Improving the efficiency of photosynthesis has the potential to help attain a net reduction of atmospheric carbon dioxide (CO₂). Cyanobacteria are an enticing target phylum as they contribute an estimated twenty five percent of global photosynthesis. Under ideal conditions, cyanobacteria grow and reproduce rapidly yielding numerous generations over a relatively short time span. Most research on cyanobacteria carbon fixation has been conducted under increased concentrations of CO₂. In contrast, this research investigated: 1) whether cyanobacteria subjected to CO₂-limited conditions will produce successive populations that have improved carbon fixation efficiency, 2) the viability of those adapted populations in present day atmospheric conditions, and 3) whether the survivors fix carbon at an increased rate compared to control cyanobacteria. To answer these questions, control cyanobacteria were maintained in ambient air conditions while an experimental population of cyanobacteria was developed under a range of CO₂-limited conditions. Half of the adapted populations were then returned to ambient air conditions. The rate of carbon fixation under both CO₂-limited and ambient air conditions was approximated by measuring biomass. This research could provide a laboratory-scale proof of concept for net reduction of atmospheric CO₂ by low energy biological means. This method could also eliminate the need for direct gene manipulation by capitalizing on an evolutionary process. Future experiments could replicate this study with different species of cyanobacteria to develop regionally compatible cyanobacteria with more efficient carbon fixation resulting in a net reduction of atmospheric CO₂ in an environmentally sustainable manner.

Eclipsing binaries are systems in which two stars orbit and pass in front of each other. They are important astrophysical tools we utilize to measure fundamental properties of stars, such as their masses, radii, and temperatures. Here, we analyzed photometric data acquired from the Kepler satellite in order to model the light as a function of time of specific eclipsing binary systems. We selected these targets from the Villanova Kepler Eclipsing Binary Catalog. For each system, we used a least-squares optimization method to determine the best fit solution between the model and the observed light curve. Our light curve model has a total of 13 parameters. They include stellar elements such as sum of radii and flux ratio, as well as orbital elements such as period and eccentricity. In addition to providing orbital solutions, our models can be used to search for the presence of additional bodies in the system, such as a third star or a circumbinary planet.

Retinitis Pigmentosa, a progressive neurodegenerative disease, is a significant contributor to loss of vision due to retinal degeneration. The retina is made up of light sensing cells called rods (for night vision) and cones (for day vision). In patients afflicted with this disease, there is a degeneration of rod photoreceptors over time, which leads to a decreased visual field and night blindness. At a certain point, the loss of rod cells leads to the breakdown and loss of cone cells, which are responsible for color vision. Mutations in the rod gene Rhodopsin have been linked to the development of this disease. By down regulating this defective gene, the degeneration of rods would likely be prevented. Subsequently, cone degeneration would also be prevented, limiting the loss of vision in afflicted individuals. The expression of Rhodopsin is controlled by a nuclear hormone-like receptor transcription factor called Nr2e3. In collaboration with another lab (Dr. Sheng Ding, UCSF), we have identified small drug-like molecules that can block Nr2e3, and we have called them CA88, CA95, and CA97. We predict these antagonists will lower the expression of rod genes. Wildtype mouse retinas were treated in culture with CA88, CA95, or CA97. The use of these small molecules resulted in the significant down regulation of a number of rod genes. These genes include Rhodopsin, NRL, NR2E3, and GNAT1.  Stained tissue sections further confirmed a decrease in Rhodopsin with treated retinas.  When retinal ex plants were done using mice with a P23H mutation in the Rhodopsin gene, treated retinas were found to have a significantly thicker photoreceptor layer than non-treated, indicating the ability for these compounds to prevent retinal degeneration. With a way to reliably down regulate problematic genes such as Rhodopsin, a potential avenue for treatment of humans affected by Retinitis Pigmentosa is opened.

