A quadrotor is a small air vehicle propelled by four rotors, or propellers. It is capable of vertical flight, as well as hovering and smoothly changing direction. The quadrotor is more versatile than a fixed-wing air vehicle, as it can move through environments that would limit a larger and less maneuverable vehicle. This research aims to create a successful autonomous computer-based controlling system for a quadrotor's flight. By implementing this technology, the quadrotor could move freely in environments unsafe for human flight controllers. Researchers developed and executed experiments to determine vehicle properties to improve control safety and robustness. In order to create a flight control system that will successfully maneuver the quadrotor without the use of a remote control, the quadrotor's inertia and thrust properties were ascertained. With the inertia and thrust data, controlling the quadrotor with high precision will be possible. The quadrotor's inertia was determined by measuring its rotational period using a photogate timing mechanism and a flashlight beam. Its inertia was found on three principal axes: x, y, and z. A thrust curve was determined for the quadrotor by measuring the thrust produced at each throttle setting using a force transducer. The resulting inertia and thrust properties allow for a deeper analysis of the quadrotor's abilities. In addition, an optic flow sensor will contribute to the quadrotor's flight capabilities. The sensor was calibrated and code was implemented to create communication between the sensor and a computer. When attached to the quadrotor, the sensor rapidly photographs the quadrotor's surroundings, detecting changes in altitude, rotation, and velocity. The optic flow sensor will help stabilize the quadrotor's position and allow it to maneuver away from objects in its flight path.

Mobile video communication has been popularized by applications such as Skype and Facetime, but the technology suffers from resource limitations both on the device and on the cellular network. Transmitting high quality video requires high bandwidth and battery draining processing power on mobile devices. These requirements hurt the user experience by creating high data cost, reducing call time, and limiting use to high speed networks such as WiFi. My research contributes to the MobileASL (American Sign Language) project that applies video compression to solve these issues specifically for mobile sign language communication. The deaf and hard-of-hearing community can benefit immensely from a mobile video chat application as ASL is a visual form of communication. We conducted a web study investigating sign language comprehension and intelligibility of video transmitted at four low frame rates (1, 5, 10, 15 fps) and four low bitrates (15, 30, 60, 120 kbps). The purpose was to determine how much video quality can be reduced before compromising sign language comprehension and intelligibility. The study found intelligible sign language video can be transmitted at frame rates and bitrates much lower than the current recommended standard for sign language video communication (25 fps at 100 kbps or higher) without diminishing the user experience. These findings strongly suggest that the recommended international standards are too high and can be reduced while maintaining intelligibility.

The progression and development of Singapore as an independent country has been a topic that draws in mixed reactions amongst the local and international community. As remarkable as Singapore’s economic growth has been, the avenues for political expression are limited. The goal of my project is to understand how the Singaporean public uses social media to voice their political opinions when significant restrictions and censorship are in place. Unlike in past decades, the rise of social media has allowed for a new outlet of voice in political opinions. I will examine closely if people can be empowered to voice their political opinions with social media tools. I will record two Skype interviews per age group with Singaporeans ageing from teens, twenties and fifties and using a wide range of online responses on selected social media sites such as Facebook and Twitter. This will allow me to draw the connections between the political voices of Singaporeans and social media. I want to compare the responses I get over different generations to examine whether the rise of social media change people’s attitude towards their political expression. Furthermore, I want to extensively look at the responses the people I interview and their reactions toward the comments made within social media sites. This would allow me to understand whether social media sites would be a platform to share and extent their views or an outlet to vent that otherwise serves no “actual” empowerment of their political views.

Since neuronal morphology is linked to neuronal function, the nervous system goes to great lengths to ensure that neurons achieve their proper shape, and failure to do so is associated with many cognitive disorders. However, the precise regulatory mechanisms underlying the coordinated expression of certain genes in a given cell type, at the right amount, and at the exact developmental time is one of the longstanding questions in developmental biology. MicroRNA biogenesis is a common mechanism by which cells regulate gene expression, often by “tuning” levels of target gene products, allowing for fine regulation of protein levels over a broad dynamic range. From a genetic screen for mutations in fruit flies that affect dendrite morphology in sensory neurons, we identified a novel Dicer-1 allele that causes stereotyped dendrite defects, including deregulated growth and defects in dendrite self-avoidance. Dicer-1 encodes a type III RNA endonuclease that is required for processing many types of small regulatory RNAs, including microRNAs. Time-lapse imaging and quantitative analysis of the dendrite patterning in Dicer-1 mutant sensory neurons reveals that there is a significant increase in the number and overall length of dendrite branches as well as an increase in dendrite-dendrite crossing-over, especially at late stages of larval development. Interestingly, mutation in a gene (pasha) that functions upstream of Dicer-1 to process a subset of miRNAs recapitulates the exuberant branching, but not the dendrite crossing phenotype of Dicer-1 mutants. We hypothesize that different classes of miRNAs regulate dendrite branching and dendrite self-avoidance and we plan to use microarray analysis of Dicer-1 and pasha mutants to identify the pathways regulated by these different classes of miRNAs.

Marine ecosystems are vulnerable to anthropogenic influences due to increased stresses from climate change and habitat destruction. Fish farming, aquaculture, and the pollutants of antibiotics and organic matter produced by them are one influence that has been observed to affect local marine wildlife leading to increased resistance to bacterial pathogens and increased algae cover. Rocky Intertidal Zones of the Pacific Northwest are environments that are under intense thermal and desiccation stresses. The unique organisms that inhabit these areas have adapted to live under these high stress conditions. I researched the effects of fish farms and oyster farms on the health of rocky intertidal communities, by quantifying shifts in species richness and biodiversity, near the aquaculture sites. The research took place in Barkley Sound between January 26th and February 2nd in 2013 on rocky beaches near fish farms, oyster farms, and control sites away from aquaculture locations. Ecosystem health was determined by evaluating species richness, bio diversity, and presence of keystone predator, Pisaster ochraceus, using standard quadrant surveys. I collected water samples for Solid Phase Extraction and Liquid Chromatography Mass Spectrometry to determine concentrations of anthropogenic antibiotics released from fish farms. I hypothesized that the presence of antibiotics will decrease biodiversity and species richness in rocky intertidal communities. Determining what effect and how strong of an impact these influences have on the environment may help define future environmental policies and fish farming protocols.

