Midfacial hypoplasia (MFH) is a disorder of severe underdevelopment of the upper face. This problem is significant because MFH can lead to a deformity that impedes chewing, feeding, and breathing. Although it is known that MFH can occur due to gene mutations, teratogens, and trauma, it is unknown how these insults affect anterior growth of the face. Using a novel pig model, this project aims to isolate the location of structural changes to the skull caused by MFH. We first determined if MFH in pigs is isolated to the face, and then identified the specific bones of the face that are altered by MFH. To determine if MFH is isolated to the face, we measured and compared the length of the braincase, mandible, and upper face in pigs with MFH to that of normal pigs. We then measured and compared the dimensions of individual facial bones, including the maxilla, premaxilla, nasal bone, lacrimal bone, and zygoma. All measurements were done on dry skulls with calipers and compared using t-tests. Our initial qualitative comparison of 6 normal and 6 affected pigs has found that MFH is isolated to the face, with the premaxilla, maxilla, nasal bone, and lacrimal bone shortened. The zygoma and palatine bones were normal. We hypothesize that our qualitative comparison of approximately 35 MFH pigs and 115 normal pigs will show similar results. Identifying the bones affected by MFH will help us to hone in on the specific tissue changes and mechanisms that cause MFH, and to discover better treatments for this condition.

 Host restriction factors are components of the innate immune system that play a vital role in inhibiting viral infection. One such example is a family of antiviral proteins, APOBEC3s, that inhibit retroviruses such as HIV by hypermutating the genome through cytidine deaminase activity. There are seven members of the APOBEC3 (A3) family found in primates, A3A-A3H. Each of these APOBEC3s vary in their protein expression levels and antiviral activity Antiviral activity of these proteins depends on expression levels and ability to be packaged in budding virions. A3C, in particular, is of interest because it is highly expressed and packaged but lacks potent antiviral activity when compared to its A3 counterparts. Moreover, when we examined A3C expression across primate evolution, we found that many primates encoded only unstable versions of A3C. Preliminary data, on the other hand, suggests an alternative role of A3C in modulating the effects of the more potent A3 proteins, A3D, A3F, and A3G. Coimmunoprecipitation assays suggest that A3C interacts with other A3 proteins, and subsequently decreases the packaging of the potent A3s into budding virions thus inhibiting their antiviral activity. Future experiments include removing endogenous A3C from cells to determine if the antiviral activity of other A3’s increases in the absence of any A3C. These data suggest that A3C has evolved to fine-tune the amount of antiviral activity of other A3 family members, thus allowing for better control of these potential mutagenic proteins.

Early home life and classroom environments are crucial to lifelong success. Family structure, opportunities for learning, and socioeconomic status (SES) influence experiences within the home. Further, SES impacts the resources that a student has access to, which can shape academic support and learning opportunities. Factors such as family climate, caregiver occupation and education, and parenting style have been shown to influence academic self-regulation and achievement. Literature has also pointed to the importance of relationships with peers and teachers on academic and social success. Few studies have examined how both of these environments impact student life into adulthood and litte research has explored social success in terms of feelings within interpersonal relationships and self-efficacy. The goal of the present study was to retrospectively explore experiences in the home and school environments throughout formative, developmental years and success later in life. Participants (n = 149) were asked about their family structure, SES, home learning environment (HLE), experiences in three separate academic eras, academic success, feelings in relationships, and self-efficacy. This study fills a paucity in the discussion of academic success by exploring a new measurement tool: the academic ladder, which examines a student's own perception of their achievement in relation to their classmates. Results confirm the impact of early experiences in the home and at school on later academic and social success. Interestingly, caregiver factors do not significantly impact students' interpersonal success as much as relationships with teachers and peers. Results also show that SES does not have an effect on opportunities for learning in the home; however, caregiver educational attainment affects those opportunities. Both HLE and caregiver variables have an effect on self-perceived academic success. Continuing to examine how educational experiences and environmental factors impact students' well-being will help develop intervention programs that best prepare youth to succeed throughout life.

