Females use many different sanitation products, including tampons and pads. However, it is speculated that some of these everyday products for some women may contain heavy metals and other chemicals. Lead is a heavy metal that presents a danger as can cause cancer and mental inefficiencies. Chromium is said to cause dermatitis and skin irritation. These metals are often thought of to be threatening in water and soil. However, man-made products such as tampons and sanitary napkins/pads can contain these heavy metals. Using standards from both metals and ICP technology, or an Inductively Coupled Plasma machine, analyzed the feminine hygiene products for chromium and lead. In my analysis of the hygiene products there does not seem to be a concerning amount of heavy metals, even with an increased mass analyzed. Very small amounts of chromium and lead were found in both pads and tampons. There appeared to be more lead than chromium in tampons, yet not a large amount to report stark differences.

The purpose of this research is to generate immersive, natural-looking environments from geoengineering data that can be viewed on hardware-constrained virtual and mixed-reality platforms. Current mixed and virtual-reality technologies, such as the Microsoft HoloLens, are constrained by limited hardware resources. These constraints set limits on the realism and quality of immersion of virtual reality environments. Thus, no software previously existed to intelligently render immersive 3D terrain on hardware-constrained virtual and mixed reality devices. Through research in terrain generation and 3D rendering, the Viewpoint Generator application was created that can accurately and realistically render 3D environments. To render the terrain, 3D environments generated in Unity, a game rendering software, are pre-processed on a host machine. The 3D terrain is sliced into a grid containing individual slices. For each slice of terrain, a set of concentric panoramas and a skybox are generated. These static components require relatively little power to render. Performance was benchmarked through simulations in Unity and on-device with a Microsoft HoloLens, with a minimum frames-per-second (fps) requirement of 60 fps to prevent nausea induced by slow rendering. These components form the Viewpoint Generator application that can be deployed to hardware-constrained devices, which allows users to explore areas of a 3D environment not previously possible on hardware constrained devices. Applications for the Viewpoint Generator include uses in civil engineering and environmental restoration and visualization. Large-scale environmental projects too large to convey through static 3D renderings or by human imagination can now be explored in an accurate and realistic virtual environment. As the Viewpoint Generator is designed to operate on compact devices, it is easily deployed to remote environments. The Viewpoint Generator sets the foundation for development in procedural environment generation based on geoengineering data, allowing new visual insight into civil engineering and environmental restoration projects.

Global warming is drastically increasing glacial ice loss and retreat rates.  Rapid glacier melting has been destabilizing valley walls in recent decades, as glaciers are debutting from the bedrock causing landslide induced tsunamis.  On October 17, 2015, an enormous landslide collapsed in Taan Fiord, southeast Alaska.  Some of the landslide debris covered the terminus of tidewater Tyndall Glacier, but most entered the waters of the fiord, triggering one of the largest tsunamis ever recorded on Earth.  The impacts of the tsunami ranged from scouring the ocean floor, to stripping forest cover down fiord to elevations exceeding 50 m asl.  Following the event, high-resolution satellite imagery revealed extensive subaerial white patches ~8 km down fiord that disappeared in subsequent months.  We interpret these patches as relict, formerly buried glacial ice that was uncovered during the tsunami.  Following erosion of an insulating veneer of sediment, these bodies rapidly melted, forming large kettle holes.  High-resolution multibeam sonar bathymetric mapping (a type of sonar that creates seafloor maps) of an adjacent embayment revealed dozens of subaqueous kettles, up to ~15 m deep.  

Predator-prey models provide invaluable insight into interspecies relationships and fluctuations in population sizes, but like all models, must rely on simplifying assumptions that reduce complex natural processes to functions with explanatory and predictive utility. Logistic equations for population growth predict future population size as a function of current population size and competition for limited resources; the related Lotka-Volterra equations use similar assumptions but with predator-prey interactions limiting population growth. In North America, the Canada Lynx-Snowshoe Hare cycle is an ideal demonstration of interconnected predator-prey population sizes. When vegetation is plentiful, hares have the resources to bear many litters of offspring and they provide a high level of nourishment to lynx. Lynx and hare populations increase in number until vegetation becomes scarce and predation by lynx reduces the size of the hare population. At this point, hares are too scarce to sustain lynx population growth and lynx numbers decrease while plants repopulate the region. Lotka-Volterra equations capture this cyclical relationship but assume genetic uniformity between individuals and no age structure in the population. Extensions of predator-prey models have incorporated age structure but not genetic variation. My model examines the dynamics of this system when both aging and genetic variation for fitness are incorporated into predator-prey dynamics. Using the statistical programming language R, I present a simulation of predator-prey dynamics with these two additional parameters—variation in relative fitness among individuals and age structure. Analysis of “the hare that never got caught” is an inquiry into the influence of age structure on fitness. More broadly speaking, this work attempts to model the effect of aging on the efficiency of natural selection and provides a basis for future research regarding the role of aging in evolutionary biology.

Traumatic brain injury (TBI) is an illness that affects people in all walks of life, from everyday citizens to soldiers in combat, and both young and old. Among all cases of TBI, there are some patients who recover quickly and some patients who take a long time to see any improvements, suggesting a range of what we call “TBI resistance”. To see if we could identify a genetic basis to this variation, we used the fruit fly, Drosophila melanogaster, as a model of TBI resistance. Specifically, we used a set of fly strains captured in Raleigh, North Carolina, and commonly known as the Drosophila Genome Reference Panel (DGRP). The DGRP is a sequenced set of inbred flies that researchers around the world experiment on, thus establishing a universal platform to identify genes associated with natural variation for a wide range of fly traits. For our study, we created a spring device to model TBI in flies. The device consists of vial of flies connected to a high resistant spring which propels it towards a hard pad causing damage. We compared the mortality rates between the different lines of flies. We hypothesized that we would see some lines display resistance and some lines display sensitivity. This turned out to be true, and we have already identified candidate genes associated with this variation. As a next step, to study TBI resistance on a cellular and molecular level, we will perform metabolomics with both resistant and sensitive lines to see if there is a significant difference between metabolite expression. The expression of certain metabolites in resistant flies, compared to sensitive flies, could hold the key to understanding how resistance is acquired against TBI and we will be one step closer towards understanding ways to protect people from the effects of TBI.

