Tree lines play a vital role in plant community composition in montane ecosystems. Over the past several decades, increasing annual temperatures have led to shifts in tree lines in montane environments. However, little is known about how local topography may have an effect on tree line advance. My research incorporates historical and repeat, ground based and aerial photography to assess the change of alpine tree line in a range of topographical conditions in Mount Rainier National Park over the past century. My study quantifies changes in tree cover and tree-line elevation in ridge and cove environments of the park. To track treeline change, historical and recent photographs were aligned, and areas of the photograph were broken up into polygons based on their small-scale topography. Random points were overlaid in these polygons to assess the rate of change of tree line shift. By looking at the change in tree cover in each random point relative to the polygon type, we are able to determine the amount of tree thickening that has occurred. We predicted that tree lines on sun exposed ridges will shift more quickly than those in cove environments. Snow is prevalent for longer periods of time in concave valleys limiting the amount by which the trees can shift up. Our results thus far indicate that small-scale ridge regions have the highest rate of change for tree line shift followed by cove. Subalpine meadows often occur in cove topography. Tree thickening in these regions over time may impact the wildflower populations and decrease species richness in subalpine meadows. In all, our research adds to the growing body of evidence that tree lines are moving up in elevation as well as provides the National Park Service with information about tree line influences on the plant communities of the park.

The plant hormone auxin plays a role in nearly every aspect of plant growth and development. Auxin facilitates interactions between two protein families: the transcriptional repressor Aux/IAA family and the auxin receptor TIR1/AFB family. TIR1/AFB proteins act as the substrate recognition subunit of SCF ubiquitin ligase complexes. SCF^TIR1/AFB-auxin-Aux/IAA interactions lead to ubiquitination and degradation of Aux/IAA proteins, allowing transcription of auxin-responsive genes. Each of these protein families is comprised of many functionally distinct members, allowing auxin to drive numerous developmental responses in plants. This complex network can be decomposed and signaling dynamics of individual pairs of TIR1/AFB and fluorescently-labelled Aux/IAA proteins can be measured in a yeast synthetic system using time-lapse flow cytometry. This dynamic analysis can give insight into the behavior of developmental networks in planta. However, of the six TIR1/AFB genes in the model plant Arabidopsis thaliana, only TIR1 and AFB2 induce degradation of Aux/IAAs in yeast. We aim to engineer a variant of AFB5 that is functional in this synthetic system, as AFB5 is known to be the target of many agriculturally important herbicides, but little is known about its role in development. We hypothesize that AFB5 is non-functional in yeast because it cannot form an SCF complex with the native yeast proteins. This is potentially caused by the extended N-terminus of AFB5 or the sequence divergence within AFB5’s SCF binding domain. To test these hypotheses, several N-terminal truncations of AFB5 and chimeric AFB5 proteins with the SCF binding domain replaced by that of AFB2 or TIR1 will be individually tested for their ability to induce degradation of Aux/IAAs in yeast. Functional variants will allow identification of key AFB5-regulated Aux/IAAs and associated developmental networks. Additionally, this work will guide engineering and allow functional characterization of the remaining Arabidopsis AFB genes and AFB genes from other plant species.

Hox complex genes constitute an essential and ubiquitous component in the construction of the animal body. Despite their wide range of body plans, every member of the bilaterian clade utilizes these key genes to pattern the anteroposterior (AP) axis, with one potential exception - radial echinoderms. In addition to the possession of an adult radial body plan, Echinodermata are also mostly characterized by indirect development, beginning their lives as bilateral larvae, which undergo radical metamorphosis into a radial adult. The echinoderms, outside the sea urchin, Strongylocentrotus purpuratus, remain poorly studied, and it is unknown how classically bilateral planning mechanisms like hox are involved in patterning these very different life stages. To help begin to resolve this, we present in situ hybridization data of four hox genes present in the indirect developing bat star, Patiria miniata in its larval stages. Hox expression was observed in the posterior during the development of larval forms, similar to the expression patterns seen in other bilaterian animals. These results suggest that, despite a greatly divergent radial body plan of the adult, echinoderms use many of the same developmental mechanisms found in bilateral organisms to pattern their larval stages prior to metamorphosis.

In cells, phosphorylation of p120 catenin causes it to dissociate from cadherin transmembrane proteins, which leads to the activation of downstream pathways and cell motility. We have mutated amino acids in p120 catenin in order to locate the functions of specific sites of phosphorylation in zebrafish embryos. The phosphorylated tyrosine amino acid, Y335, in p120 catenin is a target of the phosphatase "PTP-PEST” and controls epithelial cell motility and Rho GTPase activity in colon carcinoma cells. We designed a knock-out of normal activity by mutating the tyrosine to a phenylalanine, which cannot to be phosphorylated. We also mutated Y335 in p120 catenin to a glutamic acid (E), which mimics the negatively charged phosphate. These mutants were transformed into bacterial cells and the isolated DNAs were transcribed into mRNA. We have also injected zebrafish eggs with the mRNAs to analyze the effect of these mutants on development. We have also mutated several other serine and threonine phosphorylation sites on p120 catenin including, S252, T310, and S312 to determine if the mutation to an alanine or to a glutamine will result in altered downstream activity. We have injected mRNAs with the S252A and S252E mutants into zebrafish eggs and determined that the S252E mutation rescues a knockdown of the endogenous p120 catenin, while the S252A mutation does not. The results suggest that phosphorylation of S252E is required for the migration of presomitic cells to the dorsal axis. In fibroblast cells, phosphorylation of p120 at T310 promotes adhesion junction disassociation, allowing cells to mobilize in a “treadmill” fashion. We used p120 catenin mRNAs with the mutations T310A and T310E to measure their impact on cell motility in zebrafish. These individual mutations may give insight on the downstream effects p120 catenin in cell motility, including morphological bone abnormalities and metastasizing cancer cells.

This study explores the cognitive effects Bisphenol-A (BPA) has on the mature Helisoma trivolvis, a Ramshorn pond snail common in North America. BPA is a synthetic hormone used in plastics, making it ubiquitous around the world. BPA is easily leached into water and accumulates in many aquatic habitats, making this pond snail a prime candidate for research. BPA has been shown to interfere with the natural estrogen activity in the brain of pond snail embryos leading to developmental complications and premature death. This study focuses on the cognitive effects that BPA has on mature Ramshorn snails. Specifically the snail’s ability to form short-term memories in response to a negative stimulus. An operant conditioning procedure was used to assess the memory capacity of the mature snails in a range of BPA-contaminated conditions (10-800 µg/L). We raise two consecutive generations of snails both separated into five populations. Each generation had a control group containing non BPA treated water and four other groups with BPA concentrations of 10, 200, 600 and 800 µg/L solutions. Memory deficits were correlated with BPA concentrations. The results from this study add to the growing understanding of both the potential cognitive impacts of BPA as well as potential ecological consequences of BPA contamination.

Masting refers to annually variable seed production; whereby plant species release large quantities of seeds one year, followed by one or more years of significantly lower seed production. Seed masting behavior is thought to be evolutionarily favorable, a technique for survival. Two main theories exist to explain mast seeding, predator satiation and increased pollination. The purpose of this research study was to determine A) if a group of six conifer species within Mt. Rainier National Park exhibit mast seeding behavior (i.e. synchronized seed production over large areas, annual variation in seed production exceeds annual climate variation); B) Whether seed viability is greater in 'boom' years than 'bust' years (which would support wind pollination efficiency as an evolutionary driver of masting); and C) whether these patterns vary by species and/or elevation. We examined six species of conifers: Abies amabilis, Callitropsis nootkatensis, pseudotsuga menziesii, Thuja plicata, Tsuga heterophylla, and Tsuga mertensiana. Data was collected from 108 seed traps located in 18 stands at multiple elevation ranges within Mt. Rainier National Park. Seeds were sorted based on tree species, and classified as filled (viable) vs. unfilled (not viable). We then calculated mean total seed production for each stand and used correlations to assess how correlated annual seed production is across 18 stands. Next, we compared annual variation in climate within each stand, to assess whether species showed higher variation in seed production in comparison to climatic variation. Finally, we compared results for our six focal species to assess species specific similarities and differences. Understanding the mechanisms behind masting is important, as masting can control tree population demography, and influences ecosystem dynamics. Moreover, our study may provide greater understanding of the implications of climate change on masting dynamics for forests at Mt. Rainier National Park.

Argonaute (AGO) proteins are known to function in many small RNA pathways. AGO4 (Argonaute 4), a specific Argonaute protein, is mostly used for transporting small interfering RNAs (siRNAs) in the RNA-directed DNA Methylation (RdDM) pathway in Arabidopsis thaliana. siRNAs are primarily used for RNA regulation, such degradation of mRNAs in a cell. After directing the siRNA to the appropriate DNA location, AGO4 proceeds with recruitment of Pol V and DRM2 for methylation of the DNA, resulting in silencing genes. ago4 mutants are generally more vulnerable to harsh stresses, but recent phenotypic analysis suggests they demonstrate a better survivability under cold stress. Currently, we are investigating whether COR genes are present at higher baseline levels than the non-mutants and if they play a major role in this phenotype difference. Using RNA extraction and PCR with COR78 genes, we will measure the present baseline COR78 in each plant and draw a comparison. We expect that the mutants have a higher baseline of COR78, thus allowing them to have a better survivability in colder temperatures. Although additional investigation is required, COR gene interactions have a vast network that triggers later responses that might affect cold temperature resistance.

