National calls have been made to strengthen our nation’s STEM workforce by improving preparation and increasing graduation rates. At Portland State University (PSU), Oregon’s largest urban university, over 60% of students transfer from community colleges and the large majority do not live on campus. Transfer students may perceive a loss of support and a drop in GPA during their first term post-transfer, elements of what is known as “transfer shock.” As part of a newly-awarded NSF S-STEM grant, we aim to measure if high-impact STEM support programs can mitigate factors related to transfer-shock and support student sense of belonging. Direct impacts of the S-STEM program are being assessed qualitatively (e.g. focus groups, reflections), and preliminary results for our first cohort of S-STEM Scholars indicate strong bonds among the cohort and feelings of success. To examine how students supported by the S-STEM and other high-impact STEM programs compare to other PSU STEM students, a survey measuring self-efficacy, scientific identity, scientific values, STEM involvement, and sense of belonging was broadly disseminated to students in Fall 2018 and will be repeated in Spring 2019. Initial survey results (n=933) allow us to compare student responses for students supported (n=93) or unsupported (n=840) by programs such as the S-STEM. We will also compare traditional four-year students (n=291), community college transfer students (n=398), and four-year college transfer, returning, and post-baccalaureate students (n=240). Preliminary results indicate that students supported by high-impact STEM programs such as the S-STEM report significantly higher sense of belonging, both at PSU and in STEM groups. Efforts implemented by the S-STEM program to improve STEM student experiences academically, financially, and socially, particularly to the most vulnerable populations, will ultimately improve and diversify the STEM workforce.

Fluctuating temperature patterns due to climate change could negatively impact the survival of species whose sex is determined by environmental cues rather than genetic factors. Species whose sex is determined by ecological cues or social interactions fall under the Environmental Sex Determination (ESD) category, while the Genetic Sex Determination (GSD) category includes species whose sex is determined by genotype at conception. There are numerous published examples of teleost fish species that rely on ecological factors for sex determination, but no studies have explored the extent to which the annual killifish Austrofundulus limnaeus, a species without sex chromosomes, relies on ESD. A. limnaeus inhabit ephemeral ponds in Venezuela, South America that experience extreme daily fluctuating temperatures. Climate change could affect this delicate lifecycle by disrupting seasonal temperature patterns that alter sex ratios or exposure to temperatures beyond their tolerance range. Therefore, it is essential to determine what impact temperature and social interaction may have on sex determination in developing A. limnaeus. To explore ESD, A. limnaeus larvae were exposed to constant temperatures of 20 and 30°C, and a daily fluctuating temperature regime from 20-30°C from hatching until the display of secondary sexual characteristics. Some fish were grown in isolation while others were grown in small groups. Fish grown in isolation at 30°C exhibited female-biased sex ratios with 64% developing as females whereas 69% in 20°C and 61% in fluctuating temperatures exhibited male-biased sex ratios. Ongoing experiments are being conducted to explore the possible interaction between temperature and social cues for determining the sex in this species. A. limnaeus has a relatively higher tolerance to fluctuating temperatures due to their ephemeral pond environment, and thus represents an opportunity to explore how even the most tolerant of species may respond to global climate change, especially in the context of ESD.

ovine Leukemia Virus (BLV) is a disease that affects US beef herds and large-scale dairy herds. A recent studied found correlations to the presence of BLV particles and human breast cancers. Although no actual retroviral insertion (zoonosis) was found in tissue samples, this raises concerns about BLV consumption in from infected dairy samples. To investigate this phenomenon, the prevalence of BLV from raw dairy milk samples will be analyzed. Western blotting will be used to look for the major reactionary viral glycoproteins, gp51 and gp24. Controls were designed for blotting to subclone the coding region of gp51 or gp24 into bacterial expression vectors from a plasmid containing the entire bovine viral genome. Subcloning and quality assays were confirmed first by restriction digestions, PCR then also will be sent for sequencing. The expressed glycoproteins along with infected cell culture samples will then be used in blotting procedures as positive controls while analyzing raw milk samples collected from farms.

Photoperiod is utilized in plants to control seasonal responses such as flowering. Flowering of Arabidopsis is promoted in long day conditions (LD), late spring to summer, but not in short day conditions. Arabidopsis thaliana is our model organism because of its short generation time and simple genome which allows us to apply our findings to other species. One of the major factors that determines flowering time response to the different lengths of photoperiods is a gene, FLOWERING LOCUS T (FT). FT is induced around dusk in laboratory LD conditions. In natural LD conditions, there is an additional induction of FT in the morning. Although the molecular mechanism behind flowering regulation is the most characterized in Arabidopsis, the mechanism behind the expression of FT in the morning under natural LD conditions is not fully understood. Investigating these mechanisms will help us to understand how Arabidopsis plants flower in spring in nature and ultimately better the accuracy of experiments that are run indoors. The regulation of expression levels of transcription factors may be important for this FT induction. Through RNA sequencing analysis, we found eleven transcription factors within genes that were found to be differentially expressed between laboratory LD conditions and natural LD conditions. Analysis through quantitative polymerase chain reactions (qPCR) will hopefully yield results pointing toward a transcription factor that is important for the regulation of FT expression. 

Conservative estimates suggest that food production must increase by 60-70% by 2050 to keep up with population growth. This challenge to global food security is compounded by a lack of knowledge of how crop species will respond to a changing climate. The Nemhauser Lab has been studying how the photoreceptor Phytochrome B (phyB) directs the allocation of plant resources in response to environmental stimuli like elevated CO2. I have focused on studying this phenomenon in Brassica rapa, a member of the mustard family that includes a large variety of popular vegetables such as broccoli, cauliflower, Brussels sprouts, as well as varieties used for oil production. B. rapa plants with mutations in the phyB gene make fewer seeds, have a lower chloroplast density, photosynthetic rate, total chlorophyll levels, and stomatal index. To better understand how phyB is involved in seed yield, I am characterizing ovules and gynoecia (female reproductive organ) development in phyB deficient B. rapa plants. To understand how phyB plays a role in other processes relating to or impacting resource allocation such as chlorophyll levels, I will identify genes differentially expressed between wild type and phyB deficient B. rapa plants. This will ultimately lead to the identification of potential targets for engineering more resource-efficient and higher-yielding crop varieties.

The Arbuckle karst system consists of caves, microfractures, and hydrogeologic barriers. Isopods in the genus Caecidotea inhabit the pools of water within the groundwater system. Young Caecidoteas travel through microfractures, and small populations move from one cave system to the next. Over the time these fractures close, causing the populations of Caecidotea to be isolated and potentially drift genetically. The sampled distinct populations have become morphologically distinct, but it is yet to be determined if they also have become genetically distinct species. Genetic classification may also provide a more timely identification of fracture closing. DNA Barcoding using the Cytochrome Oxidase subunit 1 (COX1) gene will provide the percent of divergence in the samples obtained from different populations/locations; however, the chitin-heavy exoskeleton of isopoda could make it difficult to have DNA extractions that are “clean” (without protein) and decent yield. An extraction method was used proteinaseK (protK) and high salt to release the DNA followed by ethanol precipitation to concentrate the extract. For DNA Barcoding, the COX1 gene sequences need a PCR protocol with the robust primers is crucial. We plan to explore various primer sets for the optimal amplification.

Many plant species are known to undergo masting, where individuals within a species all produce a large amount of seed in a single year, with a sharp drop off in reproduction in the following years. Masting may be beneficial to plants by suppressing seed predator populations in low seed production years, allowing for seeds to escape predation in high seed production years. Masting is likely associated with climate, although this is poorly understood. In this study, I will use herbarium specimens to tackle questions related to masting in five plant species: Tsuga heterophylla, Pseudotsuga menziesii, Thuja plicata, Rubus spectabilis, and Rubus parviflorus. Specifically, I will note the number of cones, seeds or berries on herbarium specimens, as well as specimen size and the year it was collected. I will use these data to 1) examine patterns of masting in focal species as compared to field data from Mount Rainier. I hypothesize that herbarium specimens will show a similar pattern of masting as field data, with trees showing stronger patterns than shrubs. Next, I will use these data to 2) compare masting patterns to annual climate. I hypothesize that warm temperatures lead to masting the following year, and that masting has increased in frequency. Finally, I will 3) assess the relationship between masting and bird species that eat seeds and berries (e.g. grouse, jays), to determine whether masting influences population dynamics of higher trophic levels. I will do so by comparing masting patterns with bird count data from the Audobon Society. I hypothesize that population sizes of birds that rely on seeds and berries will be greater in mast years. This study provides additional information for how we might expect entire ecosystems to be affected by climate change, including resource distribution and population health.

There has been significant concern regarding the global effects of climate change, especially on plant communities, which are influenced by individual plant species responses. Warming temperatures are having large repercussions for plant biodiversity, with rapidly changing environmental conditions causing shifts in species ranges and phenology. To better understand the implications of this phenomenon on plants, many studies have investigated responses of individual species to climate change. One approach that has grown in recent decades is the use of functional leaf traits, which are indicators of plant performance and reproductive capacity. Specific leaf area (SLA), the ratio of fresh leaf area to dry leaf mass, is one such trait that is attributed to plant growth and photosynthetic capacity, and found to be correlated with climate. We assessed the relationship between climate and SLA for Vaccinium ovalifoilum, a shrub that is prevalent in the montane ecosystems of Mt. Rainier. To accomplish this, we gathered SLA using samples from the Burke Museum’s herbarium collection whose distribution will be delineated across three elevational bands. Altitude was used as a proxy for climate due to variable environmental conditions found across elevation—namely temperature and precipitation—and the collection location of specimens allowed us to obtain temperature and snow accumulation data. With this information, we compared the variation between the three established elevational bands in which the specimens fell under. We hypothesized that as elevation increases, SLA will decrease, attributing this trend to a limited growing window to support high photosynthetic capacity as a result of later snowmelt and lower temperatures. Our results offered insight to understand how climate change may potentially affect plant functionality and guide future research to analyze how changes in individual species may influence community coexistence in the upcoming years.

A hatchery’s purpose is to supplement falling populations of wild fish, mitigating human impact. However, the effect operating a stream-based hatchery has on the immediate stream environment is not well understood. Varied hatchery designs make it difficult to find a consistent way of assessing an establishment. This project used the idea that consistency is key to evaluate the impact hatcheries made by examining water of the the influent and effluent flow. Water was sampled from where it entered, transitioned, and exited three different fish-bearing hatcheries. Hatcheries were classified into three general water-system types, gravity-fed, spring-fed, and flow-through. Water status was evaluated by measuring electric current, dissolved oxygen, pH, temperature, and bacterial content. In addition to unique location characteristics, containment mitigation measures and extenuating circumstances were considered when evaluating the data. The results showed the trend of influent to effluent water in all three hatcheries increased in temperature while the levels of dissolved oxygen, electric current, and pH decreased. Similar result trends were also found between alike water-system types, although with the small sample results are inconclusive. This study is not meant to be a stand alone. With the inclusion of more locations the data will begin to form an averaged scale which could be referenced for the effectiveness of certain hatchery designs and contaminant mitigation techniques. Having this data-set would eventually serve as a resource for future hatchery construction projects.

