Why are urban forests not replacing themselves?  For example, recent surveys demonstrate that adult trees are dying faster than new saplings are recruiting in Seattle (Washington), implying that the health of local coniferous forests is in decline.  Extensive resources are spent planting trees to combat this problem, but the underlying causes of this "lost generation" of trees remains unknown.  We investigate factors limiting seedling establishment of native conifers (Thuja plicata, Tsuga heterophylla) in Seattle, and use results to suggest strategies resource managers can use to address the "lost generation" problem.  We examine the effect of removing non-native English Ivy (Hedera helix) and adding mulch to understand what is limiting conifer regeneration, and to explore possible management techniques for improving growth and survival of transplanted seedlings.  We measured survival, general health (visually assessed), and height as response variables to the two treatments.  As of yet, no studies have empirically tested both of these factors.  We observed the highest transplant survival rates in areas where mulch was added, for both focal species.  Surviving transplants in the mulch treatment were also healthier than the transplants with no mulch added.  Ivy presence did not affect health or survival of either species, but it did affect growth of Tsuga heterophylla.  Treatments affected growth of the two species differently.  Growth of Thuja plicata was not affected by either treatment.  For Tsuga heterophylla, however, growth was highest in the ivy-removed treatment, but was not significantly affected by the presence of mulch.  Our results suggest that seedling survival is limited by a lack of mulch and that competition with invasive understory plants may limit growth for some species.  Our recommendations for park management are therefore that restoration transplants should be paired with mulch addition, as well as Hedera helix removal for Tsuga heterophylla, to maximize survival and growth.

Measuring client adjustment throughout psychotherapy has been supported as a method to improve client outcome upon cessation of treatment. Weekly assessments inform the clinician how the client is responding to therapy and illuminate when adjustments to treatment may be necessary.  The Evidence-Based Assessment System for Clinicians (EAS-C) is a computerized outcome tracking system that allows psychotherapists to measure weekly progress and instantly view results with their clients in session. While there are excellent measures for tracking general psychological adjustment, many are too lengthy and arduous to facilitate completion on a weekly basis. Therefore, we created the seven-item Brief Adjustment Scale for EAS-C. We hypothesized a high correlation between the BASE-7 and the Outcome-Questionnaire 45.2, an established measure of psychological functioning. Furthermore, we hypothesized participants would report more willingness to complete the BASE-7 and would rate it as easier to complete than the OQ-45.2. Adult participants were recruited through the online survey website, Mechanical Turk, and completed the BASE-7, OQ-45.2, and an acceptability and utility questionnaire online. The BASE-7 correlated highly with the OQ-45.2, indicating high concurrent validity. Participants rated the BASE-7 significantly more acceptable than the OQ-45.2, suggesting participants would be more willing to complete the BASE-7 on a weekly basis. Participants’ ratings of the utility of the BASE-7 and the OQ-45.2 were not significantly different, indicating participants believed both measures would adequately communicate levels of psychological distress to a mental health provider. These findings demonstrate that the BASE-7 is a valid tool for measuring psychological distress that may be more suitable for weekly administration than lengthier measures. As a brief outcome measure, the BASE-7 is a promising new tool that may be used to inform both clinician and client of treatment progress over time.

Augmenting course material to be relevant and accessible to students is a ubiquitous challenge throughout academia. We aimed to design, develop, and evaluate the effectiveness of activities meant to promote the learning of difficult concepts in Anatomy and Physiology. More specifically, we focused on the neurophysiology chapter of an open access Anatomy and Physiology course sponsored by the Carnegie Mellon Open Learning Initiative (OLI). This course is being created for pre-nursing students attending community colleges. We used the six-level schema of Bloom’s Taxonomy, a module addressing the knowledge and development of intellectual skills, to design learning activities that encouraged students to analyze, synthesize, and evaluate concepts rather than simply recall, explain, and define them. By compelling students to work at higher cognitive levels during the learning process, we hypothesized that there would be a corresponding elevation in critical thinking skills and a deeper understanding of the material. Our curriculum design strategy was informed by cognitive science research that shows increases in learning efficacy when students are motivated to work at higher cognitive levels. Assessments were designed to align with these higher cognitive level learning activities. Our learning activities were tested by Anatomy and Physiology students using Carnegie Mellon’s OLI course. The Carnegie Mellon course uses an innovative digital dashboard platform which allowed us to track individual student’s understanding of concepts before, during, and after using our materials so that we were able to analyze their success and effectiveness. We revised our learning activities based on these results.

People always say ‘never talk about religion at a party,’ this is true even for college students. But if you’re a female in college, talking about religion is not only taboo, it’s unheard of. After being brought up by parents with two different ideologies, Christianity and Islam, I set out with this research project to better understand what role religion plays for my other female peers. Analyzing predominantly what their chosen theology means to their identity, how they advocate for their faith, how their ideology intersects with dating and what they perceive to be the biggest misconception about them for being religiously affiliated. I chose women who were students at UW from a variety of majors who identified with either Christian or Islamic based faiths, since this is where the majority of my previous research and experience has been. My primary methods were through long-form interviews, ethnographic observations and interacting with them on a daily basis as they moved their lives and their faith. Hearing about the challenges these women overcome on a daily basis just for identifying with a particular religion has solidified my hypothesis that ideology plays a pivotal role in their undergraduate career. Based on my research thus far, it has proven that it affects them in regards to their academics, involvement on campus and their interactions with their peers on campus. Further research will yield more information about the depth that these affects have taken. Overall, the outcomes have also been both surprising and inspirational to see how these women embrace, advocate and represent their faith. This work aims to open up and spark some dialogue about what religion means to college students and how societal framework does not always accurately represent these identities.