With concern about climate change increasing, assessing how plant reproductive success is impacted by increases in temperature is crucial in order to fully understand how climate change influences ecosystem structure and dynamics. This study measures how population variation and the climate of different elevations affect the capsule size and seed mass of the high-elevation plant mountain monkeyflower, Mimulus tilingii, at Mt. Rainier National Park. If climate is the primary limiting factor determining the range of M. tilingii, plants within the species’ climate range will produce the most abundant capsules and seeds whereas plants grown outside the species’ distributional range will produce smaller amounts. Sample seedlings were planted at two elevation sites: 1)  M. tilingii’s range center and 2) below M. tilingii’s range to mimic the increase in temperature due to climate change. Populations were categorized as either within-population (for crosses within the same elevation site) or between-population (for crosses between the two elevation sites) with equal amounts at both sites. This study quantifies M. tilingii’s reproductive success both in the context of the site as well as the population type, allowing for comparisons on these two levels. Results show that parent plants from the lower site produced more flowers and grew faster, indicating that plants in the lower elevation site might be more successful. These unexpected results suggest that M. tilingii may be better adapted to a warmer environment and that climate change might even be beneficial for this reason. Determining the exact impact of temperature on reproductive success is crucial not only for measuring the species’ fitness but also for understanding how these new adaptations will play an even bigger role in competition for resources among different plant species and how those new interactions will alter the ecosystem as a whole as the climate warms.

CYCLOIDEA (CYC) is a member of the TCP family of transcription factors, whose name stands for TEOSINTE BRANCHED 1, CYCLOIDEA, and PROLIFERATING CELL FACTORS.  The members of this transcription factor family are involved in regulating plant growth and cell proliferation by binding to DNA. Previous studies show that CYC has duplicated at least twice in the core eudicot angiosperms and that the CYC2 paralog is involved in controlling flower symmetry. The goal of our research was to characterize duplications of CYC in Rhododendron, with the long-term goal of seeing how these duplications affect flower symmetry. To accomplish this task, we used the R. williamsianum genome sequence to design primers specific to each paralog in order to PCR-amplify the CYC genes from four Rhododendron species, representing two subgenera (Hymenanthes, Rhododendron). Amplified products were cloned and sequenced to recover all alleles. We used our Rhododendron sequences and sequences from the conserved TCP and R domains of other species as out-groups in a Bayesian analysis to reconstruct the gene tree. From this tree, we have identified 2 main duplications in Rhododendron CYC genes as seen in other core eudicots. We also found that the CYC2 paralog has undergone at least 2 gene duplications and that the CYC1 paralog underwent one. Future research will focus on finding when CYC2 duplications occurred in rhododendrons and determining if, where, and when these CYC2 duplicates are expressed in Rhododendron flowers.

Chiroptera (bats) forms the second most diverse branch of mammals, with over 1,300 species documented. Bats play important roles within the environment because they feed on a wide range of prey items, ranging from fruit, nectar, to insects and blood. One of the main drivers of species diversification in bats is the structural specialization of the cranium and jaw muscles, which allow bats to produce adequate bite forces to exploit and process different types of food. This study investigated differences in bite force and prey hardness among insectivorous free-tailed bats (Family Molossidae), and the factors explaining the breakdown and processing of their meals through physical digestion. The bite forces of seven Costa Rican molossid species were measured and compared with the degree to which insect exoskeleton was broken down in their feces. The size of the exoskeleton particles in the fecal samples gave clues as to how much bats chewed and broke down their meal, whereas the thickness of these particles was a proxy for insect hardness. We anticipate to find a clear correlation between exoskeleton particle thickness and size across species, which would support the prediction that the size and morphology of the skull and teeth have an effect on the food these bats can consume. A relationship between the thickness of the insect exoskeleton particles and bite force would indicate that each bath species is specialized to feed on certain types of insects with varying level of exoskeleton hardness. Our results will provide clues to understanding feeding behavior of free-tailed bats and the role of morphology on species ecology.

Improving the efficiency of photosynthesis has the potential to help attain a net reduction of atmospheric carbon dioxide (CO₂). Cyanobacteria are an enticing target phylum as they contribute an estimated twenty five percent of global photosynthesis. Under ideal conditions, cyanobacteria grow and reproduce rapidly yielding numerous generations over a relatively short time span. Most research on cyanobacteria carbon fixation has been conducted under increased concentrations of CO₂. In contrast, this research investigated: 1) whether cyanobacteria subjected to CO₂-limited conditions will produce successive populations that have improved carbon fixation efficiency, 2) the viability of those adapted populations in present day atmospheric conditions, and 3) whether the survivors fix carbon at an increased rate compared to control cyanobacteria. To answer these questions, control cyanobacteria were maintained in ambient air conditions while an experimental population of cyanobacteria was developed under a range of CO₂-limited conditions. Half of the adapted populations were then returned to ambient air conditions. The rate of carbon fixation under both CO₂-limited and ambient air conditions was approximated by measuring biomass. This research could provide a laboratory-scale proof of concept for net reduction of atmospheric CO₂ by low energy biological means. This method could also eliminate the need for direct gene manipulation by capitalizing on an evolutionary process. Future experiments could replicate this study with different species of cyanobacteria to develop regionally compatible cyanobacteria with more efficient carbon fixation resulting in a net reduction of atmospheric CO₂ in an environmentally sustainable manner.

The rise of multidrug resistant bacteria necessitates finding alternative therapies against bacterial pathogens. Virulence in many pathogenic bacteria are predicated on their ability to communicate and act in unison. In a phenomenon known as quorum sensing (QS), a threshold mass of bacterial cells produces an amplified chemical signal that triggers the collective expression of a new phenotype, such as enhanced virulence. Therefore, inhibiting QS, without preventing cellular growth, may be a recourse against drug resistant bacteria. Marine invertebrates found in warmer waters, such as the Australian reef and Indian Ocean, have shown quorum sensing inhibitory (QSI) potential. However, most marine invertebrates in the Pacific Northwest’s Puget Sound have not previously been screened for QSI compounds. This research presents the findings for QSI sources among Puget Sound’s marine sponges and tunicates, using a bacterial reporter strain to screen for QSI activity. We used the reporter strain Chromobacterium violaceum (ATCC 12472), which uses the QS signal n-Acyl-homoserine lactone (AHL) to produce its purple pigment. QSI activity was screened for by overlaying the reporter strain with a sponge or tunicate sample. Subsequent absence of pigment in the indicator strain suggested the presence of a QSI compound. Promising compounds were then extracted and identified using analytical techniques. These results help expand the catalogue of known QSI molecules from marine sources, advancing potential therapies against existing and future antibiotic resistant pathogens.

We know that climate sensitivity can vary within species, but the factors that influence which climatic variables influence population dynamics remain unclear. In this study, I am assessing whether macroclimate influences the climate sensitivity of three prominent conifer species: Pacific silver fir (Abies amabilis), mountain hemlock (Tsuga mertensiana), and Alaska yellow cedar (Callitropsis nootkatensis) on Mt. Rainier. I am analyzing tree core data from three high elevation sites. Each site is located in a distinctly different climatic area on the mountain. I am comparing standardized tree growth to climate variables (mean growing-season temperature, total growing-season precipitation, snow duration, etc.) using linear mixed effect models. This will determine how influential climate variables differ by location and by species. Gaining more insight into which climate variables have the greatest influence on growth in different areas will allow us to better predict how specific plant populations will react to ongoing climate change. Moreover, studying tree communities at high elevations is particularly important, since behavior at treeline will determine whether a species’ range expands, contracts or shifts. Range expansion of one species could lead to the crowding or elimination of another. For example, conifer range expansion on Mt. Rainier could negatively affect the alpine wildflower meadows, a major attraction for tourists. Widespread range contractions could also decrease forest density and potentially reduce the ability of those forests to sequester carbon from the atmosphere. Thus, with better predictions of tree shifts, we can make more informed management decisions for ecotourism and conservation.

Little is known about mammalian diversity in North America during the mid-Cretaceous (Albian-Cenomanian, 120-90 mya). This was an important interval in mammalian evolutionary history, during which metatherian (including marsupials) and eutherian (including placentals) mammals first appeared in North America and multituberculates (a now-extinct group of mammals) began to radiate. Unfortunately, our understanding of this period is poor because mid-Cretaceous mammal-bearing fossil localities are sparse in North America. Accordingly, each newly discovered specimen from this interval could provide important insights into therian and multituberculate diversity and their early stages of evolution. Recent paleontological fieldwork in the mid-Cretaceous (ca. 100 mya) Wayan Formation of eastern Idaho has led to the recovery of 30 mammalian specimens, including 15 metatherians and 13 multituberculates. These specimens, all isolated teeth, were discovered in situ and in the lab. Previous work by myself and other members of the Wilson Lab has focused on describing three metatherian species from this sample, as well as documenting a new occurrence of the genus Targheedelphys. Here, I focus on describing the multituberculates and analyzing their taxonomic diversity, as well as comparing them to those from a larger, contemporaneous sample from the Mussentuchit member of the Cedar Mountain formation of central Utah. Some of the Wayan specimens are attributed to new species and others are referred to previously known species. Current results indicate that multituberculate and metatherian diversity is approximately equal, with three species observed in each group, and each occupying close to fifty percent of the local fauna. The similarities and differences in taxonomic composition and diversity between these two localities will give us important insight about mid-Cretaceous mammalian evolution in North America. Additionally, this information fills a gap in the timeline of mammalian evolution that will further our understanding of mammal evolution through the K-Pg and onward into the Cenozoic.