Pollution from human influences is a growing problem in the Chehalis River and tributaries causing deleterious effects on stream health. Stream microbiomes are composed of diverse collection of microbes that play an important role in keeping the surrounding riparian zones and life within the streams healthy and thriving. Stream water has been facing a decline in quality from the leading cause of pollution from agriculture and manufacturer run-offs. Although there have been many studies relating to run-off pollution affecting streams, there are few in-depth studies done on the taxonomy and functionality of microbes in urban water ecosystems, so it is important for this to be further investigated. With the use of 16s rRNA sequencing, each sample site presents two years of data included to indicate differences both by season (Fall, Summer) and sample site. At the phylum level, every season consists of a primary microbial signature shared amongst the sites. These phyla are Proteobacteria, Bacteroidetes, Actinobacteria, Firmicutes, Verrucomicrobia, and Tenericutes. From the family data, common to nearly all sites are the Flavobacteriaceae, Comamonadaceae, and Oxalobacteraceae. Families prevalent at many sites in various combinations include Flexibacteraceae, Crenotrichaceae, Chitinophagaceae, and Verrucobacteraceae. This project presents a two-year microbiome analysis of Alder and Fry Creek to develop trends for the seasonal variation in urban water ecosystems due to human impacts.

As climate change progresses, increasing temperature is expected to have community and population-level consequences. The temperature-size rule predicts shifts in both community and population structure to favor smaller bodied organisms over larger bodied organisms as temperatures increases. We investigated this hypothesis in the context of rocky intertidal invertebrate communities on San Juan Island, and examined changes in community and population structure over the past 45 years. We replicated historical ecology studies on the abundance of six intertidal species; three of which body size data was also collected. These species included grazing and predatory molluscs (Katharina tunicata, Nucella lamellosa), anemones (Anthopleura elegantissima), and crabs (Hemigrapsus nudus, Pugettia gracilis, Pagurus sp). Additional abundance data was collected on smaller molluscs (limpets, littorine snails). Predicted decreases in body size were not apparent in populations of K. tunicata., N. lamellosa, and A. elegantissima. However, when comparing abundances, shifts in community structure towards smaller-bodied organisms were apparent. We observed an increased abundance of smaller-bodied gastropods and crustaceans (limpets and Pagurus sp), but a decrease in K. tunicata abundance, one of the largest grazers in this system. This research highlights the potential for a variety of community and population responses including both stability and variability in the face of climate change.

Increasingly, over the past half century, antibiotic resistant plasmids have spread to a large range of bacteria increasing the demand of new antibiotics. On average, once an antibiotic has been released into the public market, a strain that is antibiotic resistant evolves within a few years. Even though the constant production of new drugs and treatments provides some temporary solutions, a better solution would be to investigate and understand bacterial plasmid mechanisms. Through my research in the UW Biology Kerr Lab, I have been exploring how bacteria maintain plasmids that contain genes encoding for antibiotic resistance. Plasmids are extra-chromosomal pieces of DNA that require the host cell to allocate energy for their general maintenance. Prior theoretical research suggests that, to avoid this allocation of resources, the host should lose antibiotic resistant plasmids over time when the plasmid is no longer beneficial to the host’s fitness, for example when the antibiotic is no longer present. We found that many plasmids across multiple bacterial species persist in their hosts, even in the absence of selection for the plasmid. Currently, I am testing whether changing the environmental conditions experienced by the host/plasmid pairs, specifically from a nutrient-rich to minimal media, will affect the persistence of antibiotic resistant plasmids. This research provides important data that will allow us to have an easier time combating antibiotic resistance.  

Water temperature is one of the largest factors of hatchery efficiency, and this can vary greatly depending on the source of the water. Warming waterways is thought to be a problem with salmonid hatcheries in the Pacific Northwest. For this study, we compared the effects of water source (Lake Aberdeen vs VanWinckle Creek) as well as temperatures on the mortality rates of Oncorhynchus mykiss. Water temperature data was collected from 2015, 2016, 2017, and 2018 to compare the effects of temperatures and water source on the mortality rates of O. mykiss. Microscopy was also used in an attempt to find and identify Tetracapsuloides bryosalmonae, the parasite known to cause Proliferative Kidney Disease in salmonid fishes. This parasite is believed to be a major contributor to high summer mortality rates. We collected multiple morbid and recently deceased juvenile O. mykiss, and examined these samples using a hematoxylin and eosin staining of the kidneys and gills. Initial findings suggest no significant impact of lake versus river water for this specific disease, however gram staining and biochemical assays indicated a presence of a bacterial fish pathogen: Flavobacterium columnare. Because of this, future directions include broadening the scope to a greater variety of infectious diseases. If factors influencing development of PKD can be identified, preventative actions can be taken to lessen the mortality rates and allow for a larger amount of fish to be successfully raised each year.

Plants take up silica over the course of their lives along with other essential nutrients in the water that they absorb through their roots. The silica becomes deposited within their tissues in the form of solid bodies (phytoliths); when the plant dies and decays, phytoliths are left in the soil where they can fossilize. Fossil phytoliths preserve the original morphology of plant cells and can be used to reconstruct past vegetation. The Middle Miocene Climatic Optimum (MMCO) was a major global warming event that happened ~17-14.5 million years ago. Researcher have reconstructed the climate of the Santa Cruz Formation in Patagonia, Argentina during this period as warmer and drier. While we would expect the vegetation to become more open (i.e., grassy or shrubby versus forested), phytoliths from the Santa Cruz Formation tell a different story; in particular grass phytoliths (and therefore grass abundance) seem to decrease through time, but also become smaller. Some researchers have noticed that grasses tend to respond to reduced water availability with reduced cell size. Therefore, we hypothesize that the reduced size of grass phytoliths observed in the Santa Cruz Formation during the MMCO is due to increasing aridity. However, because this trend of decreasing cell size was only noticed by qualitative observation, we need to quantitatively assess significant changes in cell size. To do so, I studied and imaged grass phytoliths under a microscope, categorized them by subfamily/tribe based on their shape, and measured their size. I then statistically compared the phytoliths from younger and older strata to test whether there was a change in size through time. This work will be used to predict how our current global warming event may impact plant life based on the trends of the past.

High rates of forest conversion and fragmentation have placed many endemic species in the rainforests of Sri Lanka under threat. Ceratophora is an endemic and endangered/critically endangered genus of lizards containing five species, and C. aspera has the widest distribution spanning four forest regions, making it an ideal candidate species for broader conservation management projects. The goal of this project is to study the phylogeography of C. aspera across its range in the forests of southwest Sri Lanka to assess the genetic variability of the remaining populations across two lowland areas, the submontane zone (Sabaragamuwa Hills), and the montane forest zone (Central Hills). Analyses of genetic data are important for understanding the relationships between geography and genetics and to determine where populations are connected and fragmented. During the 2018 and 2019 field seasons, tail clippings were collected from wild lizards. In the University of Washington's Biology Department, DNA sequencing of mitochondrial DNA (ND4 gene) was used to measure genetic diversity within and among populations, and to estimate phylogenetic relationships. Genetic diversity is highest (6%) between the population from Hiyare (lowlands) and the Sabaragamuwa Hills (submontane zone). There is also strong evidence for highland and lowland groups. Populations from Hiyare, Sinharaja and Gilimale show no intra-population variation. Sri Lanka has pledged to reforest 200,000 ha of degraded forest to create forest landscapes under the Bonn Challenge, and to increase forest cover to 30% unde the Paris Climate Agreement. Phylogeographic profiles of endemic species, such as C. aspera, are critical for forest restoration strategies as they identify priority areas for reforestation and inform connectivity strategies based on the need to maintain metapopulation structure and genetic diversity. 

Acoustic signals are essential for communication, advertisement, and reproduction in a variety of organisms. However, their successful transmission is limited by the environment in which they are produced. My research investigates the acoustic adaptation hypothesis, which proposes that to maximize transmission efficiency, animals evolve vocalizations with characteristics that minimize degradation and attenuation (loss of volume) in their native habitat. This hypothesis predicts that birds of open habitats will exhibit vocalizations with higher frequencies and larger frequency ranges than birds of forest understory habitats, because fewer obstructions and more low-frequency ambient noise in open areas favor successful transmission of higher-frequency signals. I tested this prediction by recording and analyzing the vocalizations of 63 bird species living in open and forested habitats around Monteverde, Costa Rica. I found that on average, bird species of open habitats vocalized at significantly higher and broader ranges of frequencies than birds of forested habitats, suggesting that vocalization transmission efficiency helps shape avian communities and their response to habitat transformations.

Automatic scales are designed to weigh and count animals when they step on or cross the device. This means that high quantities of data may be collected when researchers cannot be present, with minimal interference to study subjects. However, remote and automated data collection requires verification of the quality of data before analyses. We use automatic scales in Punta Tombo, Argentina to weigh Magellanic penguins (Spheniscus magellanicus). Our scales record the time that each penguin crosses, and if certain conditions are met, they record a weight. We verified our data by comparing counts from automated scales with counts from a video recording of penguins crossing the scales. Over twenty hours of video footage were made during a 17-day period where penguins were recorded crossing automatic scales in the morning, midday, and evening on different days. We then counted the number of times a penguin was present in the video and not recorded by the scale. We expect that the proportion of penguins missed will be higher in the morning and evening when more penguins cross the scales, and lower around midday when fewer penguins cross the scales. The scales are designed to record weights when one penguin is present. When several penguins are on the scale or cross rapidly, the scale does not record a weight and may not record the correct number of penguins. Preliminary results support our prediction, with 75% and 78% of birds crossing the scales recorded during the morning and evening respectively, and nearly 100% of birds crossing the scales recorded at midday. By comparing the counts and the times between the scale and the video recording, we can determine how many penguins are missed, count the total number of penguins crossing the scales, and identify when most penguin crossings occur.

This project aims to influence the next generation of flying robots by first studying how moths use multi-sensory information to increase their agility. These different types of multi-sensory information include visual- and touch-based feedback, which are influenced by forces such as those from flapping wings and changes in body posture (which affect a moth’s inertial distribution). In addition, flying insects are known to control orientation via torques arising from at least three distinct affordances: by varying aerodynamic center of pressure, by changing body posture to alter center of mass location, and by swinging body segments or limbs to harness inertial torques. We hypothesize that these sources of control are integrated in parallel to increase robustness and agility, are weighted according to behavioral context, and are tuned to body morphological parameters. To investigate this flight behavior, we first built a test apparatus to apply rapid pitch movements to a tethered flying moth, Manduca sexta, while having a minimal effect on a moth’s inertia and natural flight patterns. This system allows us to measure the torque exerted by the moth’s flight forces and body movement. Closing the loop between measured torque and applied movement enables control of the forces experienced by the moth. Projected video is used to simulate a changing environment and create a haptic-type interface for the moths. The video can provide a visual experience to either match the mechanosensory experience or provide sensory conflict (i.e. a mixed reality environment). The next engineering challenge is to design and build a system to electronically control and monitor the motion of the moth. After this, cameras and sensors will be used to record data that will contribute to a more realistic understanding of how the principles of animal flight can be used in robotics.