This study explores the cognitive effects Bisphenol-A (BPA) has on the mature Helisoma trivolvis, a Ramshorn pond snail common in North America. BPA is a synthetic hormone used in plastics, making it ubiquitous around the world. BPA is easily leached into water and accumulates in many aquatic habitats, making this pond snail a prime candidate for research. BPA has been shown to interfere with the natural estrogen activity in the brain of pond snail embryos leading to developmental complications and premature death. This study focuses on the cognitive effects that BPA has on mature Ramshorn snails. Specifically the snail’s ability to form short-term memories in response to a negative stimulus. An operant conditioning procedure was used to assess the memory capacity of the mature snails in a range of BPA-contaminated conditions (10-800 µg/L). We raise two consecutive generations of snails both separated into five populations. Each generation had a control group containing non BPA treated water and four other groups with BPA concentrations of 10, 200, 600 and 800 µg/L solutions. Memory deficits were correlated with BPA concentrations. The results from this study add to the growing understanding of both the potential cognitive impacts of BPA as well as potential ecological consequences of BPA contamination.

Transformations over assembly code are common in many compilers. Such transformations are useful in applications ranging from peephole optimizations to software fault isolation. These transformations are also some of the most bug-dense compiler components. Such bugs could be eliminated by formally verifying the compiler, but state of-the-art formally verified compilers like CompCert do not support assembly-level program transformations. This paper presents Peek, a framework for expressing, verifying, and running assembly-level program transformations in CompCert. Peek contributes four new components: a lower level semantics for CompCert x86 syntax, a liveness analysis, a library for expressing and verifying peephole optimizations, and a verified peephole optimization pass built into CompCert. Each of these is accompanied by a correctness proof in Coq against realistic assumptions about the calling convention and the system memory allocator. Verifying peephole optimizations in Peek requires proving only a set of local properties, which we have proved are sufficient to ensure global transformation correctness. We have proven these local properties for 26 peephole transformations from the literature. We discuss the development of our new assembly semantics, our liveness analysis, representation of program transformations, and execution engine, describe the verification challenges of each component, and detail techniques we applied to mitigate the proof burden.

Amnesic shellfish poisoning is the result of eating seafood contaminated with domoic acid, produced by toxigenic diatom species from the genus Pseudo-nitzschia. In the summer of 2015, abnormally large assemblies, known as super chains, of Pseudo-nitzschia australis appeared in the massive algal bloom that swept up the Pacific Coast. This affected commercial and recreational shellfish harvesting and cost millions of dollars in shellfish sales. Due to their recent appearance, knowledge of P. australis super chains is extremely limited. Here, we investigate the prevalence of super chains in Puget Sound and along the Pacific Coast. The deep chlorophyll maximum, DCM, is a layer in the water column that is often found to contain a high volume of photosynthesizing phytoplankton.  A collection of electronic devices that measure conductivity, temperature, and depth (also called CTD) was deployed to determine DCM, from which plankton samples were collected. Scanning electron and light microscopy were used to identify P. australis species and to examine the morphology of their associated bacteria. Most surveys have been conducted during the late summer when blooms are at their peak. By conducting our survey in the late winter, we have had the opportunity to measure P. australis super chain prevalence during what is typically a less active season. Our results provide novel information of P. australis super chains and their associated bacteria during a season that has been so far neglected. In addition, our diverse sample sites in Puget Sound and along the West Coast present a systematic survey and allow us to make regional comparisons. This study lays a foundation for more comprehensive research of super chains in the future. 