Alzheimer’s Disease (AD), the most common form of dementia, is the sixth leading cause of death in the United States. With a prevalence of over five million cases, the number of AD patients is expected to increase as a new diagnosis of AD is made every sixty-six seconds. Early symptoms include short-term memory loss and gradually progress to devastating deficits in cognition, temperament, and behavior. AD is a neurodegenerative disease linked to the accumulation and aggregation of two proteins, Aβ_1-42 and hyperphosphorylated Tau, which form the characteristic amyloid plaques and neurofibrillary tangles found in the brains of AD patients. Previous studies support the notion that genetic variation underlies the wide array of phenotypes observed among AD patients, and several genes have been discovered to cause early onset AD. In sporadic (late onset) AD patients, it remains unknown what effects natural variation may have on the expression and severity of the AD phenotype. To explore the influence of genes on AD, our study utilizes a Drosophila model of AD that allows us to express both the Aβ_1-42 and Tau peptides in the fly eye. Expression of AD-related proteins in the eye leads to degradation of the hundreds of ommatidia that make up the fly eye. To quantify the extent of ommatidial degradation, we use a computer program, ImageJ, which measures the size and circularity of each ommatidium. To introduce natural variation, the AD fly is crossed with flies from the Drosophila Genetic Reference Panel (DGRP), consisting of 192 fully sequenced isogenic lines. By comparing the Aβ_1-42 and Tau-induced degradation in each background, we can identify naturally occurring modifiers of the AD phenotype. We have already identified promising hits, which could eventually help in the development of novel targeted therapies.

Parkinson’s Disease (PD) is an age-related neurodegenerative disorder that leads to progressive decline in motor control. Tens of thousands of new cases are diagnosed each year. Many cases of PD are linked to chronic exposure to rotenone, a commonly used pesticide. As an inhibitor of complex I in the mitochondrial electron transport chain, rotenone causes deterioration of dopamine-producing neurons in the substantia nigra (part of the midbrain). Studies suggest that there is a genetic component to how likely one is to develop symptoms in response to rotenone exposure. To test this hypothesis, we used the Drosophila Genetic Reference Panel (DGRP), a set of 192 fully sequenced inbred lines of the fruit fly, Drosophila melanogaster. Exposure of Drosophila to rotenone has been shown to cause dopaminergic-specific degeneration, similar to the pathology observed in PD patients. When fed highly concentrated rotenone-infused food, we see significant variation in rates of survival among female flies from different lines of the DGRP, allowing us to capture natural variation in response to rotenone exposure. After most of the DGRP has been tested, we will carry out a genome-wide association study to identify specific genetic variants associated with rotenone resistance. In this way, we hope to uncover genetic factors that could point to specific mechanisms behind PD pathogenesis. With further related research, new genetic pathways could lead to new drug targets.

Previous research has found associations between alcohol consumption and male perpetration of sexual assault. About 50% of male adolescent and college age perpetrators report they were under the influence of alcohol at the time of the incident. Additionally, research suggests that young adults who perceive same-sex peers as engaging in alcohol-related sexual behavior report elevated rates of risky alcohol-related sexual behavior. However, little is known about whether alcohol-related perpetration is associated with having favorable views toward the prototypes (i.e. images of the type of person who engages in a risk behavior) of alcohol-related sexual behavior. This study investigates whether favorable prototypes will have a positive association with participant’s identification as a perpetrator. We hypothesized that having more favorable prototypes, and feeling more similar to, typical males who engage in sexual behavior after drinking would be positively associated with perpetration. To test this, we utilized a data set comprised of a national sample of young males (n=463) ages 18-20 that completed a one-time online survey about health and risk behaviors. Participants were asked to report the number of times in the last 12 months they forced or attempted to force sexual contact on an individual who was too drunk or out of it to stop what was happening. Participants also reported on a 6 point scale how much the following words: "smart", "popular", "mature", "careless", "attractive", and "risky", describe their image of a typical male their age who has sex after 4/5 or more drinks. They rated how similar they are and how often they think about this typical male. Hierarchical regression analyses were conducted to determine the association of prototype favorability and alcohol-related sexual assault perpetration. Results from this study may provide insight about alcohol-related perpetration, which in turn could shape interventions.

The North Atlantic right whale (Eubalaena glacialis, NARW) is among the most depleted species of whale existing today, with a current estimated population of only 450. Ship strikes and entanglement issues remain the predominant cause of mortality for this critically endangered species. Thus, understanding NARW distributions, and their overlap with human activities, are a top priority for management and conservation efforts. This study analyzed passive acoustic data collected within the migratory corridor from Cape Hatteras, NC to Brunswick, GA from Oct 2015 - June 2016 as part of a comprehensive seasonal distribution look at NARWs along the Western North Atlantic coast. Four lines of 5-8 Marine Autonomous Recording Units were deployed, stretching across the shelf, in the first deployment of a three year, continuous acoustic monitoring effort. These units were processed using the Low Frequency Detection and Classification System (LFDCS), and detections were screened for daily NARW presence. The results of this study show seasonal movements to and from their calving grounds while passing through Georgia, South Carolina, and North Carolina. Off the coast of Georgia and North Carolina, NARWs are detected primarily on inshore recorders from November to March, suggesting the species take paths closer to shore while migrating. However, in late April, the groups travelling north take a path further away from the Cape Hatteras, NC shore. NARWs were picked up predominantly on inshore recorders throughout all four lines of MARUs, further supporting that critical habitats exist close to the coast in southern US waters. This information provides a better understanding as to where NARWs are spatially and temporally located, which is essential in minimizing human impacts on the species.