The Blue River of south-central Oklahoma is a spring-fed stream that drains much of the eastern Arbuckle-Simpson Aquifer, and is one of only two free-flowing rivers in Oklahoma with little to no anthropogenic influences on the flow of this river. Not much is known about the structure and composition of fish communities in the upper reaches of the Blue River. In collaboration with The Nature Conservancy, assessments of fish in riffle habitats of the Blue River were conducted adjacent to the Oka’ Yanahli Nature Conservancy Preserve in the summer of 2018. Fish samples collected were processed, individual fish were identified to species based on morphology, and biological metrics were calculated. A total of eighteen species of fish were collected from the riffle stream habitats in the upper reaches of the Blue River. The relative abundance of each species was calculated, and the Central Stoneroller (Campostoma anomaum) was highest in abundance, the Orangebelly Darter ranked second in abundance, and the Orangethroat Darter ranked third. The Orangethroat and Orangebelly darter were more likely to be found in areas in the riffles where river bed particles were in the small to large cobble size range (60 to100millimeters). The two darter species did not show any difference in preference for current velocity in the riffle habitats. The two darter species co-occurred in riffle microhabitats as indicated by the positive correlation between the numbers of each darter species collected across all seine hauls. Looking at biota in this river could give insight into how different habitats function in a free-flowing river, and more specifically, what is could potentially happen in riffle habitats of the Blue River because these areas will be the first stream habitats affected if flows are reduced from anthropogenic withdrawals of water from the Arbuckle-Simpson Aquifer.

Auxins are a class of bioregulatory hormones which impact nearly every aspect of plant growth and development. Indole-3-acetic acid (IAA) and one of its corresponding receptors (TIR1) have been shown to be involved in seed germination, lateral root formation, stem elongation, fruit set and development, along with numerous other developmental processes. In an effort to more effectively study auxin-dependent pathways, Torii et al. developed a synthetic version of the IAA/TIR1 receptor pair which was shown to act independent of the endogenous pair in Arabidopsis. Here, I extrapolate our synthetically engineered auxin-receptor pair into a model system with agricultural and environmental implications (e.g. Solanum lycopersicum- tomato) and aim to test whether we are able to 'hijack' endogenous auxin signaling in tomato to precisely modulate auxin-dependent, spatiotemporal developmental outcomes. These findings could shed some light onto the vastly complex, auxin-dependent developmental process in Solanum lycopersicum and provide a tool to study auxin's specific role in varying developmental processes such as stomatal formation, leaf morphology, temporal flowering and fruit setting.

Dravet syndrome (DS) is a severe form of childhood epilepsy caused by a mutation in the SCN1A gene, which encodes the NaV1.1 voltage-gated Na+ channel. This channel is present in most GABAergic neurons, the main inhibitory neurons in the brain. Reduced activity of the channel in DS leads to loss of inhibitory activity in the brain; this, in turn, leads to seizures and developmental deficits. Through previous research using the mouse model of DS, the de la Iglesia lab has demonstrated that DS also affects circadian rhythms, which are the endogenous biological rhythms synchronized to the 24 hour day. These symptoms are likely caused by the loss of NaV1.1 in a sleep regulatory center called the suprachiasmatic nucleus (SCN), a set of cells which functions as the ‘master clock’ of the circadian system of mammals. However, the de la Iglesia lab found that selective deletion of the SCN1A gene from the SCN fails to replicate the abnormal circadian phenotype. We believe that these mutant mice are phenotypically normal either because there is a compensatory increase in the expression of another sodium channel, NaV1.3, or because the targeting strategy does not reach all cells within the SCN. To test the first hypothesis we employed in-situ hybridization to visualize the expression of the genes that code for NaV1.1 and NaV1.3 channels in either SCN-specific knock outs or their wild type littermates. My results will help explain the phenotype seen in the SCN-specific SCN1A mutants and determine whether developmental compensatory mechanisms are important in the SCN of DS mice.

Most organisms show a roughly 24-h cycle in their physiological and behavioral processes, called circadian rhythms, generated endogenously through the ~24h cyclic expression of genes known as clock genes. Clock gene expression oscillates in the master circadian clock of mammals – the suprachiasmatic nucleus (SCN) - and nearly every cell of the body. Typically, circadian clocks and the rhythms they sustain are ‘entrained’ by the 24-h light-dark (LD) cycle. Our lab has found that fear can also behave as an entraining factor. We observed that when mice or rats need to leave a safe nesting area to access a foraging area, they forage and feed during the dark phase of the LD cycle. If the foraging area is rendered dangerous with random uncued footshocks during the active dark phase, the animals’ foraging and feeding activity shifts to the light phase. My goal is to understand the neural circuits and molecular processes involved in fear entrainment. I have analyzed the expression of clock genes in animals exposed to nighttime fear and control animals exposed to daytime fear; this allowed me to assess the circadian rhythm of expression of clock genes of interest (Per1 and Bmal1) in the SCN and amygdala, and I found that the amygdala entrains to fear but the SCN does not. I have also performed trials with brain-specific-knockout mice and found that nocturnal fear entrainment requires an intact molecular clock. My current experiments use a more specific knockout strategy of viral injections into the brain to determine whether a functioning circadian oscillator in the basolateral amygdala (BLA) or the SCN is needed for nocturnal fear entrainment. These experiments serve to unmask the molecular mechanism of fear entrainment and could also help understand the mechanisms linking fear and anxiety disorders to problems with circadian rhythms and sleep.

Asymmetric cell division (ACD) is an integral process that multicellular organisms use to create cellular diversity. For instance, stem cells use ACD to form differentiating sibling cells while recreating the stem cell in order to maintain the stem cell pool. Defects in ACD can result in a variety of diseases ranging from neurodevelopmental disorders to cancer. Using Drosophila melanogaster neural stem cells (neuroblasts) as a model to study cellular asymmetries, we recently found that hydrostatic pressure is an important factor contributing to ACD. However, the mechanisms and proteins that regulate hydrostatic pressure are unknown. Based on our previous results, I hypothesized that Na+/H+ antiporters are involved in establishing hydrostatic pressure. To examine this hypothesis, I tested the function of four Na+/H+ channels in Drosophila using RNAi knock-down experiments and subsequent live cell imaging. This imaging allowed visualization of fluorescently tagged myosin and microtubules--two critical components of the cell division process. I found that knocking down each of the four antiporters results in a bent mitotic spindle, delayed division times, and centrosome abnormalities. I conclude that the four antiporters play a role during ACD in fly neural stem cells. To validate these results, I will use CRISPR/Cas9 gene editing to develop deletion mutants and EGFP-tagged versions of the four antiporters—two crucial steps in studying the regulation of Na+/H+ channels. Further in the future, I will use CRISPR/Cas9 to create optogenetically controllable Na+/H+ antiporters, such that I can use light to control hydrostatic pressure in Drosophila neuroblasts. I also plan on measuring the  intracellular pH using genetically edited Drosophila, as disruptions in pH could cause the described phenotypes. These studies will provide mechanistic and functional insight into how hydrostatic pressure contributes to successful ACD.

In the last decade, a large amount of studies have been done using virtual environment (VE) because of the increased control over the sensory stimuli used and the detailed observation of the associated behavioral and sometimes neuronal responses. In this study, we placed honeybee in a VE and exposed them to visual stimulus in closed-loop. We showed that honeybees are able to fixate the stimulus regardless of the level of feedback fed to the sensors(e.g., the gain between the animal motion and the stimulus motion on the VE). Our next step is to investigate how different neuromodulators such as the octopamine and dopamine, may be important for fixation and adaptation to the different level of sensor feedback. Octopamine (OA) is key in modulates physiological process in invertebrates including honeybees. Recent studies have identified OA neurons that are critical for visual behaviors and that increase their activity during active behavioral state. To identify the effects on octopamine and dopamine (DA) on honeybee’s ability to fixate, we are injecting bees with OA, DA or their respective antagonists in a visual processing brain area. Potential results of this study will impact the fields of neuroethology, providing insights on the modularity of neural processes and the feedback between sensory and motor pathways.

Methanol is a common pollutant in freshwater ecosystems due to its widespread use in industrial operations, fuel, antifreeze, paints, and insecticides, and being a result of the burning of garbage. As a bioindicator species, Daphnia magna health indicates changes in aquatic ecosystem health. They are an important part of the food web, eating algae, and as a food source to insects and fish. No previous studies have examined the effects of the pollutant methanol on Daphnia heart function and mortality. This experiment examined the effects of varying methanol concentrations on heart function and mortality of Daphnia magna. It was hypothesized that methanol significantly affects the heart and mortality rate of Daphnia. Fifteen experimental biospheres were used in each trial, with three jars for each of the five concentrations. The biospheres were filled with deionized water and methanol in concentrations of 0 ppm (control), 822.6 ppm, 1644.5 ppm, 3289.0 ppm, 7119 ppm. In a second trial, the concentrations were 0 ppm, 822.6 ppm, 1644.5 ppm, 205.7 ppm, and 411.3 ppm. Heart and mortality rates were observed and recorded for each trial over 4-8 days. For each jar, videos were recorded for 15 seconds each and heart rate was counted, and mortality counted every other day. Based on the survival and heart rate differences, it was concluded that as methanol concentrations increase, the heart rate of Daphnia varied but didn’t respond linearly to concentration levels. Additionally, higher concentrations of methanol negatively affect survivability, although the initial control groups had somewhat high death rates. This study highlights the negative impact of methanol pollution on Daphnia because a negative impact on Daphnia affects the whole freshwater ecosystem. Indeed, in Lake Washington, Daphnia represent a major source of nutrients for juvenile Sockeye Salmon, making Daphnia indispensable for their growth.

Spatial variation in soil abiotic conditions at plant range limits may be important in determining how plant range limits will respond to climate change. One reason for this is that plants are known to change many characteristics of the soil around their roots in ways that influence the growth of other plants.The range limit of subalpine fir is expected to shift into subalpine meadows as the climate warms. Our goal for this project is to describe the abiotic soil qualities of a subalpine forest habitat and a subalpine meadow habitat on Mount Rainier to explore how these characteristics may affect the predicted range shift. We hypothesize that soils from subalpine meadows will have less organic matter and therefore less phosphorus, a lower carbon to nitrogen ratio, and less water holding capacity than soils from the subalpine forest. We will develop a protocol for measuring water availability and implement it on soil samples obtained from around the roots of subalpine fir trees in both the forest and meadow sites on Mount Rainier. We will use standardized tests to obtain the organic matter and phosphorus measurements. If our hypothesis of lower nutrient availability and water retention in meadow soils is supported, this may suggest that subalpine fir growing in the meadows have a greater dependency on fungal symbionts for obtaining soil resources. This would have important management implications given that suitable fungal symbionts are expected to be rare or absent at range limits.

