In the last 30 years temperature has risen 0.6°C per decade in high latitude regions, twice as fast as the global average. This extreme warming is causing perennially frozen ground (permafrost) to thaw, thereby changing subsurface hydrology and exposing previously stored, deep millenial-aged soils to microbial activity. These changes are stimulating greater organic matter mineralization and emissions of potent greenhouse gases (GHG), carbon dioxide and methane (CO₂ and CH₄). The magnitude of soil carbon mobilization is poorly contained, in part because it is unclear what fraction of GHGs are emitted to the atmosphere directly, versus released to above ground aquatic networks. To better define the role of streams in the changing arctic carbon cycle, we explored headwater stream carbon chemistry in 10 individual catchments situated in a remote and understudied subarctic landscape of interior Alaska. We found an unexpected, positive relationship between CO₂ and CH₄ across streams, with concentrations peaking in the summer for CO₂, and fall for CH₄, suggesting stream emissions peaked when soil active layers were deepest and permafrost carbon layers were most hydrologically engaged. The positive relationship between surface water temperatures and the concentration of each gas reflected these strong seasonal shifts in stream GHG content. Organic carbon content in stream water was also linked to CO₂ but not CH₄, indicating potential differences in sources and sinks of each GHG that are currently being explored with ongoing stable isotope analyses. Taken together, our findings show that closer-than-expected coupling of CO₂ and CH₄ may make some streams much greater emissions hot-spots than others, and that accounting for seasonality is critical for understanding the greenhouse gas budget of individual streams. 

While there is an abundance of computational tools for protein design, the vast majority of them focus on static structures. Data for the most probable rotamers of an amino acid are often obtained from mining its appearances across crystal structures, which do not take into account the native dynamics or conditions of a protein. Additionally, conformational secondary structure propensities are often derived from the frequency that an amino acid appears within a certain range of dihedral backbone angles in static structures. However, these data do not emulate realistic conditions, because proteins are dynamic and surrounded by solvent; thus, incorporation of dynamic data should improve the design process. Wrangler, our in-house software for peptide design, integrates dynamic data for both rotamers and secondary structure propensities. The data are obtained from molecular dynamics (MD) simulations in explicit water, taking into account interactions with surrounding solvent to better sample the most probable conformations. Several amyloid peptide aggregation inhibitors were designed using Wrangler’s scoring metrics to validate the software. These inhibitors were shown via MD simulations to better retain secondary structure than our current standards. Future work involves synthesizing the peptides in the wet lab to determine whether they experimentally perform better than our current inhibitors.

The Lyman-alpha power spectrum has previously been used to constrain the Universe’s initial conditions and particle constituents (such as the amount and mass of the dark matter) and the temperature of intergalactic gas (which constrains reionization processes). To further improve these constraints, we use another Lyman series transition (Lyman-beta). The Lyman-beta absorption cross-section is lower than that of Lyman-alpha so it probes the intergalactic medium at higher densities where Lyman-alpha features are saturated. Therefore, the Lyman-beta forest allows for a better measurement of the slope of the temperature-density relation, allowing additional constraints on reionization and the subsequent thermal evolution. In this work, we present an analysis of the Lyman-beta power spectrum using the VLT/XSHOOTER XQ-100 Legacy Survey.

Wildfires play a major role in the structure and composition of landscapes and the general ecology of the Pacific Northwest. The Klamath-Siskiyou eco-region in northern California and southern Oregon has been experiencing an increase in the frequency, scale, and intensity of wildfires in recent years. Understanding the effects of wildfires on small mammal communities is an important, yet understudied, aspect of the response of wildlife to wildfires. In 2014, two wildfires burned areas on and adjacent to a long-term study area of wildlife. We will investigate the effects of these wildfires on the occupancy of small mammals such as Neotoma fuscipes, Glaucomys sabrinus, and Tamiasciuris douglasii, using occupancy analyses of data collected during fall field seasons using track plate stations. The longitudinal data set that we have includes years of data before the fires occurred, allowing us to disentangle any effects of the wildfires from any naturally occurring variation. This research is important in determining what lasting effects these increases in wildfire frequency are going to have on predator-prey dynamics.