In recent years, gravitational waves have yielded insights across many fields, from the expansion of the universe and black hole populations to the origin of heavy elements and nuclear physics. The Laser Interferometer Gravitational-Wave Observatories (LIGO) are michelson-type interferometers formed by two, 4-kilometer-long arms with suspended test masses (mirrors) at the ends. The test masses reflect high-power lasers to be combined at the intersection of the two arms and create an interference pattern, which is sensitive to gravitational waves passing through the interferometer. For a stable interference pattern, the test masses must be oriented precisely; the low frequency orienting of the test masses is done using optical levers (OpLevs). They consist of optics that launch light from a diode laser which reflects off the test mass and hit a quadrant photodiode, which measures the tip and twist of the test mass as a function of beam spot displacement. However, this measurement has elevated noise at low frequencies, limiting its accuracy. The reduction of this noise by a factor of 10-100, would allow for a more accurate orienting of the test mass. The source of noise is likely to be found in the fiber optics connected to the launching telescope. To isolate this noise I recreated parts of the LIGO OpLev setup with a level of positional noise well below LIGO's current OpLev noise at 0.1 Hz (below a nanometer per square root hertz). To achieve noise at this level I have designed a low noise pre-amplifier, improved the physical stability of the setup, and analyzed data to identify the noise sources. With this reduced noise setup we plan to search for the source of LIGO's OPLEV low frequency noise. Reduced noise would increase the uptime of the observatories thus increasing the number of gravitational wave detections.

This research project relates to my faculty mentor Dr. Michael Honey's involvement in deep south Civil Liberties / Rights organizing from late 1969 until roughly 1976. This activity got him on the radar of the Federal Bureau of Investigation's "Counter-Intelligence Program" (COINTELPRO); a series of covert and, at times, illegal projects aimed at surveilling, infiltrating, discrediting, and disrupting American political organizations and people deemed subversive such as feminist organizations, anti–Vietnam War organizers, activists of the civil rights movement, and a variety of organizations that were part of the broader New Left. Although Dr. Honey was a known subscriber to MLK's non-violence doctrine and his political activities were primarily constrained to participating in marches, fundraising, and distributing pamphlets, this still garnered him a 800 page FBI file. This includes agents illegally wiretapping his home, going through his mail, and writing detailed notes of every civil liberties meeting he attended. What made this situation remarkable was that it was not a unique experience. Mass surveillance on Americans was mundane in the FBI at that time. This research is in support of a full length book project underway by Dr. Honey documenting his experiences through this time, using it as a framework to tell the history of the period. Currently, the main goal of my research is to analyze this 800 page file in addition to several boxes of miscellaneous, period specific, primary documents. This includes decoding FBI serial numbers, cross-referencing known agent handles, and pulling information applicable to the book. In addition to this, I plan to create a table of contents for the file and fit the surveillance record into the timeline I have been organizing of the other documents. This project contributes to the mass of literature on the period by demonstrating how this federal operation effected everyday Americans.

In cities throughout the developed world the dizzying rate of urbanization has led to a growing instability in housing fueled by a lack of affordability. A survey of 200 global cities by the Lincoln Institute of Land Policy revealed that 90% were considered unaffordable, based on the standard of a house price being more than three times the median income. This paper will analyze and compare factors impacting affordability in residential real estate markets in Singapore, Vancouver B.C., the Seattle-Bellevue-Tacoma MSA, and Copenhagen. Preliminary research indicates that the primary drivers leading to a lack of affordability are an insufficient supply to meet demand, geographic limitations, household costs rising faster than incomes, demographic impacts from population growth, ageing, and shifts in household composition. The financialization of housing has resulted in its commodification, a means of accumulating wealth and as the security for financial instruments traded on global markets, which has in turn decoupled housing from its primary connection to local markets. The primary intent of this project is to advocate for long term strategic policy changes to affect affordable housing solutions that address both the supply and demand side of housing markets, as well as advocating for a unified national housing policy that places housing as a human right.