Seattle’s Combined Sewer Overflow (CSO) system discharges approximately 100 million gallons of untreated sewage and storm water runoff into its waterways annually. The sewer system includes two combined waste streams: waste from sewer basins, which captures storm water runoff, and wastewater from buildings and industry. Pollutants in the effluent such as human waste, automotive by-products, pesticides, and pharmaceuticals can degrade ecosystems. To determine the impact that CSO outfalls have on Seattle’s waterways, this study tested for pollutant levels in sediment near two discharge areas: Elliott Bay and the western end of Seattle’s Ship Canal. Sediment samples were collected using a Van Veen grab, then handled and stored using sterile, inert materials to avoid contamination. Sediments were tested for heavy metals including mercury, via cold-vapor atomic absorption, and lead, via inductively coupled plasma mass spectrometry. The organic pollutants ammonia, nitrate, and phosphate were quantified via automated calorimetry. Laboratory testing for pollutants was done in accordance with EPA guidelines or standard analytical methods. Results were compared to the Washington Department of Ecology’s Sediment Management Standards. Preliminary results suggest that lead and mercury levels do not exceed the Department of Ecology’s sediment quality standards, while cadmium levels are slightly above or below recommended levels at each site. This data can be used as a baseline to help better understand the contribution of CSOs to pollution levels in these areas. More research will be necessary to determine the extent of damage to ecosystems near the outfalls.

Organic acids are crucial factors in creating the aromas and flavors in wine, each adding their own qualities and characteristics. Winemakers regularly use various forms of technology to quantitatively determine the contents of wine. Analytical tools such as enzymatic spectrophotometry, paper chromatography, and high-performance liquid chromatography offer methods to quantify chemical components including acetic, malic, lactic, tartaric, and citric acids, as well as sulfates and sulfites. Although ion chromatography (IC) has not been a widely studied method to analyze organic acid content in wine, it offers the potential to simultaneously analyze multiple ions with greater specificity and sensitivity than other approaches. This project examines the various ways that IC can be used to analyze the components of wine, allowing for further application within the wine industry. The malolactic fermentation process was tracked to measure the changes of malic and lactic acids within the wine. Sulfites and sulfates were measured as the wine was exposed to oxygen during the aeration process. The results show that IC provides greater accuracy than paper chromatography and enzymatic spectrophotometry, the most commonly used methods in wineries. This increased accuracy provides additional knowledge that allows winemakers to further understand and evaluate the chemical components in the wines that they create. This is a useful step towards making the characterization and marketing of the wines less subjective.

DNA origami is the fabrication of biochemical structures using DNA as the building material. Using base pair design principles, DNA can be synthesized to self-assemble into dynamic objects such as a piston. The resulting creations have potential applications in nanotechnology including drug delivery, enzyme immobilization, photolithography, environmental restoration, and biocompatible devices. The goal of this project was to design a nanoscale mechanical spring and determine the parameters for spring constant and size. First, a spring comprised of multiple columns of double-stranded DNA was designed and fabricated. Size measurements were taken and morphology was verified using a transmission electron microscope. To measure the force constant of this structure, the 5’ end of the first column was functionalized with a thiol group which was then bonded to a gold cantilever tip on an atomic force microscope (AFM). This construct was brought very close to a magnesium substrate and allowed to bond. Force measurements for the spring were taken via AFM by slowly retracting the cantilever from the substrate. The spring force constant was calculated from this data using Hooke’s law in order to predict the amount of work that the DNA nanospring can perform when included in a complex nanostructure. The nanostructures created in this project can be used in conjunction with other DNA origami designs in order to create increasingly complex machines on the nanoscale.

The rise of multidrug resistant bacteria necessitates finding alternative therapies against bacterial pathogens. Virulence in many pathogenic bacteria are predicated on their ability to communicate and act in unison. In a phenomenon known as quorum sensing (QS), a threshold mass of bacterial cells produces an amplified chemical signal that triggers the collective expression of a new phenotype, such as enhanced virulence. Therefore, inhibiting QS, without preventing cellular growth, may be a recourse against drug resistant bacteria. Marine invertebrates found in warmer waters, such as the Australian reef and Indian Ocean, have shown quorum sensing inhibitory (QSI) potential. However, most marine invertebrates in the Pacific Northwest’s Puget Sound have not previously been screened for QSI compounds. This research presents the findings for QSI sources among Puget Sound’s marine sponges and tunicates, using a bacterial reporter strain to screen for QSI activity. We used the reporter strain Chromobacterium violaceum (ATCC 12472), which uses the QS signal n-Acyl-homoserine lactone (AHL) to produce its purple pigment. QSI activity was screened for by overlaying the reporter strain with a sponge or tunicate sample. Subsequent absence of pigment in the indicator strain suggested the presence of a QSI compound. Promising compounds were then extracted and identified using analytical techniques. These results help expand the catalogue of known QSI molecules from marine sources, advancing potential therapies against existing and future antibiotic resistant pathogens.

