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

Nudibranchs are shell-less mollusks that live in marine environments where water movement produces variable flow forces. Having to deal with these forces has contributed to the evolution of diverse mechanisms that help organisms withstand the effects of strong currents. In this study we investigated how the distinctly shaped bodies of two nudibranchs change with the speed of the water flow. Two species of dorid nudibranchs were placed into a flume tank and exposed to low and high flow speeds. Photographs of the specimens were taken inside of the flume tank from different angles and at different flow speeds in order to analyze different features of their bodies. We found that the overall body shape for both species tested changed with increasing flow, becoming more compact. The nudibranchs seemingly acquired a body shape of a streamlined bump (half teardrop shape), which is known for its drag reducing properties. Understanding these types of interactions could help in improving the design of scientific equipment used in challenging marine environments.

Despite extensive research on the evolution of adaptation and diversification, the underlying mechanisms remain poorly understood. Thus far, studies have shown conflicting results, suggesting that evolution within a particular ecological niche can both constrain or encourage an organism's ability to diversify and access other niches. Further investigation of the processes that generate specialists and generalists may shed further light on the evolutionary forces that drive organisms toward wider or narrower niche space. In order to explore these evolutionary trajectories, I utilize a well-studied experimental system involving distinct phenotypic variants of bacterium Pseudomonas fluorescens SBW25 and its naturally associated bacteriophage SBW25Φ2. By evolving Φ2 on different, but closely related hosts, and comparing phage fitnesses in native and foreign environments (hosts), I plan to elucidate the effects of adaptation on the creation of specialists and generalists. Pilot experiments suggest that the bacterial hosts currently being used may not be different enough to produce a discernable effect. However, by using hosts with more distinct characteristics, I expect to find evolutionary tendencies towards specialization in fixed environments/hosts. The results of this project will contribute toward the knowledge of mechanisms adaptation and diversification, and more specifically, the evolutionary dynamics between hosts and parasites.

The microscopic cyanobacteria Prochlorococcus is the smallest and most abundant photosynthetic organism in the ocean, playing a large role in the global cycling of nutrients. Prochlorococcus form ecotypes, which are genetically variable lineages with differing physiological traits adapted to various environmental niches that enable them to be so widespread. They reside in oligotrophic (nutrient depleted) waters where certain required nutrients like phosphate can be scarce, and use a high affinity phosphate uptake pathway to take in phosphate. However, this pathway cannot completely differentiate a phosphate molecule from the physiochemically similar arsenate molecule, leading to the uptake of arsenic into cells, especially when the phosphate to arsenic ratio is low. Recent work performed by my mentors has studied the two pathways Prochlorococcus uses to detoxify arsenic, the efflux detoxification pathway, which was previously known, and the recently discovered putative methylation pathway, and they have found that strains of Prochlorococcus have different genomic capacities for arsenic detoxification. We are currently testing that genomic capacity for arsenic detoxification correlates to relative arsenic tolerance among lab strains of Prochlorococcus by batch culturing and comparing growth inhibition rates of four Prochlorococcus strains that differ in the pathway genes they contain, MED4, NATL2A, AS9601 and SS120. By inoculating the cultures in three different conditions with variable arsenate concentrations and calculating the inhibition rates, we will answer if Prochlorococcus genomic capacity correlates to relative arsenic tolerance. This would have impacts on how we look at the global circulation of arsenic because the two arsenic pathways have varying outputs that affect the circulation of arsenic and can influence the bioaccumulation of arsenic in upper trophic levels.

Pseudo-nitzschia is a diverse and cosmopolitan genus of diatoms composed of 37 species and known for its production of the neurotoxin domoic acid (DA). The phylogeny of the Pseudo-nitzschia genus is complex due to the presence of cryptic species complexes and the frequent discovery of new species. In previous phylogenetic studies, large subunits of ribosomal RNA (LSU) were used as a genetic marker to estimate how Pseudo-nitzschia species were related to one another. We sought to reevaluate the phylogeny of Pseudo-nitzschia both through recreating a LSU tree that accounts for recent discoveries made about the genus, as well as using the rbcL gene, which encodes the large subunit of the carbon fixation enzyme, ribulose-1,5-bisphosphate carboxylase oxygenase (RuBisCO), in order to better understand the evolutionary relationships within the genus. Both trees provided better resolution in the branching pattern of Pseudo-nitzschia species and identified the presence of a third clade within the genus. Each clade had distinct morphological and physiological characteristics, such as cell size, frustule morphology, pigment content and DA production, which further supported the branching order. Metatranscriptomic reads obtained from four stations along a transect ranging from the Washington coast to the open ocean were placed on the rbcL tree and reflected a biogeographical distinction between the clades. The resolution provided in these phylogenies reflects the importance of continued identification and sequencing of new species. Furthermore, the phylogeny of the rbcL shows that it is an excellent marker for both phylogenic comparison as well as community profiling in the environment.