White-nose Syndrome (WNS) is a wildlife disease caused by the pathogenic fungus Geomyces destructans that has resulted in the mass mortalities of North American cave bats. One clinical sign of WNS is wing necrosis.  Geomyces destructans may secrete proteases that degrade tissue, thus reducing wing strength and elasticity. We isolated Geomyces destructans extracellular enzymes from an in vitro system and applied enzyme solution to bat wing tissue. The toughness, strength, and elasticity of tissues was assessed with tensile testing. Protease activity was assessed with SDS-PAGE and peptide mass fingerprinting by MALDI-TOF MS. Protein profiles generated by SDS-PAGE indicate higher solubilized protein in treated samples. Major bands were identified as integumentary proteins by MS. Tensile testing did not detect damage, but Geomyces destructans proteases may cleave host integument.

Geomyces destructans is a psychrophilic (cold-loving) fungus that causes cutaneous infections in cave dwelling bats and high mortality in North American populations. Geomyces pannorum is a closely related psychrotrophic (cold-tolerant) species that is a rare skin pathogen of vertebrates. Cold-adapted organisms adjust lipid synthesis to lower membrane viscosity and thus survive unfavorable habitats. Lipid profiles, or lipid class composition, may partially explain ecological niche and G. destructans pathogenicity to bats. Additionally, profiles are species specific and may be utilized to differentiate closely related species and detect disease. We incubated Geomyces at 5°, 8°, 15°, 18°, and 22° C and isolated fungal lipid content. Broad lipid classes were determined to be primarily sterols, free fatty acyls (FFAs), and triacylglycerides (TAGs). Geomyces destructans produced higher proportions of unsaturated 18 carbon TAGs than G. pannorum. Geomyces produced more 18:3 (18 carbon, 3 double bonds) TAGs at five degrees than at higher temperatures. Geomyces destructans made higher proportions of TAGs at its growth limits, suggesting alterations in lipid synthesis to decrease cellular toxicity and reproductive effort. Furthermore, these results indicate Geomyces alter lipid structure to survive cold temperatures by increasing lipid unsaturation. Future studies should focus on temperature optima of enzymes involved in TAG synthesis and disruption of lipogenic metabolic processes. Lipid profiles among multiple Geomyces species should be further investigated as a method of disease detection.

Iron-oxide magnetic nanoparticles (MNPs) with tuned magnetic properties can enable novel diagnostic and therapeutic technologies such as magnetic particle imaging and hyperthermia. In order to optimize the magnetic properties of MNPs, organic synthesis methods are required. However, these organic synthesis methods render the nanoparticles hydrophobic and unusable for biomedical applications. To make MNPs functional in biomedical applications whilst retaining their magnetic functionality, they must be transferred to the aqueous phase using a biocompatible polymer. In this work, MNPs will be coated using a biocompatible PEG-ylated amphiphilic polymer: poly (maleic anhydride-alt-1-octadecene) or PMAO-PEG. To ensure the PMAO-PEG is a well suited polymer coating for MNPs, various molecular weights and molar ratios of PMAO-PEG are synthesized and characterized to study the effects of PEG surface density and molecular weight on MNPs. By altering the density of the polymer used to coat and phase transfer MNPs, effects such as the solubility, circulating life, colloidal stability, dosage frequency, and proteolytic degradation rates of MNPs in the biomedical applications are studied using data obtained from Gel Permeation Chromatography (GPC) and Fourier Transform Infrared Spectroscopy (FTIR). Molecular weight distributions of the various polymers are obtained from the GPC to evaluate the conjugation success after PEG-ylation. In addition, FTIR was used to identify known and unknown materials in the samples, determine the quality and consistency of samples, and to determine the amount of components in samples.

We are studying the roles of the p120-catenin protein in zebrafish development. p120-Catenin has a critical role in adhesion and migration by associating with E-cadherins and small, Rho family GTPases. The regulatory domain of p120-catenin contains 8 tyrosine and 8 serine or threonine residues that can be phosphorylated. To date, the function of these phosphorylation sites has been controversial. In cell cultures there is evidence that phosphorylation of 6 serine sites cause adhesions to recover quicker as well as form stronger connections. Some studies, however, claim that phosphorylation of these serine residues has no effect on adhesion. Tyrosine phosphorylation has been associated with nascent adhesions suggesting its role in adhesion formation, while its presence in carcinoma cell lines implies a role in cell motility. By selectively blocking phosphorylation at these 16 residues we hope determine the roles for the phosphorylation of serine and tyrosine residues in adhesion and migration of cells during embryogenesis. We mutated mouse p120-catenins at tyrosine residue 228 to phenylalanine, and at serine residues 252 and 268/288 to alanine via site-directed PCR mutagenesis. We inserted the DNA into PCS2+ vectors containing the fluorescent protein mcherry, and translated the mutant DNA into mRNA. We injected one-cell zebrafish embryos with an antisense morpholino RNA, complimentary to a splice-site region of endogenous zebrafish p120-catenin. Injections of this morpholino effectively knockdown the expression of newly translated p120-catenin mRNAs, and inhibit normal somite formation and axis extension during development. Co-injection of a wild-type mouse p120-catenin mRNA with the morpholino showed nearly normal development. Preliminary data suggests that co-injection of Y228F p120-catenin mRNA with the antisense morpholino RNA also produces nearly normal phenotypes. We will be testing the localization and function of the other mutated p120-catenins. This research could have important implications in development, treatment of some cancer types, and wound healing.
 

