

Computer face recognition and identification is an important problem with numerous applications in intelligent user interfaces, security, and accessibility. For example, identification of faces can be used for access to restricted areas, authentication without keyboards, and personalized interfaces. Traditional algorithms that solve this problem identify faces individually or use co-occurrence information for a given set of people (For example, person X is often photographed with person Y). However, such systems have many errors, and cannot generalize well to people the system has not seen together previously. In contrast, humans are much better at this because we have "common sense." We can look at a photograph and recognize that people tend to photograph with family, friends, and co-workers. We can further guess why the photograph (birthday, conference) was taken, and even where (person's house, a certain park). This abstract knowledge is very difficult for computer algorithms to learn because there are not sets of these "rules" available explicitly. In our work, we tackle this problem using structured relational graphs like Freebase, a large online graph of billions of facts about the world. Given many specific examples of people who are in photographs together and data about those photographs, we can see what connects these people on graphs like Freebase, and generalize to the "common sense" rules that are notoriously difficult to learn. Then, given a new image and possible candidates for identification of people in it, we can compute the most likely set of correct identifications. We can also hypothesize unknown faces to our existing faces. This allows us to learn, on-the-fly, a new recognizer for that specific person. Finally, by knowing relationships behind photograph subjects, we can discover and generate useful contextual information about the photograph, such as location and possible reason for the photograph. Broadly, this means that computer systems can more accurately identify meaning behind photographs; a problem that has been historically hard for computers to accomplish.

The mammalian cortex is composed of excitatory and inhibitory interneurons which regulate the firing of action potentials in the brain. Excitatory neurons increase the likelihood of an action potential in other cells while inhibitory neurons decrease this probability. Excitatory transmission develops first, resulting in electrical activity in the form of waves, which are important in the formation of neuronal circuit formation until the development of inhibition shuts down this spontaneous activity. While excitatory and inhibitory neurons are born in different locations in the brain, those that are born on the same day of development migrate and find each other in the same cortical layer. Excitatory neurons originate in the dorsal ventricles and migrate radially towards the plial surface. Inhibitory cells originate from the medial ganglionic eminence and migrate tangentially to the cortex where they then migrate radially to find their correct cortical layer. This project explores the idea that spontaneous electrical activity helps drive this organization. Tbr1 is a transcription factor shown to be important in neuronal layer finding. By using a Tbr1 KO (knockout) mouse, we show the disorganization of the neocortex compared to normal mice by quantifying the fraction of radially oriented interneurons versus non-radially oriented interneurons. Further, we examine the implication that waves and asynchronous electrical activity play a role in layer finding of excitatory and inhibitory neurons, as demonstrated by the differences in activity between Tbr1 knockout mice and controls.

Esophageal adenocarcinoma (EAC) is a type of cancer with the most rapidly increasing incidence rate in developed nations. EAC occurs as a result of the metaplasia-dysplasia-adenocarcinoma sequence initiated by Barrett’s esophagus. In this sequence of events, patients develop Barrett’s esophagus, wherein the acidic damage of gastroesophageal reflux disease (GERD) causes the esophageal epithelium to take on an intestinal epithelium phenotype. This metaplasia can then progress to Barrett’s esophagus with either low-grade or high-grade dysplasia. Patients that develop high-grade dysplasia (HGD) are at great risk for esophageal adenocarcinoma, and hence there is a need for higher specificity in the labeling of pre-cancerous tissues for endoscopic detection. Current imaging of dysplastic lesions is done through traditional endoscopy with the use of contrast agents for differential staining. However, current contrast agents have a low signal-to-noise ratio (SNR), and dysplastic lesions are often missed. Therefore, for early detection of esophageal adenocarcinoma, we are creating a contrast agent that increases SNR via fluorophore-labeled peptides that bind specifically to tissues with high-grade dysplasia. Peptides are ideal as targeting ligands as they can bind specifically to surface proteins on dysplastic cells and increase the likelihood of clinicians obtaining biopsies of pre-cancerous tissue. In the past year, we have isolated potential peptide sequences that bind immortalized cells lines generated from dysplastic tissues. A bacteriophage library was subjected to subtractive whole cell panning for isolation of phage expressing HGD-binding peptide sequences. The phages were added in vitro to cultured cell lines of normal esophageal tissue and non-dysplastic Barrett’s esophageal tissue to eliminate those that were not selective for dysplasia. After subtractive whole cell panning, left over phage were sequenced to determine the peptide sequences on them. Future work includes binding studies using flow cytometry to demonstrate that fluorophore-labeled peptides bind preferentially to dysplastic cell lines independent of the bacteriophage.

Protein homeostasis encompasses the creation, maintenance, and degradation of proteins, and it is essential for organisms to function properly. Yet, environmental stressors can disrupt protein homeostasis, which can lead to protein aggregation. Protein aggregation has been linked to serious aging diseases such as Huntington’s, Parkinson’s, and Alzheimer’s disease. In order to gain a better understanding of the pathways important for maintaining and disrupting protein homeostasis, we subject Caenorhabditis elegans to various environmental stressors that disrupt protein homeostasis. We have found that specific concentrations of hypoxia, or low oxygen conditions, induce an increased amount of protein aggregates in C. elegans compared to animals in room air, suggesting defects in protein homeostasis. In addition, the AMP-activated protein kinase (AMPK) seems to be crucial for allowing the formation of aggregates in hypoxia. AMPK mutants that are placed in hypoxia show a decrease in protein aggregation compared to wild-type animals. Furthermore, another environmental stressor, heat shock, also affects protein homeostasis. Heat shocking C. elegans prior to the hypoxic exposure, decreases the amount of aggregates compared to worms that did not experience heat shock. However, unlike hypoxia-induced protein aggregation, heat shock does not seem to require the presence of functional AMPK in order to influence protein aggregation.

The purpose of our research is to better understand older adults’ perceptions about fall detection devices. When an older adult experiences a fall, the results can be dramatically life altering or even fatal compared to an individual in a different age group. This led us to question what views older adults have about existing measures in place to monitor and analyze falls, such as fall detection devices or other technologies, as well as what demographic factors may influence these views. Using data from a parent study, we are currently in the process of analyzing focus group transcripts to compare perceptions of older adults from high and low socio-economic status using qualitative descriptive methods. We are analyzing transcripts for common themes that may lead to the identification of areas for further study. By studying older adults’ perceptions of fall detection devices, we hope to gain a better understanding of their needs and preferences when it comes to such devices. We hope exploring and understanding demographic or other factors that affect these perceptions may lead to more open conversations on falls, and thus better our ability to customize fall detection devices and their features, and fall prevention plans for older adults.

In spite of rapid advances in detection and treatment, cancer remains one of the most deadly diseases, killing over 1500 Americans each day. The ability of cancer cells to metastasize is the driving force behind the high mortality. For this reason, early detection and improved treatment technologies are crucial to enhance the survival rate of patients. The progression of cancer pathology begins with the accumulation of DNA mutation that transforms a normal cell into a proliferating tumor cell. This unregulated cell growth is governed by disruption in reactive oxygen species, iron homeostasis, and up-regulation of ribonucelotide reductase. Studies show chelators have significant antiproliferative properties reducing tumor growth through iron chelation. Unfortunately, they also bind to iron in normal cells, therefore, there is a great need to develop chelators that bind specifically to iron in cancer cells to prevent cell proliferation. Our study focuses on the design of a new class of site-directed iron chelators using gold nanoparticles (AuNPs) as targeted molecular carriers. These AuNPs are capped with thiolate ligands that are modified using EDC/NHS coupling chemistry for attachment of chelators and targeting moieties that recognize cancer cell surfaces. We will present the synthesis strategy and characterization methods used for confirming the presence of chelators on the AuNP surface. These methods include ultraviolet-visible, fluorescence, infrared, and dynamic light scattering spectroscopies. Metal binding studies demonstrating iron uptake will also be presented.

All organisms require the pyridine nucleotides NAD(P)(H) to perform various cellular functions, but their role in methylotrophy is not well understood. Methylotrophic organisms are able to use organic substrates without carbon-carbon as a sole source of energy and carbon. In metabolism, pyridine nucleotides provide reducing power for the cell to perform redox reactions in catabolic and anabolic processes. In contrast to energy-limited modes of growth, methylotrophy is predicted to be reducing power-limited as the oxidation of methanol or methylamine is coupled to phosphorylation of ATP and energy production. Furthermore, internal concentrations of NAD(P)(H) are predicted to be saturating so the balance between catabolic and anabolic charge ratios may be of greater importance than the relative concentrations. Consistent with these predictions, fluctuations in NADPH levels are observed during as an immediate response when the facultative methylotroph Methylobacterium extorquens AM1 is transitioned from multi- to single-carbon substrates. Known mechanisms to recycle pyridine nucleotides include the decoupling of NAD(P)H using NAD(P) kinases/phosphatases or transhydrogenases and the use of enzymes with dual specificity or isoenzymes. We propose a transhydrogenation cycle between the EMC and PHB pathway to be an important mechanism to maintain redox homeostasis in M. extorquens AM1. To demonstrate this, I will use select OMIC approaches to analyze wild-type strains during succinate to methanol transitions and compare wild type to an mtdB mutant, a strain without a functional methylene-H₄MPT dehydrogenase B (MtdB). In this mutant, the assimilatory blocks on methanol and methylamine are presumably due to the disruption of a key pyridine-nucleotide producing step. These results will provide increased understanding of the mechanisms used to balance production with consumption of redox equivalents and re-distribute carbon flux in M. extorquens AM1. Insight from this work has implications for engineering methylotrophs for biotechnological applications including the production of biofuels and value-added chemicals.