Two human retroviruses cause AIDS: HIV-1 and HIV-2. HIV-2 is less pathogenic than HIV-1, with lower plasma viral loads, decreased transmission and mortality rates, and a slower decline in CD4+ T cells. Despite this, many patients progress to clinical AIDS and may benefit from antiretroviral therapy (ART). HIV-2–infected patients failing first-line ART often harbor drug-resistant strains of the virus that limit second-line treatment. Consequently, there is a need for rapid, inexpensive HIV-2 drug resistance testing that can guide second-line therapy. In this study, we optimized and validated a novel genotypic drug resistance test for HIV-2 using dried blood spots (DBS). Specimens for this project were collected as a part of an ongoing cohort study of ART for HIV-2 infection in Senegal, West Africa. Blood samples from HIV-2–infected patients were spotted onto filter paper and shipped via courier “overnight” to Seattle at ambient temperature. We then extracted viral RNA and DNA from the DBS, amplified genes of interest using nested PCR, and identified mutations at major drug resistance sites after population sequencing. After obtaining genotypes from only three of 42 (7%) of DBS from a previous protocol, we designed a new, optimized protocol and were able to genotype 10 of 22 (45%) DBS, including five of seven (71%) with HIV-2 plasma viral loads over 50 copies/mL. Drug resistance mutations V47A (protease) and M184V (reverse transcriptase; RT) were observed in 63% and 75% of genotypes, respectively – 75% had evidence of multi-class resistance to both protease and RT inhibitors. These results show that DBS genotyping can identify major drug resistance mutations in HIV-2 patient samples, thereby guiding second-line ART for HIV-2 infection. Because DBS-based resistance testing is a low-cost testing approach which provides results within a clinically-actionable timeframe, we expect that this innovation will improve HIV-2 patient care in resource-limited settings.

Diatoms are responsible for roughly 45% of all oceanic primary production and play a unique role in carbon cycling. This crucial role makes understanding their behavior and interactions vital. In the environment, diatom samples are typically xenic (marine bacteria present around and on the diatoms). These diatom-bacterial interactions have been shown to have striking effects on diatom growth rates due to bacterial release phytohormones. These plant-based signaling molecules are well characterized in terrestrial organisms but their marine impact is not fully understood. One such phytohormone, indole-3-actetic acid (IAA), is responsible for bacteria-plant mutualistic behavior on land. Previous work in our lab has shown that addition of IAA to axenic diatoms has no effect at moderate levels and is lethal at high levels. However, when diatoms are co-cultured with IAA-producing bacteria, their growth rate increased. Thus, IAA alone is not sufficient to induce increased growth. We used this information, and the known bacterial IAA biosynthetic pathway to select IAA derivatives and precursors (methyl-IAA, Tryptophol, Tryptamine, Indole-3-acetamide, indole-3-carboxylic acid, and Tryptophan) to test their endogenous expression in marine bacteria found on diatoms in the environment. Of the bacterial species tested, none expressed every compound and most expressed novel combinations. This project tests the effects of various IAA derivatives as well as a cytokinin (phytohormone),6-(γ,γ-Dimethylallylamino)purine (2ip), on diatom growth. We investigate suites of compounds, based on bacterial expression data, as well as individual compounds. We also seek to use phylogenetic tree building to identify the bacterial producers of these compounds using IAA-producing, terrestrial bacteria as a reference. Impacts of bacteria on diatom growth, blooms, behavior and the metabolites left behind from these interactions would aid in analyzing environmental transcriptomic data and ultimately result in a fuller understanding of diatoms and their response to chemical stimuli.

Kaposi’s Sarcoma-Associated Herpesvirus (KSHV) is the etiological agent of Kaposi’s Sarcoma (KS), a highly vascularized tumor predominantly made up of cells of endothelial origin. KSHV establishes a predominantly latent infection in endothelial cells in culture and in the KS tumor. KSHV latent infection alters cellular metabolism to improve the survival of the infected cells. These metabolic changes resemble a common alteration in cancer cells, termed the Warburg effect. This refers to an increase in glycolysis in the presence of oxygen and a decrease in oxidative phosphorylation. The mechanism of KSHV induction of the Warburg effect is currently unknown. Hypoxia-induced factors (HIFs) are likely candidates for KSHV induction of the Warburg effect as both HIF1α and 2α are induced by KSHV latent infection. To determine if HIF1α or 2α is required for the survival of KSHV infected endothelial cells, I constructed HIF1α or 2α knockouts using the CRISPR/Cas9 gene editing technique in a lentivirus vector. I expressed the endonuclease Cas9 and guide RNAs that lead Cas9 to cut at the HIF1α or 2α genomic sequences leading to genomic mutations in HIF1α and 2α respectively. To determine if HIF1α or 2α is required for the survival of latently infected endothelial cells, I infected the HIF1α and 2α knockout cells with KSHV and looked for cell death at 48 hours after infection. To evaluate if HIFs are required for KSHV induction of the Warburg effect, I will determine if one or both of the knockout cells produce less lactic acid and increase oxygen consumption at 48 hours post KSHV infection as compared to infection of wild type cells indicating the Warburg effect is not being induced by KSHV in the knockout cells. These results will aid in the future efforts to develop antiviral drugs by inhibiting viral latency.

Duplex Sequencing (DS) is a Next-Generation Sequencing technology employing double strand molecular tagging to reduce technical errors.The high accuracy of DS enables the resolution of low frequency mutations in nuclear and mitochondrial DNA (mtDNA). We are interested in using DS to analyze mtDNA mutations in ulcerative colitis (UC), an inflammatory bowel disease that predisposes to colorectal cancer. Tumor progression in UC is related to mitochondrial dysfunction. By sequencing mtDNA mutations in colonic biopsies from UC patients, we aim to elucidate the role of these mutations in tumorigenesis. A critical limitation, however, is the high number of low frequency mtDNA mutations present in these biopsies and the lack of appropriate computational methods to process large amounts of information generated by DS. The goal of this study was to develop computational methods to enable the extraction of mtDNA mutation information from DS data. DS identifies the reads corresponding to each strand of DNA by grouping them by their unique tags, making single-strand consensus sequences (SSCSs), which are then paired to form duplex consensus sequences (DCS). SSCS reads remove technical errors, but contain errors caused by DNA damage. The first computational method that we developed compared sequencing information from SSCS and DCS reads to assess the level and type of DNA damage in each sample. Other computational methods consisted of a program to classify mutations according to their sequence context, and a script that calculates mutation types and frequencies inside and outside the D-loop region as well as in all mtDNA genes and allows comparison of these parameters in large batches of samples. These tools will enable the processing of mtDNA DS information in a fast and high-throughput way, leading to assessment of the range of different types of mtDNA mutations in the progression of ulcerative colitis and colorectal cancer.