The position of leaves around a stem (phyllotaxy) impacts a plant’s yield, pollination conditions, and light harvesting abilities. Auxin plays a critical role in establishing phyllotaxy. Expressing sequence variants of the auxin-regulated protein IAA28 in the plant Arabidopsis thaliana led to changes in phyllotaxy, specifically in the angles between flowers along the inflorescence bolt. Normally, the IAA28 protein binds and represses AUXIN RESPONSE FACTOR (ARF) transcription factors. When auxin is present, the IAA28 protein is degraded, initiating organogenesis. I am currently using three strategies to characterize an IAA28 knockout mutant (iaa28-ko) to better understand IAA28’s role in phyllotaxy. Loss of IAA28 is reported to cause a number of phenotypes by Wang and Guo, but phyllotactic patterning has not been characterized. My first goal is to quantify phyllotaxy by using a measuring device made in the Nemhauser Lab to measure the divergence angle between siliques. I hypothesize that the divergence angles measured in iaa28-ko plants will be smaller than the wild type. My second goal is to determine the change in auxin patterning in iaa28-ko mutants by using plants expressing an auxin reporter called DR5::Venus. Because the iaa28-ko mutant is reported to have more lateral roots, and lateral root initiation requires auxin, I hypothesize a higher expression of DR5::Venus in the iaa28-ko root and inflorescence meristem than in the control. Finally, I will test the functional conservation of BIF4, the putative maize ortholog of IAA28. To determine if BIF4 is functionally similar to IAA28, I will use Agrobacterium-mediated transformation to express BIF4 in an iaa28-ko plant. I hypothesize that the BIF4 protein will fill in the role of IAA28 in the auxin pathway, rescuing the mutant. By understanding the underlying mechanisms that control the phyllotaxy of Arabidopsis, we can learn how to apply similar engineering strategies in other plants.

Changes in phenology, the timing of biological events, are a commonly observed response to climate change, generally with earlier onset of life-history events in the spring. However, high-elevation grasshoppers deviate from this pattern displaying delayed maturation over the last 50 years. To better understand this apparent paradox, we experimentally explored the interactive effects of temperature and light regimes on maturation rates of Melanoplus boulderensis, a montane grasshopper inhabiting a broad elevational cline. We generally expected warmer temperatures to speed development, but this effect might be mediated by day length, which is an important phenological cue for many species. As predicted, grasshopper maturation took longer at lower temperatures. Day length affected maturation rate at low temperatures only, with short day lengths delaying maturation. Elevation of origin did not affect maturation rate. These results suggest that if climate change allows grasshopper eggs to hatch earlier in the spring when day length is short, maturation would require longer at cool, high-elevation locations as observed. Our results highlight the importance of considering all factors affected by climate change when attempting to predict the consequences of such phenomenon on organisms.

Gastrulation is an early phase in the embryonic development of vertebrates during which the three germ layers differentiate. The movement of the cells during this phase, is mediated by actin structures stimulated by integrins, extracellular matrix, and ligands. Migration of the cell is activated by Rho GTPases and focal interactions with cadherin-p120 catenin interaction stabilizing cell-to-cell adhesion. To be more specific, the protein, p120 catenin, is required for the extension of the dorsal axis and normal migration of the presomitic mesoderm. This lab studies the molecules that define the pathways of cell migration and tissue migration in zebrafish embryos. Specifically, we are studying how various mutations affecting the phosphorylation state of p120 catenin family genes were produced by undergraduate students and their respective effects on the dorsal axis extension were visually observed. In this experiment, zebrafish embryos were injected with mutated mRNA and analyzed using our in situ hybridization of two probes. Somites were stained using the myoD probe while the presomitic mesoderm was stained using the papC probe. Staining the mutated mRNA, allowed the team to witness phenotypic abnormalities of the dorsal axis much more clearly. Quantifications of the stained somites and presomitic mesoderm will allow a statistical analysis on various p120 catenin mutants. Overall, this experiment provides a deeper understanding of cell migration during developmental processes.

Cell adhesion and motility are important cell processes that are necessary for embryo morphogenesis. Prevous studies have identified p120-catenin as a key player in coordinating cell movements by either stabilizing E-cadherin complexes to strengthen adhesion or activating cytoplasmic CDC42 and Rac1 GTPases to initiate motility. Most of these studies were done in-vitro using cells grown in a 2-dimensional plane. Comparatively, few studies have attempted to describe p120-catenin's function in a 3-D space. In an effort to investigate p120-catenin's function in embryos, we are co-immunoprecipitating p120-catenin from developing zebrafish embryos. We are specifically investigating how the tyrosine 228 (Y228) residue of p120-catenin mediates binding to E-cadherin. The hypothesis is that phosphorylation of Y228 causes p120-catenin to bind to E-cadherin. To test this, we are injecting zebrafish embryos with p120-catenin containing either an Y228F of Y228E mutation. If our hypothesis is correct, the Y228F mutation would prevent phosphorylation of the 228 residue and decrease affinity between E-cadherin. The Y228E mutation mimics the negative charge of phosphorylation and would instead cause p120-catenin to bind to E-cadherin. 

Antibiotics are present in nearly every facet of our lives including personal hygiene, medicine, food processing, and the treatment of infectious diseases. Because of this widespread exposure, antibiotic resistance occurs in dangerous pathogens around the world. Novel antibiotics are needed to combat these resistant organisms and reduce both the loss of lives and treatment costs. Most antibiotics originated in microorganisms cultured from soil, but very few novel compounds have been discovered in this environment over the last several decades. It is imperative that other environments are screened for antibiotic producing microbes. We sampled the Puget Sound, isolating and culturing bacteria from the surface. Isolated cultures were tested against reference strains of common pathogens for antibiotic potential by measuring the zones of inhibition they produced via agar diffusion. Phylogenetic analysis with 16s ribosomal RNA was used for identification of cultures with inhibitory activity. This type of analysis, especially if scaled-up, has potential to identify novel therapeutic compounds that may elude common resistance mechanisms.

As concern over antibiotic resistance continues to grow, there is a critical need to discover and develop new methods of controlling and preventing bacterial infections. Essential oils derived from the peels of oranges are known to possess antimicrobial properties. Previous research has established that limonene, the principle compound present in orange oil extract, is a particularly effective antimicrobial agent that both destroys bacteria and inhibits bacterial growth. To determine whether different varieties of oranges have varying antimicrobial potency, the efficacies of oil distilled from blood, navel, and valencia oranges were compared. Oils extracted through steam distillation were diluted with methanol to concentrations ranging from 1:20 to 1:1. Staphylococcus aureus, Pseudomonas aeruginosa and Escherichia coli bacteria were exposed to the oils using the disc diffusion method on TSA plates. The minimum inhibitory concentration (MIC) for each oil was determined using the agar diffusion method. Gas Chromatography Mass Spectrometry (GC-MS) was used to compare the relative concentrations of limonene present in each essential oil. A better understanding of the potency of orange oil as an antimicrobial agent could lead to development of novel drugs and products to be used to combat infection and prevent the spread of bacterial pathogens.

DNA origami is the fabrication of biochemical structures using DNA as the building material. Using base pair design principles, DNA can be synthesized to self-assemble into dynamic objects such as a piston. The resulting creations have potential applications in nanotechnology including drug delivery, enzyme immobilization, photolithography, environmental restoration, and biocompatible devices. The goal of this project was to design a nanoscale mechanical spring and determine the parameters for spring constant and size. First, a spring comprised of multiple columns of double-stranded DNA was designed and fabricated. Size measurements were taken and morphology was verified using a transmission electron microscope. To measure the force constant of this structure, the 5’ end of the first column was functionalized with a thiol group which was then bonded to a gold cantilever tip on an atomic force microscope (AFM). This construct was brought very close to a magnesium substrate and allowed to bond. Force measurements for the spring were taken via AFM by slowly retracting the cantilever from the substrate. The spring force constant was calculated from this data using Hooke’s law in order to predict the amount of work that the DNA nanospring can perform when included in a complex nanostructure. The nanostructures created in this project can be used in conjunction with other DNA origami designs in order to create increasingly complex machines on the nanoscale.

Intraspecific studies of morphology and performance are essential for understanding the factors that enable resource partitioning within ecological communities, yet these have received little attention in mammal ecomorphology. Sea otters (Enhydra lutris) is one of the few marine mammal species in which individual-level dietary specialization has been quantified and linked to competition and prey abundance, making them an ideal system to investigate the morphological basis of food resource partitioning. Here, we assess whether differences in cranial morphology and bite force predict dietary variation among sea otter populations. We use geometric morphometric analyses and two-dimensional bite force models to (1) estimate differences in cranial shape and bite force among the three sea otter subspecies groups, E. l. kenyoni, E. l. lutris and E. l. nereis, (2) evaluate the extent of sexual dimorphism in cranial morphology and bite force within subspecies, and (3) relate the variation in cranial morphology and bite force to available dietary information. Although some sexual dimorphism in cranial features exists, preliminary results do not show significant differences in bite force between subspecies or between male and female sea otters. These results suggest that resource-use variation may be linked to individual foraging behavior and not to differences in morphology in sea otters. However, unique cranial features leading to high bite forces may enable this species to have higher diet plasticity; higher bite force in sea otters allows for the consumption of a variety of hard-bodied prey items and allows for either generalized or specialized diets, depending on prey availability and competition.