According to the World Health Organization, every year about 3.3 million babies are stillborn and more than 4 million die within 28 days of birth. Yet the death of a baby remains a very difficult subject in contemporary American society and bereavement interventions in perinatal medicine are still quite limited. This research will expand our understanding of the role photography plays in assisting parents with the process of mourning neonatal, perinatal, and infant death. By examining the perspectives of healthcare professionals, photographers, and parents in regard to the practice of bereavement photography, the research will investigate the ways in which photographs are used and transmitted, in both the private realm of bereaved families and the public domain of cyberspace. This study aims to understand how photography is used in the process of memory making and consequently, how the act of creating memories enables emotional healing. Finally, it will explore how bereavement photography exists at the junction of two shifts simultaneously occurring in cultural practices and social attitudes: the renegotiation of the boundaries between public and private, and the development of newer, characteristically modern, expressions of grief. This work has the potential to raise awareness about this developing mourning practice and increase the efficacy of bereavement interventions in neonatal and perinatal care, with the ultimate goal of providing a more widely available framework for helping parents cope with this hitherto often unspoken of, and invisible, loss.

Although college student drinking receives considerable attention (Hingson, Heeren, Winter, & Wechsler, 2005), and depression rates are known to be high (ACHA, 2010), less is known about how these rates vary for immigrant students. The current research focuses on differences between students born outside of the U.S. and native students in drinking and mood, and is part of a larger study on developing an on-line intervention for students who have both high-risk drinking and depression symptoms. Immigrant students may experience challenges related to “acculturative stress”, or being the first in their family to attend college. These students may be at a higher risk than other college students (Buddington, 2002 ), yet few studies have investigated drinking behaviors and depression rates of this population. Some evidence suggests increased drinking in U.S. students studying abroad (Pederson, Larimer & Lee, 2010) yet it is uncertain how students who have moved here from abroad compare.  Analyses will examine whether immigrant students differ in drinking and depressed mood from native students. Study participants (N = 1,603; 57% female; mean age = 19.6 years) were students at a west coast university. The Alcohol Use Disorders Identification Test (AUDIT) was used to measure alcohol consumption and the Beck Depression Inventory-II (BDI-II) was used to measure depressed mood. 15.6% of participants reported being born outside the United States. Those born outside the U.S. reported significantly lower AUDIT scores (M=3.91 vs. M=6.80, t(1601) = 6.90, p <.001) and more depression (M=11.09 vs. M=8.50, t(1601) = 4.30, p <.001) than native students. Additionally, we will examine whether students’ immigration status and how many years they have lived in the US moderate the relationship between alcohol use and depression. An understanding of specific drinking patterns and depression rates among immigrant students could aid in the development of targeted interventions for this population. 

In a world of childhood obesity, soaring gas prices and climate instability, bicycles are quickly becoming a socially, environmentally and economically sustainable alternative to single occupancy vehicles. In May, I will be organizing chaperoned bike-trains for elementary school children in Wedgwood and Thornton Creek elementary schools, with the intention of increasing the number of children commuting by bicycle. A bike-train is comprised of elementary school children and adult chaperones riding safe and efficient pre-determined routes to school. Children learn bicycle safety, rules of the road, and riding etiquette, all while acquiring social and communication skills, as well as physical confidence. These rides also build community among adults, as chaperoning, organizing and discovering shared passions are all part of this process. While implementing bike-trains is a small-scale project, it addresses the most pressing issues of our day: health concerns, social isolation and environmental degradation. This project will examine two methods of organized bike-trains:  traditional, multi-stop routes in at Thornton Creek Elementary, and a more casual "meet and ride" route at Wedgwood Elementary. With the culmination of this project, I will compare the outcomes of both methods of bike-trains, compiling my research into a document enabling parents, teachers and staff throughout Seattle schools - and potentially worldwide - to implement bike-trains in their communities. Bike-trains, an experiment in applied research, cultivate local solutions to current global concerns.

The Short-tailed Albatross (Phoebastria albatrus) is listed as endangered under the US Endangered Species Act (ESA) due to small population size, and limited breeding range. The Short-tailed Albatross (STAL) breeds on Torishima and Minami-kojima Islands off Japan and migrates to Alaskan waters during the summer. The NOAA Alaska Fisheries Science Center’s Observer Program, in collaboration with the USFWS, instructs observers to carry out seabird monitoring activities in addition to their recording of bycatch during fishing operations. Using Observer Program seabird sightings and vessel-bird interaction data from 1993-2009, we examined potential vessel interaction threats to the recovery of the population, as well as the frequency and geographic expansion of Short-tailed Albatross sightings. Our data indicate that Short-tailed Albatross sightings increased more than the Short-tailed Albatross population during this time period (6.5% population growth per year), with observer days remaining relatively stable. We also found that incidences of discard feeding and/or vessel following are not increasing disproportionately to population size as the population continues to grow, thus it is unlikely that vessel interactions threaten the STAL population recovery. Lastly, we found that the sightings of Short-tailed Albatross show an eastward expansion since 1993, thus suggesting an expansion of this species within their historic range.

While sexual co-mingling of the races in the Americas began as early as the first cases of colonization, miscegenation remained an unspoken taboo in America until roughly the mid-century, when many cases of mixed-race couples began increasing in visibility in local communities, popular culture, and the courts. These couples found themselves thrust into the spotlight as either martyrs for the cause, fuel for the propaganda against mixed unions, or examples for popular interest pieces in magazines and newspapers. The role of news outlets in bringing public awareness to the presence of interracial relationships, for good or for bad, was crucial. This project explores newspaper articles over a 20 year period (late 1950s through the early 1970s) from three American Black newspapers: New York Amsterdam News, Pittsburg Courier, and Atlanta Daily World, and analyzes them from several perspectives, considering regional differences, date of the article (before or after the Loving v. Virginia decision), and subject matter of the article. Findings revealed several themes: emphasis on the white, female opinion, shifting generational divides, and the role of celebrity and celebrity mixed unions in public interracial marriage awareness. This project displays my discoveries in how the black community felt about interracial marriages during this period, as well as how the black media sought to influence public opinion regarding the topic.