Cranial elaboration, in the form of domes, horns, and bony bosses, has evolved multiple times in vertebrate history, including in non-mammalian synapsids, the extinct ancestors of mammals. The lack of similarly thickened skulls in living animals has meant that very little can be inferred about how these features developed or why they evolved. Here we use comparative bone histology to describe the microanatomy of Oudenodon, a 255-million-year-old synapsid with distinctive nasal bosses. We compared thin-sections from the thickened portions of Oudenodon to the non-thickened skull of its relative, Diictodon, in order to better understand how cranial elaboration developed in synapsids. We took thin sections from the thick nasal bosses as well as non-thickened regions of Oudenodon to capture changes in tissue microstructure. Then, we compared these thin-sections to similar regions of the skull in Diictodon, which lacks cranial elaboration. In the bone tissue of both Oudenodon and Diictodon, we observed a cancellous, spongey interior sandwiched between two layers of compact cortical bone. This pattern of bone is typical in many modern skulls but the thickness of the cancellous region in Oudenodon is strikingly thicker, even in regions away from the boss. We hypothesize that increased cranial thickness in Oudenodon is due to this middle expansion of spongey, cancellous tissue. As a result of the increased bone thickness, sutures in Oudenodon are deep, wide, and convoluted when compared to the relatively simple interdigitated sutures in Diictodon. These and other histologic comparisons with distantly related taxa allow us to interpret the growth and construction of cranial elaboration in synapsids, adding to our understanding of how these thickened skulls evolved. Future work can also explore the possible soft tissue covering of these bosses and domes, which may have been used for intraspecific display or combat. 

It is often assumed that terrestrial surface climate in the Arctic is largely controlled by the surface albedo. As the land surface becomes darker, it will absorb more solar energy. The extra absorbed energy is then released through longwave radiation and turbulent fluxes. If the total amount of latent heating is relatively constant, the extra absorbed radiation leads to warmer temperatures. The evaporative resistance of the land surface sets the difficultly for water to evaporate, and thus changes the partitioning between the turbulent fluxes of latent and sensible heat which could lead to a different surface temperature. These effects are known; however, it is unclear what the relative contribution of evaporative resistance and albedo are for the terrestrial surface climate. We used the albedo and evaporative resistance values derived from two common vegetation types, needleleaf evergreen trees and broadleaf deciduous trees, to simulate the climate response to a change in land surface albedo and evaporative resistance in factorial combinations. We find that changing the evaporative resistance between the two plant types has a large effect on the surface energy budget that is almost if not equivalent to changing albedo alone. Lower evaporative resistances lead to an increase of low clouds relative to higher resistance. As a result, less solar radiation reaches the surface when the evaporative resistance is lower. In contrast, the albedo controls how much of the incoming solar radiation gets absorbed. The reflection of light due to the difference in albedo is of the same magnitude as the loss of incident sunlight due to increased cloud cover under lower evaporative resistance. Our results demonstrate that realistic changes in evaporative resistance can have just as large of an impact on Arctic terrestrial surface climate as changes in surface albedo due to cloud feedbacks.

With our rapidly changing climate, plant communities are predicted to experience more variable conditions. Climate change predicts that there will be longer periods of drought followed by heavy rainfall at unpredictable intervals. With this, plants may experience selective pressures to combat the stress that come with these variable conditions, which ultimately may influence plant evolution. Phenotypic plasticity and epigenetic modification are two factors we believe may strongly influence the adaptative ability of plants. I predict that these variable conditions will promote phenotypic plasticity and epigenetic “memory” (where plants’ stressful experience can be inherited from parent to offspring), and potentially help offspring plants cope with the same abiotic stress. We have implemented an experimental design mimicking the predicted variable conditions of climate change. For two generations, we exposed plants to either drought or non-drought conditions. Then in the third generation, we took seeds from parents that experienced those conditions and exposed them to either drought, non-drought, or variable watering in a cross-replicated design. I hypothesize that there is inherited epigenetic memory, and that the different treatment groups will pass memory that will benefits plants if the offspring was exposed to the same condition its parent experienced.

The level of plastid DNA (ptDNA) declines as plastids develop from colorless proplastids to green chloroplasts. The decline in ptDNA is associated with an increase in DNA damage resulting from oxidative stress and ultraviolet (UV) radiation. 8-oxoguanine (8-oxoG) is a lesion in ptDNA that results from the oxidation of guanine. Our lab previously found a reduced amount of ptDNA in light-grown plants compared to dark-grown plants, likely due to increased oxidative stress that increases ptDNA damage. Here, our objective is to quantify ptDNA damage by assessing 8-oxoG lesions during the greening of maize leaves. We hypothesize that as plastids mature, 8-oxoG lesions increase. Our experimental outline involves the quantification of 8-oxoG by the enzyme-linked immunosorbent assay (ELISA), as well as immunofluorescence microscopy using antibodies that target 8-oxoG. We are examining plastids isolated from light-grown and dark-grown stalk and leaf tissues. As 8-oxoG lesions are one of the markers of oxidative DNA damage, our results will be used to assess DNA damage during development of maize plants. This research will provide a better understanding of role of oxidative stress in plant development

Mosquitoes primarily navigate using their olfactory system, and can use this system to form “memories” that influence their choice in hosts. When a mosquito encounters an odor, information is sent through the antennal lobes in the brain to the mushroom bodies, which are structures responsible for learning and memory consolidation. This odor-learning pathway is mediated by neurotransmitters like dopamine and serotonin. Recent research has shown that the mosquito Culex quinquefasciatus has extremely low levels of dopamine in the antennal lobes compared to other species, and is unable to learn to avoid odors associated with a negative response. This led us to predict that dopamine is essential for aversive learning in mosquitoes. We hypothesized that Cx. quinquefasciatus differed from other mosquitoes in learning ability because they were previously tested in the light and they are the most nocturnal of the originally tested species. To test this hypothesis, we conditioned the mosquitoes in the absence of light in an aversive learning paradigm to measure how frequently they chose to avoid the conditioned odor. An inability to learn regardless of light condition would indicate that the role of dopamine as a neuromodulator in the antennal lobes evolved partly to allow diurnal mosquitoes to avoid defensive hosts. Next, specific neurotransmitters in the antennal lobe were mapped using confocal microscopy, revealing their concentrations which may explain behavioral differences from other mosquitoes. Most mosquito species show some plasticity in host selection, which can lead to the transmission of animal diseases, like West Nile Virus, to humans. Mosquitoes are the world’s deadliest disease vector, killing over 700,000 people globally each year, so understanding how and why this adaptation occurs can help us understand the framework that underlies the spread of mosquito borne diseases and bring us one step closer to solving this global issue.

Skeletal reduction is a common feature among deep-sea fishes that have diversified from shallow-water relatives, such as snailfishes. These skeletal reductions may be an adaptation to environmental conditions of high pressures, low temperatures, declining luminosity and limited food availability. Snailfishes (family Liparidae) are found across a large bathymetric range (0 – >8,000 m), with intertidal ancestors giving rise to a large clade of deep-sea species. We used microcomputed tomography (micro-CT) to estimate average bone mineral density and examine jaw, pectoral girdle, and neurocranium morphology. Our results suggest at least three mechanisms of skeletal reduction: (1) reduction of bone size, (2) reduction of bone density, and (3) loss of skeletal elements. First, using phylogenetic generalized least squares (PGLS) analysis, we found that the change in cranial dimensions with depth was not uniform. While the size of the maxilla, dentary, and pectoral girdle decreased with greater depth, length of the upper premaxilla and the neurocranium did not vary with collection depth. Second, average density of the lower jaw decreased with increasing depth. Lastly, the ventral suction disc has been lost multiple times within the deep-sea lineage. While all three methods are seen in snailfishes, other groups may use some or all of these mechanisms to different extents. Some mechanisms of skeletal reduction may be more advantageous than others. The extent to which a structure is retained in deep-dwelling fishes may indicate its functional importance. Variable skeletal reduction in the family Liparidae provides insights into the physiological adaptations that allow fishes to survive in deep-water environments. We conclude that some skeletal elements are maintained at the expense of others as fishes balance the functional demands of life in the deep sea.

Asymmetric cell division (ACD), a process that generates daughter cells with different cell fates and sizes, is a fundamental mechanism for generating cellular diversity during development. We use Drosophila melanogaster neural stem cells, or neuroblasts, to study ACD. Neuroblasts provide an ideal model for ACD since they are intrinsically polarized and divide with physical as well as molecular asymmetry, resulting in a self-renewed stem cell and a smaller ganglion mother cell (GMC). Kinesins, plus-end-directed motor proteins, have previously been implicated in asymmetric cell division and spindle dynamics. However, the specific kinesins that influence ACD and the mechanism by which they do so remains unknown. Elucidating the function of kinesins in cell division will help establish a more holistic view of cell development. To learn the role that kinesins play in asymmetric cell division, we performed an RNAi knockdown-based live-cell imaging screen of most kinesins in Drosophila. We found that knocking down the Drosophila kinesin genes Klp3A, Klp10A, Klp59C, Klp67A, Klp68D, CG14535, cos, or ncd causes the mitotic spindle to bend during metaphase and anaphase. We hypothesize that this phenotype is due to the spindle being so large that it buckles under the pressure of the cell as it divides. We are currently investigating this hypothesis by imaging knockout mutants to confirm this phenotype and tagging each kinesin with GFP to study how these proteins are localized during typical ACD.

Insect pollination is crucial to agriculture and conservation, but little is known about the ecology and evolution of floral scent, which is one of the strategies that plants use to attract pollinators. Flowers that rely on insect pollinators have floral scent compositions that attract certain types of pollinators more than others. Oenothera pallida is a plant which is pollinated by both daytime and nighttime pollinators, so examining its floral volatiles gives us an idea of what attracts the different pollinators to this flower. My research examines how floral scent emissions from Oenothera palllida differ between the day and nighttime, and how these differences in floral scent emission affect the attractiveness of the flowers to different pollinators. I extracted the floral scent from Oenothera pallida that is grown in the lab. I used Porapak traps to sample volatiles from each plant for six-hour periods in the evening and in the morning, which allowed me to see the change in composition depending on the time of day. I analyzed the floral scent samples using gas chromatography - mass spectrometry (GCMS). Then I created artificial scent blends in mineral oil that reflected the scent compositions of daytime and nighttime floral scent emissions. I exposed the hawkmoths and honeybees to the different scent compositions in a wind tunnel and observed the different responses of the two species. Finally, I determined what proportion of the moths or bees were able to locate the scent source by counting the number of individuals that flew upwind and landed on the artificial flower. 