 The vast majority of current protein-based drugs involve binding a therapeutic target with an exogenous molecule that neutralizes or blocks its function. A major drawback of this approach necessitates a stoichiometric number of binding sites be administered to the patient, resulting in many caveats such as high dosage, stability, and immunogenicity. Enzymes represent an underexplored avenue for protein therapeutics with vastly enhanced potency. Proteases are essential and ubiquitous enzymes that catalyze peptide bond cleavage. While there are multiple therapies available derived from naturally occurring proteases, currently there are no novel, engineered protease therapeutics. In this work, we seek to establish a highly specific and processive protease system with traits desirable for use as a protein therapy, such as high solubility and thermostability. For this purpose, we have chosen to engineer the small ubiquitin-like modifier (SUMO) protease. The target of this protease, SUMO, is a small protein important for cell cycle regulation in eukaryotes. The mechanism for SUMOylation is analogous to the ubiquitin regulation system; these small proteins are adducted to other molecules and serve as signals for degradation or cellular localization. Removal of these tags is essential to the regulatory process, and is mediated by the highly specific SUMO protease. This inherent specificity makes the SUMO protease an ideal engineering platform. Here, we take the first steps toward unlocking the therapeutic potential of the SUMO protease by enhancing the stability and solubility of the yeast homologue. To accomplish this, we re-engineered surface residues with the Rosetta software suite. Furthermore, we have developed a novel Förster resonance energy transfer assay to allow us to monitor protease activity in real time. In addition to laying a foundation for the creation of highly selective therapeutic proteases, our work has immediate implications for the production and purification of recombinant protein in a laboratory setting.

Synthetic biology aims to engineer biological systems that perform complex tasks such as producing therapeutics and biofuels. Synthetic gene networks are developed that interact with an organism’s native genome to modify its behavior, and the design of synthetic gene networks is guided by computational models. However, the ability of computational models to accurately predict gene network behavior is limited by a poor understanding of how individual network components operate; and this often results in repeated rounds of experimental refinement. This work aims to improve the predictive power of computational models by characterizing the function of promoter sequences. We developed methods to easily detect intracellular RNA levels with high accuracy using an RNA-based fluorescence reporter. The method is used to quantitatively measure RNA synthesis rates in E. coli. This technique may be used to enable high-throughput characterization of DNA promoter sequences for use in synthetic biology applications.

Antibiotic resistance is a challenging problem in the realm of human health today. As a fundamental evolutionary phenomenon, it provides an excellent system to test adaptive evolutionary theories in a short amount of time. Thus, I explored the rise of antibiotic resistance in two evolution experiments with Escherichia coli. In the first, I asked how differences in genetic background affect the rate of adaptation to a new environment. To address this question, I generated 19 unique antibiotic resistant mutants by evolving E. coli in an environment with low drug concentration, and then exposed thousands of populations of each isolate to a high concentration environment measuring the proportion of populations that survived. Since survival in the high-drug environment requires acquisition of a new beneficial mutation, I hypothesized that high mutant survivorship indicated an isolate with more mutational options available in the high drug environment (we call this “potentiation”). Isolates with low survivorship would have fewer available mutational options (we call this “doom”). Interestingly enough, some observed differences may be due to a phenomenon known as sign genetic epistasis – when mutations have different effects in combination than individually. Preliminary data suggests a few strong cases for potentiation. I also investigated the effect of an initial resistance mutation on the consequent adaptations in a no drug concentration environment. To study this, I generated 23 unique mutants of E. coli and tracked how fitness and drug resistance changed over time in 2,200 populations. Both of these experiments help illuminate the role of historical contingency in evolution, the idea that an initial mutation may dictate an organism’s future mutational trajectory (available mutational options). Therefore, understanding both the effect of initial mutations and the underlying mechanisms of mutation acquisition is necessary in order to combat the emergence of resistant bacteria, a current human health concern.

Autophagy is the process in which eukaryotic cells selectively degrade proteins and organelles. Autophagy has been well documented in organisms ranging from yeast to mammalian cells, with demonstrated roles in response to starvation, aging, and stress. However, there has not been an effective method for measuring autophagy in C. elegans, despite C. elegans being a popular model organism for the study of disease and aging. We refined an assay that uses double-fluorescent protein tagged Atg-8/Lgg-1 to measure autophagy in both yeast as well as C. elegans. This assay reports an increase in autophagy in response to starvation in both model organisms. We then applied this to the study of nematodes containing a mutation in Rheb, an important protein in the upstream signaling cascade that regulates autophagy. Autophagy is damped by signaling through the TORC1 pathway. A mutagenesis screen revealed two different worm mutants (ENU9 and ENU10) which are predicted to hyper-activate TORC1 signaling. Using the aforementioned assay we found that ENU9 and 10 mutants have dramatically reduced levels of autophagy. This work has implications for further research in Alzheimer’s, Parkinson’s and related diseases associated with ageing and proteostasis.

High Density Lipoprotein (HDL) particles are spherical structures, which play a fundamental role in the reverse cholesterol transport (RCT) pathway, where cholesterol is carried to the liver for excretion. Apolipoprotien (Apo) A-1 is the primary protein component of HDL and plays a critical role in the RCT pathway. As lipid and cholesterol are transported from cells, they are encircled by Apo A-1, forming discoidal pre-ß-HDL particles, which subsequently undergo cholesterol-dependent maturation via Lecithin-Cholesterol Acyl Transferease (LCAT), forming spherical HDL. Man-made HDL or reconstituted HDL (rHDL) have many applications in nanotechnology, including cellular delivery of antigens and small interfering RNA. However, the large size distribution of HDL made from full length Apo A-1 raises difficulties in relation to drug delivery variability. Currently, I am using shorter constructs of Apo A-1 lacking the N-terminal globular domain as a membrane scaffold protein for nanodiscs – which resemble pre-ß-HDL particles, but differ in their more uniform size range (~3%). We hypothesize that treatment of nanodiscs containing cholesterol with LCAT will result in spherical HDL-like particles with a more narrow size window. We have demonstrated that LCAT-mediated maturation of cholesterol-containing nanodiscs yields HDL-like particles. This reveals that the N-terminal region is not necessary for maturation. Next, I aim to optimize experimental conditions for generating HDL-like structures and characterize their polydispersity via analytical ultracentrifugation. The insight gleamed from this study will establish a base line for using matured nanodsics as drug delivery vehicles with a uniform size range.

Our lab has recently developed computational methods for designing cage-like protein nanomaterials built through the self-assembly of multiple copies of two distinct protein components. This new technology holds great promise for a wide range of applications including targeted drug delivery, vaccine design, and biofuels. Moving towards these real-world applications, one desired but as of yet unrealized feature of our current designs is the ability to produce each protein component independently of one another and then trigger assembly by mixing the purified components in vitro. Obtaining this level of control over the assembly process requires that the individual protein components are stable and soluble in the absence of their designed binding partner. This property is not explicitly considered in our current design protocol. Here we present work aimed at addressing this problem by implementing a new step into our design protocol wherein we redesign the amino acid sequences of the proteins to increase the net positive charge on the surface of one protein subunit and the net negative charge on the surface of the other subunit. This supercharging approach should improve solubility by disfavoring aggregation between identical subunits of individually purified components while favoring the interactions between distinct subunits required for nanocage formation. To supercharge the proteins, we use the molecular modeling software package Rosetta to determine positions on the surface of each protein that are predicted to tolerate mutations to either positively or negatively charged residues. This information is used to automatically generate initial designs, which we then manually inspect and refine.

As we move our energy production and consumption economy towards a cleaner, “green” energy paradigm, it has become clear that research into solar energy harvesting is of real world significance. While fundamentally challenging, the capture and storage of solar energy into chemical bonds, such as hydrogen, can be envisioned as a large scale energy solution. In nature, the champion of solar water splitting for energy production and storage is Photosystem I and II (PS I and II). After a photon absorption event, the manganese oxygen evolving center (OEC) in PS II increases its reductive capacity enough to oxidize water into its oxygen and hydrogen constituents. Following the water oxidation reaction, the manganese oxidation state returns to the original to further oxidize additional water molecules. In practice however, it is incredibly difficult to create a regenerative OEC mimic, as high valent Mn is not usually stable. Therefore, our focus is to develop and explore materials which mimic the PS I and II solar water splitting reaction. α-Fe2O3 has shown great promise for the solar water oxidation half reaction. Upon photo-excitation, electrons are collected at the back contact leaving the surface of α-Fe2O3 in an oxidized state, providing a driving force for water oxidation. Additionally, upon introduction of certain catalysts, we can increase the oxidative capacity of α-Fe2O3, and thus improve the overall solar-to-hydrogen efficiency. So far, we’ve observed a significant enhancement in the oxidative efficiency with the use of a certain cobalt catalysts, and we are investigating the use of other metal centered catalysts including: nickel, iridium, silicon, tin, iron, niobium, and titanium. Ideally, we’d like to see these other metal centered catalysts demonstrate a greater increase in solar-to-hydrogen efficiency than our cobalt catalysts. We hope to, one day, apply this technology towards increasing the efficiency of solar powered fuel cells.