Neurons are specialized cells that receive and relay information throughout an organism, and the compartment that inputs the signal has multi-complex structures known as dendrites. The form of the dendrite is tightly regulated to neuron function; therefore, any abnormality that alters the structure of the dendritic arbor can lead to severe defects in neuronal function. However, the mechanisms of how dendrites develop and maintain their arborization are poorly understood. From a forward genetic screen for mutant alleles with progressive defects on dendrite patterning we identified one mutant allele that leads to a complete loss of terminal dendrites. We mapped this allele to a small genetic interval, and using complementation tests and DNA sequence analysis we identified Acsl (Acyl-CoA synthetase long-chain) as the gene affected by this mutation. Interestingly, Ascl is also associated with human X-linked mental retardation (XMR), but to date the role that Ascl plays in dendrite development has not been investigated. Here we report the phenotypic analysis of the Acsl mutant, effects of Acsl knock down in neurons, and our plans for functional analysis of Acsl in dendrite development.

Dendrites are branched extensions of the cell body of a neuron that act to receive and process synaptic or sensory inputs. The elaborate branching pattern of the dendrite is a hallmark of neural type, and has a considerable impact in determining what signals a neuron receives, and how these signals are integrated. Alterations of dendrite morphology can lead to abnormalities in neuron function--dendritic defects are associated with neurological disorders such as Ret syndrome, Fragile-X syndrome, and Down syndrome, and in many cases the dendrite pathologies are progressive. Therefore we set out to identify mutations that result in progressive defects in dendrite growth and stability with the hope that the genes affected by these mutations and the processes in which they regulate will provide new insight into human disease. A series of complementation tests using chromosomal deficiencies, as well as meiotic mapping have been used to map one such mutant (cc215) to a small chromosomal interval. In addition, we have performed a non-complementation screen to determine other alleles that affect the same gene mutated in cc215. Complementation tests and sequence analysis are currently being performed to classify the gene affected by this allelic series, which will allow us to investigate the underlying cause(s) of the dendrite defects in the mutants.

Nanoimprint lithography (NIL) has become a widely used technique in fabricating nanoparticles using a top-down approach with several advantages over bottom-up chemical methods, including being able to precisely control particle shape, size, structure, and composition. Using NIL, synthetic antiferromagnetic (SAF) nanoparticles can be fabricated using multilayer deposition techniques, imprinting, liftoff, and particle release into water with limited defects. The particles can also be coated with a functional polymer so that they can be used in a number of drug delivery systems. However, common NIL techniques often make it difficult to add functional coatings to the particles after the particles are released in water. Deposition methods for different layers, as well as using silicon molds that introduce defects and irregularity in particle size are other pitfalls that can be corrected using a new approach. The nanoparticles (~300 nm diameter) were homogeneously patterned using a mold to etch disk-shaped nanoparticles on a silicon substrate with layers of titanium and magnetite deposited on its surface via magnetron sputtering to contribute to the antiferromagnetic properties of the particles.  The fabrication process is extensive and utilizes many clean room processes, including nanoimprinting, dry etching, undercutting, multilayer deposition, liftoff, and polymer coating, though polymerization was not explored in this study.  Following, release techniques were used to produce a monodisperse and homogeneously-sized sample of high moment, multilayer particles in water with high saturation magnetization and low toxicity. Final results to determine the effectiveness of the particles were determined by studying the magnetic properties of the nanoparticle solution sample in the presence of an external magnetic field. With antiferromagnetic and useful imaging properties, functional biomagnetics could become a highly useful material system. Future work in this field includes biofunctionalizing the particles to modify in-solution behavior and implementing them into various biomedical systems, depending on how small the particles can be made using NIL.

The Salish Sea is critical habitat for the endangered population of Southern Resident Killer Whales (SRKW). One of the primary threats to SRKW recovery is underwater noise pollution from boat and ship traffic. Killer whales rely on acoustics to communicate, navigate, and to forage in their underwater environment. The increasing levels of underwater noise have the potential to mask the SRKW calls and echolocation clicks, resulting in compensation (i.e. increasing the loudness of calls and using echolocation more or less frequently). This study investigates the potential effects that boat and ship traffic may have on SRKW echolocation. If SRKWs are experiencing masking while actively using echolocation, it is expected that there will be a significant difference between echolocation click rates in a quiet underwater environment and click rates produced in an underwater environment filled with noise pollution. Passive acoustic monitoring was used to record SRKW acoustics and measure the received levels (RL) of underwater noise. Visual boat and ship counts were conducted during acoustic recordings to quantify the amount of traffic in the study area (Whale Watch State Park, San Juan Island, WA). These data sets are being tested to determine if there is a significant correlation between the RL of underwater sound and boat and ship traffic, and if echolocation click rates change in respect to the RL of underwater sound. The anticipated results are that boat and ship traffic will be directly connected to the increases in RL of underwater sound and that masking will be impacting SRKW use of echolocation. Southern Resident Killer Whale population recovery is faced with a number of threats, however underwater noise pollution is one that we, as a society, can directly impact. Consequently, it's extremely important for us to understand how underwater noise pollution can affect this endangered population of killer whales. 

Organic Photovoltaics (OPVs) provide a potentially cheap and clean option to harvest energy from the largest source of energy available - the sun - however they are still fairly inefficient when compared to inorganic photovoltaics. Attaching fluorine to the polymer backbone has been shown as an effective way to increase the open circuit voltage (Voc) and power conversion efficiency of the devices by lowering the highest occupied molecular orbital of the polymer. However, the impacts of fluorine attachments on the other properties of active layer, like morphology under different processing conditions and electrical properties, have not been fully studied. Knowing this information will help the future designs and processing of donor-acceptor polymers for OPV application. In this project, three structurally identical polymers, with zero, one, and two fluorine attachments (named P0F, P1F, and P2F) were studied. The morphological impact of fluorine attachments are studied by varying the ratio of PCBM (a widely used and promising acceptor) and these three polymers as well as the solvents used when processing through atomic for microscope (AFM). Hole features were found on the surface of the thin film. The density of and depth of the holes were found to correlate to the number of fluorine attachments and processing condition respectively. Future works are being done to investigate the reasoning behind the device efficiency with the attachment of fluorine and differentiating whether this is due to these physical morphologies or bandgap manipulation being the primary contributor to a higher efficiency. The influence of fluorine on the dielectric constant of the thin film and operation of OPVs will also be studied. 