Pacific cod (Gadus macrocephalus) is the target species of a large fishery in North America that ranges from Alaska to California. In a recent genetic sequencing study, very high divergence among Pacific cod from different geographic areas was observed in what appears to be the Zona pellucida sperm-binding protein 3 (ZP3) gene. In many other vertebrates, the ZP3 gene codes for proteins that are significant to reproduction, and this gene may be an important factor in the context of the species' life history and management. To increase resolution of how ZP3 varies across the Pacific cod range, this project investigates the entire coding sequence in Pacific cod from four geographic areas: Kodiak Island, Prince Williams Sound, Hecate Strait, and the Washington Coast using PCR and Sanger sequencing. Differences in amino acids and protein structure were identified. It appears that there are significant differences in the ZP3 gene between southern and northern populations of Pacific cod. Understanding these patterns is important for future studies of how differences in the ZP3 gene may affect reproduction and population connectivity.

Cerebral malaria (CM) is a multifactorial disease with lethal neurological complications plus increased risks of cognitive and neurological impairments making CM a leading cause of childhood neuro-disability. The malaria parasite, Plasmodium falciparum, accounts for most mortality from malaria, and primarily kills children under five in sub-Saharan Africa. The deadly CM complication develops when red blood cells infected with parasites (iRBCs) bind to the endothelial cell wall in brain microvasculature. This process of parasite sequestration via cytoadhesion is mediated by the parasite ligand, P. falciparum erythrocyte membrane protein 1 (PfEMP1) encoded by a family of 60 var genes. An individual parasite, however, strategically undergoes allelic exclusion to express only a single distinct PfEMP1 variant. PfEMP1 proteins possess the ability to bind relatively few host receptors despite seemingly limitless sequence diversity. Requirements for maintaining binding surfaces conserved in structure and binding potential despite significant sequence diversity remain a mystery. Understanding these requirements will be critical for developing therapeutics to mitigate disease severity. A subset of PfEMP1 proteins associated with severe/cerebral malaria bind highly conserved regions of the host receptor, endothelial protein C receptor (EPCR), and inhibit binding of its natural ligand, activated protein C (APC). There are six PfEMP1 subdomains that bind EPCR (CIDRα1.1 and CIDRα1.4–1.8 domains), which share limited sequence identity among PfEMP1 variants. The data so far suggests the presence or otherwise absence of a coiled coil domain within CIDRα1 determines binding to EPCR. Our study uses computational and molecular biology tools to investigate the molecular and structural determinants for malaria parasite adhesion to EPCR. 
 

Organisms face a range of stressors over the course of their lifespans. As with most traits, we see significant variation in response to stress even between individuals within species. In our attempt to explain differences in stress responses between individuals, the Promislow lab studied the metabolome, the total profile of all small molecules in an organism, and found variation in stress response is correlated with variation in contents of the metabolome. Indeed, in a study of peroxide resistance in the fruit fly, Drosophila melanogaster, we found resistant flies tended to have increased galactose levels, compared to sensitive flies. This observation led to the novel hypothesis that flies fed supplemental galactose will have increased peroxide resistance compared to control flies. For this experiment, we chose flies among the most sensitive and resistant lines examined previously because the most sensitive flies, with low galactose levels, may show increased effects of supplemental galactose on lifespan. In this experiment, flies feed on food with varied galactose concentrations, including a negative control without galactose. We then place the flies into media with peroxide or water, the control. We record the number of flies that die in each condition multiple times a day, and the death rate provides a quantitative measure of peroxide resistance. By comparing the death rate of flies within a line kept in varying concentrations of galactose exposure, we can test the effect of galactose on resistance. If our hypothesis is correct, the flies receiving supplemental galactose should die at a slower rate than those without additional galactose. However, it is possible flies receiving supplemental galactose will die at faster rates, suggesting galactose makes flies more sensitive. Determining whether galactose makes flies more resistant or sensitive to peroxide may prove to be important in counteracting effects of oxidative stress in other organisms.

The incorporation of trivalent ytterbium ion (Yb³⁺) impurities, or dopants, into nanoscale materials is of significant interest due to the unique optical properties of the Yb³⁺ ion. The electron configuration of Yb³⁺, 4f¹³, is associated with just one f-f electronic transition (²F_5/2↔²F_7/2) that is narrow and lattice-independent with an energy of ~1.27 eV. This makes luminescent ytterbium doped colloidal semiconductor nanocrystals, which are solution processable, ideal for use in silicon-based solar energy applications like luminescent solar concentrators. Doping colloidal nanocrystals with ytterbium ions, however, is not necessarily sufficient for creating a material with luminescent ytterbium. It is necessary for ytterbium to be sensitized by energy transfer from a visible light absorber in order to be emissive. Previous synthetic work indicates that the most promising route for sensitizing ytterbium is the direct doping of ytterbium ions into visibly absorbing host nanocrystals such as chalcogenide semiconductors. Incorporating ytterbium ions into chalcogenide semiconductor hosts, however, poses a significant synthetic challenge. Additionally, it is essential to optimize synthetic reaction conditions such as growth temperature, growth time, coordinating solvent used, precursor concentration in coordinating solvent, and ytterbium dopant concentration in order to produce a material with luminescent ytterbium. These synthetic variations are informed by physical characterization of the morphology, absorbance, and photoluminescence of previously synthesized ytterbium doped colloidal nanocrystal samples by transmission electron microscopy, absorbance spectroscopy, and photoluminescence spectroscopy, respectively. It is expected that current efforts to optimize these synthetic parameters and interface ytterbium doped colloidal nanocrystals with compatible ionic materials in a process known as ‘shelling’ will allow the reproducible creation of a novel nanoscale material with bright ytterbium luminescence at room temperature. Upcoming fundamental studies of these ytterbium doped colloidal nanocrystals will probe the dynamics of energy transfer by time-resolved photoluminescence spectroscopy and provide insight into the kinetics of ytterbium sensitization.