Current methods for staging chronic kidney disease are deficient because they lack specificity and sensitivity. Two potential renal biomarkers, cinnamoylglycine (CG) and hippuric acid (HA) are dietary metabolites cleared by the kidneys. These two compounds are potentially more sensitive indicators of kidney function because they are shown to require active secretion into the ultrafiltrate by the renal tubules. The purpose of this project was to develop and validate a liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for determining the concentration of CG and HA in serum for use in future clinical research studies. Samples were prepared by precipitating serum proteins with acidified acetonitrile followed by phospholipid removal using solid phase extraction. Compound separation was achieved with ultra-high performance liquid chromatography utilizing a reverse-phase T3 column with a gradient mobile phase. Detection and quantification were accomplished by isotope dilution-tandem mass spectrometry operated in positive electrospray mode. The transitions monitored were 206.04>131.04m/z and 181.03>105.01m/z for CG and HA respectively. The lower limit of quantification (20% CV) for this multiplexed assay was established at 0.028 ng/mL and 1.2 ng/mL for CG and HA, respectively. Linearity studies achieved an r² value >0.97 for both analytes. The mean analytical recovery was 62% for CG and 64% for HA. The following studies used concentrations of CG and HA at 44.67 ng/mL and 7063.05 ng/mL respectively: intra-assay imprecision (CV, n=20) was 5.05% and 4.36%, inter-assay imprecision (CV, n=20) was 11.90% and 5.89%, and total error was 12.92% and 7.33% for CG and HA, respectively. This LC-MS/MS method demonstrates good performance and excellent analytical specificity for detecting and quantifying CG and HA in serum. The next phase is to implement this method into a clinical research study and explore these analytes as improved biomarkers for staging chronic kidney disease.

Acute myeloid leukemia (AML) is a type of blood cancer. This disease is treated by chemotherapy and bone marrow transplantation, but mortality rates remain high and new therapies are needed. Because gene expression in AML differs from person to person, it is possible that personalized therapies can be designed by understanding how gene expression predicts drug sensitivity. Previous studies tested the sensitivity of 14 human AML cell lines and 30 primary patient samples to 160 chemotherapy drugs, and utilized computational approaches to identify genes that are correlated with the sensitivity to specific drugs. In my project, I am evaluating several of these predictions by silencing gene expression in AML cell lines with a tool called short hairpin RNA (shRNA), which is used to bind and degrade the expression products of genes called messenger RNA (mRNA). I will then test the ability of drugs to inhibit growth in cells that have undergone gene silencing versus control cells that have not undergone gene silencing. If we successfully validate these gene expression-drug sensitivity relationships, they could lead to personalized clinical treatment approaches in AML.

The past 40 years has seen extraordinary growth amongst the Latino population in Washington State. Our study asks why the population of Latinos is increasing and what is driving the migration of Latinos to Washington State. After analyzing data from the U.S. Census from 1970-2010, we revealed that in the last decade the Latino population has risen in some Washington counties as much as 300%. Although the information from these government sources account for the general Latino population, the Latinos who are undocumented in the United States are more difficult to track. In lieu of these numbers we were able to access non-traditional data through a Seattle-based Latino organization that works with this specific population and confirmed the continued growth. Furthermore, the overall increase in the Latino population has seen the most dramatic rise in three Western Washington counties: King, Pierce, and Snohomish. Other data sources such as the Washington State Department of Financial Management and the U.S. Bureau of Economics revealed that since the 1970’s, industries such as construction and hospitality services in King County, port labor in Pierce County, and farming in Snohomish County were attracting this population. In addition to labor opportunities, we believe that the increase of Latinos in these counties can be attributed to the absence of restrictive immigration legislation such as laws set in place in states like Alabama and Arizona. Moreover, Washington’s liberal social tendencies and geographic location deflects much of the anti-immigrant sentiment that makes news headlines in states along the U.S. – Mexico border. According to a Pew Research study, by 2020 Latinos in the United States will account for approximately 19% of the population – a number that is likely to increase in Washington State and continually change the population, economic, and social landscapes.

Conifers are an important part of the forest industry and are extensively planted for timber production. However, high crop yield demands and increasing environmentally stressful conditions such as heat, drought, and water salinity have caused an increase in the use of chemical fertilizers and water, which can be expensive and unsustainable. A possible alternative to fertilizers is the use of nitrogen fixing endophytes. Endophytes are bacteria or fungi that live within a plant, establishing a mutualistic relationship in which they can provide growth stimulation through production of growth hormones, nitrogen fixation, enhanced nutrient uptake, and protection from potential pathogenic colonizers. Prior studies have demonstrated that the use of fungal and nitrogen fixing endophytes significantly increases growth in many crop plants grown in the presence of abiotic stresses. In this study I have inoculated Douglas Fir seedlings with various strains of nitrogen fixing endophytes. Because confirmation of inoculation is essential, some of these endophytes were marked with a fluorescent marker (GFP) to confirm inoculation using fluorescent microscopy. Once inoculation was confirmed, conifers were grown in nitrogen-free or nitrogen-low soils and solutions to compare growth and measure nitrogen levels in plant tissues between inoculated and uninoculated conifers. If these endophytes prove to be beneficial for increasing conifer growth, they could be used as a sustainable alternative to chemical fertilizers and in turn, aid in the mitigation of climate change on forestry ecosystems and the environment.

Cells and organisms must adapt to a variety of conditions to ensure survival. These adaptations have led to the evolution of a set of genetic stress response pathways, many of which have co-evolved to affect longevity. One of these pathways is the hypoxic response pathway, which is important for the response to diminished oxygen and is controlled primarily by the hypoxia inducible factor-1 (HIF-1). HIF-1 is a highly conserved transcription factor whose stabilization promotes increased lifespan and healthspan in C. elegans. Despite HIF-1 being highly conserved, similar stabilization of HIF-1 in humans leads to von Hippel-Lindau (VHL) syndrome, a disease characterized by increased tumor formation. Although the effects of global activation of the hypoxic response are well-documented, the tissue specificity and important downstream targets necessary for benefits or disease remain largely uncharacterized. My project focuses on the proteins downstream of HIF-1 that act to affect health and longevity. Work in our lab shows that multiple genes downstream of HIF-1 in C. elegans are sufficient to increase worm longevity when overexpressed in the absence of HIF-1 stabilization. One of these downstream genes that modulate worm aging is flavin-containing monooxygenase 2 (FMO-2). FMO-2 is a phase 1 xenobiotic metabolizing enzyme that may also play a role in protein homeostasis. We have found that the expression of FMO-2 either ubiquitously or in the intestine and head excretory glands of C. elegans increases lifespan and healthspan. My project involves further characterizing the FMO-2 protein by testing its role in resistance to stress and improving healthspan. In addition, I am contributing to epistasis experiments to determine whether FMO-2 acts in any other aging-related pathways. In characterizing FMO-2 in this way, my project seeks to better understand this protein in the context of health and longevity.

Chronic allograft injury has replaced acute rejection as the leading cause of renal graft failure following transplantation. Graft failure is of special importance to pediatric patients since they typically require multiple grafts in their lifetime and therefore will benefit from graft life extension (Smith et al, 2010). A relationship has been demonstrated between subclinical Cytomegalovirus (CMV) and subclinical Epstein Barr Virus (EBV) and chronic allograft injury previously. This relationship could lead to insight into the mechanism of chronic allograft injury. To characterize the relationship between subclinical infection and chronic allograft injury we measured T-cell specific response to subclinical CMV and EBV infections. A panel measuring three aspects of T-cell response: activation, memory, and cytokine response, was proposed and validated. T-cell response was quantified using flow cytometry on stimulated whole blood samples from study participants in an intracellular cytokine staining assay. Analysis of T-cell activation, memory, and cytokine production was done using a Boolean gating strategy on FlowJo software. Twenty-six patients are currently enrolled, with whole blood samples being collected every six months over the course of twenty-four months. We are in the process of banking, processing, and analyzing the samples. After all of the patient samples have been analyzed for T-cell memory, activation, and cytokine production, we will quantify the relationship between T-cell response and subclinical viremia. This data will be compiled in conjunction with the GFR, kidney biopsies, and CMV/EBV PCR data to create a longitudinal history, allowing us to understand how CMV and EBV viremia contributes to chronic allograft injury.

Tuberculosis (TB), an infectious disease caused by the bacterium Mycobacterium tuberculosis (Mtb), kills nearly 2 million people a year and is a major cause of morbidity and mortality worldwide. The increasing prevalence of multi-drug resistant (MDR) strains that fail to respond to all currently available drugs underscores the critical need for new therapeutic strategies. DNA topoisomerases (topos) are a class of enzymes responsible for maintaining the correct topological state of DNA molecules by modulating the degree of supercoiling through the breakage and reforming of covalent phosphodiester bonds in the DNA backbone. With the precedent-setting success of several anticancer and antibacterial drugs that target topos, focus in TB research has increasingly turned to these enzymes as new potential targets for chemotherapy. In this study, we isolated Mtb topoisomerase type IA (MtbTOPA), a subclass that only acts on single-stranded DNA (ssDNA), as our target of interest. At least one type IA topo activity must be present in every organism for resolving topological obstacles that require ssDNA cleavage, and fortuitously, Mtb happens to only encode one type IA, further validating MtbTOPA as a high-value drug target. We have cloned, expressed, and isolated highly purified recombinant MtbTOPA protein for enzymatic studies and work is currently underway to solve its crystal structure to aid in target-based approaches to drug development. In efforts to develop a high-throughput screen (HTS) for identification of small molecule inhibitors of MtbTOPA, we have collaborated with the Global Alliance for TB Drug Development (GATB) and leading structural genomics centers to gain access to large compound libraries as well as to accelerate the drug discovery process. We adopted a HTS method based on fluorescence resonance energy-transfer (FRET) and requisite MtbTOPA mutants were designed. It is our hope that the HTS will identify several hits that can be developed into novel TB drugs.