Antibiotics are present in nearly every facet of our lives including personal hygiene, medicine, food processing, and the treatment of infectious diseases. Because of this widespread exposure, antibiotic resistance occurs in dangerous pathogens around the world. Novel antibiotics are needed to combat these resistant organisms and reduce both the loss of lives and treatment costs. Most antibiotics originated in microorganisms cultured from soil, but very few novel compounds have been discovered in this environment over the last several decades. It is imperative that other environments are screened for antibiotic producing microbes. We sampled the Puget Sound, isolating and culturing bacteria from the surface. Isolated cultures were tested against reference strains of common pathogens for antibiotic potential by measuring the zones of inhibition they produced via agar diffusion. Phylogenetic analysis with 16s ribosomal RNA was used for identification of cultures with inhibitory activity. This type of analysis, especially if scaled-up, has potential to identify novel therapeutic compounds that may elude common resistance mechanisms.

As concern over antibiotic resistance continues to grow, there is a critical need to discover and develop new methods of controlling and preventing bacterial infections. Essential oils derived from the peels of oranges are known to possess antimicrobial properties. Previous research has established that limonene, the principle compound present in orange oil extract, is a particularly effective antimicrobial agent that both destroys bacteria and inhibits bacterial growth. To determine whether different varieties of oranges have varying antimicrobial potency, the efficacies of oil distilled from blood, navel, and valencia oranges were compared. Oils extracted through steam distillation were diluted with methanol to concentrations ranging from 1:20 to 1:1. Staphylococcus aureus, Pseudomonas aeruginosa and Escherichia coli bacteria were exposed to the oils using the disc diffusion method on TSA plates. The minimum inhibitory concentration (MIC) for each oil was determined using the agar diffusion method. Gas Chromatography Mass Spectrometry (GC-MS) was used to compare the relative concentrations of limonene present in each essential oil. A better understanding of the potency of orange oil as an antimicrobial agent could lead to development of novel drugs and products to be used to combat infection and prevent the spread of bacterial pathogens.

 Glioblastoma multiform (GBM) is the most common and aggressive malignant primary brain tumor and accounts for about 70% of new cases of primary brain tumors in the US annually.  Current treatments are very aggressive and have a high risk of systemic toxicity due to non-specificity of current cancer therapeutic agents. Iron oxide nanoparticles (IONPs) have shown great promise as versatile targeted drug delivery vehicles for effective cancer treatment.  In this research presentation, the development of two multifunctional IONPs for targeted GBM therapy will be discussed.  The first is an IONP covalently conjugated with anti-cancer drug, gemcitabine (GEM), using hyaluronic acid as a bridging molecule.  The second is an IONP conjugated with carboxylated ß-cyclodextrin and loaded with paclitaxel (PTX) via hydrophobic interactions.  Both IONPs were conjugated with chlorotoxin (CTX), a GBM targeting agent that can cross the blood-brain barrier (BBB), and fluorescent dyes.  Through characterization by TEM, DLS, and HPLC, the IONPs showed small size, high stability, and proper drug loading.  More importantly, the GEM-conjugated IONPs showed prolonged blood circulation time and BBB permeability in vivo.  The PTX-conjugated IONPs showed enhanced cell killing of the GBM cells and drug-resistant GBM cells compared to the free drug.  The two multifunctional IONPs have shown great promise for effective treatment of GBM.