Minimally invasive surgical (MIS) techniques, such as laparoscopic surgery (performed through small incisions using specialized tools), are an integral part of modern medicine and the future of surgery. Technologically advanced tools such as MIS robots are promising to replace or augment existing MIS manual tools. MIS robots improve on manual surgery, as they can incorporate increasingly sophisticated features such as force feedback for surgeons, automatic identification of diseased tissues, and partial automation of surgical tasks. These features can reduce patient pain, recovery time and thus healthcare costs by eliminating unintended damage to tissue and providing surgeons with tools to perform surgery more effectively. Each of these new features either requires or would greatly benefit from an accurate mathematical description of the dynamic mechanical properties for the tissues with which surgeons interact. Dynamic tissue property quantification requires that we apply a range of forces to the tissue and measure the resulting displacements. We have designed, built, and calibrated a device capable of collecting the necessary data to obtain an equation relating applied force to tissue displacement for any tissue of interest. We will process the data obtained from this device using an advanced signal processing and system identification algorithm (unscented Kalman filtering), which will evaluate the fit to the data recursively over time. This will allow us to maintain accurate results as the tissue properties change over time. This setup allows us to collect and analyze data from tissues including (but not limited to) in vivo abdominal organs in pigs. In addition to being an important study that has not been performed in the literature, the real-time collection and analysis of this data could have profound implications in partially automating surgery.

M dwarf stars, which are smaller, dimmer, and redder than our Sun, are the most common type of star in our galaxy. Like our Sun, these stars exhibit activity due to inherently strong magnetic fields at their surfaces. In M dwarfs, this activity is often classified by the emission line strength of the first transition of the hydrogen Balmer series (H alpha). We examine a sample of five equal-mass M dwarf wide binaries; these “twin” stars should have nearly identical stellar properties and therefore have very similar spectral features. We hypothesize that these stars should exhibit nearly identical properties in H alpha. If our hypothesis proves false, it means there are unexpected dynamics present in the binary system. In initial observations to classify these objects, we found that the M dwarfs in each binary, which were twins in every other way, showed very different levels of H alpha emission. To examine the range of H alpha line strengths we obtained a time series of optical spectra using the Astrophysical Research Consortium’s 3.5-meter telescope at Apache Point Observatory in New Mexico. In each binary, the slightly less massive star exhibits stronger mean H alpha, consistent with large survey results. Using data from 70 hours over 14 nights, we determined our stars have a characteristic variability timescale of around 2 hours; indicating our sample is active on shorter timescales than the typical rotational period.

When massive stars reach the end of their lives, they erupt in enormous explosions known as supernovae, leaving behind clouds of shocked gas and dust known as supernova remnants (SNR). The primary technique to measure the mass of the progenitor star requires waiting for the star to explode and examining pre-explosion Hubble Space Telescope archival images of the site, which may or may not exist. This technique is constrained by rarity of supernovae, and as such only ~25 progenitors have any mass constraint whatsoever in the literature. We employ an alternative technique in which we examine color-magnitude diagrams of the regions surrounding known supernovae to measure their star formation history. We then use this star formation history to assign an age to the progenitor star.  By employing stellar evolution models, we convert this age to a mass. Because we do not rely on identification of the specific progenitor star in the images, we are free to apply our technique to cataloged SNR, drastically increasing the number of available targets. We apply our method to ~135 cataloged remnants in the nearby spiral galaxies M31 and M33, representing a dramatic increase in the number of currently known masses. We examine the distribution of these derived masses and comment on implications for supernova physics.

Embryonic stem cells are isolated from the early developing embryo and are capable of forming the different cell types found in the body. Understanding how these cells develop and maintain their specialized state is critical to understanding how they function. We hypothesize that embryonic stem cells acquire a unique metabolic state that aids them in maintaining their specialized state. Using two distinct mouse pluripotent states, embryonic stem cells (ESC’s) and epiblast stem cells (EpiSC’s) representing cells isolated from the inner cell mass of the blastocyst and the epiblast, a later stage in embryonic development, we found that EpiSC’s are much more glycolytic in terms of their energy usage compared to ESC’s as measured by oxygen consumption and extracellular acidification rates. Furthermore, using quantitative polymerase chain reaction experiments, we found that genes key to regulating and maintaining high rates of glycolysis are significantly upregulated in EpiSC’s compared to ESC’s. We showed that the overexpression of HIF1α, a known key regulator of these glycolytic genes, in ESC’s is able to shift the ESC’s towards a more glycolytic metabolic state and cellular morphology reminiscent of EpiSC’s. In addition, transition of ESC’s to EpiSC’s using the known chemical inducers Activin and Fibroblast Growth Factor 2 revealed that changes in the expression of metabolic genes occur prior to changes in expression of cell fate markers, which suggest that a metabolic transition in the ESC’s may be key in its transition to an EpiSC-like state.

Understanding stem cell maintenance is crucial for delineating conditions such as tissue loss, aging, and cancer. Using the Drosophila female germ-line stem cell (GSC) model to observe stem cells in vivo, several extrinsic and intrinsic factors have been demonstrated to regulate maintenance of Drosophila GSCs; they have also been found to be conserved in mammalian systems. The search is on for novel regulatory factors of stem cell maintenance with the hope of extending our understanding to stem cells in mammalian systems. My project involves the characterization of the molecular function of Pineapple eye gene (Pie), a novel regulator of GSC maintenance. Through a loss-of-function screen in GSCs, it has been demonstrated that mutations of pie result in GSC maintenance failure. The amino acid sequence of pie revealed that it contains ring-domains suggesting possible E3 ubiquitin ligase function. Such proteins are key components of the ubiquitination pathway, which are involved in protein tagging and degradation. To test pie’s function as an E3 ligase, I am using a novel assay that employs the fact that bacteria do not have endogenous ubiquitination pathway and therefore utilizes Escheria coli as an in vivo system to express the components of the ubiquitination pathway and detect the formation of ubiquitin chains, a key indicator of E3 Ligase activity. I have demonstrated that the expression of pie’s ring-domains without a substrate is not sufficient for the detection of ubiquitin chains. I will now test whether the full length pie is necessary for proper ubiquitination. Further, I will also test whether pie’s functional domain needs a substrate in order to function effectively. Successful characterization of pie can reveal new pathways to target for conditions involving stem cell maintenance.