Dental caries is the breakdown of tooth enamel that causes cavities and is the most common chronic disease in children and adolescents between the ages of 6 and 19 years. Therefore, much work is being done to combat caries. We believe that the scanning fiber endoscope (SFE) developed in our lab can be used to improve the detection of early caries in children. The SFE is a small flexible probe that scans low-powered RGB laser light. It performs high-contrast high-resolution imaging and dual laser fluorescence spectroscopy with 405- and 532-nm laser excitation on both in vitro and in vivo teeth. My project focuses on the development of a calibration standard to use with the SFE in an upcoming clinical trial to be conducted at the UW Center for Pediatric Dentistry. A photostable calibration standard was created to match the fluorescence pattern of dental enamel. Spectral measurements of the standard will be taken before and after collecting data from patients' teeth with the SFE to monitor the instrument's behavior. This will allow us to account for drift in measurements and ensure that we can draw accurate conclusions from our data. 

Breaking waves dissipate energy in the form of turbulence and bubbles, and are important to many fundamental processes at the air-sea interface. Breaking waves are also a hazard to safe operations at sea and to the survivability of coastal structures. Recent buoys developed at the Applied Physics Lab are designed to study the dynamics of a breaking wave. The buoys are mounted with a number of instruments, including a camera pointed down at the surface of the water. Until now, there has been no useful, automated method to correlate these images with underwater measurements. Using MATLAB, I have produced an algorithm that analyzes the images taken by SWIFT drifters during deployment. Images with breaking waves and breaking rates during each deployment are outputted. I accomplish this through a ‘scoring’ system combining three image-processing techniques. The images go through brightness detection, searching for the signature white color encountered when a wave breaks, as well as through texture analysis. If the images pass certain thresholds for these analyses, points are awarded to their score. The images then pass through glare detection algorithms that remove points from their score if certain thresholds are met. This provides a method for identifying images, with various levels of certainty, which contain breaking waves. This method of scoring and a system of manual checks minimizes the number of false positives, increasing the algorithm accuracy. This algorithm is starting to be put to use on data sets, adding valuable information to current research at the APL. Much of the current area of study is the mouth of the Columbia River, on the Washington-Oregon border, but these devices have been deployed worldwide, including a study this summer in the Arctic Circle. Studying these breaking waves adds a wealth of information to coastal engineering applications and study of air-sea interactions.

The vertebrate body forms through a process called embryogenesis. In my research, I focused on the establishment of body length during embryogenesis of the model organism zebrafish (Danio rerio). Under normal conditions, the cells of the developing body intercalate towards the back, or dorsal side, of the embryo, and extend longitudinally to grow the body axis. One observed defect in this process blocks cell intercalation, thus leading to underdeveloped bodies, which is known as a convergent extension phenotype. In my research, I studied the role of Microtubule-Associated Serine/Threonine kinase-Like (MASTL) RNA in body axis formation. Because of a known role for MASTL in regulating chromosome segregation, I hypothesized that overexpression of MASTL would interfere with normal cell function and lead to a convergent extension phenotype with a shortened body axis in the developing zebrafish embryo. To test this hypothesis, I injected embryos with different concentrations of RNA and allowed them to develop. Overexpression of MASTL shortened body lengths at all but the lowest concentration of RNA. I then chose a low but effective concentration of MASTL RNA, injected embryos and quantified embryo length. Finally, I performed RNA in situ hybridizations, a process by which labeled probes are used to localize specific RNA transcripts in embryos. Using a variety of labeled probes, I found in addition to shortened body length, the distribution of the prospective spinal cord cells and muscle cells were abnormal in MASTL-injected embryos. The results of these experiments clearly show that overexpression of MASTL leads to a convergent extension phenotype. To continue this research, I will look at whether or not MASTL affects body length formation through Protein Phosphatase 2a, a known target of MASTL. The results of my research will lead to a better understanding of the role MASTL in cell intercalation and vertebrate body elongation.

Autism spectrum disorders (ASD) are neurodevelopmental disorders with symptoms related to social communication and repetitive behavior. One aspect of social communication that is particularly challenging for children with ASD is pragmatic language including the ability to clearly convey narrative information to others. Narrative language, such as story telling, is a type of pragmatic ability that utilizes cognitive-linguistic planning and coordination of information. The first objective of our study is to compare the narrative language abilities of typically developing children to children with ASD. Our second objective is to test the relation between narrative abilities and severity of symptoms within the group with ASD. Seventy-five 6 to 11 year old children with idiopathic ASD or typical development participated. Groups matched in age, IQ, and sex ratio. Narrative language samples were extracted from a longer diagnostic interview, the Autism Diagnostic Observation Schedule (ADOS). Scoring of narrative language skills was based on the coding system developed by Reilly and colleagues. Symptoms were assessed via the ADOS, the Autism Diagnostic Interview-Revised, Social Responsiveness Scale-2, and Repetitive Behavior Scale-Revised. We expect to find a lower level of narrative ability in the group with ASD, given previous reports of pragmatic errors , misinterpretation of key events, and dysfluencies among children with ASD. For the second objective, we predict that there will be a correlation between the narrative level and social symptoms, such that better narrative ability relates to fewer symptoms. In the repetitive domain, we expect to see more repetitive behaviors with relation to lower level of narrative ability by looking at dysfluent speech, which entails repetitions and self-corrections. Our results may lead to future studies regarding narrative ability in speech interventions towards children with ASD. 

Von Willebrand factor (VWF) is a multimeric blood glycoprotein involved in the process blood clotting. Its primary function is to be an adhesive proteins that platelets can bind to a wound site. In the Sniadecki lab, VWF is used as a matrix protein for capturing platelets under shear flow in a microfluidic device for blood coagulation studies. Currently, VWF is purchased from a company and coated on the surface of the microchannels. High molecular weight VWF has a higher ability to form a clot, while low molecular weight VWF has a lower ability. Since the VWF comes from a commercial source, the purity of its molecular weight weight is unknown. The goal of my project is to improve the VWF coating by purifying VWF from Enzyme Research. We hypothesized that low molecular weight VWF does not support clot formation and that high molecular weight VWF will show more clot formation than the control vWF in the microfluidic device. My research efforts have been to purify VWF using the fractionation gel filtration technique developed by Professor Dominic Chung’s lab at the Puget Sound Blood Center. The gel filtration technique can isolate the vWF according to size. Gel filtration was done using a 10x10 Sephacryl 500 Column. After the filtration process, vWF of different molecular weights are then applied primarily to the surface of PDMS so that platelets can bind to them under fast flow, in order to measure forces of platelet clotting. We found that there is a link between the molecular weight of the vWF and the rate of clot formation. Low molecular weight vWF does not support clot formation and that high molecular weight vWF will show more clot formation than the control vWF.

Cognitive rehabilitation has been shown to be effective on cancer survivors after cancer treatment. Some evidence suggests that older adults may be more adversely impacted by chemotherapy. The purpose of this study was to examine whether age may be a moderating factor on cognitive rehabilitation effectiveness among cancer survivors. Participants were survivors 6 months or more post active treatment, and were randomly assigned to an immediate treatment group (treatment) or a wait list (control). A battery of cognitive tests and questionnaires, both computerized and by hand, were given before and after a seven-week group-based memory skills intervention, which was specifically designed to improve memory and thinking abilities. 45 subjects completed all measures and were divided by age into “middle age” (21-60 yrs.; N=23) with mean age of 51.3 years and “older adults” (60+ yrs.; N=22) with a mean age of 67.1 years. Results indicated that both middle age and older adults improved over time for immediate and delayed verbal recall (list learning task) (p < .05). Significant improvement for sustained attention (digit symbol) (p < .05) and working memory (digit span) (p < .05), however, was observed in the middle age group only.There was a significant interaction effect of F (1,43) = 5.83 for the digit span total, with only the middle age group showing an improvement. Our results suggest that there was some difference in improvement of cognitive thinking and memory between the two age groups. Although both groups improved on measures of verbal memory only the younger adults improved on measures of attention. Our results may help guide future cognitive rehabilitation programs to target specific areas of cognition that may be more likely to respond to treatment. This will help patients have a more accurate expectation for cognitive rehabilitation goals.

The lateral habenula (LHb), is an important regulator of midbrain dopaminergic systems that are known to be involved in cocaine reinforcement. The LHb exerts an inhibitory effect on dopaminergic neurons in the ventral tegmental area (VTA), though interestingly LHb-VTA projections are known to be glutamatergic (excitatory). The rostromedial tegmental nucleus (RMTg), a recently identified GABAergic (inhibitory) nucleus, that receives direct excitatory inputs from the LHb, has been proposed to be the source of this inhibition of the VTA. Here, firstly, we injected rats with anterograde TAMRA-Lys-Dextan and retrograde FluoSphere tracers in the LHb and RMTg, respectively and demonstrated that the LHb indeed projects to both the VTA and RMTg. Secondly, since the RMTg has no known anatomical boundaries, we gauged the anatomical location of the RMTg using expression of the transcription factor cFos, a marker of neural activation in response to cocaine. A significant increase in cFos expression was found in rats injected with cocaine (10 mg/kg i.p). Finally, we utilized the Designer Receptor Activated Exclusively by Designer Drug (DREADD) technology, to investigate the role of modulating the activity of the LHb on cocaine-self administration. Rats were implanted with jugular venous catheters and trained to self-administer cocaine (0.75 mg/kg/infusion). We found that DREADD-mediated transient silencing of the LHb through the activation of inhibitory G-protein-coupled signaling pathway with clozapine-N-oxide increases cocaine self-administration. In contrast, activation of the excitatory G-protein-coupled signaling pathway decreases self-administration on a progressive ratio schedule. We further show that inactivation of LHb inputs to VTA neurons have no effect on cocaine self-administration. We now propose to investigate the role of LHb projections to the RMTg using a dual-virus strategy using a combination of Cre-dependent DREADD’s and canine adenovirus expressing Cre (that gets transported retrogradely) to specifically target the LHb to RMTg projections for DREADD-mediated modulation on self-administration.

