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.

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.

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.

In the model organism Arabidopsis thaliana, the B-class genes of flower development are responsible for proper formation of petals and stamens in a flower. Studies in Thalictrum thalictroides, a representative of the sister lineage to all other eudicots provides insight into the ancestral function of the B-class genes. Unlike Arabidopsis, the flowers of T. thalictroides lack petals, and yet the sepals are large and colored similar to petals. Here, we investigate the function of B-class proteins in T. thalictroides through the study of the horticultural mutant known as ‘Betty Blake.’ The ‘Betty Blake’ mutant phenotype consists of many non-petaloid (green) sepals and carpels but no stamens. We have previously shown reduced expression of most B class genes in ‘Betty Blake’, yet we were not able to find any meaningful mutations in these loci. Therefore, we hypothesize that an upstream regulator of the B-class genes may be mutated in ‘Betty Blake’. UNUSUAL FLORAL ORGAN (UFO) is a known upstream regulator of the B-class genes and is therefore a logical candidate. We hypothesize that the UFO mutation is the cause of the B class phenotype in ‘Betty Blake.’ The investigation of B-class function in this non-core eudicot has provided us with insight into the evolution of gene regulatory networks affecting ectopic petaloidy and stamen identity that we will continue to pursue in future experiments.

The plant genus Thalictrum (meadow-rues) contains numerous shifts in ploidy number, ranging from diploid (2x) in the earliest diverging species to 24x in recently derived species. Polyploidy can result from a whole genome duplication event within an individual (autopolyploidy) or following a hybridization event (allopolyploidy). The rates and evolutionary consequences of these two mechanisms of polyploidy are currently under debate, and I am therefore attempting to estimate their relative roles within this genus using a phylogenetic approach. The current Thalictrum phylogeny relies on chloroplast DNA and nuclear ribosomal regions, which tend to underestimate the role of hybridization due to maternal inheritance and concerted evolution patterns, respectively. I am using single-copy nuclear genes to uncover potential hybridization signals in Thalictrum’s evolutionary history. This information will be used to compare the relative numbers of autopolyploids and allopolyploids in the genus. I hypothesize that allopolyploidy played a larger role in shaping the diversity of this genus, due to its potential for differential survival and reproduction as a consequence of immediate, novel gene expression in hybrid progeny. Furthermore, this analysis will estimate the hybrid origins of particular alleles within a species. In the future, this information will be applied to questions on the evolution of genes involved in flower development after whole genome duplications.

 The first floral mutations ever documented, double flowers have been prized for centuries for their beauty. The double mutant variants ‘Shoaf’s Double’ and ‘Cameo’ are found in Thalictrum thalictroides, a member of the buttercup family. The purpose of this research is to determine the genetic mutation underlying this desirable phenotype. We predicted that a mutation in a C-class floral organ identity gene would cause the homeotic transformation (conversion of one organ type to another) of stamens and carpels to petalloid sepals in this species. C-class genes are also involved in floral determinacy, the termination of floral organ growth, which is why double flowers appear to have a second flower nested inside the first. As expected, the expression of the C-class gene ThtAG1 was greatly reduced in our mutants. Finding no changes in the coding region from wild type, we further investigated the entire genomic locus, where we found evidence of the action of a transposable element in both mutants. In ‘Shoaf’s Double’ a Mutator Like Element (MuLE) has inserted itself into a regulatory intron of TthAG1, disrupting its function. In ‘Cameo’ a ‘footprint’ at the exact same place in the sequence indicates that the same element may have jumped out, deleting a section of the intron. We hypothesize that the double phenotype in ‘Cameo’ is likely due to the accumulation of mutations before the MuLE jumped out. Since the MuLE’s transposase is expressed in ‘Shoaf’s Double’ (but not in wildtype), these results illustrate the rare case of an autonomous transposable element underlying a regulatory mutation that results in a visible phenotype. We hope that our work will provide insight into the genetic basis for the double phenotype of popular commercial flowers such as roses, camellias and carnations.