MicroRNAs (miRNAs) are small noncoding RNA molecules that post-transcriptionally regulate gene expression. MiRNA biogenesis involves two key ribonucleases, Drosha and Dicer. I am investigating the Drosha enzyme. Previous research from the Ruohola-Baker lab reveals that reducing levels of Drosha in stem cells significantly reduces levels of some miRNAs, while only slightly reducing levels of another group of miRNAs. This surprising result led us to conduct a bioinformatics analysis to identify characteristics that differentiate these two groups of miRNAs. We discovered structural differences, specifically that bulges in the central region of miRNAs were more frequent in heavily reduced miRNAs than in miRNAs that were not affected. My mentor, Henrik Sperber and I propose a model explaining why miRNAs with mismatches (bulges) in the central region of the sequence are more sensitive to reduced levels of Drosha than rigid miRNAs with no mismatches in that region. To test whether a bulge causes differential miRNA processing when Drosha is the limiting factor, I am adding and removing bulges to primary miRNA transcripts, overexpressing them in cells with low Drosha levels, and comparing their mature levels using qPCR. In addition, I am testing whether in nature cells vary Drosha levels as a mode of regulation. A previous study shows that T cells at specific stages of differentiation reduce Drosha expression by as much as 10 fold. My own bioinformatics analysis reveals that certain tissues in mice have an 8-fold reduction of Drosha. To see whether reduction of Drosha levels correlates with differential microRNA processing, I am using microarray data to find subsets of microRNAs that have dramatically reduced levels when Drosha expression is significantly low. With my research, I hope to discover a potentially novel mechanism of regulation in which cells alter Drosha levels to selectively process a subgroup of miRNAs.

A dance, a piece of art that is naturally ephemeral, is very difficult to preserve. Though it can be partially captured through film or notation, neither of these two-dimensional forms of archiving fully encapsulates the experience of a dance for either audience or performer. The only way to truly bring a dance to life is to perform it. Because a dance is at once a living participant and observer of the cultural context in which it was created, as well as a work of art, by researching and performing historical dances we can reach a more complete appreciation of culture past and present. A great part of the research done to better understand the historical role and importance of a dance will in fact come through the act of meticulously recreating the art work in the present day. This year the Chamber Dance Company researches and performs eleven works of dance by choreographers Ethel Winter, Helen Tamiris, Mary Wigman, Ruth St. Denis, Jean Erdman, Susan Marshall, and Louis Falco. We look for insights that elucidate historical issues of the time through embodying the movement. For example, in St. Denis' work we see cultural appropriation of Orientalism; in Tamiris we look at how and why a white Jewish American woman made dances about African American oppression; and in Wigman's work how dance was able to slip through the iron fist of Nazi censorship. This presentation will be a preview of the choreographed works to be performed by the Chamber Dance Company in October 2012.

Kaposi's Sarcoma-Associated Herpesvirus (KSHV) is a gamma2-herpesvirus that infects humans and can cause tumors in immunosuppressed individuals. Rhesus rhadinovirus (RRV) is a related herpesvirus of macaques that is similar to KSHV, but has significant differences as well. While KSHV infections are predominantly latent with only low levels of spontaneous replication, RRV replicates much more readily. For this reason, RRV is a useful tool in studying the mechanisms of reactivation and replication of rhadinoviruses. We sought to identify the regulatory promoter elements of the replication and transactivator (Rta) gene, which induces the lytic stage of the virus. To find this, we transfected cells with different length clones of the Rta promoter region and tested the activity using luciferase assays. We identified a potential binding site of the transcription factor Sp1 and tested its function through mutagenesis. Our results indicate that the Sp1 binding site is required for high level promoter activity suggesting that this is an important regulatory element within the promoter sequence. We also tested the activity of the RRV Rta promoter in the presence of the RRV latency associated nuclear antigen (LANA), a gene known to inhibit replication through suppression of Rta expression in KSHV. We found that with LANA present, the activity of the Rta promoter decreases significantly. Because Rta has a critical role in viral replication, the regulation of the Rta promoter by the cellular factor Sp1 and the viral gene LANA may have important implication on the RRV life cycle.

Gliomas are invasive, fatal brain tumors that can be detected using magnetic resonance imaging (MRI). However, MRI does not reveal the entire size of tumor. By using a mathematical model developed by Kristin R. Swanson and colleagues, glioma growth can be quantified from the diffusion rate of the tumors cells, the net proliferation rate, and the carrying capacity of the tissue. These parameters are unique to each patient and can be determined by measuring the tumor volume from different MRI modalities as they change over time. Our lab collects data from patients consented to our study and records information about what treatments a given patient receives, since this can affect how the image appears. In my role as a member of the measurement team, I examine patient images to determine the extent of tumor burden on a given date. To obtain these measurements, I use Calcmri, a MATLAB program developed by our lab. Depending on the modality, enhancement on MRI slices can indicate tumor volume as well as other fluids. Calcmri can adjust the intensity threshold at which MRI enhancement will appear, which allows me to isolate the tumor and specify a region for the program to measure. I measure a series of two-dimensional cross section images in order to calculate a combined into 3-dimensional volume. These measurements are used to model the growth of the tumor, “in silico”. Our lab uses information from these models to discover clinical applications, such as to suggest more accurate treatment dosages and to predict life expectancy, which follows an overall goal to better capture the extent and invasion of tumor burden than what appears on MRI.

The harmful bloom-forming alga, Heterosigma akashiwo, has a dual-stage life cycle, transitioning between a vegetative, motile stage in the water column and a resting, non-motile stage in the sediments. Previous observations have revealed a large shift in neutral lipid content as cells transition between vegetative and resting life stages. The relative neutral lipid content per cell decreases as cells enter the resting stage, followed by a rapid synthesis of neutral lipids once cells emerge from the resting stage. Neutral lipid bodies are thought to be a source of cell energy reserves. The purpose of my research is to study how fatty acid profiles shift in H. akashiwo during these life cycle transitions. Understanding changes in fatty acid profiles is important in understanding how cells respond to changes in environmental conditions and how lipids are used in metabolic processes. In this study, two strains of H. akashiwo (CCMP 452 and UWC 13.03) are signaled to enter the resting stage by putting cell cultures into the dark at 10 °C for 18 days. Resting cells are activated by exposing the cultures to growth supporting conditions of light and increased temperature (12 °C). Cell viability and relative neutral lipid content is determined by staining with the SYTOX-Green DNA stain and the BODIPY505/515 neutral lipid stain, respectively, using flow cytometry. Fatty acid profiles are determined using an established gas chromatography- mass spectrometry method developed in the Cattolico laboratory. I will report on the outcomes of the fatty acid profiling for H. akashiwo over the alga’s dual-stage life cycle. I anticipate distinct change in the fatty acid profiles between these life stages.