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 concentrations in sediment pore water, but are not killed. These results contrast sharply with observed efficacy in the field, i.e. mortality 72-96 hours post application and subsequent reductions in burrow counts. Understanding the factors governing efficacy in the field may improve control. We exposed 10 adult female shrimp that had burrowed within native sandy sediment to IMI (Nuprid® 2F) for 96 hours simulating the theoretical maximum pore water concentration (146 ppb) associated with an application of 0.5 lbs active ingredient [ai] per acre. We compared the response of the shrimp to that of an equal number of negative controls, and five shrimp in a comparable pore water-only exposure, and five in clean seawater. Behavior was monitored daily and water quality was measured at the end of the test. As expected, all shrimp in the water-only IMI exposures were overtly affected, but survived. Eighty percent of the shrimp exposed to IMI within their burrows died, whereas 90 percent of the negative controls survived. Dissolved oxygen (% saturation) varied among treatments (clean seawater: 51-69.6%; seawater + IMI: 42.4-57.4%; clean sediment surface water [alive]: 4.1-20.1%, [dead]: 3.4%; sediment + IMI surface water [alive]: 5.4, 57.9%, [dead]: 4.2-65.4%). 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 move water within the sediment.

Solar energy is arguably the most promising source of renewable energy because it is thought to be both the cleanest and most abundant source. There are several types of solar cells including organic, inorganic, and hybrid organic-inorganic solar cells. While inorganic solar cells have high efficiencies, good charge carrier mobilities, and relatively long charge carrier times, their expensive production and materials competition with the microelectronics industry has kept their prices high. Organic solar cells are solution processable, applicable to flexible substrates, and have the promise of being relatively cheap to produce. However, their relatively low charge carrier mobilities and short exciton diffusion lengths prevent them from being used as an alternative to inorganic solar cells. Hybrid organic-inorganic solar cells have been introduced as a substitute to both organic and inorganic solar cells in order to overcome the short-comings of each. Inorganic semiconductors are used in hybrid photovoltaics as the acceptor in the solar cell due to the ease of changing the size and shape, and therefore the bandgap, of these semiconductors, which allows them to contribute to the photocurrent of the cell while enhancing the conductivity. This project addresses the synthesis of cadmium selenide (CdSe) nanotetrapods, which may facilitate control of direction of electron motion in the active layer of the cell. The reaction time, growth temperature, ligand type, and monomer concentration were used to control the synthesis, and the effects of each variable on the size and shape of the tetrapods were studied via transmission electron microscopy (TEM).

In this study, we attempt to gain a better understanding of how poly(3-hexylthiophene) (P3HT) nanowires self assemble in solution. P3HT is used as the primary p-type donor in conjunction with phenyl-C61-butyric acid methyl ester (PCBM) in bulk heterojunction polymer solar cells. During self assembly, individual P3HT chains begin to kink after about 40 monomer units into an S-like shape. These S-shaped chains interact with one another via pi-pi interactions and form nanowires with widths typically between 20 and 70 nm and heights between 3 and 5 nm. In an attempt to improve device efficiency, we would like to exhibit greater control over the size of the nanowires. Controlling the morphology of the nanowires would allow us to improve the efficiency of the device. Thus, we demonstrate a method to create self-assembled nanowires from 12.5, 16, and 28 kDa molecular weight P3HT. P3HT solutions were made with a concentration of 1 mg of polymer to 2 mL of solvent (anisole and chloroform in a 4:1 ratio). These solutions were then heated at 80°C and thoroughly mixed for 16 h. After mixing, the solution is removed from heat and allowed to self-assemble for several days. Finally, the solution is then spin coated onto a silicon dioxide coated silica substrate. The samples were analyzed using atomic force microscopy to provide detailed information about the surface coverage, width, and height of the nanowires.

Until recently, little research has been done on C-S bond formation in transition-metal catalyzed transformations compared to other carbon-heteroatom bonds such as C-N, C-O, and C-P. As sulfur-based coupling partners (thiol and disulfide for example) tend to poison transition-metal catalysts, development of C-S bond formation has been slow. However, a recent nickel-catalyzed system shed new light on this difficult transformation. In this context, C-H functionalization is a sustainable and straightforward approach to sulfur-containing heteroaromatic production. C-H activation is a process whereby a carbon-hydrogen bond is cleaved, thereby allowing the exposed carbon atom to form new bonds. Thus, in order to expand the above research of C-S bond formation toward development of short synthesis for fused thiophene systems, focus was placed on a palladium catalyzed cascade-type reaction system. C-H activation reactions can and have been manipulated to work in a cascade-type fashion. By combining cascade-type methodology with the reduced environmental impact of C-H activation, these fused thiophenes can be synthesized cleanly and efficiently. The test substrates in this work are O,O-diethyl S-phenyl phosphorothioate and 4,4,5,5-tetramethyl-2-(thiophen-2-yl)-1,3,2-dioxaborolane. Both substrates were chosen because they contain sulfur, thereby aiding the C-H activation process. By effecting a C-H activation with a palladium catalyst at one of the ortho carbons of the phenyl ring with the boronic ester of the thiophene, the first C-C bond will be formed. In the time immediately after this first transformation, the now-changed palladium complex is able to insert into the S-P bond of the phenyl-based compound. This step sets up the second reaction, whereby the phosphorothioate directing group is cleaved along the S-P bond and the resulting thiol is coupled to a carbon atom to close the ring. This molecule is known as benzo[b]thieno[2,3-d]thiophene.

The basic functional unit of the nervous system is the neuron, which contains two highly specialized compartments, the axon and dendrite. Dendrites received synaptic/sensory inputs, and the dendrite arborization pattern has a profound influence on the type and number of inputs a dendrite can receive. We are studying dendrite patterning in the Drosophila peripheral nervous system (PNS), with a particular focus on the role that non-neuronal signals play in shaping dendrite development. In the Drosophila PNS, sensory neurons grow on top of a monolayer of epithelial cells, which provide instructive cues to shape dendrite patterning. To date, there are plenty of tools available to genetically label and manipulate neurons, but few tools are available for genetic manipulation of epithelial cells. My goal is to design a reporter construct that will specifically label and facilitate targeted expression of transgenes in epithelial cells. To this end, I am assembling a modular plasmid construct which contains a minimal promoter, an enhancer sequence which we have found to be sufficient to direct epithelial expression, and the coding sequence of green fluorescent protein or other genes of interest. After assembling the construct, I will use germline transformation to generate transgenic flies and test the efficacy of the construct. If successful, this will represent the first epithelia-specific transcriptional reporter, and will provide a template for assembly of additional tools for studying dendrite-epithelia interactions.