 This project presents the development of a new process flow in the Washington Nanofabrication Facility to create a magnetically neutral Nuclear Magnetic Resonance (NMR) test device for use at the Department of Energy (DOE) Pacific Northwest National Labs (PNNL). At PNNL, within the Environmental Molecular Sciences Laboratory, the devices are used to characterize environmental contaminants, like radioactive isotopes, using NMR spectroscopy. The devices being developed are to be superior in uniformity and layering a stack of thick copper sandwich with a precisely deposited aluminum layer. The project includes computer-aided design (CAD) and fabrication of a precision mask set for fine resolution that limits irregularities in the test structure that could adversely impact the NMR measurement. The fabrication process starts with an electroplating seed, photolithography, and thick electroplating of copper. Following plating, chemical mechanical polishing is performed to yield an atomically smooth surface. After this, a precision thickness aluminum layer, that cannot be conventionally electroplated, is deposited and patterned via a lift-off process. This project will also be a primer for more industry-focused capabilities for the WNF with eventual development of through-silicon vias (TSVs) for research applications.

Cocaine and other drugs of abuse have destroyed the lives of many individuals as those who take such drugs struggle with the powerful vice of addiction. Such drugs have been shown to cause changes in the brain, specifically in the cortex and the striatum, which has been linked to the manifestation and maintenance of addiction. Within the striatum there exists cell populations of neurons, which vary in their outputs to the brain and are regulated by glutamate inputs from the cortex. The involvement of these individual cell populations in addiction, including how they are regulated by cortical glutamate, is not yet fully understood. In order to investigate this issue, I collect data in and run rat behavior experiments with rats that have been treated with viral vectors, which temporarily decrease neuron activity in specific cell populations when activated by specific ligands. After the behavioral data has been collected I process the tissues by slicing the brains and stain them with techniques such as immunohistochemistry. Then I determine if the vectors were actually present in the expected cells due to their fluorescence after immunohistochemistry procedures. In some of the work that I have done with Kerry Kerstetter we have found that decreasing activity in cortical glutamate projections to the striatum resulted in an increase in motivation for cocaine. A better understanding of the intricate pathways involved in drug motivation will allow for better treatment and care for those suffering from addiction. Our hope is to provide more information on such pathways to help progress the development of future treatments for victims of addiction.

Youth in the U.S. juvenile justice system are faced with various physical and mental health disparities, such as sexually transmitted diseases, and mental illness. Youth are at elevated levels of risk of contracting chlamydia and gonorrhea. People under 25 years old make up 15% to 30% of HIV cases (Morris, et al., 2006). It has also been found that many externalizing disorders such as attention-deficit/hyper-activity disorder, conduct disorder, and oppositional defiant disorder are also associated with delinquency (Wareham & Boots, 2012). Given these health disparities, it is essential that consistent health care be readily available and accessible to this high-risk population. However, many communities do not have efficient resources to identify possible factors that hinder the consistency of health and mental health care for adjudicated youth. The current research project focuses on risk factors preventing continuity of health care (both physical and mental) among youth in the King County Juvenile Justice system. Through analyzing and coding over twenty qualitative interviews, risk factors preventing youth’s access to care are identified. The study explores how factors such as lack of knowledge on how to navigate the medical system and youth’s rights to independently access care, create unique barriers for youth seeking and receiving care. As a result of these obstacles, many high-risk youth receive much of their primary care while in detention facilities. Based on analyzing the interviews and a literature review on programs fostering access to health care among adults, I will propose a model to promote continuity of care among this high-risk youth population.

As the NFL was going into a lockout in 2011, linebacker Ray Lewis made the controversial statement that crime rates would rise if the NFL season was lost. Mr. Lewis said, "There's too many people that live through us," and that without football teams to follow, those people would turn to crime. At the time, there were many arguments provided on both sides of the issue, but no empirical research was done. Studies have shown that professional athletes commit more crimes during a lockout; and that children with access to sports programs are less likely to grow up committing crimes; but no one has ever tested the claim that a professional sports team has an effect on the crime rate in the area in which it is based. My experience living in a Seahawks-enamored Seattle in 2013 has motivated me to take Mr. Lewis's assertion one step further and investigate whether the success of a pro sports team can raise or lower the crime rate in its city. I look at more than just the relationship between winning percentage and change in crime rate (note that I cannot compare nominal crime rates, due to the varying base levels of crime in metro areas as diverse as New York and Denver). Other measures I investigate are margin of victory or closeness of playoff race, as perhaps a more dramatic season gives the fans more to live vicariously through. Despite some relationship between winning percentage and playoff success of a team and the city's crime rate, I can't show a significant enough correlation to conclusively say that the NFL influences the rate of crime. While this doesn't have any direct implications on the NFL or on policy makers, I believe that my results are enough to encourage further study of the issue.

In liver transplantation, increased overall fat content in donor livers causes poor graft function and lower patient survival post-transplant. Longer waiting lists combined with a shortage of organs has resulted in transplant surgeons considering moderately steatotic livers as a part of extended donor criteria. Clinically, the fatty infiltration is diagnosed by the lipid droplet size. Macrovesicular steatosis refers to large droplets or vesicles that distort the nucleus, while microvesicular steatosis refers to droplets equal to or less than the size of the hepatic cell nucleus. While macrovesicular steatosis negatively impacts graft function, livers with microvesicular steatosis result in patient outcomes that are almost the same as that of nonsteatotic livers. Therefore, a method to quantify the amount and droplet size of hepatic steatosis can be an innovative tool for transplant surgeons. In our previous studies, sound speed and attenuation correlated with the presence of visually observable fat. However, significant variabilities were discovered in the attenuation. The next step in this research involves exploring the effect of lipid droplet size on attenuation, using an attenuation spectroscopy method developed in colloid science research. If the total fat content is known, mixture rules based on a volume average of the fat and non-fat components can be used to estimate the intrinsic attenuation at a given frequency. Beyond this estimate, excess attenuation attributable to interactions between fat and non-fat phases of the mixture can be estimated using a coupled-phase model. Here, we quantitatively evaluate the excess attenuation caused by small lipid droplets by comparing attenuation measurements of well-characterized dairy products with model predictions. Results confirm that sub-micron sized lipid droplets produce a measurable amount of excess attenuation at 1 MHz. These results suggest that analogous measurements may be made in quantifying the amount of microvesicular steatosis present in livers with known overall fat percentage.

Staphylococcus aureus is a Gram-positive bacterium that colonizes the nose and skin and causes a variety of infections in humans. The acquisition of resistance to many first line antibiotics has made S. aureus increasingly difficult to treat. Previous studies have shown that an S. aureus enzyme called nitric oxide synthase (NOS) is necessary for both colonization and infection in animal models. The goal of the present study is to determine the role of NOS in staphylococcal physiology. We treated the S. aureus strain COL and an isogenic mutant strain lacking NOS with several redox-active compounds including menadione, paraquat, and pyocyanin. The minimal inhibitory concentration (MIC) of each agent was measured in liquid culture. A NOS mutant was substantially more sensitive than wild-type S. aureus to menadione, and menadione-resistance was restored by treatment with exogenous nitric oxide. In contrast, NOS mutant and wild-type strains were equally sensitive to paraquat. As both menadione and paraquat are redox cycling reagents that generate superoxide radicals, this observation suggests that the menadione-sensitivity of the NOS mutant is unrelated to superoxide. The NOS mutant also appears sensitive to pyocyanin, which blocks the electron transport chain. We hypothesize that nitric oxide regulates electron flow through the electron transport chain, most likely by inhibiting terminal oxidases. Further studies will investigate the effect of electron transport inhibitors that target NADH-dehydrogenase (rotenone) or the F₀F₁-ATPase (DCCD), and the effect of mutations that impair cytochrome assembly or the regulation of redox metabolism, in wild-type or NOS mutant bacteria. ATP and NAD/NADH levels will be monitored in parallel to determine effects on energy generation and redox balance. These studies will reveal how endogenously generated nitric oxide maintains redox homeostasis in bacteria and may lead to novel strategies to treat or prevent S. aureus infections. 

The inequalities and marginalization of people with disabilities is an issue with global scope. Environmental influences and socially derived assumptions shape the way disability is defined and experienced cross-culturally. Statistics shed light on significant disparities throughout various countries. According to United Nations Enable (2006), 10% of people in the world have some type of disability. Of this entire population of people with disabilities, 80% live in developing countries. Further, out of the estimated 200 countries in the world, only 45 have disability-specific laws such as anti- discrimination. In this research, I examined the driving factors behind this disparity through a cross-cultural comparison of disability advocacy efforts. In particular, I looked to countries that have experienced shifts in policy that directly influenced people with disabilities. I identified disability advocacy taking place in South Africa in a post-apartheid context, Ukraine in a post-soviet context, and the US in post-ADA context (Americans with Disabilities Act). Through rhetorical/discourse analysis of the imagery and language used on nongovernmental groups’ websites, I examined how shifting power dynamics have situated people with disabilities in South Africa, Ukraine, and the US and how these patterns manifested in online communications.

This study analyzes the color complex which is defined as psychological fixation about color and features that lead African-Americans to discriminate against each other. There is a lack of dialogue around how history has turned African-American women to focus towards hurting each other through colorism - skin color biases. This research asks how issues of colorism within the African-American community lead to concerns of self-acceptance and perception of beauty among young African-American women. I expect to find evidence of the effects of the color complex and determine how young Black women perceive beauty in order to frame their identity. The findings will fill a gap in existing research by challenging the work of earlier researchers, who have looked at the existence of colorism among African-American women today and look farther into how this issue has been and is affecting their perception of beauty in relation to the acceptance of themselves. 