The need for energy efficient chemical reactions is growing in response to the world’s energy crisis. Reactions must not only be high yielding but also require low energy input. Many redox processes of interest involve the transfer of electrons from the surfaces of electrodes and need an electrical input as driving force. The ability to promote redox reactions photochemically would greatly reduce the energy input needed. As of yet, interfacing electrochemical reactions with colloidal photosensitizers in order to promote them photochemically has not been done. This project experiments with CdSe quantum dots as the colloidal photosensitizer by absorbing visible light from an LED light source and transferring an electron in order to reduce ferrocenium to ferrocene as a model reaction. The goal of this project is display the ability of CdSe in the productive electron transfer promoted by visible light to ferrocenium. Knowledge of this model system can be applied to more complex reactions in the future and the work done here will help understand how to drive industrial chemical reactions via sunlight. 

Oxidative stress arises from an imbalance between reactive oxygen species and an organism’s ability to avoid or repair the damage caused by these reactive molecules. The fruit fly, Drosophila melanogaster, demonstrates varying degrees of resistance to oxidative stress. To understand the genetic basis of this variation, our lab analyzed a collection of inbred, fully sequenced Drosophila lines, the Drosophila Genetic Reference Panel (DGRP), and tested the associations between resistance and each of more than two million single-nucleotide polymorphism (SNP) markers throughout the genome. We found a particular SNP at the second chromosome located within the gene u-shaped (ush), had the strongest statistical relationship with oxidaive stress resistance. We then hypothesized that this gene contributes to the degree of resistance in the flies. For my research, I am evaluating this hypothesis by comparing the peroxide resistance of two sets of genotypes to confirm if the SNP at 2L:531863 bp contributes to the trait. For this comparison, I used two groups of lines, one with the ‘resistant’ and the other with the ‘sensitive’ version of the SNP, and distributed mated females from each line into vials with or without peroxide added into the food. I counted the number of dead flies at regular intervals and used these data to calculate the mean lifespan for each line, where lifespan is a measure of peroxide resistance. If both groups show similar lifespans, it suggests that this particular SNP does not affect peroxide resistance and I may test other SNPs at nearby loci with a similar procedure. However, if the two groups show significant differences in resistance, this result would support the connection between the SNP and peroxide resistance. I would then go on to manipulate the expression of ush using RNA interference to test whether changing mRNA levels impacts peroxide resistance.

Studies have shown that alcohol consequences are associated with alcohol-related sexual consequences. Studies on young adults have found that alcohol use is linked to risky sexual behavior , and alcohol-related sexual consequences are common. Women absorb and metabolize alcohol differently than men, and literature has found gender differences in alcohol consequences. However, gender differences in alcohol-related sexual consequences and the association between alcohol consequences and alcohol-related sexual consequences have been understudied. The current study will examine (1) gender differences on subscales of alcohol consequences and alcohol-related sexual consequences and (2) associations among alcohol consequences and alcohol-related sexual consequences by gender. We hypothesize that women will exhibit higher scores than men on the subscales of academic/occupational consequences, blackout drinking, impaired control, risk behaviors, and self-care. Additionally, we hypothesize that women will exhibit higher scores than men on the subscales of disregard of personal boundaries, neglect to use birth control, and sex with someone they just met. The current study used baseline data from an intervention study focusing on drinking and sexual behavior among a national sample of young adults (N = 402), who completed an online survey. Participants reported if they experienced alcohol consequences (21 items), such as “While drinking, I have said or done embarrassing things.” Additionally, participants reported if they experienced alcohol-related sexual consequences (41 items), such as “I had digital sex I later regretted.” Regression analyses for count outcomes were conducted to test gender differences in alcohol consequences and alcohol-related sexual consequences, controlling for alcohol use and sexual behavior. Spearman correlations were also conducted. Results will provide a better understanding of the relation between alcohol and alcohol-related sexual consequences and help shape interventions for reducing behavioral risks.

Previous research has found that alcohol consumption among young adults is linked to an increased likelihood of engaging in risky sexual behaviors, including unprotected sex. When examining the likelihood of safe sex practices, additional research has found that having sex at a younger age (<14) is associated with a lower likelihood of using contraception. However, there is a gap in the literature around how number of sexual partners plays into this relationship. The current study aimed to investigate the association between age of first sex and number of lifetime sexual partners with condom use after alcohol consumption. We hypothesized age at first sexual experience would be positively correlated with condom use during penile-vaginal, anal, and oral sex while under the influence of alcohol in the past three months. Additionally, we hypothesized that the number of lifetime sexual partners would be negatively correlated with condom use in the past three months after alcohol consumption. To test these hypotheses, the present study (n = 1002) used data from a national sample of young adults, ages 18-20, who completed a one-time online survey. Participants were asked age at first penile-vaginal, anal, and oral sex as well as their number of lifetime sexual partners. Additionally, participants were asked number of times they had sex in the past three months after consuming alcohol and of those times, how often they used a condom. Regression analyses were conducted to determine the association between first age of sexual encounter and likelihood of using a condom, as well as number of lifetime partners and the likelihood of using a condom, both after consuming alcohol. Results from this study may help us understand how previous sexual experience is related to the likelihood of practicing safe sex after alcohol consumption.

Previous research has recognized a link between drinking alcohol and later negative consequences such as physical, legal, academic, interpersonal, and sexual problems. Despite the well-known risks linked to heavy drinking, young adults continue to engage in risky drinking behavior especially when they have positive attitudes about heavy drinking. However, little is known about why the relationship between alcohol-related consequences and drinking exists. We propose that attitudes act as a mediator between consequences and drinking. We hypothesize that the more alcohol-related consequences a young adult has experienced, the more favorable their attitudes will be towards drinking, which will ultimately lead to more drinking. To test our hypothesis, a national sample of 1002 young adults aged 18-20 were asked to complete an online survey on young adult health, including drinking attitudes and alcohol consequences. Participants reported the number of drinks they consume on a typical week, the frequency of drinking they consider acceptable, and the number of drinks they consider acceptable to consume in one sitting. Additionally, participants reported whether or not they experienced any alcohol-related consequences in the past 3 months, including but not limited to: “blacking out”, vomiting, a hangover, or driving a car while drunk. In order to test mediation, bootstrap estimation multiple mediation analysis (SPSS Process macro) will be used. Results of this study will provide a better understanding about young adults’ cognitions regarding alcohol-related consequences and may help shape interventions by allowing individuals to draw from their past experiences to guide their future decision-making.