Differentiated human embryonic stem cells (hESCs) demonstrate the potential for regenerative medicine and drug discovery utilizing rationally assigned cell fate. But hESC are limited by the technical difficulty of recapitulating an ever growing set of cellular phenotypes using a finite set of pluripotent cell lines. The resulting molecular deficiencies limit the ability of differentiated cells to integrate into host tissue, and diminish the translational potential of findings based on differentiated hESC. Induced pluripotent stem cells (iPSCs) can be derived from patients with or without genetic disorders, and have much greater use for drug discovery and basic research, and patient derived iPSCs are less prone to rejection by host tissue. However, iPSC generated by insertion of genes into the host genome, increasing risk of rejection and limiting maturation of iPSC-derived cells. RNA-induced pluripotent stem cells (RiPSC) offer a solution to problems of genomic modification by inducing pluripotency exclusively through the transfection of mRNA. MicroRNA (miRNA) exhibit widespread regulation of mRNA translation and degradation, and do not directly alter the genome. A bioinformatics study curating publicly available microarray data for components of the miRNA biogenesis pathway, pluripotency factors, and miRNA expression will generate hypotheses about the functions of miRNA and relevant proteins, with a focus on differentiation and neural cell fate. Quantification of miRNA and mRNA expression in hESC and RiPSC during retinal differentiation will support or disprove hypothesized relationships between protein and miRNA expression. Transfection of miRNA will be used to determine the ability of these miRNA to enhance differentiation and maturation of retinal cells. Additionally, the resulting retinal progenitors will be implanted into mouse retina, directly testing the potential of miRNA to improve clinical outcomes of stem cell based therapies for the nervous system.

The geographic ranges of species are strongly influenced by climate. As temperatures increase, species are expected to shift poleward in latitude and upward in elevation, a prediction supported by observations of range shifts in recent decades. Species interactions also play a crucial role in setting geographic ranges of global biomes, and could be critical in determining the response of species to climate change. Due to limited data on interspecific competition in the boreal biome, Earth's largest land biome, it is largely unclear how climate change will affect the range limits of the individual tree species that occupy it. In recent decades, spruce trees (Picea engelmannii) have increased in abundance at high elevation locations formerly dominated by larch trees (Larix lyallii). This change is thought to result from improved climatic conditions for spruce establishment but has not been tested. I hypothesize that spruce have higher establishment rates than larch where the two co-occur when temperatures are high. To test this hypothesis, I will harvest 120 stems of each species at locations in the North Cascade Mountains in the summer of 2012. I will then count the number of annual growth rings for each sapling to determine establishment year. Next, I will model the relationship between establishment rates and climate in different decades of the last ~100 years for each species. Finally, I will compare the establishment-climate relationships of the two species to infer how the relative abundances of the species might shift with warming. These results have large-scale implications for changes we should expect to see in global biomes as warming continues. In particular, this hypothesis suggests that spruce will replace larch as climate change progresses.

Autophagy, or “self-eating”, is a process cells use during times of stress or starvation to break down their own proteins or organelles to provide the required nutrients. I focused on the autophagy-related protein 13 (Atg13), a regulatory protein that controls the initial stages of autophagy. Specifically, I was interested in defining the distinct roles of the N and C-termini of the Atg13 protein. Using Saccharomyces cerevisiae expressing the full length, N-terminal, and C-terminal half of Atg13, I tested how these protein domains affected autophagy processing. To monitor this I looked at the autophagy dependent processing of aminopeptidase 1 (Ape1) and alkaline phosphotase 8 (pho8). Western blots were used to monitor the changes in Ape1 protein length after processing, and a colormetric phosphatase assay measured autophagy-dependent increases in pho8activity. Using these techniques I found that the two domains of Atg13 play distinct roles in the process of autophagy.

The diatoms are a prolific and productive group of phytoplankton belonging to the Phylum Heterokontophyta. They are responsible for ~23.5% of global primary production and their high photosynthetic capabilities depend on their abilities to synthesize chlorophyll. A key step in the biosynthesis of chlorophyll is catalyzed by the enzyme 'light-dependent protochlorophyllide oxidoreductase’ (POR). Early in the evolution of diatoms, the gene encoding this enzyme (por) was duplicated, resulting in two homologous but later divergent genes: por1 and por2. We aim to create a comprehensive heterokont por gene phylogeny to determine whether the gene duplication event occurred before diatoms diverged from sister taxa in the Heterokontophyta, early in diatom evolution, or in only one diatom lineage. Additionally, this phylogeny will allow us to determine the effects of natural selection in shaping the evolution of these genes. Preliminary studies suggest that positive selection acted in the past on both por1 and por2, though these protein sequences are now conserved within diatoms. To create this por gene phylogeny, we will sequence the por genes of various organisms representative of the major orders within the diatom class, Bacillariophyceae. Additionally, we have successfully sequenced numerous representatives of other Heterokont classes that will serve as the background to the Bacillariophyceaen gene phylogeny. These studies require the cultivation of various strains of algae, DNA extraction, PCR with por specific primers, and gene sequencing.

