This research uses multi-agent simulation to explore the sustainability of different types of water supply networks. Sourcing, collection and storage, treatment, and distribution are all defining components of water supply chains. A functional water supply chain is one that supplies water to the end user in sufficient quantity and of sufficient quality. Factors such as pressure-driven leakage, fluctuating water supply, and seasonal water quality issues all affect water availability and delivery. To explore how water supply networks compare on a systems level, each supply chain type is modeled using a stochastic, multi-agent simulation platform. This platform allows statistical analysis of water supply systems under varied internal and external system conditions to gain insight into the strengths, weaknesses, and potential sustainability of each type of network. This research enables side-by-side water supply network comparisons that are unavailable in the real world, and is applicable to water supply network design and re-design.

Identifying the sources of sediments that make up an archaeological site can be useful for understanding changes in site formation processes. Changes in site formation processes can relate to climate change and changes in the human use of the site. We analysed sediments from Klipfonteinrand, a Middle Stone Age site in western South Africa and sediments from seven potential source locations in the surrounding landscape. We used an acid digest procedure to extract elements from the sediments and identified and quantified 34 elements in the sediment extract using ICP-AES. Our results revealed elemental profiles of major geologic units in the landscape and changes in the source of sediments in the archaeological deposit. We explore the implications of these changes for our understanding of palaeoclimate, human history and human-environment relations at this site.

Geoarchaeological analysis of sediments collected during recent excavations of Khao Toh Chong, (KTC), rockshelter in Southwestern Thailand has provided detailed results describing the natural and cultural processes influencing site formation and occupation. This region has a complex history of sea level change during the Holocene but the prehistoric human responses to these changes are not well understood. Palaeoclimate records are sparse because of the lack of typical proxies such as pollen cores. To better understand the human-environment relationship in prehistory, this study characterized the sediment profile and utilized changes in stable carbon isotope ratios of soil organic matter (SOM)  to identify and interpret shifts between ancient C3 and C4 vegetation communities. These two types of plant communities may indicate palaeoclimatic conditions with periods dominated by C3 plants representing cool, wet, and cloudy climates and periods dominated by C4 plants representing hot, dry environments. The stable isotope data are interpreted in context of other geoarchaeological analysis and the material culture recovered from the site. This is the first study of stable carbon isotopes in SOM at an archaeological site in mainland Southeast Asia. These palaeoclimate and archaeological data, in combination with sea level data, give us a more detailed understanding of the human-environment dynamics in this region.

This study focuses on how the global efforts of a politically active and increasingly visible movement of adult autistic activists are challenging the common framing of autism and shifting the contemporary autism debate. Common representations throughout the autism field contextualize the autistic experience through diagnostic categories of difference, constructed primarily by psychologists, neurologists, educators, and service providers. These characterizations are determined through observational criteria such as delayed communication, repetitive physical behaviors, and marked deficits in social skills. While the deficit mindset dominates the media and the public perception of autism, there is a lack of attention and research on how the social impact of these ‘perspectives from the outside’ influence the lived experience of autistic adults. This work counters the hegemonic deficit interpretation by investigating the multiple meanings of autism, and studying whether politicized tensions over autistic representations—and misrepresentations— influence public conversations surrounding service delivery, treatment design, and provisions of care. Drawing on qualitative cultural research methods including narrative, textual and image analysis, as well as ethnographic field notes, this study critically analyzes the lived experience of adult autistics and their efforts to re-humanize public assumptions about autism while living in a society, they suggest, that stigmatizes their experience as emotionally isolated, socially deficient, and mentally diseased. I analyze the socio-political discourse of autism and the conflicting representations put forth by medical professionals, mainstream media, institutions, scholars, and—autistics. These contradictory interpretations produce a cultural system of difference engaged in debate over autistic autonomy, self-determination, and justice. To critically engage this ‘culture war’ this inquiry considers who has the right to speak for the autistic community? Whose values are characterized as authentic by the public? Finally, this investigation asks, can autistics redefine autism and how will this definition reframe their position in political discussions about them? 