As the population of older adults in the United States grows, more ways are being explored to encourage an active lifestyle and promote healthy living. Many malls and other sites across the country have established walking programs that provide people ways to get exercise and fulfill social needs. The purpose of this study is to explore quantitatively the numbers and types of people who participate in these programs as well as to describe the physical environment in mall and non-mall settings with walking programs. This study will make use of a modified SOPARC tool, a tool originally designed for assessing park and recreation areas. The tool will be used to capture information on walkers’ observed sex, approximate age, ethnicity, activity level and usage of mobility aids. Information will be collected about the external and internal conditions at the walking sites including information on accessibility, safety and features of interest to the walker. Results will include data gathered at 10 mall and five non-mall sites in five states. It is hoped that the results of this study will show what types of people are using these programs as well as features that are common among the various sites. To date, one mall audit has been conducted. Of 39 walkers observed over 15 minutes, 61% of walkers were male, 77% were older adults, and 74% were of observed Caucasian ethnicity. This site also played special music for the walkers and has an information kiosk where walkers can sign in and record their miles walked. Challenges to older walkers include uneven walking surfaces from the transit stop and small writing on the mall wayfinding map. It is hoped the study will provide a basis to help tailor walking programs to target certain populations and ideas for optimal walking settings to inform a best practices guide for existing and new walking programs.    

Colicins are a family of antimicrobial toxins that are produced by E. coli. The colicin gene is carried on a small circular DNA molecule, called a plasmid, along with a gene encoding an immunity protein. The immunity protein binds and neutralizes the antimicrobial colicin in a highly specific manner. Bacteria lacking the plasmid (and thus lacking immunity) are killed by the colicin. The immunity and the colicin are mutually dependent on one another, creating a system that seems unable to evolve. If either changes then they will no longer fit together, which in this system would result in the death of the cell by its own colicin. However, evidence shows that there are many different pairs of colicin and immunity proteins that share common ancestors, suggesting that diversification has occurred. How is this diversity possible if the system seems evolutionarily trapped? Our research looks at the idea of promiscuous protein intermediates. Under this hypothesis, the immunity changes first so that it can bind both its original colicin as well as another distinct colicin protein, we then attempted to recreate this possible evolution pathway in lab by evolving our own colicin-immunity pair. Using directed evolution we first evolved a “broadened” immunity protein then a matching colicin through error-prone PCR, which created a diverse collection of mutated colicins. Then we screened for matching colicin-immunity pairs. In pursuit of our novel protein, we generated and screened over 6000 colicins and have successfully isolated two potential novel colicin proteins.Through sequencing analysis, we know that the two potential novel colicin genes each have two nonsynonymous mutations.

Carboxylic acids are ubiquitous in chemistry and used in a variety of industrial applications, ranging from polymer precursors to food preservatives. Modern routes to synthesize these compounds often involve specialized equipment, harsh conditions, and potentially toxic reagents. An alternative synthetic route is the aldehyde-water shift reaction, in which an aldehyde is oxidized by water to form a carboxylic acid and molecular hydrogen. The use of water as both solvent and reagent could potentially reduce the impact of aldehyde oxidation on the environment, especially when compared to the routes . A series of iridium-, rhodium-, and ruthenium-based complexes have been synthesized and investigated for activity in catalyzing this reaction. Using ¹H NMR (proton nuclear magnetic resonance) and GC-FID (gas chromatography) to analyze reaction products, we have observed many of the catalysts to disproportionate aldehydes to alcohols and carboxylic acids in competition with the desired dehydrogenative oxidation to carboxylic acids. Mechanistic studies and catalyst optimization for dihydrogen production are presented.

Autism Spectrum Disorders (ASDs) are genetically heterogeneous neurodevelopmental disorders largely characterized by impairments in social interaction. Many with ASD face other comorbidities, including sleep problems. Prevalence of sleep problems in those with ASD are significantly greater than typically developing children and range widely from difficulties falling asleep to parasomnias. Although many studies investigate the link between sleep and autism, none have considered variability in sleep differences as a function of the genetic variability of the disorder. The underlying assumption for this project is that behavioral variability, such as differences in sleep problems, observed in ASD is a function of the genetic variability in ASD. Chi square analysis was conducted using data collected about sleep problems in a medical history interview from a large, well characterized and genotyped sample of children with ASD to determine the prevalence of sleep problems in ASD as a function of genetic subtype. Those individuals with similar, recurring gene mutations were further examined in order to view whether sleep problems (both pervasiveness and type of sleep issue) may be a specific phenotype related to that gene mutation. Using ANOVA, gender differences in sleep presentation were also examined.  Results from this study may serve as a starting point to evaluate other wide ranging comorbidities, such as gastrointestinal illnesses, as a function of the genetic differences present in those with ASD.

Precasting concrete uses a controlled environment known as a precast plant to create concrete members more quickly and carefully than could be done on a construction site. Precasting is a huge industry innovation avoiding onsite complications. This process leads to better quality concrete products that are faster and cheaper to make. While this practice is already well established in industry, some of the more precise material properties are not exactly known, including the relationship between applied stresses and resulting displacements, known as the modulus of elasticity. Because plants accelerate curing using heating, material properties are affected and difficult to determine. To investigate modulus of elasticity, freshly poured concrete samples were subjected to heating, and the modulus of elasticity was measured and compared against unheated concrete samples more analogous to an onsite concrete pour. This was accomplished by using a compression testing machine applying controlled loads according to American Society  for Testing and Materials standards and recording the deformations of both heated and unheated samples. Testing occured at regular intervals up to 56 days after the concrete was poured in order to capture the time dependency of the modulus of elasticity as the concrete cured. With a fuller knowledge of this specific property, a material model will be created to better equip precast plants in predicting precast concrete behavior, such as intentional upward bending to resist eventual bending in the opposite direction. A more accurate model will also give a better idea about stress losses in prestressing cables, which strengthen concrete members by providing a clamping force to prevent cracking or failure. Cable stress changes when concrete deforms, and is also affected by heating. With an improved understanding of the material behavior during curing, precast plants will be better equipped to precisely manufacture the concrete products that make modern infrastructure possible.

Carbon dioxide (CO₂) is a greenhouse gas that traps radiation in the Earth’s atmosphere. Increasing levels of CO₂ in the atmosphere can lead to a warming of the Earth’s surface and can affect a number of processes that affect climate patterns. Terrestrial ecosystems contain 3 times more carbon than the atmosphere, and each year forests release more than 10 times the amount of CO₂ to the atmosphere through soil respiration than fossil fuel emissions. Although these large natural soil respiration fluxes tend to be balanced by fixation of atmospheric CO₂ through photosynthesis, the carbon balance of forests under future climate is still unknown. In order for scientists to better model the role of forests under future climate change, an improved understanding of the amount of carbon that is allocated and stored in different components of forest ecosystems is needed.This project aims to provide a more thorough understanding of whole-plant carbon allocation in temperate forests. While trees may allocate up to 50% of their photosynthetically fixed carbon belowground, carbon allocation belowground has been historically overlooked. In particular, very few studies have quantified the amount of carbon allocated to mycorrhizal fungi – the symbiotic fungi found on tree roots that provide the plant with water and nutrients in return for sugars (carbon). We employed three distinct methods (including new isotopic techniques) to quantify carbon allocation to mycorrhizal fungi across a range of New Hampshire forest types. Preliminary results show that in nutrient poor conifer forests, mycorrhizal fungi may receive as much as 30% of the total plant carbon. This is one of the first studies that will quantify carbon allocation to mycorrhizal fungi under a range of natural forests.

Protection of old buildings is one of the tools for reinforcing well-being of our communities and ensuring their sustainable development. Today, older built stock is challenged by demands for rapid urban growth and modernization, and so are challenged cultural identities of our neighborhoods. Preservation of historic urban fabric is necessary as transformations and growth occur. The question this project seeks to answer is how can we secure balance between protecting authentic character and ensuring economic vitality in historic urban cores? The primary methods are assessment of historic properties in the Old Town Neighborhood of Redmond and research of effective placemaking solutions among downtown revitalization case studies. The final report features a set of design suggestions regarding the public realm within Old Town's Historic Core and is meant to help preserve, promote, and celebrate the neighborhood. This project is a part of a planning process intended to develop architectural design standards for Redmond’s Historic Core.

It has been hypothesized that there is a correlation between the flexibility of amino acids in a protein and their conservation. Inflexible residues tend to be structurally important and thus less tolerant of change. By this theory, mutations at these positions are expected to typically be deleterious. The Dynameomics project is an ongoing effort by the Daggett Research Group to characterize protein folding space through molecular dynamics simulations of representatives of all known protein structures or folds. The representative domains are organized such that the lowest rank fold (rank 1) represents the highest populated fold – with each subsequent rank representing fewer structures. We have used a novel software module to calculate residue flexibility directly from the relevant molecular dynamics simulation files. The resulting data were used to test the hypothesized correlation between conservation and flexibility. Analysis of the entire dataset showed that hydrophobic residues and Cysteine were relatively conserved on average. Hydrophobic residues are generally found in the less flexible core of the protein while Cysteine residues form highly inflexible disulfide bonds. Thus, residues expected to be inflexible were conserved on average – providing support for the tested hypothesis, with the caveat that the standard deviations were large. To avoid these large variations, analysis of individual proteins was needed. Calculated correlation coefficients allowed for the quantification of how well each simulated structure agreed with the hypothesis. Work is now being done to characterize the difference between the various ranks of Dynameomics in terms of this conservation-flexibility relationship. We anticipate that a better understanding of evolution at the amino acid level of proteins will help us to better predict the impact of mutation. Combining this information with rotamer information can allow for the creation of tools useful in the field of protein design and engineering.

