Plants respond with a sink stimulation of photosynthesis when colonized by bacterial and fungal mutualists, which compensates for costs of carbohydrate allocation to the microbes. Problems may arise when light is limited and plants cannot increase photosynthesis. We hypothesize that under such conditions the costs for maintaining the mutualism outweigh the benefits, which ultimately turns the beneficial microbes into parasites exploiting resources and reducing host fitness. We study these plant-microbe interactions under different light availabilities using lima bean plants, rhizobia (nitrogen-fixing bacteria), and mycorrhizal fungi. In our study, we apply two levels of light (full light and light intensity reduced by 50%) and four levels of microbial inoculation (sterile soil, rhizobia, mycorrhiza, and rhizobia x mycorrhiza). Fitness-relevant plant parameters are measured including plant vegetative growth as well as flower and seed production. Our study will provide first insights into potential shifts in functional interactions between plants and plant-associated microbes under light limitation.

The composition and abundance of lipids preserved in lake sediments provides information on the past environment, and changes in this geochemical signal through time may be driven by climate. To understand precipitation changes in the Pacific over the last few thousand years, sediment cores have been collected from lakes on multiple islands, including Poza de Los Diablos and Pozas Verdes on Isabela Island in the Galapagos. Lipids from these sediment cores were solvent-extracted, individual compounds were identified by gas chromatography-mass spectrometry (GC-MS), and abundances of these compounds were quantified using a gas chromatograph-flame ionization detector (GC-FID). Poza de Los Diablos data reveal elevated concentrations of both middle and long chain-length n-alkanes from approximately 1450 to 1850 AD, and indicate an enhanced contribution of material from both aquatic and terrestrial plants during this interval, which may be caused by shifting hydrologic patterns. However, these changes might also reflect a local event such as an altered flow path for surface water due to river or wave erosion. To improve our understanding of paleoenvironmental changes indicated by the Poza de los Diablos data, lipids from cores taken from nearby Pozas Verdes were also extracted and analyzed by GC-MS and GC-FID. Due to their close proximity (<1 km), any climate event that affected Posa de Los Diablo would have also affected Pozas Verdes, but with significantly different modern salinity (Diablos = 10, Verdes = 40) and ecology, each lake is likely to have responded quite differently to changing precipitation patters. By analyzing both records together we seek to improve our interpretation of the past environment.

With global temperature predicted to increase by 1-6 degrees C by 2100, the question of how species will adapt to such a rapidly changing environment is becoming increasingly urgent. Some of the most widely observed responses to climate change have been changes in phenology, or the timing of life-history events such as the timing of migration, flowering, or mating. These apparent adaptations may be the result of genetic evolution or plasticity, and while both can prevent a species from extirpation during rapid environmental shifts, they vary markedly in their long-term effects on population viability. The Pacific salmon, Oncorhynchus, are one group of organisms whose survival is intimately linked to climate conditions. Because salmon die after they spawn, their entire life cycle depends on the success of one spawning season, which in turn depends on their ability to migrate up rivers to spawn during months favorable to their survival. Even small increases in water temperature and flow rates can greatly increase pre-spawning mortality for these fish. Using existing knowledge of Chinook life-history and fine-scale climate projections for the Columbia River Basin, together with an eco-evolutionary model, we assess the potential for Chinook salmon to shift their migration timing to adapt to future climate change. We hypothesize that Chinook are likely to have the evolutionary potential to allow them to avoid spawning during the warmest times on a long-term scale. While this is reassuring for the survival of pacific salmon, in general the extent of adaptability will depend on the life-history of the organism of interest.

The process of cellular reproduction is dependent upon precise timing and coordination of regulatory events. Oscillations in cyclin-dependent kinase (Cdk) activities drive the cell cycle by regulating changes in the phosphorylation states of protein substrates. This dynamic and intricate signaling network of protein phosphorylation is a central component of the cell-cycle control system and enables the cell to modulate cellular functions and processes. Despite extraordinary advances in depth of coverage, phosphoproteomics experiments have struggled to expand in breadth, often comparing thousands of phosphorylation sites between only two moments in time. Such snapshots provide a biased view of the highly dynamic phosphoproteome and ignore important contextual information. To meet this challenge, we are developing robust and reproducible phosphoproteomic methodologies and utilizing mass spectrometry to study the changes in S. cerevisiae phosphoproteome over the course of the cell cycle. I first analyzed the reproducibility of the sample preparation techniques and data acquisition methodologies, which are key factors in the ability to distinguish true differences between different samples. Repeat analyses of 10 identical samples consisting of the entire yeast phosphoproteome were conducted, and preliminary results show that about 70% of the total identified phosphoproteins and 37% of the total identified phosphorylation sites were detected in all 10 repeat analyses with a variance in quantitation of less than 5%, indicating an accurate measurement of changes across the runs. I am now collecting global measurements of relative phosphorylation and protein changes in 5-minute intervals over the entirety of the cell cycle in a synchronously growing population to identify and quantify the proteins present at each time point of the cell cycle. This research will provide a wealth of information on the dynamics of proteome and phosphoproteome regulation throughout the cell cycle and unlock new insights into the biology of defective checkpoints in cancer.