Pollination syndrome refers to suites of floral traits that influence biotic or abiotic vectors transporting pollen from one flower to another. These traits typically include flower color, position, shape, size, scent and reward. Scent is a major component of pollination syndrome, as the volatile organic compounds (VOCs) that compose “scent” often attract pollinators or deter predators. The genus Thalictrum in the Ranunculaceae (buttercup family) includes both insect- and wind-pollinated species, enabling comparisons of the role of scent in floral diversification among recently diverged taxa with distinct pollination syndromes. To characterize floral scent, we identified and compared the bouquet of VOCs emitted by insect- and wind-pollination species, as well as by floral vs. vegetative tissue. Scent was collected from tissue samples by traps in a filtered air system, then eluted and analyzed with gas chromatography mass spectrometry. Quantitation and emission rate were calculated to generate floral bouquets. Electroantennograms were performed on selected compounds to examine pollinator response. Focusing on eleven species representative of the two pollination syndromes and spanning the Thalictrum phylogeny, we identified ten key compounds of which five are deterrents against herbivory, two are pollinator attractants, and three have unknown functions. Given that these scent profiles consist primarily of defensive rather than attractive compounds, we hypothesize that repeated transitions from insect- to wind-pollination in Thalictrum may be due to the breakdown of an ancestrally weak insect pollination syndrome. Moreover, scent bouquets appear to follow phylogenetic patterns more so than pollination mode. The variation in distribution of VOCs across species in a phylogenetic framework allows us to test evolutionary patterns of compound co-option during evolution.

Every plant needs Nitrogen to grow. Nitrogen is usually given through synthetic fertilizer which is expensive and causes a lot of environmental problems. Synthetic fertilizer is bad for the envieronment not only it need a lot of fossil fuel to make the high temperature and pressure condition for Nitrogen reaction, but also excess Fertilizer will bring blooming algae to the surround ponds, which will make the organism in the water die out because lack of Oxygen since the sunshine cannot get through algae and help underwater plants to photosynthesis. Since previous research in the lab showed that endophytes isolated from Willow and Poplar trees can promote growth of crops such as pepper, tomatoes, and sweet corn under low nitrogen conditions, we hope that Endophyte can reduce or completely substitute synthetic fertilizer of other commercial plants, such as corn. Endophytes (microbes living inside plants) can produce phytohormones and provide fixed nitrogen for plants. My research focuses on corn, a bioenergy crop species typically grown with large inputs of fertilizer. I screened ten commercial varieties of corn and compared the growth of endophyte inoculated plants with the uninoculated controls, in low nitrogen soil. In one variety of corn there was increased biomass in the inoculated plants compared to the controls. Currently I am testing which isolate is responsible for the plant growth promotion. These findings will have a great impact on commercial production of corn in a sustainable way.

The Society for Ecological Restoration, University of Washington Student Chapter (SER-UW), has for the past several years been restoring a forested site near the North Campus Residence Halls. After years of hard work clearing the area of invasive species, SER-UW has begun an effort to share the site and their ideas of habitat and biodiversity revitalization with the community at the University of Washington. The big question for the group now is, can we turn the restored forest into a community space for use and recreation? As the Design Intern for the group, I am utilizing my background as a Landscape Architecture student to create a design that will activate "new" space, as it was inaccessible prior to invasive species removal, and allow for an exciting interaction with, and interpretation of, a Northwest Forest experience. I have performed as a mediator for SER UW, to turn their ideas and desires for the site into design. I set to work discovering how to establish the site as an interpreted and useable site for the community. I developed drawings, diagrams, a prototype sign, and a site plan, then held a work shop with SER UW to discuss the preliminary design. From there, and through a meeting with the Campus Landscape Architect, I created a fourteen page report including details and guidelines of the site design. The design focuses on programs of community gathering and art, as well as elements implemented to influence interaction with the site. Through our design, SER UW will create a legacy at the Whitman Walk Restoration Site. The site will be sustainable from the active involvement and care of the Whitman Walk through students who grow to appreciate the site and find a sense of belonging there. Whitman Walk will grow a greater understanding of the significance of ecology in its visitors for many years to come.