Organic acids are crucial factors in creating the aromas and flavors in wine, each adding their own qualities and characteristics. Winemakers regularly use various forms of technology to quantitatively determine the contents of wine. Analytical tools such as enzymatic spectrophotometry, paper chromatography, and high-performance liquid chromatography offer methods to quantify chemical components including acetic, malic, lactic, tartaric, and citric acids, as well as sulfates and sulfites. Although ion chromatography (IC) has not been a widely studied method to analyze organic acid content in wine, it offers the potential to simultaneously analyze multiple ions with greater specificity and sensitivity than other approaches. This project examines the various ways that IC can be used to analyze the components of wine, allowing for further application within the wine industry. The malolactic fermentation process was tracked to measure the changes of malic and lactic acids within the wine. Sulfites and sulfates were measured as the wine was exposed to oxygen during the aeration process. The results show that IC provides greater accuracy than paper chromatography and enzymatic spectrophotometry, the most commonly used methods in wineries. This increased accuracy provides additional knowledge that allows winemakers to further understand and evaluate the chemical components in the wines that they create. This is a useful step towards making the characterization and marketing of the wines less subjective.

3 million Americans and 65 million people worldwide have been diagnosed with epilepsy. In two-thirds of these patients, the causes of epilepsy, and therefore the therapeutic targets, are unknown. Recently, de novo mutations in the EEF1A2 gene, which encodes for a protein translation regulator, were found in several individuals with pediatric epilepsy and intellectual disability. In order to study how a mutation in this gene causes the neurological defects, we generated mutant eef1a2 zebrafish using the CRISPR/Cas9 method. Zebrafish models to study diseases have gained momentum due to their genetic similarity to humans, large amount of offspring in each generation, easy genetic manipulation and amenability to large-scale drug screens. Our initial in situ hybridization studies showed that eef1a2 has a limited expression pattern in the developing zebrafish that includes neurons involved in movement and escape behavior. To understand whether the mutation causes observable behavioral dysfunction or seizures, we tracked wild type (WT) zebrafish and heterozygous and homozygous mutants in various behavioral assays and genotyped tracked fish using Sanger sequencing. We are expecting that the mutants to have defect in movement and escape response. In a future study, the electrophysiology of the forebrain will be recorded to determine whether eef1a2 mutants reveal abnormal electrical discharge characteristic of a seizure. These studies with the zebrafish model will provide more insight about the EEF1A2 protein and its neurological function, and may lead to a better understanding of epilepsy etiology and the design of targeted therapeutic approaches.

Animals and humans collect and process information from their environment using a host of sensory modalities to maintain control of movement. Such integration of information is exceedingly challenging for the control of flight in insects, which is inherently unstable. We use insects as a model system for understanding how multiple sensory inputs influence flight control. While vision is necessary for flight, its processing time is too slow for effective fight control. Thus insects use a faster sensory modality that encodes mechanical information (inertial forces). We use a combination of experimental and theoretical approaches to reveal the precision, sensitivity, and rapid processing speeds of inertial sensors in flying insects. In particular, we suggest that wings not only serve a role as propuslors, but by virtue of the mechanosensory neurons in them, provide a key sensory role for inertial forces. We hypothesize that the wing mechanoreceptors of the hawkmoth (Manduca sexta) rapidly and precisely extract mechanical information necessary for flight control. We further hypothesize that such encoding properties are similar to those in wing evolutionary predecessors, halteres (a sensory organ that is known to be a gyroscopic organ) in flies. To test our hypotheses, we recorded the electrical activity of wing neurons subject to a mechanical stimulus. We used methods from computational neuroscience to characterize the encoding properties (the stimulus features that drive neural responses). We found that nearly all neurons respond rapidly with 5 ms precision and they are extremely selective for the temporal pattern of the stimulus. These results are similar to those found for halteres, and suggest a novel finding that wings serve the dual function of both actuation and sensing. These results reveal a new interpretation of movement control in animals and can serve as inspiration for the next generation of flight systems.

Motor behavior is the result of neural programs emerging from the Primary Motor Cortex (PMC). To generate behavioral outputs the PMC integrates exogenous and endogenous sources of variance. Electrical activity from the PMC has been effectively used to operate minimally invasive brain-machine interfaces (BMIs) that can operate prosthetic limbs to achieve basic motor outcomes such as operating a joystick.  Further development of neuroprosthetic technology will rely on a deep understanding of sources of variance to the PMC and how the PMC compensates for this. The circadian system regulates physiology and behavior within the 24-hour time frame and it represents a predictable source of endogenous variance for the generation of motor behavior. The specific pathways by which the circadian clock(s) may modulate PMC motor programs is not understood, but preliminary results from our lab show that the circadian system modulates the PMC electrical activity associated with wheel running in mice. We implanted electrocorticographic (ECoG) electrodes onto the PMC of mice and recorded electrical activity while they ran on a wheel at different circadian times. This showed that the PMC electrical signals associated with wheel-running are modulated in a predictable manner by the circadian system. I propose to replicate these experiments in mice with a malfunctioning circadian clock. I hypothesize that the canonical molecular circadian clock is essential for this modulation. To test this hypothesis, I used ECoG electrodes to record PMC electrical activity of Bmal1^-/- mice, which have no copies of the clock gene BMAL1, and their wildtype (Bmal1^+/+) littermates. This determines whether the circadian modulation of the PMC depends on an intact molecular circadian clock. Understanding the regulatory effects of the circadian system on PMC brain wave activity is crucial for the design of BMIs and their effective operation throughout the 24-hour day.

Many plant-pollinator interactions are thought to depend on coordination between the timing of plant scent emission and pollinator activity. Certain plants of the genus Petunia exhibit rhythmic scent emission based on the circadian clock, but little is known about the role of the clock in pollinator behavior. The pollinator of Petunia axillaris, the hawkmoth Manduca sexta, is thought to be nocturnal based on mostly anecdotal evidence. To understand the temporal relationship between Manduca sexta and P. axillaris, it is necessary to first determine the precise timing of hawkmoth activity. We hypothesized that moths would display circadian timing in their flight behavior, complementing the timing of scent emission from P. axillaris. To test this, we observed the flight behavior of male hawkmoths in response to 12-hour light/12-hour dark conditions, continuous dark, or continuous light. The moths were entrained to the 12-hour light/12-hour dark cycle during their pupation and their first two days post-cocoon emergence, and they were introduced to a wind tunnel on the third day for the experimental conditions. The number of moths flying within a ten-minute period was recorded continuously for one day or every four hours for three days. Hawkmoths exhibited flight activity only during the subjective night phase of continuous dark conditions. This rhythm was maintained over multiple days of continuous darkness, demonstrating that it is not dependent on light input. We also examine how desynchronizing the clocks between plant and pollinator affects pollination success, and lastly if it’s possible to induce a pollinator shift by shifting the timing of scent release.

Stomata, valve-like pores encircled by guard cell pairs on the plant epidermal surface, serve as the primary gateway for gas exchange with the environment as well as water movement through the vasculature. During organ morphogenesis in Arabidopsis thaliana, the differentiation process from an unspecialized protodermal cell to a fully mature pair of guard cells, in addition to the coordination of proper stomatal spacing and density in the epidermis, is regulated by a complex signaling pathway that involves a series of interactions between positional signaling peptides and transmembrane receptor kinases. The secreted signaling peptides EPIDERMAL PATTERNING FACTOR (EPF) 2, EPF1, and STOMAGEN (EPFL9) play major roles in this differentiation pathway. Previous studies have extensively investigated the functions of EPF2, EPF1, and STOMAGEN; however, the effective range of these peptides after secretion has yet to be determined. Here, we use a Cre-lox Gal4 recombination system to induce site-specific mosaic overexpression of our target peptides in the Arabidopsis epidermal layer, in which induced recombinant cells are positively indicated by fluorescence. Preliminary results have confirmed the efficacy of the Cre-lox system as well as consistency of stomatal patterning phenotypes with the overexpression of each peptide. Using this system, we will visualize and quantify the distance over which EPF2, EPF1, and STOMAGEN can influence stomatal patterning in Arabidopsis.  By better characterizing the peptide activities that regulate stomatal patterning in plants, this project can lead to novel insight on the relationship between stomatal development and plant productivity, which has potential applications for agricultural innovation.

Flowering plants exhibit diverse forms of floral symmetry that represent many independent changes throughout their evolutionary history. The selective and genetic basis to these changes has provided scientists with a complex puzzle that Darwin once referred to as an “abominable mystery.” Recent genetic studies began to uncover the genetic causes for this mystery, revealing the presence of certain genes that show correlations with this evolutionary trend. One such gene, the CYCLOIDEA (CYC) gene, has been identified as a major contributor to changes of floral symmetry. We have found this gene in the sequenced genome of Rhododendron williamsianum where it has experienced multiple duplications. The goal of my research is to identify the main duplications in one of the CYC copies (CYC2) in the Rhododendron genus. I accomplished this by using polymerase chain reactions to isolate any CYC2 copies present in two species from each of the subgenera of Rhododendron: Hymenanthes, Azaleastrum, Therorhodion, and Rhododendron. I then used cloning and sequencing to obtain the sequences of the CYC2 copies from each of the sampled species. I will conduct a phylogenetic analysis of these sequences in order to reconstruct a gene tree that will display a summary of the main CYC2 duplications that have occurred in the genus and when they emerged. Preliminary results from four species sampled thus far show that two independent duplications in CYC2 have arisen in both Hymenanthes and Rhododendron. My expanded analysis, sampling species from additional subgenera, will provide a more thorough history of this gene and its duplications throughout the genus. This will allow for more robust testing for correlation between symmetry and gene duplication in the future.