MicroRNAs (miRNAs) are crucial regulators of gene expression in plants and animals and play a critical role in many biological processes, including nervous system development. From our previous study of Drosophila melanogaster peripheral sensory neurons, we found that miRNA bantam is both necessary and sufficient in epithelial cells to initiate an epithelia-derived signaling pathway that regulates dendrite growth. Using miRNA sensors, which report the location on miRNA activity, we found that bantam activity is developmentally regulated in epithelial cells. We hypothesize that this developmental regulation of bantam activity is the result of transcriptional regulation of bantam, and we aim to investigate this using bantam transcriptional reporters. To this end, we are developing bantam transcriptional reporter constructs in which the bantam transcript has been replaced by different reporter genes, such as GFP or Luciferase, while preserving the cis-regulatory landscape. We will use these reporters to monitor bantam transcript levels over developmental  time and, pending the outcome of these studies, we will use the reporters to identify trans-acting factors that regulate bantam transcription.

For thermoelectric (TE) applications, oxides possess certain advantages over conventional intermetallics, including excellent high-temperature stability, low toxicity, and a complex structure, which aids in lowering the thermal conductivity. Recently, it has been found that SrxBa1-xNb2O6 (SBN) holds potential for use in high-temperature TE applications (e.g., waste heat recovery). In our work, a solution combustion synthesis (SCS) process was devised to fabricate SBN with a range of Sr:Ba ratios in order to ascertain an ideal SBN composition for optimum TE behavior. The SCS method, which is highly amenable to mass production, allowed for good control of the SBN stoichiometry, and the as-processed powders were found to possess good single phase purity. Powders processed with different SBN compositions were subject to conventional sintering followed by reduction. The TE properties of each SBN composition were then tested and compared. Preliminary results of our acquired data suggest a decrease in the thermal conductivity as the Ba content is increased, likely due to the larger mass of Ba when compared to Sr. From the obtained results, an ideal SBN composition was determined having the optimal TE performance. Field assisted sintering (FAST) was then employed to processed SBN powder having the optimum composition, and the TE properties of the SBN from both conventional sintering and FAST were compared.

Organic electronics is a growing area of research that investigates the properties and applications of conjugated polymers and conductive small molecules. Devices made from organic electronic materials can be flexible, inexpensive to process, and have lower weight compared to inorganic devices. Prominent synthetic techniques for conjugated polymers, including the Suzuki reaction, Heck reaction, and Kumada coupling, utilize a palladium or nickel complex as the catalyst. When the reaction completes, organometallic molecules and metal nanoparticles remain stuck in the polymer, decreasing the efficiency of resulting devices by acting as charge trappers or photo quenchers. The potential commercial success of organic electronics is highly dependent on their efficiency, and so the impurities need to be removed. A palladium-catalyzed model Suzuki coupling reaction of bromobenzene and phenylboronic acid was analyzed by 31P-NMR both before and after the post-synthetic addition of thiuram disulfide (TMTD). Pd(PPh₃)₂Br₂ dibromide was present in the solution prior to the post-synthetic disulfide addition, but not after. When TMTD or diphenyl disulfide were added directly to metal catalyst in chloroform, the resulting product precipitated out; the solubility of the product was different from the reactants. The change in solubility indicates that disulfide molecules can behave as metal scavenger for residual palladium or nickel catalyst. In order to restore the performance of organic polymers, scavenger molecules are used post-synthesis. This additional step isolates palladium or nickel atoms and changes their solubility, allowing them to be separated from the polymer. The performance of disulfide-based metal scavengers added to catalyst-metal-contaminated conjugated polymers is discussed.

Bacteria play important roles in marine nutrient cycles. However, most marine bacteria are uncultured and little is known about their specific functions in marine nutrient cycles. Environmental members of the gamma proteobacterial sulfur oxidizer (GSO) clade have the genetic potential to use energy from sulfur oxidation to assimilate carbon, suggesting that they contribute to carbon and sulfur cycling in the oceans. Here we report the isolation and initial characterization of an open ocean representative from the GSO clade. Our isolate, GSO-NP4, was purified and its identity confirmed by 16S rRNA gene analyses. This isolate grows to relatively low cell densities (2 x E5 cells/ml) and has a doubling time of approximately 19 hours. Six 1L cultures were required to obtain 3.1g of DNA for genome sequencing. Six to twelve additional 1L cultures were established to obtain enough DNA to sequence the complete genome of GSO-NP4. Genomic information of this isolate is essential for future studies to determine the roles of GSOs in marine carbon and sulfur cycles.

Previous research has shown that adults demonstrate better memory for novel music from their own music culture as opposed to music from a foreign culture. This passive learning imprinted upon kids as they grow up in a certain musical culture its known as “enculturation”. Visual information has also been shown to impact musical memory in adults. Pertinent visual images may augment the encoding process of music and lead to greater recall abilities. In this study, we will include a visual component to the audio information presented. This addition will test the facilitation of visual information to the musical memory of culturally unfamiliar music in adults. Using four video/audio excerpts of musicians performing music in a classical Chinese style and four video/audio excerpts of musicians performing western (classical) style music, we tested the audio and visual memory of adult human subjects in culturally unfamiliar and familiar music. To test them we used twenty-four test items (twelve true tests and twelve false tests) in audio or video format. These different test items can be prepared in three different combinations: audio/audio, AV/audio, AV/AV. Preliminary data demonstrated significantly better overall memory for culturally familiar music. However, music memory scores were higher in the audio condition than in the AV condition in culturally unfamiliar music tests. These results indicate that adding visual information does not aid in musical memory of culturally unfamiliar music. Dichotomous from our initial hypothesis, it is possible that this occurred due to the dominance of visual memory in encoding, or that auditory and visual stimuli provided too much novel information for effective recall.