This exploratory study investigates levels of stress among informal caregivers of cancer patients and the amount and kinds of social support they received while providing care. Previous research indicates that informal caregivers, defined here as family members or friends providing care to loved ones, often times experience extended periods of stress that can be reduced with increased social support. Social support includes the instrumental, informational, appraisal, and emotional forms of assistance caregivers provide. The aim of this study is twofold: to examine why previous social support services at a care facility in the Pacific Northwest had fluctuating participation rates, and to find strategies to strengthen social support for caregivers through understanding the levels of stress and support they experienced. I hypothesize that fluctuation was due to a lack of knowledge of support services and receiving support outside of the agency. I use a mixed methods design with a quantitative survey and a qualitative focus group component. Participants are given surveys inquiring information about the levels of stress they experience in their daily lives and the amount of support received from others. The focus group consists of guiding questions including open-ended questions about their experiences with caregiving, levels of stress, coping methods, forms of social support, observations on health changes, and perceptions of supportive services. I expect to find that caregivers receiving social support from family and friends will report experiencing less stress compared to caregivers that primarily receive social support from healthcare professionals. Overall, this study provides a deeper understanding of the extent to which caregivers feel social support and highlights barriers to social support service use at an organizational level. These findings have implications for existing knowledge on caregiver support and increases the knowledge base of stress and support of informal caregivers.

Dyslexia is a complex disorder that interferes with a person's ability to read and spell with no consensus as to what causes it. The typical person processes language in the left hemisphere and is either right or left handed while very few people have ambidextrous tendencies. Our hypotheses are two-fold. First, that competition between the brain's two hemispheres underlies dyslexia. Second, that this competition is evident in cortical activation during reading tasks as well as performance speeds during hand motor tasks. To test our hypotheses, we collected data from 52 adult participants (19 with dyslexia, 33 controls) who underwent electroencephalography (EEG) measures during a word reading task and also performed an alternating keytapping task.To investigate Hypothesis 1 (lack of lateralization is associated with dyslexia), we categorized our participants' EEG data according to typically vs atypically lateralized language activation patterns. Higher than expected numbers of adults with dyslexia in the atypical hemisphere activation group would be consistent with our hypothesis. To investigate Hypothesis 2 (correlations between the two modalities), we calculated a relative lateralization score for each of these task types and tested the correlation between these two scores for significance. Evidence of correlations between these two measures would yield higher than expected numbers of participants with dyslexia in the ambidextrous group as well. Evidence for both of our hypotheses will provide important insights into the biological underpinnings of dyslexia, pointing to disorganized brain circuitry in affected individuals. 

Calbindin D9k is a calcium binding protein that contains a helix-loop-helix motif, called EF-Hand. Members of the EF-Hand family are involved in calcium uptake and regulation of functions within the neuroendocrine and muscular systems. As calcium is involved in many cellular processes, such as muscle contraction and nucleotide metabolism, the function of these calcium-binding proteins is of great biological significance. Nuclear magnetic resonance spectroscopy (NMR) can provide a measure of protein dynamics, such as order parameters, that describe the residue-level mobility of a protein, including that of the backbone amide groups. These order parameters are often translated into conformational entropies, enabling an assessment of the entropic changes associated with unfolding or binding events. NMR studies that probe the stability and cooperative binding of calbindin D9k provide evidence that a temperature dependence of order parameters can identify regions of the protein that exhibit linear or nonlinear stability as a function of temperature. I will use molecular dynamics simulations to characterize the dynamics of Calbindin D9k and provide atomic level detail of the protein’s temperature dependent behavior over a temperature range of 3 to 63 Celsius. I will be comparing order parameters calculated from the simulations with experimentally derived order parameters for both the calcium loaded and unloaded states to determine the effects the calcium ions have on protein stability and conformation. Residues instrumental in calcium binding and structural stability are expected to exhibit smaller reductions in order parameters while non-structural regions should exhibit larger and more erratic reductions through increasing temperature. This study will further our knowledge of the dynamics of calcium binding proteins and offer an estimation of the free energy contribution that conformational entropy provides ligand binding. It may also be possible to extend these results to other calcium binding proteins known to act in disease and calcium deficiencies.

The Muon g-2 experiment hopes to test the difference between the experimental and theoretical values of the anomalous magnetic moment of the muon (g-2) out to a greater statistical precision than has been previously accomplished. Such a discovery would provide strong evidence of new physics such as dark photons, supersymmetry, or possibly something not yet considered. During the experiment, muons are injected into a large superconducting ring. A muon decays to an electron and the electron curls to the inside of the storage ring and strikes an array of lead fluoride crystals. When an electron hits a crystal, it produces light that is proportional in intensity to the energy of the electron. The energy and the time of its arrival help to indicate the direction of the spin which is used in the calculation of g-2. My research investigates how light is propagated and distributed in these crystals and how different reflective or absorptive wrappings affect this distribution. I measure light yield and pulse width, which correspond to two different extremes of wrapping material. For maximum light yield, I use a special reflective white paper called Millipore, while shorter pulse widths are achieved using an absorptive black Tedlar paper. I have developed a 2x2 array of crystals coupled to light sensitive photomultiplier tubes. This setup, which is configured for easy switching of the wrapping material, captures cosmic ray muons that hit the surface of the earth. Capturing these muons simulates the conditions of the experiment. I analyze the resulting data by fitting the pulses and extracting the functional form of the light distribution. The results of this research will ultimately contribute to the development of more complete theories of the fundamental building blocks of the universe.

Recovery of the Pacific Northwest native Olympia oyster (Ostrea lurida) population after a near-collapse in the industry has been slowed due to several factors. Though no longer the prominent oyster along the west coast of North America, the Olympia oyster remains an important commercial, cultural, and ecological species. Effective conservation efforts are dependent on understanding the oyster’s physiology and distribution. Establishing detailed genomic resources is crucial to enhance effective management of the Olympia oyster. This study aims to extend existing research on the Olympia oyster transcriptome by characterizing the gonadal transcriptomes male and female oysters. Resulting contig sequences were compared with ProtKB/Swiss-prot database and further annotated with Gene Ontology associations. Furthermore potential genetic markers were identified. These resources add to genomic tools available for future conservation of Ostrea lurida and provide novel insight into reproductive function in bivalves.

Mitochondria are essential organelles in eukaryotic cells and are most commonly known for their prominent role in energy production. In addition, mitochondria are involved in other important cellular processes such as lipid biosynthesis and apoptotic cell death. Mitochondria also have dynamic properties including fusion, division, and movement, which are all essential to maintain mitochondrial function. Given the plethora of essential cellular activities that require mitochondrial function, it is not surprising that defects in mitochondrial function are implicated in many different human diseases and disorders including diabetes and myopathies. Mitochondrial movement is important for the distribution of mitochondria, which is important in all cells, but especially important for asymmetric cells such as neurons. Transport is also required for mitochondrial fusion – the two organelles must move close enough to each other to fuse. Mitochondrial fusion in particular is required to maintain mitochondrial DNA and therefore, mitochondrial function. We are interested in the mechanism of mitochondrial movement and the connection between mitochondrial fusion and transport. Mitochondria move on microtubules using a complex of proteins. Miro 1 and Miro 2 are anchored to the mitochondrial outer membrane and interact with two adaptor proteins, TRAK1 and TRAK2. The TRAK proteins also interact with Kinesin, which binds to the microtubules and mediates microtubule-directed movement. Understanding the assembly and regulation of this complex and the stoichiometry of its components will provide insights into the mechanism of microtubule-directed mitochondrial movement. Our goal is to clone TRAK1 and TRAK2 complementary DNA (cDNA) into expression vectors for protein production in Escherichia coli cells and then to develop a purification protocol for TRAK1 and TRAK2. This will facilitate biochemical analysis of the mitochondrial motility complex.

Ion thrusters have a wide range of applications because of the small amount of fuel needed in order to make large delta-V maneuvers. One possible ion thruster concept is for use in the upper Martian atmosphere which is comprised of mainly CO_2. At lower orbits where the atmosphere is still faintly present, an ion thruster could be used to provide constant thrust, and keep a low orbiting satellite in this orbit for an extended duration without the satellite falling due to the drag caused by the upper Martian atmosphere. The research being presented is on an air breathing low mars orbit electrostatic ion thruster concept that uses trace amounts of CO_2 in the upper Martian atmosphere as the plasma fuel source. Our team has designed, built and tested an ion thruster testing this concept. The ion thruster has a cylindrical chamber with an inner chamber diameter of 4.8 inches. The plasma is created by ionizing CO_2 gas with emitted electrons from a tungsten filament cathode in a 12 inch diameter vacuum chamber. A two screen electrostatic grid is used to control the plasma and accelerate ions in order to produce thrust. The ion beam is neutralized using another tungsten filament cathode. Four separate power supplies were used in order to create the plasma, supply voltage to the electrostatic grids, neutralize the ion beam, and create the axial magnetic field that controls the electrons inside the thruster. The high velocity ions that are generated by the thruster are emitted in a controlled fashion that then produces thrust. This thrust was calculated by using the measured power going to the neutralizer cathode, and the particle exhaust velocity. The exhaust velocity was calculated from the separation between grids, and the potential difference applied across the grids.