The broad association of neurological disorders, epileptic symptoms, and dysfunctional bone regulation in both animal and human studies support the hypothesis that neurological activity in the brain affects the formation and remodeling of bone throughout the body. In mice, brain-specific deletion of the PTEN gene has been shown to induce an overactive P13K-Akt-mTOR pathway, resulting in macrocephaly, hypertrophic neurons, and epileptic symptoms with persistent seizures. In this study, we present evidence that brain-specific knockout of the PTEN gene induces abnormal skeletal activity in mice. Total volume was significantly increased in knockout mice in the proximal tibia (p<0.01) and mid diaphysis (p<0.01) compared to wildtype controls, while tissue mineral density was significantly lower in knockout mice for both tibia locations (p<0.01). Effects of PTEN deletion were highly localized and compartment specific, as evidenced by the significantly lower trabecular bone volume in the proximal tibia (p<0.05) but significantly higher bone volume in the mid-diaphysis (p<0.05). Given the association of brain-specific PTEN deletion with seizure-like cortical activity, as well as the known influence of skeletal nerves on bone cell function, these studies provide an essential first step toward understanding the role of cortical brain activity in regulating bone metabolism. Further research into the brain’s role in bone homeostasis could be fundamental in treating bone diseases such as osteoporosis.

The high antigenic diversity HIV-1 presents an enormous challenge for vaccine design as effective vaccines must be broad and potent in order to recognize and effectively counteract diverse circulating HIV strains. The identification of broadly neutralizing antibodies to recognize and counteract these diverse strains provides optimism for the ability to elicit broad and potent responses against HIV via vaccination. PGT128 is one such antibody and has been shown, in combination with other broadly neutralizing antibodies, to improve neutralization coverage of both viruses transmitted heterosexually and vertically, i.e. from mother to infant. Thus it is crucial that we understand the molecular determinants of the virus that leads to its sensitivity to broadly neutralizing antibodies. We studied viruses from longitudinal time points, one at 21 days post infection and one from 560 days post infection, of one infected individual who displayed increasing sensitivity to PGT128. Using nested PCR to create chimeras between the two viruses, we found that the loss of a single potential N-linked glycosylation site in the V1 region of HIV envelope conferred sensitivity to PGT128. This emphasizes the importance of N-linked glycosylation sites in conferring PGT128 recognition.

While it is acknowledged that individuals of intersecting marginalized identities experience compounded prejudices, most of the research on intersecting identities has focused on the intersections of gender and race. In two studies, we seek to explore the intersection of weight and race on perceptions of American identity. This study builds on previous research findings that Asian Americans are perceived as less American than people of any other racial group. Furthermore, because Americans are stereotyped as overweight, we hypothesized that heavier Asian Americans would be perceived as more American and less likely to be in the US illegally than their thinner counterparts. Photos of Asian American and White American men were edited to create heavier and thinner versions of each man. University of Washington students viewed either a heavier or thinner version of one of the men and assessed his American identity and perceived documentation status. The heavier Asian American men were perceived as more American and less likely to be in the US without documentation than thinner versions of the same men. Weight did not influence perceptions of White men’s American identity or documentation status. These studies demonstrate that Asian Americans who gain weight may surprisingly be buffered from prejudice directed at those who are perceived as less American.

Essential tremor (ET) is a very common and problematic tremor disorder that affects over five million people worldwide. It is not a harmful or fatal disease, but because it can greatly impact the quality of life of older adults. Treatment for essential tremor varies depending upon the level of magnitude of the tremor, and high levels of magnitude could possibly prompt usage of deep brain stimulation (DBS). A device that could collect data could also double as a control for deep brain stimulation in more severe cases of ET. It is because of this reason that a diagnosing wrist device is being developed. Most cases of ET involve tremor in the upper limbs, and so a wrist-mounted or upper-arm-region device would be most logical. My goal was to successfully have a piece of hardware capable of graphing simulated (or actual) tremor in real time into a figure in the program MATLAB. The hardware consists of an inertial measurement unit (IMU) and an Arduino microcontroller hooked up to the computer. Wireless capabilities were also planned in the hardware of the final prototype. This device was proposed to be integrated into fabric of some type and fastened somewhere on the human arm for testing. The prototype developed is a glove with the externally attached sensors and microcontroller, and I was responsible for designing, testing and iterating plans of this device, as well as coding in Arduino and MATLAB to collect and graph data from the device in real time.