We investigated how grading treatment, self-evaluation versus peer-evaluation, on weekly practice exams (PE) in an Introductory Biology course affects the advice students give to improve academic performance. We hypothesize that students who suggest more resources and study strategies perform better on course exams because they are aware of how improvements need to be made and what resources to use. Students in the class (approximately 550) take a PE on Thursday and then grade the PE responses on Friday. The grading groups were split up into two treatments: half of the class self-evaluated whereas the other half evaluated their peers’ responses. In addition, they were prompted to answer two questions: 1) Pick a single thing that you/this student should work on. 2) What resource should they consult before the next exam? We used this information to explore how study strategies and resources that students suggest relate to their test scores. To analyze the responses, we created specific codes corresponding to student answers. Results of the codes indicate that the students’ responses fall into four categories for question 1 and two sets of categories for question 2 (with three and two codes in each set). When asked to provide ways to improve PE performance, the four specific codes were being descriptive, increasing knowledge of content, interpreting the question, and time management. When providing resources, the two sets of categories were active versus passive resources and expert, peer, and self resources. Over the course of ten weeks, students who suggested more strategies and resources tended to perform better on exams. As well, both self-evaluators and women in the course suggested more strategies and resources than peer-evaluators and men respectively. Given this study, instructors can better understand what resources students are utilizing but also which study strategies tend to be more successful for students.

Joubert syndrome (JS), a rare recessive genetic disorder, is characterized by abnormalities in the cerebellum and brainstem. Notably, JS is a ciliopathy because the known causative genes have products that localize to the primary cilium, a vital organelle acting as the nexus between many signalling pathways. Understanding more about JS will provide insights into this emergent group of disorders revolving around the cilium. Causal mutations for JS need to fulfill three criteria: They need to be rare, deleterious, and present in both alleles (copies of a gene) in the patient. Patients in our cohort are sequenced for rare deleterious variants (RDVs) to identify variants that satisfy the first two criteria. To determine whether the segregation pattern of the variants satisfies the third criterion, we sequence both parents, each of whom should carry one of the variants. My research uses next-generation sequencing to determine the segregation pattern for families in whom RDVs have already been identified. Specifically, I am using molecular inversion probes (MIPs) to target-sequence putative causal mutations in the parents and then using the sequencing data to determine the segregation pattern of these variants. If the MIPs data show RDVs for a causative gene are on the same allele, then the variants cannot be the cause of JS in the family and we will have to consider other variants or perform additional sequencing to identify the causal mutations. The data will likely show that the mutations are in both alleles because the mutations targeted with MIPs are mutations that have passed the filters for being rare and deleterious and are robust candidates for being causal. Ultimately, the goal of my research is to elucidate the genetic basis of JS in hopes of improving risk recurrence analysis, prenatal diagnosis, and help discover biological mechanisms of JS.

Both content knowledge and problem-solving strategies are important components for academic success in biology. All problem-solving strategies begin with the ability to understand the problem being presented. In the context of biology, this means identifying the core concept being asked in complex questions. Identifying keywords, words that are important or significant, can help students identify these core concepts. The purpose of this study was to explore how well students can identify keywords and if this ability is correlated to exam performance. Students in an Introductory Biology course took weekly practice exams (PE), after each PE they either graded their own or a peer’s PE. In addition, students were asked to “identify the keywords in the question that should have caused you to provide the complete and correct answer given in the key”. This experimental design also allowed us to explore how grading an anonymous PE affects quality of students’ keyword selections. Students’ keyword selections were compared to a keyword rubric created by the research team. Data was coded by two researchers to 90% inter-rater reliability. On average, students only correctly identified 39% of keywords each week. Multiple regression models were used to explore correlations between correct identification of keywords and performance on both PEs and course exams. Interestingly, students who self-graded were more consistently engaged with the keyword activity as compared to peer-graders. In both cases, percent keywords correct could predict overall exam performance. These results indicate that if instructors want to help students improve their problem-solving skills of complex biological problems, helping students recognize keywords may be one solution. Furthermore, identifying which students have trouble simplifying complex exam problems and helping these students improve their ability to identify keywords may be beneficial in addressing learning disparities within large introductory classes.

Student-graded practice exams (PEs) have been used to facilitate learning in large classrooms. In a large introductory biology class, we investigated the impact of self vs peer-grading of PEs. We hypothesized that students who graded their own PEs would grade more accurately than peer graders because they are more motivated and reflective in their grading. Over time this more accurate grading would lead to increased performance on course exams. One question from each week’s PE was graded by a team of experts. We calculated PE grading accuracy by comparing the expert grade to the grade assigned by the student. We analyzed the correlation of PE grading accuracy with exam performance. For each metric we investigated the impact of treatment, incoming GPA, and student demographics (e.g., gender, socioeconomic status, first generation, race/ethnicity) using general linear models. There was no difference in average expert PE grade between the two treatments. Incoming GPA was the only significant predictor of expert PE grade with GPA positively correlated with expert PE grade. There was a significant interaction between incoming GPA and treatment on grading accuracy. Students with high GPAs who graded peers consistently underestimated their peers’ PE performance. Students with lower GPAs who graded peers either graded similarly to experts or slightly overestimated their peers’ PE performance. Students who graded their own PEs more accurately predicted their PE performance regardless of incoming GPA. There was an interaction between GPA and treatment on course exam performance, as high GPA self-graders earned more course exam points than high GPA peer-graders. Average GPA students earned the same amount of course exam points regardless of treatment. Given these findings and the logistical complications of peer-grading in large classes, instructors can use the more easily administered self-grading method of providing feedback on low-stakes practice exams.