Differences in the morphology (size and shape) between sexes in mammals is common and serve to provide advantages in various contexts. Size differences can be allometric (Rensch’s rule), where females are typically larger in smaller species and vice versa. In bats, females are generally larger, although this does not follow an allometric pattern. Instead, it is suggested that selection for mobility and efficient parenting drive sexual dimorphism in bats. Ralls’ ‘Big Mother’ hypothesis suggests that larger size in female bats is due to a need for mobility during reproduction. Bat flight behavior is highly influenced by wing morphology. Therefore, in addition to size differences, females may have different wing shapes, which reduce the load of the fetus during pregnancy. Consistent with the big mother hypothesis, size typically varies more in the wings (e.g., forearm length) as opposed to other body size measurements (e.g., skull length). In this study, I compare cranial, body, and wing size differences between male and female little brown bats (Myotis lucifugus). I also analyze shape differences in the wings between the sexes, using a geometric morphometric approach. Using digital photographs, I placed 14 homologous anatomical landmarks on the wings and body of 83 bats (33 female, 50 male). I use a generalized procrustes analysis in order to obtain shape variables from the digitized landmark configurations. I used t-tests to compare cranial and body size measurements, and I use a procrustes anova to test for differences in the wing shape between males and females. I found significant female-biased differences in forearm (p < 0.01), wingspan (p < 0.01), and total length (p < 0.05) measurements. Wing shape measurements are still in progress. Our results may contribute to growing evidence that sexual dimorphisms in bats are related to selection for mobility during pregnancy and lactation.

Drepanosauromorpha is an extinct group of reptiles known from the Middle to Late Triassic (237–212 MA). The clade currently includes seven genera (Avicranium, Dolabrosaurus, Drepanosaurus, Hypuronector, Kyrgzsaurus, Megalancosaurus, and Vallesaurus) that are known from fossils collected in Europe (Italy, UK), North America (Arizona, New Mexico, New Jersey), and Asia (Kyrgyzstan). The first described drepanosauromorph, Drepanosaurus unguicaudatus, was based on a flattened holotype preserving most of a complete skeleton. Subsequently described drepanosauromorphs display the following diagnostic features: the length of the chevrons (ventral spines below the tail vertebrae) is substantially longer than corresponding tail neural spines, the cervical (neck) vertebrae are heterocoelous (saddle-shaped articular surface), the cervical ribs are absent as distinct ossifications, and the chevrons are fused to their respective centra. In recent years, both three-dimensionally preserved partial skeletons and isolated material of drepanosauromorphs have been found across both Europe and North America. These discoveries have helped shape our understanding of the biology and diversity of drepanosauromorphs. However, comparing isolated, three dimensionally preserved specimens to the more complete, yet two dimensionally preserved articulated specimens is difficult due to differences in preservation. Here, we describe a new drepanosauromorph species from the Chinle Formation in Petrified Forest National Park, Arizona based on the left second manual ungual (claw) . Some of the characteristics that distinguish this claw from those of most drepanosauromorphs is its size. It differs significantly from all known Drepanosaurus specimens (like the Italian holotype and the Hayden Quarry Drepanosaurus) because of the ventral placement of the cotyle (articulation surface), the height of the claw, the lack of compression along the pre-axial/post-axial plane, and a furrow along the midline. This new taxon not only highlights unsuspected morphological variation within Drepanosauromorpha, but also helps sheds light on the evolutionary history of smaller-bodied reptiles within Late Triassic ecosystems.

The interactions between pollinators and plants have a strong correlation to the fitness and reproductive success of both parties involved. These interactions are responsible for most of plant reproduction by seeds and they also drive evolutionary diversification of both plant and pollinator species. Wind turbulence plays an important role in navigation by smell, which is important for many pollinators while locating flowers. Climate change may alter wind patterns, which in turn may affect the ability of pollinators to locate flowers. The goal for this project was to determine the effect of wind on pollinator success. We determined the visitation rate of pollinators at Oenothera pallida flowers in the field by analyzing infrared camera videos recorded last summer at a field site in Grant County WA. Next we ran a multiple linear regression to determine the effects of wind speed, temperature, humidity, and ozone levels on floral visitation rates. Pollinators of Oenothera pallida include the hawkmoths Hyles lineata and Manduca sp., various bee species including Andrenids, Apids, Lassioglossum sp. and Megachilids, Bembix wasps, and various flies. Wind speed is the strongest variable that affects pollinator visitation at different times of day, which implies that changing wind patterns significantly impact plant-pollinator interactions.

Human pathogenic viruses are responsible for nearly all recent pandemic diseases. We set out to search for viral protein sequences that could be important for tissue tropism. To achieve this goal, human pathogenic viruses were classified according to the tissue they infect (pulmonary, gastrointestinal, etc.) — irrespective of whether they were enveloped or non-enveloped RNA or DNA viruses. Next, we developed a customized amino acid sequence alignment program to speed up protein-sequence comparisons and alignments in each viral category. We identified the conserved seven amino acid motif, VAIVLGG, in both Old World and New World alphaviruses. Our further analysis localized the VAIVLGG consensus sequence on the adherence spikes of the chikungunya virus (CHIKV), a well-known mosquito-borne arthrogenic member of the Old World alphaviruses which caused a recent chikungunya fever outbreak in Florida. Our further search revealed that this sequence is located within the viral region involved in its binding to the newly-discovered human CHIKV receptor. In light of the fact that several ongoing clinical trials are aimed at developing vaccines against CHIKV, it is tempting to entertain the idea that our identified VAIVLGG consensus sequence might potentially be used to serve as a single-antigen for producing a pan-vaccine effective not only against CHIKV but also the following alphaviruses: Onyong-nyong, Semiliki Forest, Ross River, Mayaro, VEEV, WEEV, EEEV, and Sindbis.

I present a baseline assessment of the plant family Melastomataceae along an elevational gradient of the Llanganates-Sangay ecological corridor in central Ecuador. Conservation efforts within this corridor aim to preserve the high levels of diversity and endemism present in the region. Melastomataceae, as the third most diverse plant family in Ecuador, contributes valuable biodiversity, biomass, and ecological services to the ecosystems of this corridor. On Cerro Mayordomo (max elevation: 3,383 m), 300 m transects were established at four different elevations, and six 5x5 m plots were assessed along each transect (600 m² assessed total). All melastome species encountered in plots were grouped and counted based on morphological characteristics. My findings reveal a positive correlation of melastome diversity and abundance with elevation up to 2,500 meters. At 3,000 meters, species diversity decreases sharply, but total abundance remains high. Jaccard, Sorenson, and Morisita-Horn similarity indices indicate dramatic changes in melastome community composition over even slight differences in elevation. Eighteen species of flowering melastomes belonging to four genera were found, revealing a subset of the family's astounding diversity in this region. The results of my study will be used to inform future conservation efforts and ecological studies in this incredibly unique and important Andean corridor.

Organisms in the ocean depend ultimately on phytoplankton as it is the base of the marine food web. Through the use of satellite imaging, indicators of photosynthesis such as chlorophyll-A are used as an index of primary production in the ocean over large areas and variable time scales. Phytoplankton is dependent on large-scale ocean processes such as water temperature and water column mixing. Such estimates might provide insights in food availability for larger predators that eat plankton eating fish such as the Magellanic penguin. Located on the southeast coast of Argentina, Punta Tombo is among the largest breeding colonies for Magellanic penguins. The Boersma Lab at the University of Washington has studied the colony since 1982 and have determined reproductive success for 35 years. Although many factors influence the overall success of the colony, starvation of chicks is responsible for 40% of chick deaths. Through the use of spatial analysis tools, we have looked at chlorophyll-A patterns and seasonal water temperature variation around Punta Tombo and compared these two variables with reproductive success of Magellanic penguins. We expect a strong positive relationship between the two datasets: water temperature and chlorophyll-A. Further we expect that when values are higher closer to the colony, reproductive success of birds is higher, and parents forage closer to the colony.

Insects use feedback from multiple sensory modalities to control their motor output. Hawkmoths are crepuscular insects that fly in low light conditions, hovering over flowers as they pollinate and feed from them. They use their long and flexible mouthpart, the proboscis, to explore flower surfaces and feed from a tiny nectary opening in these flowers. We asked how moths combine visual and mechanosensory feedback to find the nectary opening in flowers. To test the effect of light level on their efficiency in locating the nectary we combined 3D printing technology to generate artificial flowers, with micro-sensing technology that allowed us to detect the proboscis tip inside the nectary, and computer vision techniques to track the motion of hovering moths at two different light levels; 0.1 lux (moonlight) and 50 lux (dawn/dusk). Using a combination of low light videography and machine vision, we quantified how floral exploration changed between visits, and between the different light levels. We also measured the length of time moths took to find the flower nectary each visit. We found that moths took less time to find the nectary at lower (moonlight) levels compared to higher (dawn/dusk) levels. Hawkmoths are typically active in low light conditions, hence the higher light levels might be adversely affecting flight control. Moreover, preliminary reconstruction of their flight paths suggests that moths hovered over the flower in tighter trajectories under lower light conditions, as compared to the higher light conditions. These results suggest a decreased control over their flight motor output at higher light levels, resulting in reduced hover feeding. These behavioral differences have led us to a series of questions looking at the physiological effects of the different stimuli.

Drosophila alpha-tubulin acetylase (dTat) is an enzyme that covalently modifies microtubules by addition of acetyl groups to the microtubule lumen. Prior studies demonstrated dTat is essential for mechanosensation in Drosophila. Mutation of alpha-tubulin lysine 40, which is covalently modified by dTat, similarly compromises mechanosensation, but our preliminary results suggest that alpha-tubulin 40 mutation and dTat mutation differentially affect some forms of somatosensation. Consistent with this observation, recent studies suggest that dTat may additionally regulate microtubule stability independent of its enzymatic activity. Whether this non-enzymatic function of dTat influences neuronal function remains to be determined. In my studies, I aim to determine the relative contributions of enzymatic and non-enzymatic functions of dTat to somatosensory function in Drosophila larvae. To this end, I have assayed requirements for dTat function in a variety of larval mechanosensory and thermal responses, which are governed by defined classes of somatosensory neurons. For each of these behaviors, I used transgenes to resupply dTat function to dTat mutant flies, comparing the ability of wild type and enzyme-dead versions of dTat to support neuronal function. Results from these studies provide an entry point to understanding enzyme-independent function of dTat.

 Twelve replicate populations of the bacterium Escherichia coli have been evolving in Lenski's Long-Term Evolution Experiment (LTEE) for over 67,000 generations in a shared nutrient limited environment. The evolved bacteria grow 70% faster than their ancestor but experience a decrease in number produced during a growth cycle. This is consistent with a trade-off between growth rate and yield (here defined numerically). We explore if populations are constrained by their previous ecolution, and if populations with high growth rate can evolve to have a higher yield (and if so, does this happen at a cost to growth rate?). We do this by adding population structure to growing populations, where selection is relaxed on growth rate and strengthened on yield. Water-in-oil emulsions provide a structured environment where millions of nutrient-filled droplets are isolated by an oil phase. We manipulate population structure by inoculating droplets with either one bacterial cell (low starting density) or more than two bacterial cells (high starting density). We observe that selection acts on faster growing cells in our high density emulsion treatment and higher yield cells in our low density emulsion treatment. We also observe a change in cell size: cells in the high density emulsion treatment get bigger over time, and cells in the low density emulsion treatment get smaller. We explore if there is a relationship between cell size and growth rate/yield trade-off.