Approximately 54 million Americans have some form of cognitive or physical disability. This minority status crosses lines of age, gender, race, ethnicity, sexuality, and socioeconomic status. We are all subject to becoming disabled, should we experience illness, an accident, genetic difference, or the effects of aging. Despite such large prevalence, we are faced with limited and stereotypical images of disability as a problem that should ideally be fixed or eliminated. Such a view is the medical model, which contrasts with a more inclusive view of disability, the social model. The social model holds that being disabled is a neutral form of human difference. Problems come from the lack of accessibility for disabled individuals in a society built predominantly for people without disabilities. My project uses the social model framework; first, I will analyze representations of disability in contemporary media. This uncovers marginalizing portrayals of disability that manifest in television today, such as pitying attitudes, “supercrip” depictions, and disability as a burden. Second, I will use focus group methods to examine perceptions of disability among UW students with and without disabilities. I will ask students to interpret various media portrayals of disability and examine salient patterns among their responses. I hypothesize that students will tend toward stereotypical generalizations consistent with the medical model of disability. I predict these results will demonstrate a need for students to develop skills for critical media consumption. With the results of this project, we can identify points for intervention and reframing of harmful stereotypes about disability.

Mosquitoes are the principle disease vector of malaria, yellow fever, and dengue fever, which are responsible for more than a million deaths worldwide annually. This makes controlling transmission a global health priority, and underscores the importance of understanding their behavior. Although it is known that olfaction is the main sensory modality mosquitoes use to select prey, many behavioral patterns, such as changing prey preferences, suggest that associative learning has a role in mosquito behavior. Previous research has established mosquito’s affinity for human scent and characterized their olfactory receptors, but little is known about the neural substrates and molecular underpinnings that modulate olfactory learning. To gain insight into the importance of olfactory learning, I have been introducing controlled perturbations into the larval mosquito nervous system and assaying their behavior using a classical conditioning model. This is achieved through genetic manipulation and injection of drugs with known targets. Initially, I have focused on the role of dopaminergic neurons, because they are known regulators of associative learning in other species. To this end, I have developed microinjection techniques that allow for delivery of silencing RNAs (siRNAs) to knockdown dopamine receptor expression. Using this approach, I have found that Dopamine receptor deficient animals, as well as those injected with Dopamine antagonists, are unable to learn like their untreated counterparts. Knockdown animals suffer a much higher mortality rate in survival experiments that test their ability to avoid predation, underscoring the importance of these receptors in vivo. Currently, we are using cell biological approaches to visualize the relevant neurons. Together these data show that larval mosquitoes are able to learn within days of hatching, and that dopamine plays a crucial role in facilitating aversive learning. In addition to clarifying the mechanistic basis for olfactory learning, these findings may ultimately enhance the development of vector control strategies.

The development of best practices in instruction, defined by student learning outcomes, requires evaluation of student engagement. How can engagement be measured? Student engagement or disengagement is manifested in body language and behavior. Educational studies that employ behavior to evaluate engagement often subjectively rely on a classical perception of how an engaged student behaves; however, recent work suggests that traditional engaged-behavior patterns can fail to account for student-reported engagement, as attentiveness may have many manifestations. Our research pioneers an objective approach to identifying and evaluating student behaviors that function as accurate indicators of engagement level. Using video recordings of Biology 200 students in lecture, student behaviors were catalogued. These same students were surveyed to determine their perceived engagement. The completed catalogue indicated both the presence and frequency of behaviors unique to individual target students, allowing us to compare students’ self-reported engagement level with their corresponding behaviors. The combination of in-class engagement self-assessment and objective cataloguing of behaviors presents the opportunity for quantitative analysis of each behavior’s ability to serve as a hallmark of engagement. Analyses are in progress to determine the predictive power of classical engaged-behavior patterns, and to identify the behaviors most strongly correlated with student-reported engagement. Our purpose is to provide the educational field with a method for analyzing student behaviors as a means for quantifying engagement, and to lay the groundwork on which a widely applicable engagement evaluation tool can be developed in the future.

Red-tailed Hawks (Buteo jamaicensis) and American Kestrels (Falco sparverius) are sit-and-wait predators that rely on perch-sites to forage efficiently. Overwintering Red-tailed Hawks and American Kestrels use available perches (i.e., utility poles and wires, trees, fences, gates, etc.) to hunt for prey items in the agricultural fields in Northeast Arkansas. Observations were made from December 2011 to the present on three representative cover types: short rice stubble, soybean stubble, and fallow areas including roadsides in order to determine which perch-sites were used by Red-tailed Hawks and American Kestrels the most. Prey density and vegetation cover were also estimated in each cover type. Utility pole crossbeams at a height of 6.3 meters are the main perch-site used by Red-tailed Hawks, demonstrating the use of man-made structures as perch-sites. These perches were generally in or near short rice stubble fields, which were found to have the lowest amount of vegetation cover, and low prey density. Conversely, American Kestrels most used utility wires at a height of 4.9 meters from the ground, over fallow roadsides as perch-sites, representing an area with high prey density and vegetation cover. Although there have been documented cases of inter-specific competition between these two species, Red-tailed Hawks and American Kestrels may limit direct interaction via differential uses of perch-sites. The study gained insight into the behavioral ecology of two competing raptors in northeast Arkansas.

Mobility is a sensitive indicator of overall health in older adults. Objective mobility data can provide insight into patterns of function including sleep, behavior, and activity, which is valuable information for both individuals and their healthcare providers. By visualizing objective mobility data, providers can assess for trends that could indicate a shift in overall health in order to intervene earlier, whereas older individuals with mobility goals may benefit from feedback in order to better meet goals or sustain behavior change. The purpose of this project is to perform a secondary data analysis and determine methods for visualizing objective mobility data for both individual users and healthcare providers. Participants of the original study were older adults with a recent history of mild traumatic brain injury. Data was collected with an active sensor system requiring participants to wear a sensor device during waking hours. Working through an interface designed by the University of Washington Ubicomp Lab I aim to create a composite profile of a single participants mobility and movement within their life-space. I am using Excel to sort and create visual representations of data. Key factors to include in visualizing these data are total amounts of active versus passive time spent per participant and the participant’s mobility within his or her life-space. Data analysis is in process and prototypes for visualization are under development. With any visualization effort, it is important to address the different stakeholders’ needs and expectations. Visualizing mobility data for individuals to better understand their own activity levels requires an approach that may be different from visualization targeting clinicians to support clinical decision making. Differences include preferences for granularity of data, level of abstraction, and annotation of context specific details that complement the visualization data. This study demonstrates that visualization can maximize the utility of health monitoring data.