Breast cancer is the most common cancer in women. Even with advancing treatment techniques, breast cancer is still the cause of tens of thousands of death in the U.S. alone. Combined treatments including surgery, radio and chemotherapy are commonly implemented for breast cancer. However, the survival rate of metastatic breast cancer remains low, so new targeted therapy strategies are needed. In recent years, nanotechnology has opened a new route for targeted therapy of breast cancer. Nonetheless, some challenges still remain for nanoparticles (NPs) used in breast cancer treatments. After loaded with anticancer drugs, fluorophores and targeting ligands, NP drug delivery systems suffer from issues of size limit, stability, target cell internalization and biodegradability. Anti-human epidermal growth factor receptor 2 (HER2/neu) monoclonal antibody is a good targeting ligand for some breast cancer cells for two main reasons. Firstly, about 1/4 of breast cancer patients overexpress HER2/neu. Secondly, monoclonal antibodies have a better targeting effect than small molecule, protein and aptamer-based targeting ligands. However, the bulky size of the antibodies can change the desired physiochemical properties of NPs. Therefore, an anti-HER2/neu peptide, which is a small exocyclic peptide derived from the antibody, is utilized for targeting purposes. Moreover, paclitaxel (PTX) is a strong anticancer drug that can restrain mitotic spindle assembly and chromosome segregation, and in turn prevent breast cancer growth. Here we report anti-HER2/neu peptide-conjugated and PTX loaded iron oxide NPs (IONP-PTX-AHNP) that are small size, highly stable and biocompatible in biological medium for breast cancer treatment. Significantly, the IONP-PTX-AHNP showed targeted cell uptake into HER2/neu overexpressed breast cancer cells and PTX-mediated cancer cell death.

Understanding the genetic changes by which organisms adapt to novel and extreme environments is a central goal of evolutionary biology. One mechanism that may offer a rapid path to adaptation is hybridization: the union of two genetically distinct populations or species. Hybridization may transport beneficial genetic variation from a related species or may stimulate new variation to form within genomes, such as the mobilization of transposable elements (TEs). Transposable elements are large, repetitive sequences that can independently move around the genome, and thus mediate a cascade of large-scale changes in chromosome structure, gene expression, and gene content. I am interested in studying whether TE insertions occur more frequently in hybrid species vs. parental species and identifying the types of genomic changes TE insertions facilitate in hybrids. To do this, I am using a two-part approach in the model system of budding yeast, Saccharomyces cerevisiae. First, I am performing fluctuation assays to assess the rate of transposition in S. cerevisiae, its relative Saccharomyces uvarum, and an interspecific hybrid of the two. Second, I am using sequencing to identify novel TE insertions in hybrids evolved in nutrient-limited environments. If TEs do play a role in hybrid adaptation, I would expect to map transposition events with sequencing data and identify associated chromosome rearrangements and/or gene disruptions that may confer a fitness benefit. I also hypothesize finding higher transposition rates in the S. cerevisiae x S. uvarum hybrid clones compared to the non-hybrid parental clones. In doing so, I hope to gain a deeper understanding on the genetics of hybrid adaptation, which has yet to be studied in greater detail in the field of experimental evolution.

As environmental monitoring technology advances, people will increasingly have access to new data about their surrounding environmental quality. But, a challenging issue is the question of how can people best access the information? In this research project I focused on data collected from a new neighborhood air pollution monitoring study in Oakland, CA. Our research question is: How can we best express complex air pollution data so that it can be understood and acted upon by people with different educational backgrounds and community interests? I employed user experience research and design methods to answering this question by having the local community members at organizations like West Oakland Environmental Indicators Project, Communities for a Better Environment, La Clinica, and Bay Area Air Quality Management District respond to questionnaires and interviews related to their interest and concerns about air pollution. After gathering this information, I analyzed the air pollution data our research group and the government are currently collecting in the region. Later I used the sorted data to design personas and wireframes through Illustrator and prototyping tools for how the interface should look and have the community members test the prototypes by responding to surveys and interviews as to whether they can use the given data with ease. Lastly, I reported the results of our iterative interviews and questionnaires. I anticipate that the outcome of using user experience research and design methods will be an interface that is highly usable for the community partners in Oakland, CA. 