The dorsomedial striatum (DMS) is a brain region that functions in mediating goal-directed action but the cellular, molecular, and circuit-level substrates controlling this remain unknown. Interestingly, the kappa opioid receptor (KOR) and its ligand dynorphin (dyn) are present in about half the cells in the DMS. KOR is a G protein-coupled receptor known to have dysphoric effects through dyn. Given the effects of KOR in the DMS are relatively unknown, we investigated the role of the dyn/KOR system on goal-directed action. We hypothesized that dyn-KOR signaling in the DMS constrained goal-directed actions and motivation. To investigate, we used transgenic mouse strains engineered to express loxp sites on either side of either pre-dynorphin or KOR (pDyn or KOR cKO) genes. We performed viral intracranial microinjections in the DMS of either an anterograde AAV expressing Cre recombinase (AAV-Cre) to remove pDyn in DMS cells or an AAVretro-Cre to delete KOR in neurons projecting to the DMS. We assessed goal-directed action in these mice via instrumental conditioning at varying contingencies, as well as using a wildtype control strain. Furthermore, we utilized progressive ratio testing where the amount of nose pokes required for a reward, a sucrose pellet, increased exponentially, as a measure of motivation. A greater number of nose pokes made indicated higher levels of motivation. Next, reversal training was done where the nose poke port that is active between the two was switched to determine whether the difference in nose pokes made was due to a learning issue or a true difference in goal-directed activity. Our studies aimed to address the involvement of dyn-KOR modulation of goal-directed behavior in the DMS.

People suffering from stressful events are likely to experience negative affective states. Previous studies have shown that stress induces the release of neuropeptides including dynorphin, which acts presynaptically on kappa opioid receptors (KOR) and may act to inhibit neurotransmitter release in the limbic brain areas. In this project, we investigated the interaction between KOR and dopaminergic systems in the ventral shell of the Nucleus Accumbens (NAc) to determine how dopamine release is altered during in vivo dynorphin activation of KORs. To monitor and manipulate dopamine and KOR dynamics, we injected genetically encoded fluorescent indicators of dopamine (dLight) and KOR (kLight) respectively and implanted optical fibers in the NAc ventral shell in transgenic mice brains. In collaboration with Lin Tian at UC Davis, we also characterized the in vivo fidelity and accuracy of a newly developed kLight—version 1.2a. To light-stimulate dynorphin neurons in vivo, we injected a red-shifted channelrhodopsin, Chrimson that acts as a light-gated ion channel to depolarize dynorphin neurons. We recorded dopamine/KOR activities during behavioral experiments including Pavlovian conditioning using sucrose pellets. We hypothesized that upon dynorphin neuron activation, there will be a decrease in the amount of dopamine release in the NAc, an increase in KOR light activity and fewer motivated behaviors observed in mice to obtain sucrose pellets. Here we will present our findings measuring dopamine and kappa opioid function in the NAc. These results could have implications for neuropsychiatric diseases including depression and addiction.

Kaposi's Sarcoma associated Herpesvirus (KSHV) is an oncogenic human herpesvirus and the etiological agent of Kaposi's Sarcoma (KS), a cancer that afflicts HIV-positive individuals worldwide and is endemic in sub-Saharan Africa. KS tumor cells, known as spindle cells, originate from latent KSHV infection of endothelial cells. We have previously used a phosphor-proteomics approach to identify changes in the phosphorylation state of proteins during KSHV infection. We identified Platelet/Endothelial Cell Adhesion Molecule-1 (PECAM-1) to be significantly phosphorylated during KSHV infection as compared to mock infected cells. PECAM-1 phosphorylation leads to a cascade of signaling that promotes cell adhesion, migration, and cell survival, however, the role PECAM-1 plays to aid KSHV infection is currently unknown. To determine whether PECAM-1 expression and phosphorylation is important for KS pathogenesis, I propose to assess differences in gene expression levels with RT-qPCR, validate phosphorylation levels in vitro via western blot, and generate CRISPR-lentiviral constructs to knock out PECAM-1 and express PECAM-1 isoform variants in endothelial cells. These experiments will paint a more complete picture of how PECAM-1 interacts with endothelial cellular processes during KSHV infection. Many rounds of RT-qPCR have been conducted to asses gene expression levels with highly variable results. This indicates that some uncontrolled factor in the cell culture process is affected PECAM-1 expression levels. I hypothesize that cell density is the cause behind this variability and plan to use western blotting to elucidate differences in PECAM-1 protein levels in low and highly confluent cells.