Giardia lamblia, a microscopic flagellated parasite that causes giardiasis, is a highly divergent eukaryote in which conventional Golgi, endosomes, lysosomes, and mitochondria are absent. Similar to other parasites of medical importance, Giardia lamblia has two life cycle stages - proliferative trophozoite form and water-resistant, nonmotile, infectious cyst form. During encystation when Giardia trophozoites transform into infectious cysts, they secrete cyst wall proteins (CWP1-3) that are trafficked and processed in Encystation Specific Vesicles (ESVs). These vesicles are thought to be stage-induced Golgi in Giardia. Previous work in the lab has shown that the signaling activities of G. lamblia’s single Rho family GTPase, GIRac play an important role in regulating this encystation process. The aim is to characterize proteins in Giardia lamblia that potentially interact with GIRac, currently focusing on homologs of known players in membrane trafficking by examining their order of arrival using morphology of the ESVs based on CWP1 staining. Since this is subjective, there is a need for stage-specific molecular markers. In other eukaryotes, Rab GTPases have been established as markers of membrane identity and directionality of trafficking. Only two out of nine Giardia’s Rab GTPases have been localized and reportedly found at ESVs and based on published images, they appear to be recruited at different stages of ESV maturation. By tagging the N-terminus of all 9 Giardia Rab GTPases with fluorescent tags, we can screen them for their localization to ESVs and perform multi-color imaging to determine the order of arrival of these markers. Ultimately, this finding of stage-specific molecular markers could be a powerful tool to further suggests its potential as a novel target for drug development to treat giardiasis.

Bignoniaceae, also known as the trumpet creeper family, consists of 800 species of trees, shrubs, herbs, and lianas. Bignoniaceae diversity is highest in the Neotropics, but have a worldwide distribution in both tropical and temperate zones. Molecular phylogenetic studies recognize 8 major clades in the family. The goal of this work is to construct an updated Bignoniaceae phylogeny by gathering all available DNA sequence data in the family from previous studies, GenBank, and unpublished sources. I organized, gathered and selected genetic data that I used to create locus alignments for a concatenated matrix. Phylogenetic reconstruction of the concatenated data was done using Maximum Likelihood and Bayesian methods. With these results, we aim to better understand family-wide diversification patterns in the family. Previously recognized clades are supported, additional resolution among them is obtained, and major biogeographic events are reconstructed.

Last year, our team conducted an exploratory study to characterize the prevalence and admittance factors of STEM degrees across the U.S. with Additional Requirements to Entry (ARE). By gathering data on universities with these programs and surveying their administrators, we gained a general understanding of the state of competitive majors across the nation. We found that GPA was the most frequent criteria of admittance for these programs, which were mostly in engineering and life sciences. Furthermore, we determined that the most common reason for the implementation of these programs was limitations on faculty, funding, and administrative support. These findings suggested that further study into these programs is warranted. Thus, our current aim is to characterize the impact of these programs on the student experience at the University of Washington, particularly those of students from minority and low income backgrounds. To this end, we conducted focus groups throughout winter and spring quarter of 2019 to evaluate student experiences with competitive majors and assess whether there are consistent themes across them. We will be supplementing these qualitative data with quantitative data from survey questions administered to a large number of UW undergraduates. Because GPA is often correlated with socioeconomic or minority status, we hypothesize that these programs may discourage students or disproportionally exclude minority groups from entering high-earning STEM fields. The qualitative and quantitative data of this project will further add to our understanding of the effects and scope of competitive majors.

Sexual dimorphism is a characteristic of many organisms that is genetically encoded and typically studied as a binary trait. Biomedical research routinely categorizes subjects into “male” and “female”, and the resulting data are used to establish sex-specific measures of good health and disease. However, this practice overlooks the existence of intersexual phenotypes and oversimplifies the overlapping variation between sex-specific groups. The phenotypic expression of sex is directed by a complex orchestration of many genes. As such, it is reasonable to consider that there are more than just two discrete expressions of sex, and furthermore that the dimorphism of so-called sex-specific traits resides along a continuum. Metabolomics studies the small molecules that make up all the molecular building blocks in the body, and offers a unique opportunity to quantify sex variation that is morphologically invisible. Doublesex (dsx) is a gene that plays a pivotal role in the sex development of Drosophila melanogaster, and its absence results in an intersexual morphological phenotype. This study models sex in Drosophila melanogaster as a continuous trait by comparing metabolomic profiles for wildtype females, males and dsx null mutants using statistical analysis of metabolome data. While many studies have been conducted to understand the role of dsx in sex determination, to our knowledge no one has attempted to use this novel approach to quantify sex variation as a complex trait. Here we measure over 1000 metabolites in fly samples and test a hypothesis that some metabolites exhibit continuity between male, intersex and female phenotypes. Future work could explore the degree to which these metabolic sexual continuities exist in natural fly populations, and provide a powerful model to study factors that are influenced by sex differences more comprehensively.

Numerous interventions and genetic modifications have been shown to extend lifespan across a diversity of species. However, these studies often assume that extended lifespan is synonymous with extended healthspan. Recent research in the nematode worm, Caenorhabditis elegans, has questioned this assumption, and suggests that increasing lifespan can prolong the frailty associated with old age. This is particularly important for humans, as increasing lifespan without a corresponding increase in healthspan could spell disaster. The majority of healthcare costs are associated with aging-related pathologies, and prolonging life without prolonging health could radically inflate these costs. To parse out the genetic relationship between healthspan and lifespan, we have turned to Drosophila melanogaster, a well characterized model organism for studies on the genetics of aging. We have collected lifespan data as well as multiple measures of healthspan across these genotypes, and found a strong positive correlation between lifespan and healthspan in these flies. This confirms the importance of lifespan as the primary parameter in aging studies, and suggests that genetic interventions increasing lifespan may generally be accompanied by an increase in healthspan.

Filoviruses are a family of viruses including the Ebola and Marburg viruses which pose serious threats to global health, as evidenced by the 2013-2016 West African Ebola outbreak. Lloviu virus (LLOV) is a recently discovered filovirus associated with large bat die-offs in Spain and Hungary. Its effects on humans are unknown; however, similarities to other deadly filoviruses suggest it may have similar infectivity. Live LLOV has not been isolated, hindering vaccine research and development. The goal of my project is to develop a model “pseudotype virus” of LLOV using non-pathogenic vesicular stomatitis virus (VSV) as a backbone expressing LLOV viral envelope glycoprotein. I modified and optimized existing methods used to produce VSV pseudotype viruses by transfecting cells with plasmids expressing the VSV genome, modified to produce LLOV viral envelope glycoprotein. This pseudotyped LLOV can now be used to test vaccines against LLOV and provide insights into this understudied virus.

Mutations in the ND2 gene (mitochondrially encoded NADH dehydrogenase 2) have been linked to a reduction in efficient energy production, shortened lifespan, progressive neurodegeneration, and mitochondrial diseases such as Leigh’s syndrome. The ND2 gene codes for the production of NADH, a crucial portion of the electron transport chain in cellular respiration. Previous studies have hypothesized that mutations within the ND2 gene are responsible for mitochondrial disease development. However, previous studies have not extensively investigated how genetic variation present in a population might affect the mutant ND2 phenotype. This study attempts to understand how nuclear genetic variation can ameliorate or exacerbate the effects of mutations in the mitochondrially encoded gene, ND2. To model genetic variation in a population, the project utilizes the Drosophila Genome Reference Panel (DGRP), a set of 200 fully sequenced, inbred lines with over 4 million single nucleotide polymorphisms (SNPs) throughout the genome. These SNPs are particularly useful for Genome Wide Association Studies (GWAS). To assess the effects other genes might have on the ND2 mutant phenotype, DGRP lines were crossed with a mutant ND2 line that expresses ‘bang sensitivity’, measured as recovery time following paralysis after being vigorously shaken in a test tube. Recorded progeny recovery times varied significantly among DGRP lines, suggesting that nuclear genetic variants influence the ND2 mutant phenotype. After conducting GWAS, a list of identified SNPs associated with varying recovery times was acquired. With further study, we hope to identify which specific genes interact with ND2, what function those genes have, and whether those genes might be part of a larger regulatory pathway involving the ND2 gene.

In Arabidopsis thaliana the plant signaling hormone auxin is a major regulator of plant growth and development including the formation of lateral roots. Auxin controls the development of lateral roots by regulating the activity of transcription factors, known as Auxin Response Factors (ARFs). Because ARF7 and ARF19 mutants shows reduced formation of lateral roots, they are identified as master regulators of lateral root development. Using these ARF mutants, my project aims to understand how these regulators control early stages of lateral root development and gain insight into the role of auxin signaling in developmental specification. To investigate this, reporter lines are crossed with plant mutant lines of ARF7, ARF19, and both ARF7/ARF19 exhibiting a range of lateral root phenotypes, enabling accurate identification of lateral root specification and initiation stages. In mutants, we use bend assays to induce the lateral root developmental program in a synchronous manner. Seedlings are grown vertically on agar plates for 4 days, then turned 90° eliciting a gravitropic bend response at the root tip and leads to an eventual emergence of a lateral root at that the bent region. In mutants, temporal dynamics of lateral root program is quantified using fluorescence microscopy of reporters in synchronously induced lateral roots. Based on collected data thus far, the arf7 mutants (compared to wild type) exhibit slower onset of the specification reporter, suggesting the mutation has a temporal delay on developmental processes. As this project progresses, we will focus on temporal differences in expression of reporters that identify early specification and initiation stages of lateral root development via use of bend assays along with microscopy. Insights gained from these experiments will help us focus on stages and events in lateral root development that are impaired in arf mutants and thereby indicate on how auxin controls the developmental processes.

All around the world, humans depend on cultivating plants for medicine, food, landscaping and building materials. Understanding how plants grow helps people make more informed decisions about what to grow and how best to grow it. The plant hormone auxin plays a key role in determining almost all aspects of plant growth and development. The Nemhauser Lab has previously determined that two versions of the receptors for auxin, TIR1 and AFB2, function at different speeds in the model plant Arabidopsis thaliana. Currently, we do not know how this speed disparity affects specific plant functions. My hypothesis is that there are measurable differences in organism functions caused by this difference in molecular speed. In the past, full knockout mutants for TIR1 and AFB2 did not exist, making it difficult to answer this question. To complete my research, I developed these mutant plant lines, determined functions that can be quantitatively measured, and collected and analyzed the data. Because the auxin-signaling network affects so many plant functions, any additional information we can gain about how this network functions in the model organism helps us move towards a more complete understanding of plant growth. This could positively improve the efficacy of agriculture and other plant-based industries, as well as moving us towards other new discoveries in the field of plant growth.