The lymphatic system is essential to fluid and cell transport, immune function, and tumor metastasis. Lymph drains from body extremities into lymph nodes, via lymphatic vessels, to present antigens to lymphocytes. This can result in an immune response. The existence of tumor cells in lymph nodes is a sign that cellular metastasis has occurred from the primary tumor. I am studying lymphangiogenesis, a process in which lymphatic vessels and sinuses grow and dilate in response to antigens or tumors, thus increasing the lymph flow and capacity to transport tumor cells in lymph nodes. Recently an antibody, 10.1.1, has been discovered to recognize an antigen that is selectively and highly expressed in lymphatic endothelium. The 10.1.1 antibody specifically induces lymph node lymphangiogenesis. This binding also induces proliferation of an unknown cell type in the lymph node. In comparison to the 10.1.1 antibody, injecting a nonspecific antibody control has no effect on lymphatic sinus growth. I am therefore studying how the 10.1.1 antibody rapidly induces lymphatic sinus growth, as well as what cell types contribute to making the new sinuses. I am using the technique of immunostaining to study the effects of the 10.1.1 antibody. By taking a frozen slice of lymphatic tissue and staining it with various antibodies to detect proliferating cells and their cell type, I can identify the specific kinds of cells that are forming into lymphatic sinuses. An understanding of how these lymphatic sinuses grow could help generate therapeutic strategies for manipulation of the lymphatic or immune responses. By inhibiting sinus growth and thus limiting lymph flow, it could be possible to prevent the metastasis of cancer.

The magnitude of trade in food within an increasingly globalized world has contributed to a situation where the populations that produce food often do not receive the ultimate benefits of their labor. For example, food production in one place might primarily support the production of manufactured goods and services that benefit people in distant places. The degree to which agriculture in a certain region supports economic activities abroad varies enormously across the globe. This study aims to understand how food production supports flows within the global economic system and contributes to unequal relationships between different regions of the world. To do this, global economic flows are modeled by entering production and consumption data into an interregional Social Accounting Model and analyzed within a geographic information system. From this, we have been able to identify the most important globalized croplands and categorize regions by the “function” they serve in global webs of production and consumption similar to an ecological trophic level analysis.  These results suggest that uneven flows of embodied food production between regions may be related to global patterns of poverty and health, as well as to the prospects for a more sustainable human ecosystem.

South Africa’s KwaZulu-Natal province currently has the highest HIV prevalence in the world at approximately 30%. The University of Washington’s International Clinical Research Center is currently conducting a pilot program for a new HIV testing method, Home-Based Counseling and Testing for HIV (HBCT), to address the HIV epidemic. A mathematical model of heterosexual HIV transmission in KwaZulu-Natal was created to evaluate the long-term consequences of HBCT on HIV prevalence. This model simulates a population of susceptible and infected individuals with varying sexual activity levels and therefore, risk. The model also divides the population among twelve age cohorts and the infected individuals are further divided into three HIV stages and a final AIDS stage, as defined by the World Health Organization. The model was created in MATLAB and validated with HIV prevalence data for KwaZulu-Natal from the Joint United Nations Programme on HIV/AIDS. Preliminary results from the model indicate that HBCT will diagnose more cases of HIV than other testing methods and, with successful linkage to care, will decrease HIV prevalence in the future. While the possibility of HIV elimination by HBCT is yet to be determined, preliminary results indicate that HBCT is effective at linking infected individuals with care, including antiretroviral therapy. This work has the potential to guide health policy in South Africa, and given the newfound effectiveness of pre-exposure prophylaxis and treatment as prevention, HBCT provides a promising future for controlling the HIV epidemic.

Shrimp waste-water (SWW) is rich in nutrients that include both phosphorus and nitrogen. A significant amount of money is spent by aqua culturists to eliminate these macronutrients before the water is released into the environment. In this study, we determined whether algae, which need phosphorus and nitrogen to grow, of commercial value (e.g., for biofuel, aqua feeds or neutraceutical production) can be maintained in this waste-water stream. Experiments tested for the ability of SWW to support algal growth when these organisms were grown in: (1) COREs media (control) as well as (2) SWW media (experimental) that contain: (a) no phosphate, (b) no nitrate, or (c) no nitrate or phosphate addition(s). Three algae that grow in marine waters were tested: B. chromulina, UWC 695, and Isochrysis galbana (UWC635) in each of the medium types listed above. Cell counts were taken regularly throughout the course of algal culture growth using a BD Flow cytometer. Neutral lipids and lipid profiles were measured using BODIPY 505/515 dye and Gas chromatography–mass spectrometry (GC/MS) analysis respectively.

Currently, freight models at the state level use a four-step modeling approach, which generates trips based on origins, destinations, and land use. In the personal travel sector, models have started taking into consideration entire tours based on household demographics. Freight modeling uses this same approach despite situational differences. In an effort to improve freight modeling, this research aims to identify characteristics of freight carrier companies that determine distinct freight movements. A survey of licensed motor carriers was designed and conducted in Washington State and Oregon State. The identical surveys conducted in both states consisted of 33 questions. Respondents were asked questions regarding their vehicle fleet, locations served, times traveled, types of deliveries, and commodities. A total of 614 complete responses were gathered. An analysis of the data, using statistical software R and Excel, aims to reveal clusters of company types that can be distinguished by determining characteristics such as company size, commodity, and role in a supply chain. By identifying unique patterns among the dependent variable such as travel distance, travel times, and delivery style, the results can then be integrated into state models to more accurately predict freight vehicle routes.

Organic photovoltaics (OPVs) are a promising solar energy technology due to the possibility of cost-competitive large-scale manufacture. Polymer based devices typically have a bulk heterojunction (BHJ) architecture. However, BHJ materials degrade rapidly under typical operating conditions, contributing to limited device lifetimes. The degradation due to photooxidation of a model OPV system of poly[9,9’-dioctylfluorene-alt-(bis(N,N’-(4-butylphenyl))-bis(N, N’-phenyl-1,4-phenylenediamine)] (PFB) and poly[9,9’-dioctylfluorene-alt-1,4-benzothaidiazole] (F8BT) was studied by attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR). Photooxidation products as a function of increasing photon dose at 405 nm were identified in PFB:F8BT, PFB-only, and F8BT-only films. Degradation kinetics on these films were determined by fitting Gaussian peaks to the IR spectra and measuring changes in peak area as a function of photon dose. Preliminary results suggest that multiple carbonyl species are formed in both polymers under ambient conditions. Analysis of the data collected in this experiment will be used to potentially evaluate the chemical kinetics of the degradation process and the formation of undesired chemical species in order to find a way to extend the lifetime of the device. Gaining insight into what limits the lifetime of current solar cell materials will help to improve the durability of plastic solar cells, and thereby solar energy as a widespread technology.