Over the past few decades the budding yeast Saccharomyces cerevisiae has emerged as a prominent model for aging research. One method for measuring aging in yeast is to determine the replicative life span (RLS) of mother cells, defined as the number of daughter cells produced prior to irreversible cell cycle arrest. The Kaeberlein Lab Dissection Team has measured RLS for hundreds of thousands of yeast mother cells over the past few years. In addition to RLS, we have also recently began recording the budding pattern at end of life as an additional phenotype of interest since these mutations have been known to lead to irregular cell cycle regulation. 4 different categories are used to define the terminal morphology of yeast cells: unbudded (U), small bud (S), long bud (L), and clumped (C). From the data gathered thus far, a positive correlation has been made between the terminal budding pattern of cells with reduced RLS compared to their unbudded counterparts. Meaning contructs that stop replicating mid cell cycle (S, L, or C) live shorter lives. We speculate that genomic instability contributes to terminal arrest in the budded state, but further research needs to be conducted to confirm this theory. It will also be of interest to determine how specific genetic defects lead to altered frequencies of the 4 different terminal morphologies and their relationship to replicative life span.

 Amongst other struggles, providing health care suitable for its population's needs remains a major challenge for Nigeria as a nation today. To assess the health of the population and the use of health care services, Nigeria's National Population Commission carried out Demographic and Health Surveys (DHS) in 1990, 1999, 2003, and 2008. Knowing that several states in Nigeria have populations dominated by one of the three major ethnic groups, my project used DHS data to examine how state of residence influences health measures, controlling for all other relevant factors. I used the ordinary least squares - multiple regression method in order to separately analyze the degree of influence each independent and control variable has on determining the aggregate health measures of each state. The health measures I focused on include child malnutrition and diarrhea, female circumcision, and maternal health behavior. In the past, studies have consistently revealed that amongst the three nationally dominant ethnic groups, Hausa people suffer the worst health measures for children and mothers; however, mixed results exist for how well Yoruba and Igbo communities fare relative to each other. This study aimed to clarify the relationship between Yoruba and Igbo dominated states using data from Nigeria's most recent and largest nationally representative sample yet - DHS 2008. I hypothesized that Igbo-dominated states fare worse than Yoruba-dominated states, because the Biafran War mostly damaged infrastructure in "Igboland", and reports indicate that the Yoruba region stands more highly urbanized today, which suggests greater postwar fitness. I also hypothesized that as the number of minority ethnic groups a state hosts increases, the worse the state-level health measures will be, according to predictions from social disorganization theory. If my results support my hypotheses, then Nigeria's future health initiatives should consider health disparities along lines of ethnicity and ethnic diversity within a state.

My research examines fairness and equity in the distribution of three wastewater treatment types across seven counties in the Puget Sound region. I begin my analysis with a thorough exploration into the concepts of fairness and equity, within the context of a variety of disciplines. Drawing on this analysis, I then look into the costs of these different systems, making sure to take into account all applicable considerations, including implementation, maintenance, and repair costs. Specifically, I investigate the costs of combined-sewer systems, separated sewer systems, and onsite septic systems at the household scale. Lastly, I use Geographical Information Systems and spatial analysis to compare the costs of these systems to their spatial distribution through the subject counties, and to the household median income within their respective census tracts. This methodology allows me to uncover any inequities in the way that the costs of these treatment types are distributed, and address a specific instance of fairness within urban planning that has yet to be investigated.

As consumers continue to face high energy bills and the efficient use of resources becomes vital to the sustainability of modern society, the need for a device to intelligently manage electricity consumption grows. The Energy Saving Butler, a computer system to be installed in homes and workplaces, seeks to meet this need by simultaneously minimizing the cost and unnecessary use of electricity--all without inconveniencing the users. The Butler is true to its name: acting behind the scenes and within the confines of the household's schedule, while working to allocate electricity efficiently and discreetly. Our team has conceptualized the features and functions that will drive the future technical design of this device. Based on data from the power company and data on appliance use, the Butler can delay or initiate tasks, such as laundry and dishwashing, so that they occur at times where power rates are at their lowest. Using a complex and dynamic priority level system, this control of power allocation is designed to work within the user’s schedule. If the user is having a dinner party one night, for example, the Butler will automatically suspend its own activities so as to not interfere with any social functions. If that user also finds his or herself driving home on a cold night, that user’s smart-phone can notify the Butler when it is within a 10-mile radius, so that the Butler can turn on the home’s heating. With these and a wide array of other practical features, we feel that the Energy Saving Butler will go a long way in saving consumers' money and working to stabilize the over-burdened power grid. It’s appealing to the consumer; it’s appealing to the utility companies; it’s a step in the right direction for a more sustainable society.