When massive stars reach the end of their lives, they erupt in enormous explosions known as supernovae, leaving behind clouds of shocked gas and dust known as supernova remnants (SNR). The primary technique to measure the mass of the progenitor star requires waiting for the star to explode and examining pre-explosion Hubble Space Telescope archival images of the site, which may or may not exist. This technique is constrained by rarity of supernovae, and as such only ~25 progenitors have any mass constraint whatsoever in the literature. We employ an alternative technique in which we examine color-magnitude diagrams of the regions surrounding known supernovae to measure their star formation history. We then use this star formation history to assign an age to the progenitor star.  By employing stellar evolution models, we convert this age to a mass. Because we do not rely on identification of the specific progenitor star in the images, we are free to apply our technique to cataloged SNR, drastically increasing the number of available targets. We apply our method to ~135 cataloged remnants in the nearby spiral galaxies M31 and M33, representing a dramatic increase in the number of currently known masses. We examine the distribution of these derived masses and comment on implications for supernova physics.

Mitochondrial dysfunction and oxidative stress have been proposed to contribute to organismal aging. In the nematode C. elegans, reduction of mitochondrial function through knockdown of genes encoding components of the electron transport chain (ETC) is sufficient to increase life span. The increased longevity is not solely the by-product of decreased oxidative damage generated by the ETC, but also involves induction of the mitochondrial unfolded protein response (UPR^mt), as evidenced by the observation that life span extension requires an intact UPR^mt. The cytoplasm, endoplasmic reticulum, and mitochondria have each evolved compartment-specific signal transduction pathways to alter nuclear gene expression in response to perturbations in protein homeostasis. However, little is known about the UPR^mt and the mechanism by which unfolded proteins are recognized in the mitochondria and signal changes in gene expression. Previous studies demonstrate that knockdown of ETC components and a subset of mitochondrial proteins induce the GFP reporters for mitochondrial chaperones hsp-6 and hsp-60. To identify novel genes involved in the UPR^mt, we are performing a forward genome-wide RNAi screen using the hsp-6::GFP reporter and measuring UPR^mt activity by fluorescent microscopy. Upon completion of the screen, we expect positive hits to include mitochondrial proteins, signaling molecules, and transcription factors that regulate the UPR^mt. Consistent with previous studies, gene knockdowns that have robustly induced the UPR^mt thus far in our screen are largely components of the ETC. In addition, the screen has yielded many novel hits including genes outside of the mitochondria and of unknown function. After the screen is complete, we will validate the RNAi clones that induce the UPR^mt and perform lifespan experiments to understand how the UPR^mt is involved in the aging process. Our screen will further understanding of how the mitochondria and nucleus communicate with one another in order to maintain mitochondrial proteostasis and illuminate how mitochondrial stress contributes to aging.

"The S.P.O.T.", which stands for Students in Partnership for Organizing Transformation, began constructing a physical space on the University of Washington Bothell (UWB) campus in the fall of 2011. This space is meant to serve as a multipurpose room for recognized student organizations (RSO) to collaborate in creating a campus culture inclusive of diversity, representation and open dialogue. The purpose of this study is to critically analyze how The S.P.O.T. exists as a site of struggle, produce by the complex interplay of passionate and influential social actors including The Office of Student Life, RSO leaders, and dedicated faculty. I also document how RSO leaders negotiate public space on campus in an effort to mobilize the wants and needs of their organization. I have conducted a series of in-depth interviews with RSO leaders, participated in several UWB Club and Innovation Forums, and spent months directly observing how students attempt to understand public space on campus. Through this research I argue that The S.P.O.T., designed with the purpose of igniting social change, has itself become a powerful social actor in shaping students understanding of UWB initiatives and policies. RSO leaders must continually employ a series of strategies to maintain visibility and legitimacy in a constantly shifing sociopolitical landscape. By unraveling the unseen forces behind the creation of student spaces, such as The S.P.O.T., and exposing the limitation, as well as the potential, we can better understand how students make sense of complex social issues. This research is necessary if students, RSO leaders, and faculty are committed to increasing awareness, respect, and understanding by transforming physical space on campus.