Presently, the United States uses 19.6 million barrels of oil per day. This amount represents 25% of the world’s total consumption, making the development of an alternative biofuel one of the world’s top energy and environmental priorities. Rose Ann Cattolico’s laboratory is working to create that alternative fuel through the use of algae lipids. A number of different tests are being conducted on physiology of selected algal strains with the goal of increasing fatty acid production. A most promising algal strain has been identified. This organism (referred to as P3) was recovered from a lake in Colorado. P3 was put through reiterative flow cytometry selection, creating what is now called P4. The P4 cultures were then subjected to antibiotic selection, creating P5.5 and P5.6. My study is to: (a) determine the taxonomic identity of this organism using molecular techniques. I hypothesize that this alga is a new species in the taxon Chrysochromulina and (b) document whether P3 has mutated while in culture. To achieve these goals I will do the following experiments. (a) The closest taxonomic relatives to Chrysochromulina sp (eg. C. parva) will be compared by sequencing the 18S ribosomal RNA, psbA , and nad5 genes. The results of these experiments will help determine the relationship of Chrysochromulina sp. and other members of this taxon. (b) The divergence of “derived strains” from P3 will be determined, which all iterations of P3 – P5.6 will be examined, using the same gene set presented above. Gene sequencing will also be used to check for other iterations of P3 that have been maintained in different media. My studies will reveal whether P3 has mutated as a result of directed evolution in the laboratory.

Routine ingestion of, and contact with, myriad chemical compounds in our environment impacts all aspects of human health, from psychiatric to oncological to acute and chronic toxicities. However, health outcomes resulting from exposure events are strongly influenced by genetic variability present in genes underlying pertinent metabolic pathways. There are four genes that have been identified in the literature as playing crucial roles in multiple and interrelated biochemical pathways, and which may have broad implications for human health. These genes include DRD4, which codes for the dopamine D4 receptor and has been linked to numerous neurological conditions including addictions, schizophrenia, bipolar disorder, and Parkinson’s disease; 5-HTTLPR, the serotonin-transporter-linked region that codes for the serotonin receptor and may be involved in a host of behaviors including affective disorders and addictions; CYP2E1, a member of the cytochrome P450 family involved with the metabolism of many endogenous and exogenous chemicals including ethanol; and GSTT1, which is involved with the metabolism of toxic compounds including many carcinogens. In order to offer an accessible advanced preventative health screening tool to patients addressing numerous potential conditions, we attempted to implement a multiplexed polymerase chain reaction that would allow us to simultaneously assay these four genetic variants. We were able to combine the GSTT1 and CYP2E1 assays into a single reaction, however we were unable to find compatible reaction conditions for 5-HTTLPR and DRD4 either together or with GSTT1 and CYP2E1.

MRI is by far the most sensitive technique for screening high-risk women and assessing the extent of breast cancer. However, dynamic contrast-enhanced imaging (DCE-MRI), the standard breast MRI method, produces many false positives. As the American Cancer Society now recommends annual MRI screening for high-risk woman, estimated to affect up to 1.8 million women in the US, there is a quickly growing need to reduce the false-positive rate of breast MRI in order to reduce the number of unnecessary biopsies that could result. Our research explores the diagnostic potential of diffusion-weighted imaging (DWI), a MRI technique that depicts the diffusivity of water molecules in the tissue as a way to characterize the cellularity of breast lesions. Research has shown that DWI has the potential to increase the diagnostic accuracy of breast cancer, serving as a promising adjunct tool to DCE-MRI for reducing false positives. Our goal is to evaluate the ability of DWI for non-invasively discriminating benign and malignant breast lesions that were identified as suspicious on conventional breast MRI. Specifically, we will investigate image registration to improve alignment of DWI images, the effects of the contrast agent used in DCE-MRI on DWI measures, and the optimal diffusion sensitization of DWI in discriminating benign and malignant breast lesions. These characterizations of DWI can potentially help to optimize the acquisition and processing of DWI scans for future clinical implementation and help guide the appropriate use of DWI as an adjunct tool in radiological diagnosis of breast cancer.

The harvest of oil from large-scale algal cultivation has become an attractive source of alternative and sustainable biofuel to replace traditional fossil fuels. Understanding how algae store and breakdown their synthesized oils sequestered within specialized organelles known as lipid bodies is key to improving algae oil production. My study is to: a) propose a model alga, b) cytologically probe lipid body architecture, c) and document lipase activity gaining access to oils within lipid bodies. To select a model alga for my studies, I conducted a survey of my laboratory’s algae culture collection looking at organisms across a variety of taxa, lipid body morphology, spatial arrangement, and total number of lipid bodies. BODIPY 505/515, a lipophilic dye, was used to integrate the lipid bodies of these organisms. Chrysochromulina sp. was identified as the best model organism for its simple compliment of two large lipid bodies. Counterstained lipid bodies indicate a strong co-localization of an endoplasmic reticulum membrane with lipid bodies. Fluorescein diacetate was used as a fluorescent indicator for lipase activity. Over a 24-hr time course study, flow cytometric data showed fluorescein diacetate fluorescence increasing as BODIPY 505/515 fluorescence decreased. Cytological studies also show fluorescein diacetate localizing to lipid bodies during its peak fluorescence. These results indicate an endoplasmic reticulum membrane surrounds Chrysochromulina sp.’s lipid bodies and lipases are involved in gaining access to fatty acids through the endoplasmic reticulum membrane. In determining effective algal lipid harvesting protocols it is paramount to first understand cellular lipid usage. Developing the most efficient methods of converting algal lipid bodies to biofuels will accelerate the viability of the global transition to alternative fuel sources.