Joubert syndrome (JS) is an autosomal recessive neurodevelopmental disorder, characterized by the "molar tooth sign" on axial brain MRI. JS is caused by mutations in 35 known genes, all of which encode proteins that localize to the primary cilium, a microtubule-based organelle that projects from the surface of most cells. Our current understanding of the underlying molecular mechanism causing JS involves lack of ciliary localization of ARL13B and INPP5E, two JS-associated proteins. ARL13B is required for the ciliary localization of INPP5E. Normal INPP5E localization maintains a phosphatidylinositol subtype distribution in the ciliary membrane. My research investigates ciliary phenotypes in cell lines harboring causal mutations in C2CD3, which encodes a protein that localizes to the primary cilium’s basal body, using existing images of patient cell lines. Loss of C2CD3 function in mouse models has presented lower ciliation rates and shorter cilia lengths. Previous research in our lab on two other JS-associated basal body proteins, OFD1 and KIAA0586, identified normal ciliary ARL13B-INPP5E levels. To determine ARL13B and INPP5E localization, cells from two control and two different C2CD3 patient cell lines were grown and serum-starved, inducing ciliation. Cells were stained with antibodies to acetylated tubulin (marking cilia), and INPP5E or ARL13B (marking protein of interest). Using Fiji, an image analysis software, I “painted” each cilium by outlining the signal in the acetylated tubulin reference channel to define a mask. Using that mask, I quantified ciliary ARL13B and INPP5E. I measured ciliation rates using the number of masks divided by the number of nuclei, and cilium lengths using the “skeleton length” function. Based on data from mouse models, we predict that C2CD3 patient lines will have fewer and shorter cilia, but normal ARL13B-INPP5E localization. These expected data would exclude the hypothesis that INPP5E mislocalization is an obligate part of the biological mechanism underlying JS.

Joubert syndrome (JS) is a genetic neurodevelopmental disorder with medical features including a distinctive hindbrain malformation and developmental delay. All 35 JS-associated genes to date encode gene products localizing to the primary cilium but the mechanism behind JS is still unknown. The primary cilium serves as a cellular antenna for signaling, and when dysfunctional, can lead to the above features and more. One JS-associated gene, INPP5E, is an enzyme that controls phosphatidylinositol (PI) subtype distribution in the ciliary membrane. We hypothesize that abnormal distribution of PI subtypes PI(4,5)P₂ and PI(4)P in primary cilia is central to the JS mechanism, and therefore should be present across genetic causes. To test this hypothesis, I used fluorescently-tagged PI biosensors, domains from naturally occurring proteins that bind to different PI subtypes, and a domain from serotonin receptor (5-HT₆) that marks cilia. The PI biosensors were already tagged with GFP (green fluorescent protein) so I replaced GFP for RFP (red fluorescent protein) on the PI(4,5)P₂ biosensor, and inserted BFP (blue fluorescent protein) on the 5-HT₆ domain, allowing me to distinguish all three molecules in the same primary cilium. To do this, I removed the GFP sequence from our PI(4,5)P₂ plasmid using restriction enzymes that cut DNA then inserted RFP (amplified from a template plasmid carrying RFP) using DNA ligase. I confirmed the RFP insert by restriction enzyme digests specific for RFP and by direct DNA sequencing. PI(4,5)P₂-RFP plasmids were transformed into cells with PI(4)P-GFP and our BFP ciliary marker, then live-imaged. These tools will make it possible to determine if abnormal PI subtype distribution in primary cilia is a unifying cellular defect in JS patient cell lines. If so, we can then explore the effects of altered PI distribution and determine whether modulating PI distribution has the potential for mitigating the effects of Joubert syndrome.

According to the World Health Organization, an estimated, 780 million people do not have access to clean water sources. Disasters are another potential cause of disruption to the supply of clean water. When the safety of a water source is unknown, a cost effective method to determine water safety is necessary to reduce unsafe water related disease and death. Prior synthetic biology research has been conducted utilizing transgenic yeast as a biosensor for heavy metal detection, such as using plasmids expressing Green Fluorescent Protein (GFP) which are promoted by heavy metal binding transcription factors. While able to detect copper ions in a dose dependent fashion, the relative instability of the plasmid, reporters which are difficult to detect in situ, and limited targeting to copper and silver ions make the efficacy of the designs impractical. Using modern methods of plasmid integration and the modulation of the copper sensitive pCUP1 promoter expression we sought to produce a stable and more sensitive biosensor for the detection of copper ions in water. We successfully integrated the genetic cassette pCUP1-yeGFP into the yeast genome and produced a viable biosensor for the detection of aqueous copper. We tested this yeast strain via a cytometer after exposure to copper of varying concentrations at varied time intervals. The results showed a dose response curve that positively correlated with copper concentration in a semi-linear fashion, which indicated the pCUP1-yeGFP transgene was a viable sensitive reporter for the detection of copper. Currently, variable constitutive promoters are being altered to increase copper detection sensitivity by modulation of the expression of the metal binding transcription factor Ace1. The team is currently exploring the effect of Ace1 upregulation on the sensitivity of copper sensing. After investigating sensitivity modulation, an exploration of practical field detectable reporters, such as violacein, will be undertaken.

Over the past few years’ silicon photonics has proven to be a viable bio-sensing platform for various diagnostic applications. The small size, label free detection and ability to be multiplexed with various assays make it a very attractive technology and potential replacement for many clinical tests. Silicon photonics has proven to be a viable technology for ABO blood typing. This technology has the potential to achieve a higher level of automation than the current clinical method along with a lower run time and lower costs. Two large limitations in clinical translation of this technology are reducing the time it takes to run the assays and the amount of processing that must be done before running them. Indirect blood typing using this technology currently requires centrifuging whole blood to isolate plasma or serum to use in the assay. This sample processing can take anywhere from 20-40 minutes and is not ideal for a clinical setting. This project seeks to increase silicon photonics clinical viability by designing an inline filtration system to isolate the plasma or serum from whole blood as it is running through the assay. This would mean that whole blood would not have to be centrifuged for indirect blood typing. Instead, the blood will be filtered in the assay and then travel through a paper network for reagent delivery recently developed in the Ratner Lab. Additionally, this assay will be developed for the commercial Genalyte silicon photonic test setup. This requires the development of a custom mount for the system along with determining positioning for the paper network. This research may help to replace the agglutination diagnostic test that has been in use for over 100 years and help save medical and monetary resources as well as patient lives.