Physiological and behavioral rhythms are controlled in mammals by a central circadian clock located in suprachiasmatic nuclei of the hypothalamus (SCN). This master clock has outputs to other organs and tissues crucial to keeping the organism properly synchronized. The SCN clock is synchronized by environmental cues, most importantly is the light-dark cycle (LD). Fearful stimuli (i.e. presence of predators) can also present cyclic variations. The de la Iglesia lab has recently shown that timed fearful stimuli during the night can switch the locomotor activity rhythms of mice to the light phase, overriding their natural nocturnal behavior. Interestingly, while the expression of the so-called “clock genes” (which sustain the circadian rhythms at the molecular level) remains unchanged in the SCN, it displays a complete inversion in the amygdala, the brain region that encodes fear. Currently, we aim to determine the pattern of expression of clock-genes in peripheral organs of mice subjected to cycling fear stimuli. Using qPCR, we will assess RNA expression of the clock genes bmal1, per1, and per2 in the adrenal gland, kidney, and liver to determine whether entrainment of activity by cyclic fear also impacts peripheral clocks at the molecular level. We hypothesize that the pattern of expression the clock genes in the liver and kidneys will be modified in mice subjected to nocturnal fear, due to altered feeding and drinking patterns. However, the adrenal gland is difficult to make predictions about the pattern of expression of the clock genes given the fact that preliminary data from our lab showed that cortisol shows two peaks in mice displaying diurnal activity after nocturnal cyclic fear exposure compared to the single peak displayed by nocturnally active mice. Thus, it is unclear if we will observe an inversion peak, much like the amygdala, or a peak similar to the LD cycle.

Proper development of an organism relies on the tight regulation of gene expression in cells and errors can lead to diseases or improper growth. Corepressors interact with DNA-binding proteins and inhibit gene expression. In the model plant Arabidopsis thaliana, the corepressor TOPLESS (TPL) is a member of a deeply conserved Gro/Tup1/TLE family. I am studying which helices in TPL monomers are necessary and sufficient for homotetramerization. Additionally, I’m investigating what proteins TPL interacts with to control repression, especially mediator components and histone deacetylases (HDACs), which previous studies have identified as potential interactors. I am using a protein-protein interaction assay known as the cytoplasmic split-ubiquitin system (Cyto-SUS). In my assay, a bait (TPL) and prey proteins hypothesized to interact with TPL are attached to two halves of ubiquitin. If the bait and prey successfully interact, then ubiquitin is reformed and a ubiquitin-specific protease cleaves a transcription factor to induce expression of genes producing adenine and histidine. Successful interaction is measured qualitatively by observing growth of yeast on plates that lack adenine and histidine. Only certain helices of TPL are observed to interact with full length TPL. Specifically, truncations that are sufficient to drive repression in a synthetic yeast assay are insufficient to multimerize. This means that the multimer state is not required for repression. Secondly, we found that the N-terminus of TPL directly interacts with mediator through MED21, suggesting that TPL regulates recruitment of RNA Polymerase II. Other corepressors of the Gro/Tup1/TLE family, like Tup1 found in yeast, and the mammalian homolog Transducin-like enhancer of split (TLE) are known to homotetramerize and interact with similar regulatory elements like TPL, including: HDACS and mediator components. Understanding homotetramerization of TPL and its role in repressive mechanisms is pivotal for comprehending how corepression works across eukaryotes.

This project examines reproductive output across different wildtype genotypes in the fruit fly, Drosophila melanogaster, and how it correlates with lifespan, activity and age-specific metabolite levels. To answer this question, we used the Drosophila Genome Reference Panel (DGRP), a collection of ~190 fully sequenced Drosophila strains that have been inbred to near homozygosity. Fecundity was measured as the per capita number of adult offspring produced by female flies over 48 hours when they are 4, 8, and 12 days old, using 3-5 replicate vials for each Drosophila strain. We have shown that there is highly significant genetic variation for reproductive output. Reproductive output declines with age in most but not all genotypes. The correlation between reproductive output and lifespan was not statistically significant, suggesting that there is not a direct trade-off between survival and reproduction in this population. A genome wide association study (GWAS) identified statistically significant single nucleotide polymorphisms correlated with variation in reproductive output, although most of them were located in genes of unknown function.

Auxin is a plant hormone that promotes root branching which allows improved anchoring in the soil and nutrient acquisition. At the molecular level, auxin promotes the activity of auxin responsive transcription factors called ARFs. I hypothesize that AGL42, a MADS box transcription factor works with ARFs during lateral root formation. I used CRISPR to remove the entire AGL42 gene from the genome and characterize lateral root phenotypes in the mutant. I characterized that AGL42 is regulated by auxin signaling. This was done by spraying Arabidopsis seedlings with auxin and measure AGL42 expression levels by RT-qPCR. I predict that increasing the levels of auxin will positively impact AGL42 levels. Alternatively, AGL42 may not be an auxin-responsive gene but may itself interact with the ARFs to affect downstream auxin signaling. To test this hypothesis, I performed a co-immunoprecipitation (Co-IP) assay to determine whether the AGL42 and ARFs interact with each other. By better understanding the lateral root specification, specifically the role of AGL42, we can learn how to improve the architecture of different crop plants, increasing their ability to thrive even in harsh environments.

Alzheimer's Disease (AD) is the 6th leading cause of death in the United States. The rate of AD diagnoses has substantially increased in the last two decades. The direct causes behind the initiation of AD are still unknown; however, genetic heritability is known to be a significant risk factor. The goal of our research is to identify the genetic variants that directly influence resistance to the formation of amyloid plaques, which are believed to lead to the initiation of AD. To investigate this idea, we are performing a genome-wide association study (GWAS) using the model organism Drosophila melanogaster. Female flies expressing the human form of amyloid beta (Aβ) are crossed with male flies from each of the 200 lines that make up the Drosophila Genetic Reference Panel (DGRP), a collection of highly inbred lines. The complete genome sequence is known for each of these lines, enabling researchers to carry out GWAS to identify genes associated with variation in any trait of interest. In our case, the progeny of these crosses all express Aβ, but differ from each other with respect to their inherited DGRP genotype. These progeny undergo image analysis to measure the amount of degeneration caused by the aggregation of amyloid plaques in the eyes. Eye degeneration is scored on a five-point scale, from zero, indicating a wildtype phenotype, to four, indicating an extremely degenerated phenotype. Preliminary results show that there is variation in the level of resistance to the aggregation of amyloid plaques among the DGRP lines, which can be accounted for by the genetic variation among these lines. The ability to identify the single nucleotide polymorphisms and the resulting proteins that cause this resistance could be pivotal in identifying methods to prevent the initiation and progression of AD.

As climate change progresses, predictions of long lasting and severe droughts are projected to affect many communities. These communities are encouraged to utilize food resources that produce high yields for sustainability. Learning the key physiological differences between drought tolerant and sensitive plants may help communities like this adapt. A key difference between tolerant and sensitive plants is the efficiency of sugar mobilization. Drought sensitive plants tend to hinder mobilization of sugars while drought tolerant plants maintain this sugar flow. Here, our objective is to locate and understand where the mobilization of sugars is bottle-necked in the sensitive plants, and how that differs for tolerant plants. We hypothesize that more drought-tolerant plants display an increase in sugar mobilization resulting in higher fruit yield, faster rate of seed filling/fruit formation, and an overall greater rate of plant growth as compared to drought-sensitive plants. Our experimental protocol consists of eight different genetic lines ranging in sensitivity to drought. By reducing soil moisture content to 50%, we will induce drought and start measuring growth rates of the middle leaflet of the third trifoliate, pod elongation, seed length, and biomass of different plant tissues to determine the bottleneck of carbon and sugar movement in all lines. By contrasting this net movement of sugars across lines, we hope to observe differences indicating physiological mechanisms distinguishing tolerant from sensitive lines. Understanding these differences would help educate and improve communities who are affected by drought due to increasing climate change and overall help improve sustainability of crop production.

The Hille Zebrafish Lab studies embryonic development and is particularly interested in cell motility and adhesion. We use zebrafish as a model organism due to its small size and rapid development, as well as for having clear embryos that allow researchers to observe somites form. One way that cells can crawl is through extending filopodia with actin microfilaments. The cell is anchored to other cells with adherens junctions and can push off against these anchor points, then form new adherens junctions with cadherin and other proteins. This method of walking is used for cells to move between other cells and is highly visible in premesoderm cell walking and somite formation. Cells need to regulate both elongation and adhesion, and a protein called p120 catenin activates both cadherins (which are needed for adhesions junctions) and the proteins RAC1 and CDC42 that stimulate motility through actin microfilament elongation and filopodia formation. Our hypothesis is that p120 catenins with phosphorylated tyrosines bind to Cadherins. In our mutant p120 RNA sequences, we test the activity of phosphorylatable residues by mimicking post-translational modifications with residues that can not be phosphorylated. For example, aspartic acid can mimic phosphorylated serine. Our lab has made and injected mutated mRNA sequences for p120 catenin to test if the mutant protein is able to rescue morpholino knocked-down embryos. We predict that if the tested amino acid is necessary for binding to a motility protein, then we will see rescue in phosphorylation mimics and no rescue in dephosphorylation mimics. My project was to make a p120 mutant that is missing most of the predicted regulatory amino acids. The truncated p120 sequence is called 4A and is a splice variant of wild type p120 that starts at the fourth methionine, omitting the regulatory region containing many phosphorylatabe sites.

In this study we looked at the presence of streptomycin resistance genes, strA, strB, and aadA and the insertion sequence IS133 for the bacteria Escherichia coli obtained from the wetlands located within the University of Washington Bothell. The wetlands serve as a roost for more than 15000 crows all through the autumn and winter months. The hypothesis of this study was that the presence of antibiotic resistance may be able to spread through the vector of American crows. The genes tested in this study encode for factors that play a role in streptomycin resistance (Sugiyama, Masanori, and Osamu Nimi). The IS was tested because it would indicate presence of transposon TN5393 which in turn would suggest the presence of strAB genes on conjugative plasmids (Zhao, J., and H. Dang) and thus capable of horizontal gene transfer among the bacteria. The samples were collected from crow feces and water runoff within the wetlands. 23 water samples and 37 fecal samples, were testedby TaqMan™ quantitative PCR for the presence of the three streptomycin resistance genes, strA, strB, and aadA. Once the streptomycin genes were detected, the samples were tested to see whether the genes were located on a plasmid by testing for IS133 insertion and the TN5393 transposon. Our results show that 53% of the isolates tested were positive for strA, 57% were positive for strB, 5% were positive for aadA, 22% were positive for IS133, and 22% were positive for both strA and strB. Plasmids isolated from one water runoff sample and a fecal sample showed the presence of aadA and strB. The plasmids were successfully transformed into DH5 Alpha E. coli and were ampicillin resistant but not streptomycin resistant. These results indicate that there may have been other plasmids in the cell that rendered the samples resistant to ampicillin.