Inhibitor of differentiation (Id) is a transcription factor that negatively regulates basic helix-loop-helix (bHLH) transcription factors. Of four Ids identified (Id1-4), Id1 and Id3 have been shown to regulate glial development in the central nervous system. In the retina, there is a special type of glia called the Müller glia. Currently, it is not known whether the Ids are important for Müller glial development. Knockout studies in mice demonstrated that Id1/Id3 double knockout (KO) are embryonic lethal, while either Id1 or Id3 KO mice develop grossly normal. We investigated if Id1/Id3 are necessary for Müller glial development by performing Id1 shRNA knockdown (KD) in Id3 KO retinas. Five Id1 shRNAs were tested for their efficiency in NIH 3T3 cells (mouse fibroblast cell line), and the Western blot results showed over 90% decrease in Id1 expression using three shRNAs. We will electroporate Id3 KO retinal explants with these Id1 shRNAs and determine the effects of Id1/Id3 loss on Muller glial development. We expect to see a reduction in the number of Müller glia if Id1/Id3 play a role in their development.

In developing countries nearly 80% of all diseases are linked to water and sanitation issues; globally, over two million people die annually from water-born diarrheal disease. It has long been known that some metals can exhibit powerful anti-bacterial properties. Copper has been used for hundreds of years as a means to purify drinking water but only recently have scientists begun to elucidate the mode of action for copper induced microbial death. In 2008 the U.S. Environmental Protection Agency officially registered copper alloys as biocidal agents. Now these alloys need to be studied to determine efficacy at different concentrations and with a variety of disease-causing microbes. This study investigates the powerful bactericidal effects of copper as a low cost accessible method to purify drinking water of pathogenic waterborne microorganisms. More specifically, E. coli was used as a model organism to test the efficacy of solid copper at killing microorganisms in drinking water over variable amounts of time. Efficacy of cell death was assessed with viable plate counts. Results show that ≥48cm2 of solid copper in 100 mL of water can kill E. coli (at an average concentration of 3.1x105 CFU/mL) within 24 hours. Further research is needed to determine the optimal copper to water volume ratio as well as the precise timing of cell death. It is also essential that the copper ion concentrations remain below EPA limits of 1.3 mg/L; preliminary findings produced inconsistent values. The results of this research could be beneficial to those living in locations where safe potable water is not readily available, or for those travelling to remote or foreign locations as well as hikers and campers.

Vietnam, which is experiencing a heath transition from communicable to non-communicable diseases, has an increased burden of stroke. Understanding its risk factors, including stress, are needed. The goal of this study was to evaluate the relationship of chronic stress and stroke symptoms (which are indicative of a potential stroke) as well as hypertension and diabetes in participants ages 35 and older in Da Nang, Viet Nam. We randomly identified adults, age 35 and older using voter registration lists for inclusion in this study. Interviews and health procedures were conducted either at the local health clinic or participants’ homes depending on preference. Stress was measured using the chronic stress burden scale assessing problems occurring in five domains: problems with one’s own health, with another’s health, job difficulties, financial strain, and relationship problems. Hypertensions was defined as self-reported or measured systolic blood pressure of 140 mm Hg or diastolic of 90 mm Hg and higher. Stroke was ascertained as a self-report of symptoms related to stroke or transient ischemic attack collected by the Questionnaire to Verify Stroke-Free Status (QVSFS). Multiple logistic regressions assessed the odds of increased risk of stroke related to level of stress categorized as no stress, 1 or 2 symptoms, and 3 to 5 symptoms in unadjusted and adjusted models. After adjustment for demographic, health characteristics, as well as diabetes and hypertension, individuals experiencing stress at the highest level (3-5 domains) were more than eight times as likely to report stroke symptoms as those with no stress (OR: 8.13, 4.43-14.91). Lower levels of stress (1-2 domains) also increased significantly the risk of stroke symptoms (OR: 3.27, 95% CI: 2.01-5.34). After adjusting for diabetes and hypertension, along with other potential confounding factors, we found stress to be independently associated with risk of stroke as measured by stroke symptoms.

Stellar flares are the explosive release of energy caused by the reconnection of magnetic fields on stars. Flares release large amounts of UV and X-ray radiation, and may affect the possibility of life on exoplanets, planets orbiting stars other than our own Sun. A star's mass and age greatly affect the frequency, duration, and energy of flares. Therefore, it is important to understand these aspects for a variety of masses and ages. The age of a star is related to the rate of its rotation as well as the rate at which it flares; older stars spin much more slowly and also flare less frequently than younger stars. M dwarfs, stars less than half the mass of the Sun, are commonly used in stellar flare research because they make up the majority of stars in the Milky Way galaxy. To conduct our research, we used two months of data from the NASA Kepler spacecraft to study the light curves of one young and three old M dwarfs. We were able to identify flares in these light curves and measured their durations and energies. We found that the vast majority of flares on all four stars have a short rise time and a long decay time. We also found that flares with long durations have larger total energies, and that older stars have fewer large energy flares compared to younger stars. Through using the light curves, larger, more prominent flares were easily detectable in comparison to smaller flares. Further research would concentrate on more accurate ways toward detecting such small flares.

Rare earth element (REE) concentrations in Mount St. Helens (MSH) volcanic units remain constant (or slightly decrease) with increasing silica (from andesites to dacites). Owing to the commonly held view that REE are incompatible with typical mineral assemblages in mafic to intermediate magmas, crystal fractionation was not considered to be a viable mechanism for generating dacitic melts. Instead, partial melting of a low REE crustal source was considered more likely. REE are, however, highly compatible in apatite and there is evidence of its early crystallization in mafic to intermediate magmas. Hence, we have reevaluated models for crystal fractionation in order to determine a possible mineral assemblage (including apatite) required to reproduce REE trends. Using published partition coefficients, reasonable modal amounts of the major minerals (amphibole, clinopyroxene, Fe-oxides, and plagioclase) and 1-2% apatite, it appears possible to closely mimic the REE patterns in dacites, particularly if considering some assimilation of depleted lithologies in the deep crust.