Recent studies demonstrate that certain reproductive factors such as parity (defined as the number of completed pregnancies) are disparately associated with various pathologic subtypes of breast cancer. One factor, fetal microchimerism - the term for persistent child-origin cells in a woman’s circulation and tissues long after delivery - is generally deficient in women with unselected breast cancer and suggests a protective role. Here, we are testing the hypothesis that high-grade triple negative breast cancer (positive association with parity) will be distinctly associated with fetal microchimerism compared to low-grade luminal breast cancer (inversely associated with parity). Buffy coat specimens (n=450) were obtained from breast cancer patients and control participants aged 18-44 from the REACH project (Fred Hutchinson Cancer Research Center, PI Christopher Li). Using quantitative polymerase chain reaction, DNA extracts from these specimens were tested for the presence and concentration of Y chromosome sequence DYS14, a marker of male fetal microchimersim. In an interim analysis from the first 87 specimens, 33% (9/27) of women who developed luminal breast cancer tested positively for the presence of DYS14, as did 33% (10/30) of healthy controls. 47% (14/30) of women who developed triple negative breast cancer tested positively for the presence of DYS14. Preliminary results demonstrate a higher prevalence of fetal microchimerism in patients with triple negative breast cancer compared to control or luminal participants consistent with the original hypothesis. Additional samples will be tested. Fetal microchimerism testing may represent a novel non-invasive method to identify women with poor prognosis breast cancers.

Seabird distribution and abundance can be used as indicators of the health of the coastal ecosystem. In the Gulf of Alaska over the last four decades there has been growing evidence of climate change and ocean acidification. The largest oil spill in the United States, the Exxon Valdez, occurred here. We used data from the Coastal Observation and Seabird Survey Team (COASST), a citizen science, beached bird survey program with 14 years of surveys from beaches in the Pacific Northwest, and eight years of data from Alaska. We seek to compare U.S. Fish and Wildlife Service (USFWS) data from historical surveys in the Gulf of Alaska (1970-1989), to the current beached bird data collected through the COASST program (2005-present). Historic data include monthly surveys of sites from the Kenai Peninsula to Yakutat Bay, and one offshore island, Middleton (n>250 surveys). Current COASST data cover this same range, include additional surveys from Kodiak Island, but exclude Middleton (n>1200 surveys). These data will be analyzed to examine the differences in monthly encounter rate (carcasses/km) averaged over this region, cumulative species diversity, and oiling rate (percent of recorded carcasses that are oiled). This comparison will provide insight into possible changes in the encounter rate index in the Gulf of Alaska over the past 40 years.

Climate change is likely to affect the altitudinal range limits of conifers in the Pacific Northwest as population performance declines at lower elevations and populations expand into upper elevations. However, it is possible that populations are locally adapted, thus influencing range shift dynamics. To assess the potential for local adaptation for three conifer species, Abies amabilis, Tsuga heterophylla, and Tsuga mertensiana, we monitored bud set and bud dormancy in seedlings collected from two to three different source elevations at Mt. Rainier National Park. Phenotypic differences in bud set and bud dormancy influence the length of the growing season, and thus, have impacts on fitness. However, source elevations from which we collected seeds differ strongly in climate, meaning that the optimal climatic triggers for bud set and dormancy are likely to differ. Observations on apical (terminal) bud formation were taken for one year in a common garden at the UW Greenhouse, to correct for environmental differences. Our study thus provides a glimpse at whether or not populations of one species in different locations on Mount Rainier are producing seeds with similar or different phenological traits when observed in the same climate. If seeds of the same species from different locations have inherent differences in the timing of key ecological events, a species may experience difficulty shifting its range when between-population interactions from different elevations become necessary because of climate. Dormancy and bud set differences at the seedling level could influence how conifer population dynamics on Mount Rainier and in other places around the Pacific Northwest will change. In preliminary analyses, we found that seedlings differ in budset and dormancy by species, and there is a trend for differences by elevation within species.

Within the last 20 years, global climate change has become well accepted. Research on plant dynamics has documented species shifting their ranges to higher elevations in order to remain within physiologically optimal conditions. This general observation has motivated my investigation of elevation as a driver of life history traits within alpine and subalpine plants. Specifically I’m interested in sex-ratios among the subalpine flower Erythronium montanum. This species of flower has been shown to exhibit a unique trait known as androdioecy, wherein some individuals produce male-only flowers instead of hermaphroditic flowers. In other species this trait has been attributed to sexual dimorphism, the variability between the sexes in terms of morphology and/or phenology. The discovery of this trait in E. montanum has inspired my research project with two distinct goals: To determine whether 1) abiotic factors such as elevation, soil moisture and time of flowering and 2) biotic factors such as canopy cover, and flowering density, influence sex-ratios within E. montanum. Surveys done at Mt. Rainier in 2011 and 2012 by the Hille Ris Lambers lab provide data on multiple factors which should allow me to test a number of possible hypotheses. Preliminary data analysis spanning both elevation and flowering time, show biased sex-ratios where the number of males to hermaphrodites decreases at higher elevations, late in the season. A future look at the extent of sexual dimorphism within the population can help to shed light on the mechanism behind sex-ratio bias and increase our understanding of plant reproductive-ecology over an altitudinal gradient. As many species begin a slow but steady march up the mountain, it’s paramount that we have a better understanding of how and why life-history traits fundamental to reproduction (e.g. sexual dimorphism) vary with elevation. Ultimately, future generations and plant communities rely on what is happening today.