Membranes are used frequently in water filtration to remove bacteria and contaminants from fresh water. Natural organic matter (NOM) collects inside the permeable membrane, and causes resistance against the water flow. As NOM collects, more force is required to move water through the membrane, and the energy required to continue the process increases. When the pressure required to move water through the membrane has increased, the membrane has fouled. This project examines the filtration and adsorption of NOM in fresh water obtained from Lake Washington. Heated aluminum oxide particles (HAOPs) act as an adsorbent layer, trapping NOM and protecting the membrane from fouling. The HAOPs protect the membrane by collecting and removing NOM through deposition and backwash cycles. During deposition, twenty grams per meters squared (g/m²) of HAOPs are pumped inside a plastic, tubular membrane with a pore size of 2-3 microns. Lake water is then pumped through the membrane at a flux rate of 200 liters per meters squared per hour (lmh), and trans-membrane pressures are measured within the system. Trans-membrane pressure is measured to calculate the amount of pressure necessary to move water through the membrane. Samples are collected periodically throughout a 20 hour run time and analyzed for UV absorbance. UV absorbance measures the amount of light able to transmit through a sample of lake water; the amount of light that travels through the water correlates with the amount of contaminants or NOM that remain in the water. HAOPs successfully remove NOM molecules and protect the membrane, preventing it from fouling quickly. 

Chronic infections with Pseudomonas aeruginosa are a significant cause of deterioration of lung function in patients with cystic fibrosis (CF), and have substantial clinical importance due to their marked resistance to treatment with antibiotics. Furthermore, existing laboratory methods for testing bacterial susceptibility to antibiotics are poor indicators of clinical response to therapy, which further increase the difficulty associated with treating these infections. Current research shows that phenotypically diverse P. aeruginosa subpopulations evolve within a single patient during prolonged infection, and that clinical antibiotic therapy causes some of these subpopulations to change significantly in relative abundance. Observed changes in abundance following antibiotic treatment signify varying degrees of antibiotic susceptibility within each patient’s P. aeruginosa population as a whole, with an increase in a particular subpopulation abundance indicating resistance, and a decrease in a particular subpopulation abundance indicating sensitivity. As previous studies have only evaluated P. aeruginosa antibiotic sensitivity prior to antibiotic treatment, we attempted to demonstrate the correlation between an increase subpopulation abundance following clinical treatment and the degree of resistance to antibiotics in laboratory testing. This was done by evaluating the antibiotic minimum inhibitory concentration (MIC) of a range of isolates collected from CF patients who had undergone antibiotic therapy, using antibiotics which had been given to each patient in clinical treatment. Our results demonstrate a marked lack of correlation between relative subpopulation abundance and antibiotic MIC, with clinically resistant subpopulations showing the same or lower MIC than subpopulations which were clinically sensitive treatment. We conclude that isolates resisting treatment do not have a different MIC than isolates responding to treatment, suggesting that mechanisms other than classic antibiotic resistance are responsible for treatment resistance in the CF lung. Further studies to evaluate these mechanisms, such as biofilm formation and formation of persister cells, are currently under way.

Retrotransposons exist as genetic elements within chromosomal DNA that can replicate themselves and move to new locations within a genome, using a process involving an RNA intermediate. They are a widespread class of transposable elements, abundant in plants, fungi, mammals and yeast. One type of retrotransposon is a Long Interspersed Nuclear Element (LINE). Unlike most retrotransposons, LINEs have no long terminal repeats (LTR) and they possess a poly A tail which defines the 3’ terminus of the element. They are several kilobases long and contain two open reading frames (ORFs) encoding a gag protein (ORF1) and endonuclease and reverse transcriptase domains (ORF 2) conferring the element’s ability for retrotransposition. Due to incomplete insertion attempts, many 5' truncated copies of LINE elements are present in the Rhododendron genome. A family of LINE elements called RLINE and several related 5’ truncation fragments have been discovered in Rhododendron williamsianum. I used PCR primers to amplify the regions of the genome in R. williamsianum where truncated RLINE insertions were found. The amplified DNA was then sequenced by Sanger sequencing. I am analyzing ten 5’ truncation fragments ranging from 692- 2918 base pairs. By phylogenetic analysis of aligned sequences common to the various full-length and deleted RLINES, I will endeavor to determine the evolutionary relationships of the truncated fragments to the full length RLINE and to one another. So far, I have sequenced and compared 8 different RLINE fragments of Rhododendron williamsianum, and will continue characterizing RLINE insertions.