Atmospheric particles and gases play a large role in Earth’s climate and have negative impacts on human health. Currently, there are air quality standards for the mass concentration of particles less than 2.5 micrometers in diameter, PM_2.5. However, there are no standards for ultrafine particles, i.e. those smaller than 0.1 micrometers, even though studies have shown that ultrafines can cause negative respiratory health effects. The mass and number concentrations of ultrafines, and therefore their sources and concentrations, are not well characterized. We report measurements of ultrafine particle concentration and size distributions in Port Angeles, Washington made using a Scanning Mobility Particle Sizer (SMPS). We used the observed diurnal cycle and seasonal variations in ultrafine particle abundance to gain insights into the primary sources in this region, including traffic, wood smoke from residential heating, and shipping, among others. By analyzing data from the SMPS together with wind direction and speed, we assessed the potential contribution of specific point sources, such as the new biomass cogeneration facility or specific roadways. We conclude with a discussion of the current site location and implications for a forthcoming study in nearby Port Townsend.

Fanconi anemia (FA) is a genetically inherited disease that frequently results in bone marrow failure, a high prevalence of leukemia, and solid tumors of the head and neck that are associated with genomic instability. Abnormal chromosome configurations produced in FA cells, called radials, are diagnostic of the disease. The mechanism of radial formation is not fully understood. However, they can be induced to form by exposure of cells to agents that promote a type of DNA damage called interstrand crosslinks (ICLs), covalently bonded DNA strands caused by exposure to ICL inducing agents such as those used in chemotherapy or endogenously produced metabolic byproducts. Radials can occur spontaneously in the cells of FA patients, therefore, understanding the formation of radials, as well as their fate during the cell cycle, may help in designing effective therapies to counteract the genomic instability. The current aim is to investigate radial formation and cell recovery afterwards through careful examination and identification of structural abnormalities in chromosomes that may be a result of prior radial formation. To carry out this goal, a population study will be performed using the primary PD20 (FANCD2) cell line. Mitomycin C (MMC) will be used to induce ICLs and cells will be harvested with paired controls at multiple time points following damage. Cells will be analyzed using classical G-banding for the presence of structural and numerical chromosome abnormalities. A significant increase in chromosome abnormalities structurally consistent with radials that have gone through mitosis is expected to be observed during analysis.

Paleoclimate data suggest that anomalously cold conditions across the Northern Hemisphere (NH) and a southward shift of the Intertropical Convergence Zone (ITCZ), a major feature of the tropical atmosphere, occurred during the Little Ice Age (LIA) ~ 1350 – 1850 AD. The purpose of this research is to identify whether these climate changes are simulated by the latest Coupled Model Intercomparison Project (CMIP5) General Circulation Models, and whether they can be attributed to changes in solar irradiance, volcanic aerosols, and greenhouse gas concentrations. In each model, two types of runs are analyzed: pre-industrial control runs and last millennium runs. The pre-industrial control runs are 1,000-year runs with external forcings held at 1850 AD levels and the last millennium runs are 1,000-year runs with external forcings that change over time in accordance with paleoclimate records. While anomalous global cooling occurs during the LIA in all models, little agreement exists on the magnitude of the cooling and the changes in interhemispheric temperature gradient. In addition, changes in the position of the ITCZ are small and vary widely between models. We perform an energy budget analysis using the approximate partial radiative perturbation method to further investigate the LIA temperature and the ITCZ changes. Volcanic aerosol forcing and surface albedo feedbacks appear to be the main drivers of global cooling during the LIA, while the contribution from changes in solar irradiance is small. Changes in the position of the ITCZ are well correlated with changes in cross-equatorial atmospheric heat transport, as expected from theory.

Entamoeba histolytica is a water-born pathogen that is estimated to cause 100,000 deaths annually in developing countries. The disease is prevalent especially in tropical areas with poor sanitary conditions, and is treatable with appropriate antimicrobial medication. Therefore, detection of the pathogen is vital in diagnosis. We developed a sensitive electrochemical assay utilizing novel yeast-scFv detection probes targeted at E. histolytica parasite antigens in stool samples. I have previously tested the assay in solution (buffer and stool dilution) with several antigens and proved sensitivity. This project is a stability study of the assay assembled on the electrodes. I tested factors including temperature, pH, humidity, pressure, and light sensitivity to determine the optimal conditions for long-term storage and transport, as well as the limit that one factor can be pushed while maintaining sensitivity. The significance of this project is to maximize the assay’s shelf life and thus to minimize the cost of manufacture and transportation of the assembled product. Consequently, it will benefit clinicians and patients in poor countries where the disease is prevalent, as a broader population of people around the globe.

Transforming growth factor-beta (TGF-β) signaling in smooth muscle cells (SMC) contributes to normal vascular development but may also play a significant role in the progression of aortic disease. Accordingly, TGF-β signaling is emerging as a therapeutic target, with strategies to block TGF-β signaling proposed as a means of preventing human aortic disease, including aortic aneurysms and dissections. However, because TGF-β signaling contributes to normal vascular development, blockade of TGF-β signaling could be harmful. We hypothesized that elimination of TGF-β signaling in aortic SMC of adult mice would cause aortic disease. We used inducible Cre-lox recombination technology to knock out Tgfbr2 in adult murine SMC. Tgfbr2 encodes TGF-β receptor II, believed to be essential for all TGF-β signaling. Mice were euthanized 4-14 weeks after SMC Tgfbr2 knockout, and effects of Tgfbr2 knockout (compared to control mice) were assessed by gross observation of aortas as well as sectioning and staining of aortic tissue. We found intramural hematomas, penetrating aortic ulcers, aortic dissection, and aortic dilation as well as significant thickening of the medial wall and adventitia in the knockout mice. Our data strongly suggest that loss of TGF-β signaling in SMC has a negative effect on aortic health and support a cautious approach in pursuing blockade of TGF-β signaling as a therapeutic strategy.

In my research, I am studying what composes the identity of a city, how we can perceive a city differently from another city. In architecture studios, we learn how to design for human experiences - what it would be like to be in the spaces that we design. To design for a complete sequence of experience, I first need to understand how people experience, see and read spaces they occupy, understand their process of passive and active perceiving and sensing. The urban city is a good place to study this because it has its duration and complexity. Experiencing a city is an open ended continuous process. What you see at a certain moment at a certain time represents a snap shot of many conflicts happening in a city. To experience is to perceive. It requires both immediate sensation and memory of past experience. What people perceive is identity. The identity of a city is shaped by the physical built environments, and the identities and activities of people in these environments. Action and interaction are important because identity does not mean anything until there is interaction between differences and conflicts. I am studying the identity that defines a city from other cities; how people perceive, act and interact with the built environments, and with each other; and also how the city shapes their action and interaction through the built environments. Looking at films gives a better sense of these actions and interactions because they are visually presented. I use films to look at urbanism, the portrait of city, the life within city, and the vision of city. Using the city of Seattle as an example, I will document my own experience through this urban environment, and also observe how other people act and interact in public spaces in this city.

The purpose of this research is the development of a precisely electroplated set of vacuum capacitor electrodes for inclusion in the MAJORANA Demonstrator (MJD) - the first stage of the MAJORANA project. Funded by the Department of Energy the MAJORANA program is part of an international effort to study neutrinos, dark matter, and axions led by the UW Center for Experimental Nuclear Physics and Astrophysics (CENPA). The project focus is on making the capacitors with a physical dimension tolerance (<2 microns) that is far less than what can be obtained via machining or other comparable methods of manufacturing. The desired capacitors are made using high-aspect ratio patterns in silicon as an electroplating mold. Silicon wafers are coated with an electroplating seed layer and then bonded to each other using thermcompression wafer bonding. Thermocompression bonding is a technique used to bond wafers by applying heat and force simultaneously. Following bonding, the wafers are patterned, using a photolithography process and Deep Reactive Ion Etching (DRIE), to form the mold cavaties. Photolithography is a multiple step process that includes application and patterning of a light-sensitive material called photoresist. Next, bottom-up copper electroplating is performed until excess deposit of copper called over-plating is achieved. The over-plated structures are polished back to establish dimensional uniformity. The final step is releasing the electroplated structures via a blanket DRIE process. Successful completion of this research project will allow assembly of MJD which in turn will be used to search for neutrinoless double-beta decay – one of the rarest forms of radioactive deacy. This project will also be a primer for more industry-focused capabilities for the Washington Nanofabrication Facility (WNF) with eventual development of through-silicon vias (TSVs) for research applications and a potential foundry process for precision part creation without the limitations of machining.

There is a wide-spread belief among professionals and parents that raising children with Autism Spectrum Disorders (ASD) in bilingual households will be detrimental to their language development. Although some early studies reported an association between bilingualism and cognitive deficits, more recent studies have called these findings into question. Furthermore, the few studies of ASD and bilingualism also support potential benefits. Children with ASD from multilingual households have been shown to demonstrate increased gesturing and sociability. Our study proposes to directly investigate the relationship between bilingual environment, social ability, and language ability in toddlers with ASD. We hypothesize that toddlers with ASD who grow up in a bilingual environment will exhibit greater social ability and increased language ability compared to toddlers with ASD from monolingual households. Thirty-eight, 12-24 month-old toddlers from the UW Autism Center who were part of a larger, multisite study were categorized based on their mother’s language ability: bilingual (BL; 18) and monolingual (ML; 20). Language measures included the MacArthur-Bates Communicative Development Inventory, Communication subscale of the Vineland Adaptive Behavior Scales (VABS-II), and Expressive and Receptive Language subscales from the Mullen Scales of Early Learning. Social skills measures included the VABS-II Socialization subscale and a measure of joint attention. We will use two sample t-tests to compare social skills and language skills between the two experimental groups. This research will provide some of the first direct evidence regarding the impact of a bilingual language environment on the early social and language abilities of very young children with ASD. We hope to raise awareness towards the need for evidence-based approaches to guide professional and parents of young children with ASD.