Plants use information about daylight to align their flowering time with seasonal changes, increasing reproductive success. Long-day conditions promote flowering in model organism Arabidopsis thaliana. The gene FLOWERING LOCUS T (FT), which encodes florigen and promotes flowering, has been understood to show evening peak expression in long-day specific manner. The molecular mechanism responsible for FT regulation has been widely studied using 16-hour fluorescent white light, 8-hour dark, and constant 22°C as simplified long-day conditions. To expand our understandings on flowering regulation in nature, where multiple environmental signals synergistically regulate flowering, our lab analyzed FT expression in plants grown outdoors during Seattle’s summer solstice (15h59m daylight, 21.2°C high, average 1971 to 2000). In contrast to what has been reported under simplified long-day conditions, a morning and evening peak of FT expression was observed. Since 2014 we have succeeded in reconstructing natural double FT expression in growth chambers with 16-hour fluorescent light supplemented by far-red LED and temperature oscillation. My project addressed the effect of far-red light, as measured by the red to far-red light ratio (R:FR), on morning FT expression. Arabidopsis seedlings were grown for two weeks in chambers under constant temperature and 16-hour fluorescent light supplemented with variable strength of far-red light conditions, mimicking shade (0.25 to 0.75:1), natural sunlight (1:1) and fluorescent light (2:1). FT expression was analyzed using real-time quantitative reverse transcription PCR. As a result, higher FR ratio increased FT expression in wild-type. We are currently analyzing phytochrome mutants, lacking functional red and far-red light photoreceptors, to investigate how they are involved in FT regulation. FT function is widely conserved in angiosperms and identifying environmental inputs and the associated genes for flowering regulation in Arabidopsis under natural conditions can contribute to researching effects of climate change on flowering time in agriculturally relevant species.

Developmental phenotypic plasticity can be a vital means to buffer the sudden and persistent effects of anthropogenic climate change, through facilitation of species persistence and possible facilitation of species range shifts. Integrating our understanding of plastic physiological growth mechanisms with functional traits may prove useful for interpretation of the ecological impacts of climate change. We investigated the influence of water-stress and light limitation on leaf mass per area (LMA), leaf anatomy, and leaf gas exchange of juvenile Populus tremuloides trees. Leaves that developed while water-stressed had significantly elevated LMA, due to increased leaf density from significantly higher spongy mesophyll surface area per leaf area (A_smes/A) and reduced stomatal conductance (g_s) but only marginally reduced photosynthesis (Pmax). In shade, leaves had significantly reduced LMA, due to reduced thickness, density, and combined A_mes/A, but maintained the same A_smes/A, and reduced palisade mesophyll surface area per leaf area (A_pmes/A), which was coupled with a reduction of g_s and P_max. Furthermore, water-stressed leaves had elevated intrinsic water use efficiency (WUE_i: P_max/g_s) while the shaded leaves, despite reduced g_s, maintained similar WUE_i. Our results suggest that, under water-stress and full sunlight, greater A_smes/A conferred maintenance of photosynthetic rate possibly through reduction of mesophyll resistance (r_m), at the cost of reducing expansive leaf area (and increasing density) as leaves were more dense but were 20 % the area of control leaves. In shade, suppressing A_pmes/A while maintaining A_smes/A may be a plastic strategy to increase laminar light capture, as leaves had reduced density and thickness but were still 50 % the area of control leaves . Together, in P. tremuloides saplings, these stresses induced developmental plasticity in LMA with differing plastic underlying anatomy and function; we discuss future implications specifically in the context of developmental plasticity, growth trade-offs, and the ecological impacts of climate change.

In order to understand the paleoecology of extinct animals, it is useful to look at extant species for comparison. Due to the shared ancestry between the modern opossum, Didelphis virginiana, and the extinct marsupialiform, Didelphodon vorax, the opossum is often used as an analog for understanding the life history of D. vorax. Didelphodon vorax, which was the largest mammal from the latest Cretaceous of North America (~66 million years ago), is thought to have had an ovivorous (egg eating) or durophagous (hard-shelled eating) diet; however, little is known about its ontogenetic patterns and ecology. Therefore, we aim to construct an age series of D. vorax to gain insight into diet changes throughout its life. A mandibular bending strength analysis investigates the level of force the mandible is capable of withstanding during biting in both dorsoventral and labiolingual directions. Additionally, we can use it to determine variation in bending strength along the body of the jaw, which allows us to further explore feeding behavior. Here, we illuminate cranial ontogenetic patterns in D. vorax by examining different development stages to determine diet variation based on mandibular strength profiles. We analyzed mandibular cross-sectional properties and applied beam theory to 15 D. virginiana and seven D. vorax specimens. Each individual used in the study resulted with a relative force greater than one, which is indicative of an adaptation toward exerting forces directly on prey, whereas a ratio less than one would indicate an adaptation toward withstanding struggling motions or transverse stresses. Finally, we find similar patterns of ontogeny for both species at different tooth positions, which supports the notion that diet changes throughout ontogeny of these marsupials. Thus, comparison of mandibular bending strength between extinct and extant mammals has the ability to gain insight into their feeding behavior and morphological adaptations.

The Cretaceous-Paleogene (K-Pg) mass extinction and resulting biotic recovery mark a pivotal moment in mammal evolution. The recovery period, which spanned about 1 million years from the Puercan North American Land Mammal Age (NALMA) to the Torrejonian NALMA, represents a transition from species-poor “disaster” faunas directly following the extinction event to species-rich “recovery” faunas. Though previous research has broadly studied the faunal dynamics of the early Paleogene, the exact mode and tempo of the biotic recovery has not been well examined. To investigate the ecological trends of the “disaster” to “recovery” faunal transition, specifically changes in diet, we analyzed dental evolution within the periptychid and arctocyonid “archaic ungulate” lineages over a time period that spans from the Puercan NALMA to the Torrejonian NALMA. We measured relief index (RFI), a metric that determines the ratio between the 2D and 3D area of mammal teeth, on both the “archaic ungulates” and a set of ecologically diverse extant mammals to identify the dietary ecologies of the extinct mammals. Previous research has demonstrated a correlation between RFI and diet in extant mammals; high RFI values correspond to herbivory and insectivory, while low RFI values correspond to omnivory and frugivory. Our preliminary results suggest an increase in dietary diversity and an overall decrease in RFI during the biotic recovery. This reduction in RFI reflects a trend in “archaic ungulate” dietary preference from insectivory in the Puercan NALMA to omnivory and frugivory in the Torrejonian NALMA. The results of our study will help scientists understand how ecosystems recover from catastrophic events, such as mass extinctions, on large timescales.

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

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

The Cretaceous-Paleogene (K-Pg) mass extinction event was a pivotal episode in the evolution of mammals. It is widely held that the extinction of non-avian dinosaurs allowed mammals to evolve rapidly into ecological niches previously occupied by dinosaurs. Studies of successive mammalian faunas from northeastern Montana have detailed this pattern, showing that (1) the earliest Paleogene (Puercan 1) ‘survival’ fauna from within 80,000 years of the K-Pg boundary was species poor and included many immigrant taxa and (2) full recovery and expansion of mammalian diversity only occurred 600 to 700 thousand years after the K-Pg event. To better resolve our view of the immediate aftermath following this mass extinction event, previous studies by myself and the Wilson Lab have analyzed a mammalian fossil assemblage from the Constenius locality (UWBM C1665), which documents a ‘survival’ fauna. The Constenius locality is bracketed to within 20,000 years after the K-Pg boundary, thus providing a time-constrained view into which mammals survived the mass extinction and how quickly immigrant taxa invaded this area. Here, I add to our understanding of this fossil assemblage by identifying and describing 23 newly recovered mammalian specimens from the Constenius locality. These specimens, which include isolated teeth and jaw fragments, were discovered in situ in the field and in the lab after screen washing more than 100 kg of bulk sediment. I compared the taxonomic composition and species richness of the Constenius mammalian assemblage to those from the Worm Coulee 1 locality (UWBM C1369), which is bracketed to within 80,000 years of the K/Pg boundary and likely represents a slightly younger assemblage. The results so far indicate that species richness and relative abundance is highest in archaic ungulates and lowest in multituberculates which is consistent and further strengthens previous research done at the Worm Coulee 1 locality within 80,000 years after the extinction event.

Therapsids (mammal-like reptiles) document the transition to modern mammals and are an important study tool in examining how the past informs the present. Understanding diseases today requires understanding the deep evolutionary history in our fossil ancestors. We present an instance of dental pathology in a gorganopsid therapsid (~260 million years old). Using fossil histological techniques, we examine a gorganopsian canine and preliminary results reveal abnormal mixture of dental tissue next to the functional tooth. These individual ectopically expressed teeth have preserved tissue layers such as enamel, dentine and a pulp cavity. Based off of the histological characters of our specimen as compared to modern clinical studies we hypothesized two possible diagnoses: odontoma and enamel pearls. Enamel pearls show dento-enamel pearl nodules protruding from the enamel of a functional tooth. Odontoma presents as individual teeth with their own histological packaging (i.e. dentine and enamel). These results suggest that our specimen most likely had odontoma. In modern cases, this results in excess dentinal tissue growth and un-alignment of teeth. The cause of this odontoma in modern clinical practices is a result of either trauma or rapid tooth replacement. The canine tooth of this gorgonopsid was prone to trauma since it served to pierce prey and was subjected to intense forces. Alternatively, gorgonopsids replaced their teeth continuously. This continous replacement could have gone awry resulting in this disease. This study presents the oldest possible case of cancer in the fossil record and elucidates the evolution of such pathologies. This study has relevance in dental clinical studies because understanding how diseases operate in humans requires an understanding of how they evolved in our deep evolutionary history. 