We are interested in identifying the spectrum of mutations that arise when performing the same evolution experiment many times. We have previously grown 32 replicates of haploid yeast cells in continuous cultures under constant sulfur limiting environments for 300 generations. Mutants with increased fitness will increase in prevalence and can be characterized using an array of comparative genomic hybridization (aCGH) or next generation sequencing (NGS). To date we have used aCGH on a subset of our evolutions, and in 16/16 cultures, found amplification of SUL1, a high affinity sulfate ion transporter gene used by the cells to aid in increasing import of sulfate. We are also interested in identifying alternative means for adaptation in this environment and have evolved a a strain in which we'd knocked out SUL1 (sul1Δ). With this background, we observed SUL2 amplification in 4/4 cases in the absence of SUL1. A second focus of our work is to track changes in fitness as specific mutations arise. To assay fitness, we periodically compete an evolving culture against a Green Fluorescent Protein (GFP) expressing ancestral strain of yeast. This work has shown that the dynamics of adaptation of wt and sul1Δ yeast differ, which suggests very different fitness landscapes during the evolution for these two genotypes. Collectively these data show that SUL1 amplification is a first target of evolutionary selection and that in its absence, amplification of SUL2 becomes the primary means for adaptation in constant sulfate limitation.

Disruption of the nervous system has been widely associated with aberrant bone function. The capacity for zebrafish to undergo rapid bone regeneration following fin amputation confers unique opportunities to examine neuroskeletal signaling within a highly tractable experimental system. In this study, we developed a model of cholinergic disruption in the regenerating tail fin using intramuscular injections of Botuliunum toxin B (BTxB). The tail fin is muscularized only at the base. By administering BTxB into the base, we were able to examine remote effects of BTxB at the distal tip while minimizing the influence of impaired muscle near the regenerate. BTxB resulted in multi-faceted effects on bone regeneration in adult zebrafish. For example, BTxB fish exhibited a significant decrease in the % length of bone regrowth compared to saline controls (sal: 74.8±8.1%, btx: 35.2±4.6%, p<0.001 for treatment, n=5). The degree of inhibition was significantly more pronounced in the middle of the regenerate compared to the dorsal/ventral regions (p<0.05 for region: treatment), suggesting that the trophic influence of fin base nerves can be spatially focused to distinct fin regions. Finally, when fish were calcein stained, we found that BTxB dramatically decreased osteoblast activity in regenerating bone. Interestingly, the effects of BTxB appeared to be spatially restricted within individual rays, as evidenced by marked differences in osteoblast activity between adjacent rays. This suggests a potential role for intra- and/or inter-ray nerves in mediating the effects of nerve disruption in the fin base on osteoblast activity in the distal tip. Collectively, these studies demonstrate the capacity for focal cholinergic disruption to remotely alter bone regeneration in a multi-faceted manner. Given the genetic and optical tools for dissecting neural pathways in zebrafish, this model provides a powerful platform for identifying novel mechanisms underlying neural control of bone growth.

Previous research done in our lab found that poplar and willow trees grow in nutrient-poor soil, and they obtain their nutrients through partnership with microbes that live within them (referred to as Endophytes). We then have successfully isolated endophytes and are now exploiting them for plant growth promotion, stress tolerance. My research question is to test if inoculating poplar clone OP-367 with endophytes can help the plant survive drought condition. The experiment was set up by controlling watering schedule that simulate drought condition and compared the results of the uninoculated control group and the inoculated group. We quantified the results using measurement of wet and dry biomass, chlorophyll (SPAD readings) which quantifies the health of the plant by measuring the greenness, and maximal photochemical efficiency (Fv/Fm), which quantifies the photosynthesis happening in the plant. The implication of this project will permit better growth of plants under water stress condition. The potential of endophytes to increase drought tolerance in OP-367 poplar hybrid and or other plant species can become a potential remedy for rescuing agriculture problems in relation to drought weather condition.