Locomotion is a ubiquitous human behavior. The analysis of locomotion patterns is critical for diagnosing and monitoring musculoskeletal disorders. However, current analysis methods are limited to gait laboratories equipped with accurate optical systems and force plates. To address this limitation, this work focuses on developing a process for manufacturing low-cost, individualized, flexible foot insoles equipped with force, acceleration, and gyroscopic sensors. The approach is a three stage three-dimensional (3-D) printing process: (1) 3-D print flexible base layer with electronic compartments; (2) install electronics; and (3) 3-D print flexible closing top layer. The design of the insole with respect to the sensor location is highly modifiable, resulting in subject specific sensor layouts. Moreover, any miniaturized sensor/transducer can be incorporated in the design. The resulting structure is a flexible instrumented insole worn in the user's shoe. Currently, the main application is for real-time sensing for use with a bionic ankle prosthesis. Future applications include real-time sports analysis, sweat sensing for analysis of body chemistry, and energy conversion using piezo electric transducers. Thus, the main contribution of this work is a manufacturing process for low-cost flexible 3-D printed insoles with embedded sensors.

Systemic immune activation (IA) is a proven key factor in human immunodeficiency virus type 1 (HIV) infection pathogenesis and progression to acquired immunodeficiency syndrome. The reproductive hormone progesterone plays a role in regulating the immune system, and most cells contain progesterone receptors. Previous studies have linked high-progestogen states in women, such as pregnancy and progestin-based contraception use, to increased infectivity in HIV-seropositive women and increased HIV acquisition in seronegative women. Progestin-based contraceptives such as depot-medroxyprogesterone acetate (DMPA) can create high plasma levels of progesterone analogs. Therefore, studying DMPA use by HIV-seropositive and seronegative women may clarify DMPA’s role in HIV-related IA and genital shedding, and immune changes related to HIV acquisition. We hypothesize that DMPA increases systemic IA. Increased IA could be clinically significant by contributing to increased HIV acquisition in high-risk HIV-seronegative women, and by increasing genital shedding and infectivity among HIV-seropositive women. To answer this question, peripheral blood mononuclear cells (PBMC) were collected at three postpartum time points over six months from 120 Kenyan women with both HIV-seropositive and seronegative status, including a sub-population in each category that elected to receive DMPA for contraception. Two immunophenotyping panels were developed to measure T-cell IA and cellular subsets of interest using flow cytometry (CD38, HLA-DR, Ki-67, Bcl-2 for T-cell activation; FOXP3, CD25, CD127 for regulatory T-cells; CCR7, CD45RA, CD27, CD28, CD57 for memory subsets; CCR5 for the HIV co-receptor). With preliminary analysis completed for most samples, specific antibody populations have been gated with FlowJo software. After completion, we will compare different population percentages in the four arms of the study, observing how these change with DMPA administration. These calculations will help elucidate expected differences in inflammatory and regulatory changes in both HIV-seropositive and seronegative women with respect to the relationships between DMPA, immune activation, and HIV susceptibility and infectivity.

Cardiovascular disease is the leading cause of death worldwide due largely to the inability of the heart to respond effectively to injury through tissue regeneration. Coronary artery narrowing initiates cessation of arterial blood supply to the heart generating an ischemic injury, characterized by low oxygen and nutrient supply and the accumulation of metabolic waste. Currently, research approaches to study ischemia rely on high-cost and low-throughput in vivo models. As such, there is a need for an in vitro platform for mimicking ischemia/reperfusion injury in a three dimensional cellular environment. The research and design pursued here addresses this deficit in modeling capabilities by developing an in vitro ischemic injury and reperfusion model utilizing engineered cardiac micro tissues. Cardiomyocyte microtissue particles (MTPs) are formed through centrifugation of a single cell suspension of stem cell derived cardiomyocytes without scaffold materials into polydimethylsiloxane micro-wells. Ischemic injury is induced in MTPs by exposing tissue cultures to mineral oil layers on top of small volumes of spent culture media to restrict oxygen supply and metabolic waste exchange. This simulated injury results in an observable reduction in live cells as evidenced by a decreased live cell fluorescence signal associated with duration of injury from a calcein and EthD-1 live/dead stain. Optimization of this staining protocol for characterizing the extent of the induced injury in an adapted plate reader format is currently underway. Thus far, percent of live cells has been shown to positively correlate with normalized calcein fluorescence intensity and current efforts are directed towards increased efficacy of EthD-1 dead cell marking and sufficient tissue infiltration of the stain. Implementation of this protocol will create a baseline metric for monitoring the state of the engineered cardiac tissue during injury and reperfusion and provide a foundation for development of an accurate and cost effective cardiac ischemia injury model.