In the US, someone needs blood every two seconds, making blood transfusion a frequently performed procedure in hospitals. Transfusion of incompatible blood due to clerical error in the clinical blood typing procedure can induce a multitude of life-threatening immune responses in the recipient’s body. The most prevalent typing procedures are based on the overly simplified characterization of surface antigens on an individual’s red blood cells (RBCs) into the commonly known ABO blood type system. However, studies have shown that the antigens embedded in the RBC membrane, comprising of glycolipids and glycoproteins, are structural determinants of variations in the blood type outside of the ABO system, elucidating the limitations of current typing methods. This project follows the hypothesis that gas-phase hydrogen/deuterium exchange (HDX) MS techniques can be employed to characterize and further elaborate the structure of these RBC antigen constituents. To test this hypothesis, genotypically and phenotypically defined donor blood samples are processed to obtain RBC ghosts, containing only the membrane components with the hemoglobin removed through an osmotic lysis procedure. Glycoprotein and lipid fractionation, followed by digestion are employed to isolate carbohydrate components in preparation for HDX-MS analysis, which provides insight into structural composition of the carbohydrate antigens. Through this study, we expect to develop a deeper understanding of the variations in the carbohydrate RBC antigens which dictates the blood type of individuals. This knowledge will be crucial in developing glycobiological sensors that can be functionalized onto silicon chips used by Ratner Lab, facilitating novel blood typing techniques.

Fundamental understanding of how effector T-cells are transformed into quiescent memory T-cells is vital for developing immunotherapeutic treatments for autoimmune diseases and cancer, and for the development of vaccines against diseases such as AIDS, tuberculosis and malaria. Previous research on conversion of memory precursor effector cells (MPECs) into memory T cells has found evidence of Treg cell involvement in the process. Treg cells are regulatory helper T cells which selectively inhibit effector T cells to prevent and suppress overly strong immune responses and autoimmune responses. Research has also shown that MPECs produce their own IL-2, a cytokine involved in immune tolerance and activation. Based on these data, we hypothesize that direct interaction between MPECs and Treg cells, possibly via MPEC-produced IL-2, is required for conversion of MPECs into memory T-cells. We also addressed colocalization of Treg cells with short-lived effector cells (SLECs). SLECs are IL-2 non-producing effector cell counterparts of MPECs and do not form memory. Potential MPEC or SLEC interaction with Treg cells was visualized through immunofluorescence microscopy of the secondary lymphoid organs (spleen and lymph nodes) of experimental mice injected with lymphocytic choriomeningitis virus (LCMV). To bypass the low precursor physiological frequencies of MPECs we employed the P14 LCMV GP33-specific TCR transgenic mouse system, which is a well-regarded model system for studying memory differentiation. To test the role of IL-2 in cell-cell interactions, we used IL-2 agonist and antagonist antibodies. A detailed understanding of how Treg cells are involved in the process of MPEC to memory T cell conversion is key to developing novel immunotherapeutic treatments.

Quorum Sensing (QS) is a chemical signal based communication system by which bacteria regulate gene expression according to changes in population density. This communication mechanism is used by the environmental bacterium and opportunistic human pathogen P. aeruginosa, which is a major cause of Cystic Fibrosis (CF) lung infections. P. aeruginosa employs two interconnected QS systems: las and rhl. These systems are regulated by the transcription factors LasR and RhlR, each of which binds a unique chemical signal that further activates transcriptional regulation. LasR and RhlR together control the expression of virulence factors critical for many infection processes. In laboratory strains, the LasR and RhlR QS systems are arranged hierarchically, such that LasR transcriptionally activates RhlR. Although this QS hierarchy is common to laboratory strains of P. aeruginosa, some CF clinical isolates are capable of RhlR activation in the absence of functional LasR. However, the origin of this LasR-independent regulation remains unclear. In this study, we investigate whether the LasR–RhlR hierarchy is conserved in environmental P. aeruginosa. We collected several environmental isolates and genetically engineered them through allelic exchange mutagenesis to disrupt LasR function. We then transformed wild type and LasR-null isolates with reporter constructs that produce GFP (Green Fluorescent Protein) in response to either LasR or RhlR. In these two conditions, we measured protein levels of LasR/RhlR, signal concentrations and the production of several QS-regulated products. In most cases, we observed that RhlR activity was substantially reduced in the absence of functional LasR. The observed decrease in RhlR function is so far consistent with the idea that the QS hierarchy is a conserved feature of P. aeruginosa. However, mechanisms of quorum regulation in environmental strains may differ from laboratory strains and a proper understanding of them can potentially contribute to the development of non-antibiotic therapies.

Duplex ultrasound scanning with both color Doppler and Doppler spectral waveforms is relied upon for diagnosis of vascular disease and selection of patients for further evaluation and treatment. In most duplex ultrasound applications, classification of disease severity is based primarily on alterations in blood flow velocities. Our research group in the Applied Physics Laboratory is collaborating on the development of a Doppler Ultrasound Simulator for training and assessment of scanning skills. The ultrasound simulator allows learners to repeat examinations as many times as necessary to acquire and improve skills. With the addition of clinical cases covering a range of disease severity, this duplex ultrasound simulator will be a useful tool for training health-care providers in vascular ultrasound applications and for assessing their skills in an objective and quantitative manner. The Doppler Ultrasound Simulator extracts virtual blood flow measurements from computational flow models, with real-time scanning linked to a physical mannequin. The Simulator reproduces the key components of a clinical Doppler ultrasound examination including steering the Doppler beam, selecting the size and location of the Doppler sample volume, specifying the Doppler angle relative to the vessel axis, and adjusting the pulse repetition frequency (scale control) and baseline to avoid aliasing. My research role in this larger-scale project is to use a data processing program, MATLAB, for image reconstruction, processing and analysis. MATALB is used for the creation of 3D image volumes, which are used as the foundation for vessel reconstruction as 3D computer models. MATLAB is also a useful tool for correction of image motion artifacts. My effort in this project involves applying image correcting algorithms to create 3D volumes with enhanced vessel alignment and minimized interference from real-time shifting of 2D ultrasound images.