Drug targeting is highly advantageous because the ability to deliver drugs exclusively to specific cells or organs reduces both the dosage and toxicity effects associated with nonspecific administration. However, targeted delivery of therapeutics is still challenging due to lack of an efficient drug carrier design. Carbohydrate complexes, such as glycolipids and glycoproteins, serve as cellular markers and receptors universally found on the outer membranes of mammalian cells. These glycoconjugates distinguish different types of cells from one another and enable cellular recognition and adhesion. Both the immune system and foreign pathogens rely on these glycoconjugates to bind and enter host cells. For viruses and bacteria, adhesion to host receptors is the first step towards infection. Because of this broad physiological usage, carbohydrates must be highly diverse, with each carbohydrate corresponding to a different receptor. By mimicking nature’s mechanism of cellular adhesion, chemists are using carbohydrates to target specific cells for drug delivery. The designed glycopolymer, as a potential drug carrier, is composed of two main components: carbohydrate for targeting cells in cell-specific manner and pyridal-disulfide (PDS) groups for bioconjugation and fluorescent labeling. In the first step of the synthesis of the glycopolymer, three different glycomonomers (mannose, galactose and N-acetyl-glucosamine) have been synthesized and characterized in order to construct structurally well-defined glycopolymers. Each glycomonomer can be utilized for the synthesis of reversible addition-fragmentation chain transfer (RAFT) glycopolymers. This carbohydrate-based polymer construct has promising potential in targeted drug delivery for its reduction in toxicity and increase in drug efficacy.

Flight control in dynamic environments is a complicated task that many animals accomplish with ease. It requires rapid integration of sensory input as well as balancing long-term planning with reflexive behaviors. The giant hawk moth Manduca sexta is a useful model organism for studying flight control because its physiology is well understood and it is easy to rear in captivity and work with experimentally. In order to make flight control adjustments, Manduca constantly integrates information from slow-sensing visual sensors and fast-sensing mechanosensory organs. Both visual motion and mechanical rotation elicit strong abdominal reflexes in Manduca during tethered flight, however the exact role of the abdomen in flight is unclear. Previous work has suggested that abdominal reflexes help maintain flight stability, but it has not been shown that the abdomen is actively used for control. The goal of my research is to determine if Manduca can actively use their abdomen to stabilize the visual field. To answer this question, I have created a virtual flight arena composed of a projection system, magnetic tether, and IR sensor. The visual stimulus is projected onto an acrylic dome within which the moth is suspended by the tether. The experiment consists of a system where the moth controls the velocity of a horizontal bar displayed on the dome with its abdominal position. The bar has an initial velocity that the moth counteracts by moving its abdomen in order to stabilize the visual field. The precision of the moth’s abdominal control capabilities can then be tested by differing the initial velocities of the bar and varying the way that abdominal position controls the bar’s velocity. In addition to answering my research question, this project provides a framework to study the general multi-input multi-output problem in neural control.

Under constant volume muscle contraction myofilament overlap increases and muscle expands radially. While myofilament overlap is considered a major factor in force generation, considerably less is known about the role of myofilament expansion accompanying shortening during contraction. Recent theoretical evidence suggests that the spacing between filaments will indeed be an important determinant of force generation at any level of filament overlap, however, there are scant data that show the extent to which filament overlap changes in intact muscles. To address this issue we performed work loops on intact Manduca sexta flight muscles while simultaneously measuring myofilament spacing, force, and length using time resolved small angle x-ray diffraction imaging. Muscles were stimulated at 25 Hz and held at a temperature of 35C while simultaneously measuring length and force. Five x-ray images were taken during each wingbeat cycle for 100 contractions. These images were averaged over all cycles, and lattice spacing was measured for each phase. During work loops with a 6% strain cycle, lattice expansion changes by 2.77 ± 0.839%. Thus we do not reject the constant volume assumption, which would predict a 2.4% change in radial dimension for a 6% longitudinal strain. Taken together these data suggest that lattice expansion during muscle shortening is a critical component of muscle force generation.