The Cretaceous-Paleogene (K/Pg) mass extinction event (~66 million years ago) was a seminal episode in Earth's history. This event resulted in the extinction of up to 76% of all species and led to new evolutionary opportunities for the survivors (e.g., mammals). Accordingly, study of fossils spanning the K/Pg boundary is critical to understanding the dynamics of the extinction and resulting biotic recovery. However, K/Pg sections with vertebrate faunas are presently known only in North America. The Indian subcontinent was geographically isolated from approximately 88 MYA until 55-50 MYA, during which time massive volcanic eruptions (the Deccan Traps) occurred in western India during a four million year span across the K-Pg boundary. These eruptions and their effects have been implicated as causal mechanisms of the K-Pg mass extinction, but few studies have directly tested this hypothesis. Numerous vertebrate fossil localities have been found in India in the sedimentary rocks below (infratrappean) and between (intertrappean) the volcanic basalt flows. Historically, these fossil localities have been considered latest Cretaceous in age, but recent work has refined the stratigraphic and temporal relationships of the fossil localities. This allows us to track species diversity through time during the volcanic eruptions and leading up to and across the K-Pg boundary. In turn, these data can be compiled to determine the timing and magnitude of the extinctions within the context of Deccan volcanism and the mass extinction itself. We have compiled published records of over 1,653 fossil specimens from infra- and intertrappean localities throughout India. From the literature, we recorded demographic and locality information for our database. We will then use this database to characterize vertebrate faunal changes during the volcanic eruptions and across the K-Pg boundary in India, as well as compare the effects of the mass extinction in India with other parts of the world.

Molecular studies of plants’ photoperiodic flowering have helped improve crops in agriculture and horticulture by modulating growth patterns in plants. A photoperiod is a seasonal change in day length of daytime that is consistent from year to year. Plants maximize their reproductive success by adjusting their flowering time according to photoperiodic information. To better understand the effect of photoperiods in plants, we used Arabidopsis thaliana as a model organism. Scientists worldwide study A.thaliana due to its genomic simplicity, its fast growth and its efficient transformation by using Agrobacterium tumefaciens. In A. thaliana, the transcription of the CONSTANS (CO) gene is key for the regulation of seasonal flowering. Under long-day conditions, both transcriptional and post-transcriptional CO regulation maximize the CO protein accumulation towards the end of day, which induces the expression of FLOWERING LOCUS T (FT) gene, which encodes florigen and causes the plants to flower. TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL NUCLEAR ANTIGEN FACTOR (TCP) binding site is closely located to cis-elements of CO regulators, which indicates that they might interact in the same complex. To study the functional interaction between TCP and known CO regulators, including GIGANTEA (GI) and FLOWERING bHLH (FBH), we first studied the protein-protein interaction using yeast two hybrid analysis. The yeast two hybrid analysis confirmed protein-protein interaction between TCP4-GI, TCP4-FBH, and FBH-GI. Then, to validate the protein-protein interaction suggested by the yeast two hybrid analysis we performed flowering time measurement experiments on multiple combinations of these mutants, in order to investigate the genetic relation among CO regulators.

 

Regulation of metabolic pathways is often implicated in many normal as well as disease processes in organisms. Our previous work discovered changes in the metabolome associated with longevity in eleven different species of fruit flies. The metabolic pathways associated with longevity included gluconeogenesis, the Krebs Cycle, and amino acid degradation. However, it is still unknown how basic nutrient parameters influence metabolic pathways in flies. We used mass spectrometry coupled with liquid chromatography to quantify the small molecules present in whole fly tissue. After finding metabolites associated with age, we completed nutrition assays to determine if there were associations between nutrient parameters and metabolomic profiles. The measurement of basic nutrient parameters consisted of colorimetric assays for total glucose and protein levels. Data analysis revealed correlations between the levels of each nutrient found in whole fly tissue and corresponding metabolomic profiles. In our future work, we plan to manipulate metabolic pathways or nutrient parameters found to be significantly associated with age and observe whether there are changes in longevity.

As our planet warms, organisms that cannot migrate to more suitable habitats will be forced to adapt to the increasing temperatures or face extinction. An important question to address is how the rate of environmental change affects an organism’s chance to adapt. If an environment changes suddenly, then organisms must also adapt rapidly, whereas slower rates of change allow the organism more time to adapt. Microorganisms, such as the virus phi-6, can be utilized to answer this question because they evolve rapidly, allowing us to watch evolution in real time. We evolved phi-6 over 11 weeks to survive high temperatures. In different treatments, the viruses experienced sudden, moderate, or gradual changes in temperature. Sequencing the evolved lineages at two genes revealed multiple mutations. We added the mutations one by one to the ancestor to determine how each mutation affects thermotolerance. We find that each mutation can increase or decrease thermotolerance by a different amount. Interestingly enough, mutations that give the greatest increase in thermotolerance appeared in viruses that experienced slower temperature change. There is also a trend where viruses that experienced slower temperature change had more mutations per lineage than viruses that experienced sudden change in temperature. My results demonstrate that rate is an important parameter when taking adaptation into consideration. If the temperature increases too rapidly, there may be fewer ways for organisms to adapt, and they are unlikely to survive climate change.

The B-class genes of the ABCE model of floral development are necessary for the initiation of petal and stamen development in Arabidopsis thaliana (a core eudicot). Loss of B-class function results in homeotic conversions of petals to sepals and stamens to carpels, resulting in a female flower. All ABCE genes are activated by LEAFY (LFY), a master regulator of floral development. The F-box protein, UNUSUAL FLORAL ORGAN (UFO) is a co-factor of LFY, necessary for transcriptional initiation of the APETALA3 (AP3) lineage genes; a subset of the B-class. In the model plant Arabidopsis, the UFO mutant phenotype strongly resembles classical B-class mutants confirming UFO’s role as a regulator of AP3 genes. Although the function of the AP3 genes has been investigated in a wide variety of flowering plants, little is known about UFO outside of the core eudicots and rice. In order to gain a deeper understanding of the evolution of AP3 regulation, we are investigating the function of the UFO ortholog in flowers of the early-diverging eudicot Thalictrum thalictroides (in the buttercup family) using Virus Induced Gene Silencing (VIGS). Unlike many core eudicots which only have one AP3 homolog, T. thalictroides has three copies that arose from recent duplication events. We have previously shown that these three paralogs have a partially redundant role in stamen identity and in petaloidy of T. thalictroides sepals. We predict that the down-regulation of ThtUFO will result in a B-class mutant phenotype equivalent to a full ThtAP3 mutant knock-down. By studying ThtUFO and its effect on petal and stamen identity genes in an early diverging eudicot we hope to gain a deeper understanding of the implications of gene regulatory evolution on floral morphology.

The human Tumor Suppressing Subtransferable Candidate 1 (TSSC1) gene was first discovered in 1997 as a gene whose likely location was within a chromosomal region that suppressed tumor growth. A recent study reported that decreased TSSC1 gene expression results in increased metastasis of breast cancer cells to bone. However, the underlying mechanism by which the TSSC1 protein acts in cancer cells remains unknown. Interestingly, TSSC1 is a highly conserved protein among eukaryotes. We are using Drosophila melanogaster as a model organism to define the normal function of TSSC1. Previously, our lab showed that the Drosophila protein, dTSSC1, localizes near Trans-Golgi Network (TGN), the region of the Golgi that sorts and packages membrane and secreted proteins into vesicles for transport to post-Golgi destinations. We have also isolated two mutations in dTSSC1 and observed that they cause defective formation of the acrosome, a Golgi-derived organelle that is localized to the apical tip of mature sperm and is required for fertilization. Based on these observations, we propose that dTSSC1 acts in spermatids to regulate acrosomal protein and vesicular trafficking. We are expressing tagged membrane proteins to ask whether dTSSC1 is required specifically for trafficking of acrosomal proteins or if it has a more general impact on membrane protein trafficking. These studies use expression in the male germ line. Notably, dTSSC1 is expressed in many tissue types, similar to its counterpart in humans. Therefore, we are also investigating whether dTSSC1 mutations have effects on protein trafficking in somatic cells. Our results should define the normal cellular role of dTSSC1 in Drosophila and may also provide insight into the role of the human protein in normal and cancer cells.

Genetic robustness is the ability of an organism to gain mutations without changes to its fitness or functions. Evolutionary conditions that might select for genetic robustness are unclear, but some studies suggest that proteins that are more thermostable (able to fold properly at high temperatures) are also genetically robust to mutations. We are examining this relationship in phi-6, a virus that infects bacteria. We have evolved phi-6 for thermostability by subjecting it to high temperatures and then sequenced the viruses for mutations. We used homology-modeling programs to visualize the structures of mutated viral proteins and made predictions about the molecular basis of thermostability and genetic robustness. In order to evaluate whether the thermostable strains are genetically robust, we ran random mutagenesis on both thermostable mutants and the wild type virus. Our work shows that evolution for thermostability may be a viable mechanism to evolve genetic robustness.

Flowering time in plants is imperative to reproductive viability and is controlled by a variety of molecular regulatory systems drawing upon internal and external stimulus. We use Arabadopsis thaliana as a model to determine how plants incorporate photoperiodic sunlight cues in the production of flowers. Through the transcriptional regulation of certain molecular factors, plants are able to effectively control the temporal expression of the FT (FLOWERING LOCUS T) gene, FT protein is in leaves and then moves up the shoot apex to initiate flowering. Expression of the FT gene is initiated by a transcription factor called CO (CONSTANS) and suppressed by a protein called CDF1 (CYCLING DOF FACTOR 1) that are controlled by sunlight and the plant’s endogenous circadian clock. CDF1 inhibits CO transcription by binding to a series of four identical upstream DNA binding sites and is thought to do so in conjunction with a corepressor protein called TPL (TOPLESS). In this experiment we created a mutant background that was deficient in TPL activity in conjunction with a synthetic CO promoter fused to the bioluminescent enzyme firefly luciferase (LUC). We use this tool to assay if changes in binding site number and orientation in the presence or absence of TPL change the sensitivity of the promoter to photoperiodic sunlight inputs. We hypothesize that the removal of TPL will increase early-day CO expression regardless of daylength but CO expression will be unaffected by the amount of binding sites. We also expect that loss of TPL function attenuates CDF1 dependent repression of flowering, such that differences in CDF1 repression between different binding site architectures types will be unchanged in the absence of the corepressor. This would corroborate results from previous experiments. Should we obtain other results we might be made to reevaluate the role TPL plays in florigenesis in Arabidopsis.