Hydrogels have proven to be excellent 3D cell culture platforms, serving as frameworks for synthetic tissue substitutes. Though given the complexity of the native extracellular environment, control over mechanical and biochemical cues within hydrogels is important in mimicking the extracellular matrix (ECM), the dynamic framework about which cells function. We seek to provide spatiotemporal control over cell fate within hydrogels formed through photo-mediated oxime ligation, a novel approach to photopolymerization seldom interfering with biological species present in cell encapsulation. By conjugating a photo-cleavable ortho-nitro benzyl (NPPOC) functionality to an aminooxy group, this otherwise spontaneous reaction may be spatiotemporally regulated with UV light. Excitation of the aminooxy-NPPOC complex upon UV light exposure cleaves NPPOC, enabling aminooxy to undergo ligation with an aldehyde. We have demonstrated the successful synthesis of 4-arm poly(ethylene glycol) (PEG) molecules separately functionalized with benzaldehyde and aminooxy-NPPOC end-groups. We have additionally demonstrated hydrogel formation following UV light exposure to 4-arm PEG solutions of varying compositions, verifying photo-mediated oxime ligation’s viability as a photopolymerization strategy. Following gelation, photo-mediated oxime ligation may be extended towards the incorporation of biochemical ligands via 3-dimensionally patterning NPPOC-conjugated proteins. Combining control over hydrogel geometry and stiffness with protein patterning, this dynamic hydrogel platform will expectedly aid in better understanding cell behavior through emulating the ECM’s heterogeneity. Consequently, an improved understanding of cell-matrix interactions may aid in advancing synthetic tissue substitutes.

The current industrial agriculture model relies heavily on water and fossil fuels to create the fertilizers, herbicides, and pesticides needed to grow, as well as harvest, process, transport and distribute food to urban areas. Urban indoor agriculture systems may provide alternatives to meet nutritional demands of growing populations in urban areas by using hydroponic and aeroponic methods. Indoor methods rely on energy to operate the watering and lightning systems, and temperature controls are needed to maintain a consistent environment for optimal, healthy plant growth. Studies have shown that fungal symbionts can confer tolerance for increased temperatures, drought, high CO2 levels, and protect plants from disease. This study will investigate the role that fungal endophytes play on plant growth and water consumption in aeroponic systems by measuring the potential effect(s) that fungal endophytes (i.e.Trichoderma sp., Curvularia sp. and Colletotrichum sp.) have on Lettuce (Lactuca sativa) growth under reduced water conditions. By quantifying the differences in biomass, rates of growth, water consumption and relative water content between the infected plants and uninfected plants, we will determine if the relationship between the endophyte and the plant increases plant growth while decreasing energy usage and water dependency. New technologies applied to large scale, indoor agriculture operations could decrease water and energy requirements needed to grow food sustainably. Creating energy and water efficient systems could have substantial economic and environmental benefits, by decreasing the carbon footprint associated with agriculture models and increasing access to healthy food in urban areas.