The ocean under Europa’s crust has the possibility of harboring life. Using the available energy, I have made an estimation of the possible biomass on Europa. The available energy was calculated using the available oxidants (O₂ and SO₄^2-) and reductants in the system (H₂). This was then compared to estimates for the amount of energy life needs to survive. The estimated biomass would result in a much smaller cell density in Europa’s oceans than in Earth’s oceans; however, it is most likely that any biomass on Europa would be concentrated where there is available energy instead of being evenly spread throughout.

The prospect of life on the icy ocean world of Europa is an exciting one. A common theory is that hydrothermal vents could produce the necessary reductants for chemosynthesis to take place on the ocean bottom. However, future missions to probe for life will initially focus on the icy surface and the ocean just below the ice. We propose a ‘viral elevator’, a mechanism which functions similarly to the ‘viral shunt’ in Earth’s oceans, which could create and shuttle dissolved organic matter (DOM) to the surface through viral carriers. Current studies model Europa’s ocean with a system of currents and a sub-ice freshwater layer (Soderlund et al. 2014, Zhu et al. 2017). Our calculations demonstrate that the viral elevator could feasibly move DOM through a combination of the ocean currents and diffusion through the freshwater layer. The end goal of this research is to create a functioning model for virus-bacteria dynamics in Europa’s ocean, based on the influx rate of DOM from the viral elevator. We have modified an existing closed-system model (Max Showalter, UW) for viral and bacterial populations in Earth’s sea ice to fit the open-system environment of Europa’s surface ocean. Our new model shows how the virus-bacteria ratio changes given likely parameters for Europa’s ocean.

Post-traumatic stress disorder (PTSD) is a widespread disorder that diminishes the quality of life for millions of adults annually. Symptoms of PTSD include flashbacks and unwanted memories in those who have suffered a traumatic experience. Research labs across the world are working diligently on understanding the interactions between brain regions affected by PTSD, with much of its effects still unclear. Our lab is researching the brain’s neural interactions during traumatic events, such as in PTSD. We are studying the connection between two specific brain regions in a mouse model: locus coeruleus (LC) and dentate gyrus (DG). Both regions are crucial for understanding the neural interactions of PTSD as they are associated with many of its symptoms. The LC is responsible for modulating anxiety and arousal, while the DG is responsible for memory formation and recall. The LC does this by releasing norepinephrine (NE) during a state of anxiety or arousal. We are altering the activity of the LC via optogenetics and identifying its effect on the formation of new memories. We measure the formation of memories by analyzing the behavior of the mice after the activation of the brain region. We also track the release of NE by with fluorescent imaging of the brain after analysis of the behavior. Under a fluorescent microscope, we are able to identify the parts of the brain norepinephrine travelled to and its effect on the behavior of the mice. Data collected thus far suggests that the norepinephrine released from the LC to the DG is associated with the inhibition of memory formation and impaired recall. These findings will help us better understand the underlying neural mechanisms that cause PTSD and other neurological disorders involving memory.

Fungi in the order Erysiphales (powdery mildews) are the causal agents of a detrimental disease to over 10,000 plant species. Identifying powdery mildew species is important for answering a wide array of questions. For example, different species often require different control regimes. Accurate identification of powdery mildews is often accomplished by sequencing DNA of the internal transcribed spacer (ITS) region. The ITS region is a commonly used fungal barcode that consists of an extremely divergent region between two highly conserved regions among eukarya. To sequence these regions we require primers (~20 base pair DNA sequences) on either side of the region. These primers assist in running Polymerase Chain Reaction (PCR). In most samples there will be multiple organisms present. In order to select only the target fungi (powdery mildew) for sequencing, we need primers genetically specific to the order we are looking at yet divergent from all other organisms. The primers for the powdery mildew ITS that have previously been generated have numerous issues such as they tend to amplify other organisms and fail to sequence specimens that are over five years old. The lack of success of previous primers highlights the need for new, more specific, primers. To accomplish this task we use a combination of genomic computer programs. The programs are used to locate the locations of these primers and to analyze their chemical compositions to ensure they will be conducive for a successful PCR reaction. By viewing the PCR results we can determine if the primer was specific enough to only amplify powdery mildew DNA. New powdery mildew specific primers will greatly enhance our ability to genetically identify powdery mildew from field and herbarium samples.