Antibiotic resistance in bacteria is rapidly rising and our garrison of effective drugs keeps dwindling. As the creation of new antibiotics is incredibly time-consuming and expensive, it’s crucial that we slow the rapid evolution of drug resistance to prolong the effectiveness of our current drugs. Recent studies suggest improving current drug cycling practices by exploiting a phenomenon known as collateral sensitivity, where resistance to one drug leaves bacteria more sensitive to a second. By selecting pairs of antibiotics that exhibit collateral sensitivity, this method causes one drug to become more effective at abolishing bacteria after resistance to another drug has occurred. However, it is not known if collateral sensitivity profiles are maintained after further evolution of the bacteria; information that is crucial if we want a long-term method of combating drug resistance. Through our experiments, we aim to test the null hypothesis that collateral sensitivity profiles do not change over evolutionary time. To do this, we first isolated an array of Gentamicin-resistant Escherichia coli that exhibit collateral sensitivity to Colistin. Then we evolved our resistant bacteria for ~200 generations and measured the minimum inhibitory concentration (MIC), the concentration of drug that inhibits bacterial growth, for both drugs. By comparing the MIC values before and after our evolution experiment, we can determine if collateral sensitivity changes. If collateral sensitivity increases after evolution, collaterally sensitive drug cycling treatments could prove to be more effective than we already assume. But if collateral sensitivity decreases, the efficacy of this style of treatment may be reduced, which is important to know when designing drug cycling treatments. Knowledge of collateral sensitivity patterns will influence the way we treat patients and combat future multidrug-resistant bacteria.

Coordination of the initiation of flowering with the optimum season is important for plants in both natural and agricultural systems. In the model plant, Arabidopsis thaliana, timing of flowering is strongly regulated by photoperiod. The main factors important for flowering are CONSTANS (CO) protein, which is an activator of flowering in response to photoperiod and FLOWERING LOCUS T (FT), the direct target of CO. FT protein is a mobile factor which can initiate flowering. Additionally there is a family of repressor transcription factors, the CYCLING DOF FACTOR (CDF) transcription factors that are able to limit the timing of both CO and FT expression so that flowering is repressed during short days. Functionally, CDF expression is controlled by the circadian clock so that their effect is constrained to the morning period of the day. In the afternoon of long days, CDF protein is degraded, enabling CO and FT to promote flowering. Recently, our laboratory has determined that CDFs may require a co-repressor protein, TOPLESS (TPL) to form a repressor complex to regulate flowering genes. To explore the importance of this repressor complex on flowering time, I observed how FT, CO, and other flowering genes expression levels change over the course of development in several genetic backgrounds. To remove TPL function where flowering time genes are expressed, we created a transgenic plant that expresses a dominant negative mutant of TPL in phloem companion cells. We hypothesized that this mutant would resemble a CDF loss of function, so I compared these lines and wild type plants over developmental time. Additionally, I am investigating the genetic interactions and epistasis of TPL with other flowering time pathway components by checking the flowering time and gene expression of transgenic plants which express mutated TPL and harbor mutations in other flowering time genes.

Blowflies are a major food source of pitcher plants. The main goal of this project is to observe if scents produced by the pitchers can attract blowflies. To test the hypothesis, experiments were conducted to determine the volatiles produced by pitcher plants and if flies have a preferred scent. We collected scents from pitcher traps through headspace sampling for a period of 24 hours (+/- 1hour), and ran them on a GCMS to identify the compounds. A Y-maze choice experiment was set up to determine if flies were attracted or repelled by any particular scent produced by pitcher plants. One arm in the Y-maze is set up as control, in which the scent emitted was purely mineral oil. While the other arm contained the scent that was being tested such as DMT or benzaldehyde. Each scent that was tested included 50 trials so that results due to random chance can be reduced. Initial experiments identified that traps produce a wide range of volatiles from sweet scents like ethyl tiglate to carrion-like scents such as DMT. On average, the flies went into the side arm with DMT scent diffused into it. The observed data can be explained by the possibility that flies have preference over the scent of DMT. I plan on testing additional scents produced by traps to determine if they are detectable and attractive to pitcher plant prey.

Seasonal influenza exhibits rapid evolutionary dynamics and successful prediction of its evolutionary future is extremely beneficial for public health. In this research we proposed a method that can infer the genotypes that are likely to dominate the influenza population from a sample of genome sequences. Our approach first requires to construct a time-scaled phylogenetic tree from the genome sample. By iterating over the subclades of the phylogenetic tree, we infer the effective population trajectory for each subclade using Bayesian Nonparmaetric Phylodynamic Reconstruction by Palacios JA et al. Finally, we estimate and rank each subclade’s population growth rate which enables us to identify the genotypes with the highest growth potential. We applied our method to seasonal influenza A/H3N2 sample data from 1995-2014, which predicted the progenitor lineage of the upcoming influenza season with near optimality in 5 out of 19 years and provide informative predictions in 14 out of 19 years. The results indicate that our method could help provide useful information for influenza vaccine selection process.

The study of crop foods, such as maize and corn, offer us important insights on how to create healthier and more abundant crop yields. The initiation and maintenance of callus tissue cultures is a process essential for researching transgenic plants and is constantly plagued by contamination. The media components can influence the formation of callus, shoot, or root tissue as well as culture longevity and general health. The goal of this project is to find an optimal medium for callus formation that contains anti-microbials in order to avoid contamination and promote callus, rather than shoot or root, production. The monocots used are rice and maize. The base medium used consists of Chu N6 Basal salts, 0.7% phytablend agar, and 3% various sugars. I grew tissues on the base media with varying amounts of hormones, additives, anti-microbials, and sugar blends and assessed callus, root, and shoot development as well as the presence or absence of tissue necrosis and microbial contamination. Various tissue cleaning procedures were also tested. I hypothesize that rinsing tissues in antibiotics before plating them would decrease initial contamination and that antibiotic plates could be used to eliminate contamination from already growing cultures. The presence of various hormones and chemicals, such as 2,4-D and silver nitrate, influenced tissue differentiation when applied at certain times. The use of anti-microbials in the washing process as well as in the initial cultures has eliminated most of the contamination issues. It appears that the use of an initial growth medium that promotes callus development and a long-term growth medium to keep cultures healthy will be the key to achieving long-lived callus cultures. The ability to create and maintain these cultures allows the study of transgenic plants and their DNA.

Phytoliths are microscopic silica bodies that are produced in the tissues of many vascular plants. Over the course of their lifetimes, certain plant cells become filled or encrusted with silica that the plants have absorbed from soil. Grasses produce a diverse range of phytolith shapes that distinguish them from phytoliths produced by other plants. We hypothesized that it would be possible to distinguish certain grass clades by the unique phytolith shapes they produce and the relative abundances of these shapes. We sampled a range of grass species across the grass-family phylogeny, including from grasses that diverged early on in the evolution of this clade. We isolated phytoliths from dried grass material and created permanent slides that were examined using a light microscope. For each grass species, we counted and categorized all phytolith shapes observed and calculated the relative abundance of each shape. These counts allowed us to identify grass clades based on the relative abundances of phytolith shapes they produced. Our results are a reference collection of phytoliths found in modern grasses that can be used as a key for identifying grasses in the fossil record. When applied to deep-time vegetation studies, this information can help identify grasses from ancient ecosystems. Because the spatial distribution of grass species vary depending on environmental factors such as temperature and humidity, our work can also help provide past climatic and environmental information. Studying grasses is important because they are an important part of Earth’s ecosystems and are a major food crop for humans.

Olfaction is an important method of communication for organisms such as mice. However, metabolism is significantly influenced by the integrity of sleep and the amount of dietary fat. Here I examined whether environmental factors such as sleep and diet could affect volatile profiles, because these may in turn affect the biological signals that are relayed between conspecifics. We hypothesized that the volatile profiles in mice would change following sleep disruption and/or increased fat levels intake. A group of one strain of mice was divided into two groups: one control group with undisturbed sleep and one experimental group that underwent sleep disturbance. Each group was divided again into two groups: one received regular chow diet and the other received high-fat diet. All mice were individually housed during the 4-week treatment period, and fecal samples were taken 2 weeks after cessation of sleep and diet manipulations through solid-phase microextraction (SPME). Following gas chromatography and mass spectroscopy (GC-MS) of these samples, I analyzed the data and found differences in abundance of volatile compounds among the experimental groups. Namely, production of pentanoic acid and benzaldehyde decreased considerably as a result of sleep disruption. Several other compounds were also found to undergo change in abundance as a result of fat level in diet or from a combination of both factors. My work in this project could potentially be a starting point in investigating the metabolic pathways associated with sleep disruption and diet that are linked to the above changes in volatile production.