Individual bees often show flower constancy, specializing on a floral resource while avoiding switches to newly available resources. The familiar plant species benefits by receiving high rates of visitation even when competing floral resources become available. However, the phenology of some plants is shifting more rapidly than others in response to climate change, resulting in a changed sequence of floral resources bees encounter. To determine whether this affects plant fitness, we asked how pollinator visitation to competing plant species depends on the order in which those species bloom. We used two plant species with overlapping phenology and a common pollinator, Hypochaeris radicata and Campanula rotundifolia. We allowed Bombus impatiens to forage in floral arrays representing three phenological progressions: (1) CR Early, with C. rotundifolia decreasing from 100% to 0% while H. radicata gradually increased from 0% to 100%; (2) HR Early, with H. radicata decreasing from 100% to 0% while C. rotundifolia gradually increased from 0% to 100%; and (3) a Control with both species at 50% throughout. We quantified visitation rate to both species, and seed production by H. radicata. Overall, the number of bee visits received by both species was significantly higher when that species was introduced first than when it was introduced after its competitor. In treatments where the proportion of the early species decreased over time, the visitation rate per flower to that species increased, for both species and across all stages of experimental treatments. Seed set for H. radicata showed a similar pattern to visitation. Our results corroborate other work suggesting that individual bees learn and become specialized on a single floral resource and are slow to switch to a newly emerging resource. As a result, the flower species that blooms first can benefit from higher bee visitation and thus, potentially higher reproductive success.

Nitrogen is a commonly limiting nutrient for Douglas-fir growth in commercial stands throughout the Pacific Northwest. Fertilizer nitrogen is applied to mitigate these deficiencies though some studies estimate that only about 30% of the nitrogen is actually taken up by the trees. Knowing where the rest of the nitrogen goes will help determine the best way to fertilize trees and reduce excess use of nitrogen fertilizers. This is beneficial both to stand managers looking to reduce costs associated with fertilization and to the environment as excessive fertilization can lead to increased nitrates in water. For this study, fertilizers labeled with 15N were used to track to the movement of nitrogen within a commercial Douglas-fir ecosystem. Nitrogen-15 is a stable isotope of nitrogen and is often used to trace nitrogen compounds in the environment. Three enhanced fertilizers designed to increase fertilizer N uptake by reducing volatile loss of N and one industry standard fertilizer were used on ten different commercial Douglas–fir stands throughout the Pacific Northwest. The fertilizers were applied at same rate over a period of one year. For the purpose of this study we will be looking specifically at two of the stands. Mineral soil (up to 60cm depth) and foliage samples were collected prior to fertilization to determine the background abundance levels of 15N. Following fertilization, mineral soil and foliage samples were collected at regular intervals to quantify the amount of N15 recovered over time and final sampling was conducted one year after fertilization. Mineral soil and foliage samples were prepared and analyzed for N15. To quantify the amount of N15 taken up by each component, background abundance of N15 was subtracted from the amount of N15 recovered in both the mineral soil fractions and the foliage. We anticipate that the enhanced fertilizers will increase N uptake.

We assessed the impacts of the Carpenter Creek Estuary Restoration Project, headed by Stillwaters Environmental Center of Kingston, WA, in regard to the goals of habitat restoration and preservation. Due to diversions and development, the altered hydrology and sedimentation regime of the stream and intertidal estuarine habitats led to unfavorable conditions for local wildlife, in particular, native salmonids such as Cutthroat trout (Oncorhynchus clarkii), Coho (kisutch), Chum (keta), and endangered Chinook salmon (tshawytscha). With the completion of the first phase of the restoration in 2011, the replacement of a ten foot culvert under S. Kingston Road with a ninety foot bridge, we began gauging the efficacy of the restoration by analyzing water quality, sediment samples, rates of sedimentation, and the extent and composition of intertidal vegetation islands in relation to the presence and abundance of salmonids using diachronous data from pre- and post-bridge construction. We collected and analyzed sediment samples taken in 2011 and 2012 from thirty three transects/quadrats along the estuary banks using Wentworth’s Classification of Coarser Sediments Based on Size of Particles and a gravelometer. These data reveal a decrease in total fine sediment volumes and an increase in larger grain sized pebbles and sand more conducive to salmonid spawning. We evaluated shifts in sedimentation rates and the size and species composition of vegetation islands in the estuary using vegetation surveys and geographic information systems (GIS). We gauged fish presence and abundance utilizing on-site observation, the online Habitat Work Schedule, and reports by local individuals and organizations, with indications of increased habitat health and availability based on geospatial analyses and fish presence. The results of this study are not yet conclusive, but implicate significant progress in the creation of habitat more suitable for returning salmonids, warranting additional research and funding for the completion of the restoration project.

The field of synthetic biology aims to modularize gene-networks within microorganisms for the purpose of using them as well characterized parts in building novel, useful biological systems. Realizing this goal is vital because biology’s inherent practicality holds the key to needed energy efficient technologies. As the human population increases, energy efficient technologies will become more and more a necessity. The first step in realizing this vision of adapting biology into an engineering discipline is through properly characterizing gene expression and enzyme function within engineered and natural biological systems. To do this, I have developed a turbidostat with mixture control and fluorescence sensing capabilities. A turbidostat is a continuous culture bioreactor that maintains constant culture volume and microbe density through a feedback loop between turbidity measurements and dilution with fresh media. The constant culture environment and microbe density allows the cultured microbes to reach a “steady state” where growth and all environmental conditions are kept constant. By maintaining microbes at steady state, variables that effect microbial processes are minimized, which facilitates accurate examining of gene-network dynamics. The mixture control ability of the turbidostat allows for the concentration of a given molecule within the culture environment to be modulated through time without altering any other environment variables. Through mixture control, a molecule that acts as an input to a gene-network (i.e. an inducer molecule that initializes a gene-network) can be varied in concentration through time within the culture environment. Since most gene-networks utilize fluorescent protein production as their output, the turbidostat’s fluorometer (a fluorescence detector) can monitor the output of a gene-network while the input to the network is modulated. We believe that the ability of this turbidostat to look at the input-output dynamics of gene-networks under defined environmental conditions will yield enhanced behavioral understandings, aiding to the modularity of these systems.