While HIV treatment is improving, there are still problems associated with it. Antiretroviral therapy (ART) has unfavorable side effects, is expensive, and requires a lifelong daily pill intake. However, it has been proposed that a therapeutic vaccine could provide durable control of viremia in the absence of ART. This is a difficult approach due to the high mutation rate of the virus. Research has shown that there are conserved elements (CE) within the virus that do not change because they are important for the viral fitness. Accordingly a therapeutic DNA vaccine is being investigated that targets the CE epitopes. To address this, rhesus macaques were infected with SIV (Simian Immunodeficiency Virus), put on ART, vaccinated with four doses of DNA vaccine expressing CE, removed from ART, and their viral loads monitored. A successful vaccine is expected to reduce the viral loads to negligible amounts post ART cessation. My research project investigates the role of CE responses developed during acute infection. I hypothesize that macaques that naturally develop higher CD4+ and CD8+ T cells (types of white blood cells) with CE specificity in response to the acute SIV infection will respond better to ART and CE vaccinations. To investigate this I collected plasma and lymphocytes from the blood during acute infection and analyzed the CD4+ and CD8+ T cells using enzyme linked immunospot (ELISpot) and intracellular cytokine stain (ICS) assays. The viral loads were monitored by measuring the concentration of viral RNA in the plasma. T cell responses measured at each time point was then correlated to viral loads post ART-pre vaccinations or to CE responses measured after the final DNA vaccination by Spearmann Rank correlative test. My findings will help us better understand the significance of conserved elements in controlling the HIV and thus design better human therapeutic vaccines.

People with leg amputations who use prosthetic feet during community ambulation encounter frequent environmental barriers. Uneven ground, such as grassy fields or sidewalks in disrepair, cause excessive forces at the interface between the artificial leg and the residual limb because of torques from the ground acting on the foot. These forces can cause pain, skin breakdown, and falls. Impulsive forces may be reduced by a prosthetic foot allowing medial-lateral rotation of the foot relative to the leg. This study compared the kinetic and kinematic outcomes of an investigational prosthetic (IP) foot to the participant’s usual prostheses. Eight study participants completed a single leg balance test and 5 walking conditions with their prescribed prosthetic (UF) and with the IP foot. The participants walked lengthwise along 10% and 15% side slopes and across domes (Botts’ dots) placed on flat ground. A 3-D motion capture system tracked 36 reflective dots which were placed on key landmarks so that joint angles and spatiotemporal metrics could be computed. One participant’s data was excluded from the ankle joint outcomes. Participants reported reduced forces at the residual limb-prosthesis interface. Preliminary results indicated that the UF and IP foot perform similarly in sagittal plane motion. The IP foot increased the ankle medial-lateral rotation for 5 out of 6 participants. Future research will include comparing a participant’s UF to the IP foot in community trials while collecting activity monitoring, GPS, and logbook data.

One limitation of chemotherapy drugs is their impaired ability to penetrate tight junctions between epithelial cancer cells to access the inside of a tumor. Adenoviruses have devised a method for moving between epithelial cells by virtue of binding adenoviral fiber proteins to the human protein desmoglein-2 (DSG-2) found within these junctions. When used in coordination with chemotherapy drugs, a recombinant adenoviral fiber protein, termed JO-1, was shown to improve the efficacy of the cancer drug by opening tight junctions thereby facilitating entry of the drug into the tumor mass. Mutagenic library studies with JO-1 identified point mutations that resulted in increased affinities for DSG-2. An affinity enhanced variant, JO-4, containing a V239D mutation is currently being evaluated for tumor co-therapy. Two additional mutations were identified, one (N293S) lead to an increased association rate, and a second mutation (Y250F) slowed dissociation by stabilizing the complex between the fiber protein and DSG-2. We hypothesized that combining multiple advantageous mutations in a single protein would result in an overall additive effect on affinity and activity. Utilizing more active proteins in cancer therapy can allow for smaller doses and higher potency of chemotherapy drugs in human patients. Two proteins based on JO-4 and containing the Y250F or the N293S mutations were designed in silico, cloned, and produced in E. coli. These proteins were then characterized for functional activities based on the ability to compete with adenovirus infection and the ability to enhance chemotherapy in mouse tumor models.  We expect the proteins with heightened affinity to DSG-2 will block virus infection at lower doses than JO-4 and in conjuction with chemotherapy drugs will stunt the growth of tumors in mice compared to chemotherapy alone.