Mushroom bodies are paired structures in the brains of invertebrate phyla. They are characterized by densely packed neurons that are essential for facilitating learning and memory. Previous research using anatomical observations and immunohistology on mushroom body-like structures across arthropod species supported genealogical correspondence over convergent evolution of these learning and memory centers. The data collected so far, however, lacks representation from certain taxa, namely the crustaceans. To continue gathering evidence to further support or refute genealogical correspondence of mushroom bodies, we will examine neuroanatomical features as well as the presence of proteins required for learning and memory formation in a class of crustaceans called the malacostracans. Protein kinase A catalytic subunit alpha (PKA-Cα) is one such protein that is highly conserved in amino acid sequence and in learning and memory function across insects and mammals. Its conserved nature makes it a useful indicator for mushroom body homologs across phyla as its expression is known to be enhanced in mushroom bodies. We will be utilizing antibodies raised against PKA-Cα on brains of crustaceans closely related to insects in order to reveal structures that may genealogically correspond to mushroom bodies. Evidence suggesting that mushroom bodies are linked through homology would be supported if paired brain structures of crustaceans in multiple lineages are found to resemble mushroom bodies in morphology and protein expression patterns. By identifying mushroom body-like centers across invertebrates, we are able to make a comparison of the structures in context of the sensory environments of each animal in hopes of understanding the role of mushroom bodies in the evolution of learning and memory.

Indoleacetic acid(IAA) is a common and well understood auxin class phytohormone that promotes plant growth by increasing cell division and elongation. IAA has also been shown to increase infectious adhesion and filamentation in certain strains of Saccharomyces cerevisiae. Increased IAA production by the plant’s microbiome has been demonstrated to stimulate host and symbiont growth. The IAA production in multiple strains of S. cerevisiae from the USDA ARS library was quantified using the Salkowski colorimetric technique, then the highest IAA producing strains were treated onto corn to examine the effect on biomass growth. Preliminary results have shown greatly increased root mass and moderately increased shoot mass in treated corn. This symbiotic yeast treatment could have agricultural applications, increasing crop yields without increased application of fertilizer, pesticides, or other products that could have a negative ecologial impact or detrimental effects on the crop.

Armadillidium vulgare are terrestrial isopods characterized by their ability to conglobate (roll into a ball) as a mechanism of defense from predation. It is theorized that conglobation functions as both a defense mechanism against predation and a means to avoid desiccation in arid environments. This project tests conglobation as a mechanism of water conservation. Water-loss in A. vulgare, was investigated in the free and conglobated states. In experiment one, 40 specimens of A. vulgare were suspended in their conglobated state using dental rubber bands and kept at 30.5°C and 30% relative humidity for 22 minutes along with a control group of additional 40 specimens of A. vulgare in their free state. Water-loss rate decreased by 16.5% when specimens were in their conglobated form. In experiment two, we first varied the humidity and then temperature to test whether different conditions triggered voluntary conglobation. Four groups of 15 specimens of A. vulgare were kept at 25°C in environments of varying humidity: 18%, 30%, 46%, and 99% respectively for one hour. No voluntary conglobation was observed in response to humidity change. Finally, we observed that high temperature triggered conglobation beginning with 6% conglobating at 31.5°C and 100% at 50°C. Our findings suggest that while conglobation behavior may help to conserve water, A. vulgare conglobate primarily as a defense mechanism. Further research is needed to clarify the function and purpose of the conglobation response in A. vulgare.

p120 catenin is an adherens junction-associated protein responsible for stimulating both cell adhesion, through interactions with RhoA and E-cadherin, and cell motility through interactions with Vav-2 and Cdc-42/Rac-1. Recent research in vitro has identified selective phosphorylation as a regulation mechanism for which pathway p120 catenin undergoes, but the results have yet to be replicated in vivo. Here, I specifically focus on the effects of phosphorylation of the tyrosine at 228 (Y228) on dorsal axis extension in zebrafish embryos during embryogenesis. This was accomplished through co-injection of mutant mRNAs Y228E (glutamic acid) and Y228F (phenylalanine) alongside an anti-sense splice-site morpholino specific to p120 catenin δ1. When compared to uninjected embryos, embryos injected with Y228E and morpholino exhibited much poorer dorsal axis extension whereas embryos injected with Y228F and morpholino exhibited relatively normal dorsal axis extension. These findings suggest that phosphorylation of p120 catenin at Y228 promotes interaction with RhoA and E-cadherin, thus reducing interaction with Vav-2 and Cdc-42/Rac-1 and limiting cell motility, although the specific pathway is still unclear. I shall further validate these findings through co-precipitation of mutant p120 catenin and its binding partners by preforming immunoprecipitation (ReCLIP) of proteins obtained from developing injected zebrafish embryos. As loss of E-cadherin function is closely associated with cancer progression, the ability to facilitate E-cadherin function through phosphorylation of p120 catenin at Y228 suggests a novel method and area of study for combatting cancer.

Hydra vulgaris are some of the simplest animals with neurons and have only two thin, near transparent layers of tissue: myo-endodermal and myo-ectodermal layers. Each cell in the animal can be examined simultaneously due to their small size, simple body pattern, and stereotypical (regular and defined) behaviors. This makes Hydra great animals for examining simple signal transmission pathways from which the complex pathways in vertebrates derive. Cells in the ectoderm and endoderm use calcium signaling to coordinate contractions and cause the animal to move, but how this mechanism of cell-to-cell calcium signaling functions is not well understood. Invertebrate gap junctions, intercellular proteins that cells use to send signals to adjacent cells, are coded from the innexin gene family. It has been found that the genome of Hydra magnipapillata has fourteen predicted innexin genes. Recent data suggests some of these innexins are expressed in the ectoderm, specifically innexins 1,4,5, and 13. I hypothesize these proteins are necessary for the animal to perform coordinated contractions. To determine the role of these proteins, I used shRNA techniques to knockdown innexin expression. After examining wild type Hydra, I examined an existing line of transgenic Hydra which express GCaMP in ectodermal cells to identify when cells use calcium to signal other cells. In these animals, signals can be viewed as a wave of fluorescence passing across the ectoderm. I knocked down the genes by electroporating shRNA molecules into adult animals who express GCaMP, and will image these animals’ behavior. There should be quantifiable differences in the fluorescent waves, as I postulate that some cells will be excluded from these waves if an innexin is knocked down, and analyzing these differences should clarify the role of innexins in gap junction signaling.

Reactive oxygen species (ROS) are partially reduced oxygen molecules produced during cellular metabolism in all aerobic organisms including plants. ROS derivatives such as superoxide (O2–) and hydrogen peroxide (H2O2) cause several types of cell damage in plants. Chloroplasts and mitochondria are major sources of ROS because of photosynthesis and aerobic respiration in these organelles, respectively. Previously, our lab showed that light-grown maize plants have more damage in plastid DNA (ptDNA) and mitochondrial DNA (mtDNA) than dark-grown plants and that ptDNA and mtDNA levels decline during leaf development. Here, we hypothesize that increased damage to ptDNA and mtDNA in light-grown leaves is linked to increased ROS generation compared to dark-grown and germline stalk tissues. We used absorbance- and/or fluorescence-based assays to quantify levels of ROS in chloroplasts and mitochondria isolated from leaf and stalk tissues during seedling development. Our data suggest that light-grown leaf has more ROS than light-grown stalk, dark-grown leaf, and dark-grown stalk. Our findings indicate that highly damaged DNA is a consequence of ROS generation in light-grown leaves of maize. Overall, this research will help us further understand the oxidative damage caused by various reactive oxygen species during the development of maize plants. 

Skin plays an important function as a highly innervated sensory organ. This sensory function is critical to organism survival, but the skin, and its axons, are easily damaged and need to be repaired to maintain homeostasis. Zebrafish are an excellent model to study tissue repair because they regenerate tissue efficiently and share conserved skin architecture with other vertebrates. A cell type shown in previous lab experiments to contribute to skin repair is a macrophage like cell, the Langerhans Cell. I hypothesize that if Langerhans Cells are not present within zebrafish epidermis then tissue repair will be incomplete or delayed. I investigated these cells using two different methods. First, I analyzed mutations that cause a loss of function in genes required for Langerhans Cell development. Second, I used the transgenic ablation technique to inducibly kill Langerhans Cells in the skin by addition of the antibiotic metronidazole. I imaged fluorescent Langerhans Cells in the zebrafish epidermis in both of these genetic scenarios to quantify the reduction in Langerhans Cells. Following the completion of these experiments, we expect to see that a lack of Langerhans Cells will induce slower or halted recovery from damage. In the loss of function method, I expect that various mutants will not have as many Langerhans Cells and that following induced ablation, Langerhans Cells will die out when the drug is introduced and slowly recover following metronidazole removal. The key implication of this is finding more about our own biology that can lead to faster healing. In theory, if Langerhans Cells have a major effect on this process then knowing more about our own skin can help us translate this understanding to our own healing process.

Publication metrics have often played a major role in understanding the interaction between research, popular opinion, and public policy. The field of scientometrics has been especially successful in bridging this gap for hot-button environmental issues, such as global climate change. Here, we used publication metrics to look at another burgeoning environmental topic: marine microplastic pollution. Research into marine microplastics has risen explosively in recent years, and some governments have already introduced anti-plastics policies in response. Here, we looked into the influence of microplastics research in news outlets and public opinion. First, we searched ISI’s Web of Science for articles containing the search terms “MARINE” and “MICROPLASTIC,” and recorded the number of publications over time. Second, we used a web scraper to gather similar publication counts for popular news outlets. Finally, we gathered data on social media interest in microplastic pollution by looking at the frequency of Twitter posts containing relevant keywords over time. Differences in article and tweet lexicons were analyzed using WordSmith Tools. We hypothesized that increased published research on microplastics correlates with stronger media coverage and more social media presence. Overall, the project found a unique interplay between microplastics research and popular sources, and we discuss how this interaction might impact public policy changes.

Microplastics are fragments of plastic smaller than five millimeters in length, often created by the breakdown of larger plastic materials. The ubiquitous presence of this form of debris in marine environments has led to detrimental effects when ingested by marine organisms including false sense of fullness, impaired reproduction, and stunted growth. Microplastics are heterogeneously distributed in water, animals, and sediment, making it necessary to compare and contrast conditions when considering any biological effects. Due to the variability of microplastics across space and time, different locations may have varying types and sizes of microplastics. This study examines the relationship between anthropogenic activity and microplastics in areas ranging from low to high population density in the Salish Sea. In July and August of 2018, samples of mussels, water, and sediment were collected from ten sites around the Salish Sea. The samples were chemically digested with hydrogen peroxide over a five-micrometer filter. Debris collected by the filters was photographed through a microscope and subsequently characterized. The images were processed using ImageJ for length, width, shape (fiber, fragment, film, or sphere), and color. We hypothesized sites have different microplastic compositions and there is a correlation between anthropogenic activity and microplastic abundance. The results of this study could aid in efforts to locate point sources of specific types of microplastics in the Salish Sea and determine priority locations for marine debris management.