To test questions on the evolutionary history of a species, it is important to consider the drivers of genetic diversification that lead to speciation. Species diversification is often driven by the formation of geographical boundaries, ecological diversity, sexual preference, or a combination of these factors. However, for the Western Banded Gecko (Coleonyx variegatus), a species native to the southwestern region of the United States, few of these factors exist. Despite the lack of clear barriers to gene flow, prior research identified several distinct populations of C. variegatus in this region, though there is some uncertainty with these distinctions as they relied solely on the signal from one mitochondrial DNA (mtDNA) locus. The aim of this project is to instead use genomic data to assess the validity of the C. variegatus populations defined by mtDNA, and to investigate how these populations are distributed across the geographic region they inhabit. Using genomic data allows us to more confidently define population boundaries and assess how they have evolved through time. To explore the aim of this project, we sequenced reduced representation genomic data for 224 individuals across the range of the species to determine how populations of C. variegatus are structured. We then built species trees to assess the relatedness of these populations with respect to each other and the overall evolutionary history of the species. Our findings show that there are consistencies between both the genomic and mitochondrial data population definitions, but distinct differences are also present, with mtDNA overestimating the number of populations. Thus, relying on mtDNA data alone may be insufficient for confidently ascribing population boundaries for C. variegatus. Accurately defining populations can have great implications for the conservation of native biodiversity, but as shown by our study, relying on a single mtDNA locus may mislead this crucial process.

Cardiovascular disease is the leading cause of death worldwide. A key reason driving the high mortality of heart disease is that the heart is unable to regenerate any muscle that is lost due to injuries like heart attacks. Furthermore, there are no current therapeutics that promote the creation of new muscle. However, in the past decade, scientists have attempted to address this issue by using stem cell-derived cardiomyocytes (iPSC-CMs) to replace lost heart muscle. A key limitation preventing using this therapy in humans has been that cardiomyocytes derived from stem cells remain immature relative to adult cardiomyocytes, and these immature cells cause several complications when transplanted into an adult heart. Identifying cardiomyocyte maturation regulators is needed in order to further develop this technology and translate it to patients. Previous studies from our lab and others have identified the RNA binding protein Muscleblind-like protein 1 (MBNL1) as a key factor controlling muscle maturation. MBNL1 expression increases as the heart matures after birth and it controls expression of many critical regulators of cardiomyocyte maturation, however, MBNL1 has never been studied directly for promoting iPSC-CM maturation. In this project, I am testing the hypothesis that increasing MBNL1 expression will improve the maturity of iPSC-CMs. I am using a genetically engineered stem cell line in which I can overexpress MBNL1 and an isogenic control line to test my hypothesis. I have found that MBNL1 expression naturally increases over time in iPSC-CMs. Additionally, I have validated the MBNL1 overexpression system in iPSC-CMs. Finally, I have used this system to test my hypothesis that MBNL1 will increase iPSC-CM maturity by measuring well-described transcriptional and structural hallmarks of maturity. Ultimately, this project will aid in identifying MBNL1’s role in controlling cardiomyocyte maturation, helping further develop stem cell-based therapeutics to repair damaged heart tissue in humans.

The Davis lab is focused on understanding the pathogenesis of Parkinson’s Disease (PD), a neurodegenerative disease characterized by the progressive loss of cognitive functions and motor movements. The mutation in gene glucosidase, beta acid 1 (GBA) is associated with the genetic risk for accelerated PD progression. Prior experiments have shown that GBA deficiency accelerated protein aggregation and affected extracellular vesicles. This has led to our hypothesis that extracellular vesicles are a vehicle for the spread of protein aggregation and mutations in GBA promote this accelerated spread. To investigate this, we developed a Drosophila model of GBA deficiency (GBAdel) and a human neuronal model with induced pluripotent stem cells (iPSCs) from an individual with PD heterozygous for a null GBA mutation. With our fly model, I have conducted genotype recombination to express human Alpha-synuclein (aSyn) in GBA deficient flies in the thorax. If aSyn ended up aggregating in the brain, I compared if this process was accelerated with GBA deficiency versus the control group by measuring high molecular weight oligomers. In addition, prior research has shown that extracellular biogenesis is a result of endolysosomal trafficking which leads to the formation of exosomes in our neuronal culture and spread of protein aggregation in our fly model. We suspect that GBA deficiency affects multiple parts of the endolysosomal pathway. In our human neuronal culture model, we compared endolysosomal trafficking impairments in GBA deficient cells versus controls. To measure this, we stain cells with antibody markers for early endosomes (EEA1,Rab5), late endosomes (Rab11), lysosomes (LAMP1) and conduct confocal imaging for analysis. By understanding the mechanisms of GBA deficiency and progression of protein aggregation, we can determine new therapeutic targets to slow the rate of PD and other neurodegenerative diseases.

Variants in the genetic risk factor GBA have been shown to increase the risk of developing Parkinson’s disease (PD) and accelerate motor and cognitive decline in PD patients. To better characterize this relationship, this project investigates the mechanisms underlying the onset and exacerbation of Parkinson’s disease in patients with the genetic risk factor GBA through the use of Drosophila and human neuronal cell culture models. We use a GBA deficient Drosophila model, which exhibits symptoms of Parkinson’s disease, including neurodegeneration, motor and cognitive dysfunction, and accelerated protein aggregation. Additionally, we use induced pluripotent stem cells (iPSC) from a PD patient heterozygous for the GBA mutation. Prior work in the lab found that GBA deficiency accelerates protein aggregation, alters lipid metabolism, autophagy, and cell-to-cell propagation of pathogenic protein aggregation via extracellular vesicles (EVs). We also found that restoring wildtype GBA function in glial cells of GBA deficient flies rescues protein aggregation in the brain, leading us to hypothesize that GBA may have a neuroprotective role in glia. Because EVs are formed through the endolysosomal trafficking system, we are examining makers for endolysosomal vesicles in GBA deficient and control astrocytes. We will also observe how GBA deficient versus control astrocytes uptake and traffic neuronal EVs, and eventually test whether co-culturing wildtype astrocytes with GBA deficient neurons may reduce pathogenic protein aggregation in neurons, compared to co-culturing GBA deficient astrocytes with GBA deficient neurons, or GBA deficient astrocytes with control neurons. To perform these experiments, we will be using an automated cell culture system integrated with automated confocal microscopy to observe the survival of the cells over time before fixing and analyzing pathogenic protein aggregation in the cells by Western blot. We hope that this research helps us to better understand the mechanisms underlying the progression of Parkinson’s and explore new therapeutic targets. 

Batillaria attramentaria, a species of marine snail, is highly invasive in intertidal habitats along the Pacific coast of North America. B. attramentaria is regularly infected with a parasitic trematode, Cercaria batillariae. Parasitic infection is known to alter both physical characteristics and behavior of snail hosts, in many cases to the benefit of the parasite’s survival and reproductive fitness. I investigated the effects of parasitic infection on B. attramentaria antipredator responses. Snails were sampled from the intertidal area at Penrose Point State Park in Lakebay, Washington, and acclimated to tanks in controlled laboratory conditions. Afterchemical cues derived from a predatory crab were introduced, antipredator responses, including distance moved and reaction latency, were measured for one hour. I hypothesized that snails with parasites would display a reduced antipredator response. If there is a parasitic influence on the host, these behaviors might be advantageous to the parasite cercaria by putting them in more frequent proximity to secondary hosts and increasing the likelihood of completing their life cycle. Enhanced understanding of the parasite-host interaction can give further context to existing studies on the success of B. attramentaria, and provide additional information for current models seeking to understand the influence of this invasive species on native intertidal ecosystems.