Carnivorous plants inhabit low nitrogen soils and must consume insects for nutrition. They achieve this by using modified leaves, called traps, which can catch prey. Thus, the ability of carnivorous plants to attract prey is key for their survival. In this study, we tested the hypothesis that carnivorous plants use scents to lure insect prey. We considered two possible cases: 1) prey are lured by only trap scents, so they will only detect trap scents or 2) prey animals are lured by both trap and flower scents, so they will detect scents from both organs. We focused on Sarracenia pitcher plants, a genus that is indigenous to the southeastern United States, and their interactions with calliphorid flies (commonly known as blow flies), one of their major prey. We used electroanntenograms (EAGs) to determine whether flies were responding to specific smells. We did this by hooking up a whole fly prep to the EAG machine, pulsing specific scent compounds over the antennae, and recording the electrical responses produced by the fly. In our tests so far, we have found that flies respond most strongly to pulses of DMT, a compound which is found in the scents of traps that have captured prey. Flies also respond to beta-ionone, a compound that is found in pitcher plant flowers. Our preliminary results indicate that flies are able to detect both trap and flower scents, so this supports the hypothesis that pitcher plants use a combination of trap and flower scents to attract their prey. We plan on testing a wider range of trap and flower scents using both EAG pulses and gas chromatography - electroantennography (GC-EAG).

There are many different Danio species that each have their own very unique pigment pattern. Even though each pattern is different, they are all made up of the same pigment cell types. Different interactions between black melanophores, yellow/orange xanthophores, and iridescent iridophores establish and maintain the Danio pigment patterns. Changes in these interactions allowed the species to diverge and created their own unique phenotype. Our project is focused on determining the differences that allow for the development of different pigment patterns within Danio species, such as Danio rerio, D. margaritatus, D. erythromicron, D. choprae, D. tinwini, D. alboliniatus, D. aesculapii, and D. nigrofasciatus. One of the more obvious differences in the development of these patterns is the order in which the adult pigment cells differentiate. In some species melanophores differentiate first, while in others xanthophores differentiate first, and in some species multiple pigment cell types differentiate at the same time. Previous studies have shown that xanthophores are very important in determining the final pigment pattern in D. rerio. In order to test what roles the xanthophores have in determining the final pattern for other species we generated colony stimulating factor 1 receptor (csf1r) mutants using CRISPR/cas9 mutagenesis. Without csf1r there cannot be any csf1 signaling, which is required for xanthophore development. By knocking out csf1r we can knock out xanthophores and the cell-to-cell signaling involving xanthophores that was necessary to form the normal pattern in Danios. So far we have created mutants for csf1r in D. rerio, D. alboliniatus, D. aesculapii, and D. choprae. We have also started to quantify the phenotypes for these mutants to determine the overall effect of knocking out xanthophores. Understanding the cellular mechanisms that allow for all the different patterns in Danios will help our understanding of the evolution of different Danio species.

The switch from vegetative to reproductive development in flowering plants is tightly regulated by a complex gene network, yet little is known about how this network evolved. The Arabidopsis thaliana flower meristem identity gene LEAFY (LFY) encodes a transcription factor that activates floral organ identity genes to initiate flower development; loss of function mutants develop leaf-like structures in place of floral organs. Genes homologous to LFY have been identified in representatives of more basal land plant lineages, including gymnosperms, ferns, and mosses. Moss LFY functions in early sporophyte development; knock-outs result in the zygote being arrested at the single-cell stage with no further development. To investigate the evolution of LFY, we have generated transgenic lines in the emerging model fern Ceratopteris richardii that use RNAi to silence CrLFY expression. We have validated lines with reduced LFY expression by RT-PCR showing a delay in sporophyte development and distinct leaf development. Our working hypothesis is that fern LFY may be crucial for early sporophyte development. To find evidence for this, we are currently analyzing gametophyte and early sporophyte development in detail using microscopy to determine the timing and location of the developmental defect (i.e. in gametangia, during fertilization, or in the early cell divisions of the zygote). Our research seeks to bridge the evolutionary gap between LFY function in moss and flowering plants by looking at its function in ferns (sister taxa to all seed plants) and to ultimately investigate how it became specified for flower development.

Leigh Syndrome (LS), one of the most common childhood mitochondrial diseases, typically arises during the first year of life and results in a wide array of metabolic and motor deficiencies leading to death within a couple of years. LS is associated with mutations in any of several mitochondrially encoded genes, including NADH Dehydrogenase Subunit 2 (ND2). The ND2 gene codes for a subunit of complex I within the respiratory chain of the mitochondria. Among patients with the same ND2 mutation, the progression and pathology of LS varies widely. The variation might be due to the effects of variation at other genes that interact with ND2. To test this hypothesis, we have turned to a Drosophila model of LS, in which flies carry an ND2 loss-of-function mutation. Drosophila with the ND2 mutation experience LS-like symptoms, including decreased lifespan, metabolic dysfunction, and paralysis, when exposed to mechanical stress, termed ‘bang sensitivity’. To identify other genes that affect the ND2 mutation in Drosophila, we crossed female ND2 flies with males from the Drosophila Genetic Reference Panel (DGRP); a panel of 200 inbred, fully sequenced lines. The resulting offspring are aged 21 days and assayed for changes in bang sensitivity— the time it takes for individual flies to recover from paralysis. By comparing the effects of ND2 on the bang sensitivity phenotype in each DGRP background, we hope to identify specific genes that either worsen or ameliorate the phenotype. If successful, this study could help us identify genetic modifiers of this mitochondrial disease, and thus help us identify novel therapeutic targets.

Circadian rhythms are vital to maintaining proper mental health. This project seeks to determine whether or not cyclic fear stimuli has the ability to override the natural entrainment of the circadian system to the light-dark (LD) cycle. This work is significant because there are few environmental stimuli that are capable of overriding entrainment of circadian rhythms by the LD cycle (e.g., temperature cycles, temporally restricted food access). Our laboratory has shown that nocturnal cyclic fear stimuli are sufficient to induce a shift in the natural nocturnal foraging and feeding activity to diurnal activity. This reflects the output of an endogenous circadian clock that is entrained to the fear stimuli because the timing of these behavioral rhythms is sustained under constant conditions. Our experimental design involves three stages. First, mice are entrained to a 12:12 light-dark cycle over a seven-day period. Then, mice are subjected to random nocturnal footshocks for fourteen days. Finally, mice are released into constant conditions to determine if diurnal behavior is sustained. Future experiments will examine the role of the amygdala and suprachiasmatic nucleus in generating the nocturnal-to-diurnal shift in behavior. Ultimately, if we know how and why fear changes circadian behavior, then we can potentially create new treatments for sleep disturbances associated with mental disorders that result from trauma, such as post-traumatic stress disorder.

The cultivation of tomatoes is currently a 58 billion dollar industry worldwide. Over the past few years, tomato plants have been subjected to more severe and abrupt climatic fluctuations than ever before. In-depth understanding of the tomato leaf anatomy and physiology can have significant consequences in agriculture. Fluxes (fluid flow rate) in leaf water and sugar-conducting tissues, xylem and phloem, are challenging to visualize in real time. It is important to attempt this measurement using intact leaves as excision interrupts control of normal flow paths. The possibility that vein density and flux influence photosynthetic rate is being investigated here.  Optical Coherence Tomography (OCT) is a non-invasive imaging modality that performs high-resolution cross-sectional imaging, allowing to visualize the structure and motion in biological samples in 3D.  In this study, we have used a state-of-the-art OCT system with 7 μm resolution, operating at 1300 nm wavelength, to investigate leaf structure, venation and vein flow in live tomato leaves for the first time. The low intensity imaging beam (3 mW) is in the near IR spectral region and imaging is performed at high speed (4 ms/frame) hence, does not interfere with the leaf’s natural physiological processes. We have used Rutgers’ tomatoes for this study. To improve the image contrast in the leaf veins, we are investigating using dye and lipid particles to be taken up by the leaves

Biological diversity is known to be a key contributor in benefiting ecosystem productivity and functioning. While phenotypic plasticity (the ability of a single genotype to reflect more than one phenotype under various environments) has been the focus of numerous recent ecological literature, it is still yet undetermined what explicit roles genetic diversity versus phenotypic plasticity have on diversity-productivity relationships in ecosystems. In our experiment, we manipulated genetic diversity as well as variation in propensity for phenotypic plasticity of Arabidopsis Thaliana individuals under drought and non-drought conditions to address the following topics: (1) relationship between genetic diversity and phenotypic plasticity, (2) the relationship between genetic diversity and productivity, and (3) the impact of genetic diversity for phenotypic plasticity on productivity. Implications of this study are critical to understand ecological relationships integral for productivity and ecosystem functioning, as well as agricultural practices, in the face of projected climate change scenarios.

The ability of animals to detect minute chemical concentrations and locate odor sources is unparalleled in synthetic systems. This is especially true in the hawkmoth Manduca sexta which can track and find the source of chemical plumes with astonishing efficiency. Male moths, for example, can detect female pheromones at concentrations of 1 in 10¹⁷ molecules of air. In this work, I created a biological odor sensor by measuring the electrical activity of the neurons in a severed antenna in response to their odor detection, (a.k.a. an electroantennogram or EAG). By comparison, commercial gas sensors are incredibly inefficient, large, heavy, expensive, and have slow response times. I have developed a small quadrotor drone which uses an electroantennogram with the antenna of a Manduca sexta moth to track a chemical plume to its source. The EAG signal is measured as the voltage across the antenna and then amplified and filtered to reduce noise. The control module of the drone uses this signal in conjunction with a measurement of the ambient airflow to steer the vehicle. The drone uses a cast and surge search algorithm to follow the chemical plume upwind: flying crosswind until the chemical is sensed, flying upwind until the scent is lost, and then repeating the process. This experiment provides proof of concept that EAGs can be used to direct the flight of an aerial vehicle for the purpose of chemical localization. This provides an odor sensing platform that is many orders of magnitude lighter than commercial odor sensors. The applications of a small, reproducible, chemosensing drone are numerous, ranging from locating contraband to testing biological hypotheses of insect flight.