Cooperation is a fascinating paradox of evolution. Why would an organism incur a cost to itself in order to benefit another individual? The Achilles’ heel of cooperation is that it can be exploited by cheaters. Cheaters reap the benefits of cooperation, but do not incur the same costs as the cooperators. Cheating is therefore considered a major problem in the evolution of cooperation. One possible way of reducing the vulnerability of cooperating organisms to cheating is through communication. Communication allows individuals to cooperate only when the conditions are favorable. My research involves a form of bacterial communication called quorum sensing, which allows bacteria to accomplish cooperative tasks that require a collective action. Pseudomonas aeruginosa, an opportunistic pathogen that causes severe infections in immuno-compromised individuals and patients with cystic fibrosis, uses quorum sensing to regulate the production of toxins and enzymes. We used a wild-type cooperating strain of P. aeruginosa and several non-cooperating cheater strains to investigate the relationship between cooperators and cheaters. We predicted that the cheater strains would benefit when grown together with cooperators in a well-mixed environment, but suffer in a structured environment. We tested this prediction through competition assays in both a shaken liquid environment (unstructured) and a soft-agar environment (structured). Combined with further research, our results may suggest that communication helps a cooperating population avoid collapse when faced with cheaters.

Evolutionary biology studies how populations change over time. For evolution to occur, there must be genetic variation, ultimately from mutation. Any mutation in a given environment may have a positive, negative, or neutral effect on fitness. Evolving populations tend to increase in fitness. A metaphoric “fitness landscape” is useful for visualizing this, with genotypes linked by mutations and elevation being their fitness. Fitness “peaks” denote genotypes from which all mutations are deleterious (downhill). If the landscape is smooth (possessing only one peak) then populations will always converge there by natural selection. However, if the landscape is rugged (multi-peaked), populations might get stuck on a low-fitness peak. This population must cross the “valley” between peaks to reach the higher peak. We are studying how migration patterns between subpopulations of Escherichia coli influence adaptation. Structured populations only allowed migration between nearby subpopulations of bacteria, while unstructured migrations occurred between any of the 95 other subpopulations of bacteria. We found that structured populations reached a higher fitness than unstructured ones. My project is investigating the genetic mechanisms behind these results. Using Illumina technology, I have completed whole genome sequencing and targeted sequencing on these populations. I am using these results to determine the type and frequency of mutations acquired in structured vs. unstructured populations. We have two hypotheses explaining structure’s effect on adaptation: the Mutational Distance Hypothesis and the Diversity Hypothesis. The Mutational Distance Hypothesis predicts that there will be more mutations accumulated in the structured populations than the unstructured, whereas the Diversity Hypothesis predicts that structured populations will have greater genetic diversity than unstructured populations. This work will lead to a greater understanding of adaptation and may have medical implications concerning the understanding bacterial evolution.

Genus Rhododendron consists of over 1000 species of woody plants.  While the overall phylogeny of the genus is known, the relationships between species are not.  My research focuses on a small and unusual retrotransposon, Cassandra, and its possible use for evolutionary studies.  Retrotransposons are sequences that are able to move to new DNA chromosomal locations via mechanisms simlar to retroviral DNA replication.  Transposition involves transcription of an integrated DNA copy through an RNA product that acts as a template for reverse transcription, and finally integration of the resulting DNA at new sites in the plant genome.  Like other retrotransposons, Cassandra has no mechanism for complete excision from a site it has occupied.  Thus, once the element is inserted into a genomic site, all or part of it is retained at this position as a stable marker.  Consequently, a Cassandra insertion at a given site is a shared derived trait, suitable for evolutionary tree-building.  Ultimately, knowing these sequences of transposition may shed light on the pattern of evolutionary divergence of Rhododendron and Ericaceae plants.  Based on one insertion site, my data suggests that thus far, only a solo LTR version of the Cassandra element is found in most species of the subgenus Hymenanthes (primarily in East Asia), with an empty site found in the subsection Pontica (more geographically diverse).  Interestingly, for a few species within Hymenanthes that lack the element, another conserved insertion (approx. 450 bp) is found in the DNA instead.  Moving forward, I will look at additional insertion sites, to gain further information on Rhododendron phylogeny.