Exposure to 17a ethinyl-estradiol (EE2), an endocrine-disrupting compound found commonly in birth control and the environment, impacts both development and reproduction in fish. Although it has been established to also cause aneuploidy in those exposed, the effect of EE2 on disease resistance is not well understood. This study uses the zebrafish model to address the effect of EE2 on fish health. Embryos will have been exposed to three concentrations of EE2 (1, 10, 50 ng/L) and a vehicle control from 10-72 hrs post fertilization. At 72 hrs, embryos will have been infected with Edwardsiella ictaluri (gram negative pathogen of fish) and monitored for differential mortality. In addition, the host immune response (via induction of immune genes) is assessed on day two and three post infection using quantitative RT-PCR. Quantitative RT-PCR is a method where RNA is transcribed to cDNA using reverse transcriptase and then is then used as a template for the PCR reaction. Specifically, we will have assessed the regulation of serum amyloid A1 (SAA1-acute phase response) and the proinflammatory gene interleukin 1 b (IL1B). From previous experiments and test runs, these two genes are expected to be upregulated after the exposure to EE2 and the subsequent infection. Overall, this study addresses the hypothesis that exposure to endocrine disrupting compounds can lead to increased disease susceptibility in fish at the individual and population level.

Long intergenic non-coding RNAs (lincRNAs) have been discovered to be widespread in mammalian genomes, with thousands existing in humans alone. lincRNAs exceed 200 nucleotides in length and are capped and polyadenylated. They do not overlap with protein-coding genes, and generally exhibit poor sequence conservation across divergent species. The lincRNA cyrano, discovered in zebrafish, possesses a very highly conserved 300 nucletotide region in at least 80 species. Cyrano has also been demonstrated to be essential in embryonic development in zebrafish. Given the sequence conservation of cyrano, we hypothesized that the secondary structure of the 300 nucleotide region was conserved across divergent species. Using selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) we determined the RNA structure of this 300 nucleotide conserved region in vitro in mouse, human, and zebrafish. Four structural motifs were found to be common in all of the species. To validate the integrity of these secondary structural motifs, we aim to probe the structure of the 300 nucleotide conserved region as it exists in the cell by performing SHAPE in vivo. Currently, our findings represent some of the first steps towards understanding the roles of lincRNAs and non-coding RNAs in general. The miniscule amount of information we collectively know about this vast new enigma of the genome emphasizes the need for biochemists to tackle this issue and improve the methods at our disposal. 

Mosquitoes, such as Aedes aegypti, mainly rely on olfaction to find a host to feed on. By exploring mosquitoes’ olfactory learning abilities, we can increase our knowledge of how they choose their hosts. Using an olfactometer, we have conducted behavioral experiments demonstrating mosquitoes can associate a single odorant, 1-octen-3-ol, with a punishment. To further these results, we tested if mosquitoes would use their experience to guide their host feeding preferences, even when confronted with strong appetitive stimuli such as heat and potential blood meal. We found mosquitoes are indeed capable of aversive conditioning in the context of feeding. In this present project, we investigate if mosquitoes can learn the association between more complex vertebrate body odor mixtures (e.g. rat, chicken, human) and a punishment. After sampling the body odors of various vertebrates, we will aversively train mosquitoes to these odor bouquets. Mosquitoes are trained by simultaneously pairing the delivery of the host odor with a negative stimulus (mechanical shock), mimicking host defensive behavior. Upon training the mosquitoes, we test them in an olfactometer giving them the choice between the aversively trained odor bouquet and the solvent used as a control. To examine whether learning affects mosquitoes’ preference between two individual hosts, we plan to use both olfactometer and blood feeding assays. Further analysis of chemical profiles of the vertebrates species using a gas-chromatograph coupled with a mass spectrometer (GC-MS) will provide insights on the interspecific variability that may be used by mosquitoes to discriminate between individual hosts. These results help to advance knowledge of the behavior and biology of disease transmitting mosquitoes and provide interesting cues to develop efficient tools (e.g. bait) to fight them.