Glutaredoxins (GRXs) are small oxidoreductase enzymes that can reduce disulfide bonds in target proteins. The genome of the model plant Arabidopsis thaliana has more than 30 GRX genes, but the biological function of most of these GRXs is unknown. We previously found that a small group of Arabidopsis GRX genes is specifically activated by nitrate, a common source of nitrogen in the soil. In order to better characterize the function of one of these nitrate-regulated GRXs, AtGRX660, we generated transgenic Arabidopsis plants that continuously overexpress the AtGRX660 gene. We isolated RNA from 12 independent transgenic lines and quantified AtGRX660 mRNA levels via real-time reverse transcriptase PCR. Three elite lines displaying >100-fold increase in basal AtGRX660 transcript levels were selected for further analysis. AtGRX660-overexpression lines and wild-type plants were grown on soil in a controlled environment growth chamber for characterization of shoot phenotypes, and on vertically-orientated plates of plant growth media for characterization of root phenotypes. All AtGRX660-overexpression lines displayed a dwarf shoot phenotype, with significant reductions in shoot biomass, total leaf area, and silique length compared to wild-type plants. In addition, root system architecture was highly altered. While primary root growth was normal in the transgenic plant lines, lateral roots were almost completely absent. Phase contrast microscopy demonstrated that lateral root primordia develop in the transgenic lines, but these primordia do not elongate and emerge from the primary root. Overall, these results suggest that AtGRX660 acts a negative regulator of shoot organ development and inhibits lateral root elongation. Our findings could have agricultural relevance in plant drought tolerance, since AtGRX660 differentially affects primary root system growth (root system depth) and lateral root system growth (root system breadth).

In recent decades, increased nitrogen (N) pollution in coastal aquatic ecosystems caused by increasing agricultural and urban activities has led to extensive habitat degradation and loss, change in the structure of aquatic food webs, and higher frequency of hypoxia. Nitrogen is ubiquitous in the biosphere, entering coastal environments through multiple pathways including ground- and surface waters, plus atmospheric deposition. The fate of much of the N entering coastal environments is not well established. In particular, the magnitude of N consumed at coastal margins, versus exported to downstream estuaries is poorly constrained. It is widely recognized that inland wetlands are important N sinks, as they are sites of fixation of reduced N to inert dinitrogen gas, however the role of coastal wetlands as N sinks is more difficult to establish due to the dynamic nature of these tidal environments. Here, to better understand the role of coastal wetlands in the global N cycle, we established a high-resolution budget of nitrate (the most abundant form of reduced N) from 9/12/2017 to 10/12/2017 at First Mallard Slough within the Suisun Marsh complex, a brackish tidal marsh in the San Francisco Bay Estuary. We modelled nitrate concentrations at 15-minute intervals using a submersible ultraviolet nitrate analyzer (SUNA), and matched these estimates with simultaneous hydrodynamic measurements of water flux. Data were synthesized in Python to establish 15-minute resolution estimates of nitrate mass exchange, showing that the wetland exported a net total of 2.54 Mg of N as NO₃^2- over the complete measurement period, or 84.6 kg N per day. Contrary to other studies showing wetlands are important nitrate sinks, our result revealed that the Suisun Wetland complex was an important N exporter to the San Francisco Bay Estuary, at least over the period measured here. Longer-term observations are needed to confirm this pattern at a complete annual scale.

Sarcopenia, or age-related of loss of muscle mass and function, is associated with a decline in quality of life for elderly populations and few effective treatment options. Sarcopenia is linked to mitochondrial dysfunction and elevated mitochondrial oxidant production. We are investigating the role of mitochondrial oxidative stress in sarcopenia using a mitochondrial targeted therapeutic and a mouse model of accelerated sarcopenia. SS-31 is a mitochondrial targeted peptide that associates with cardiolipin, decreases oxidant production, and increases ATP production. Superoxide dismutase 1 knockout (SOD1KO) mice lack superoxide dismutase 1 (an enzyme that converts the oxidant superoxide into hydrogen peroxide and molecular oxygen) resulting in an accelerated sarcopenia phenotype. We are testing whether treatment with SS-31 preserves muscle function in the SOD1KO mice. We hypothesize that improving mitochondrial function with SS-31 treatment will delay the decline in muscle function in the SOD1KO mice. To test this, we are administering SS-31 to SOD1KO mice through surgically-inserted osmotic pumps for 8 weeks between 3 and 5 months of age (the published timeframe for the onset of skeletal muscle decline in SOD1KO mice) and performing in vivo muscle function measurements of the gastrocnemius before pump insertion and monthly after pump insertion for 3 months. We compare muscle functional measurements with histological and biochemical analyses of mouse tissue samples upon euthanasia and determine skeletal muscle fiber type, metabolite and protein concentrations, and muscle fiber respiration and oxidant production. We expect SOD1KO mice with SS-31 to have a lower rate of decline in muscle force production and increased fatigue resistance over time, higher max ATP production, and decreased oxidative stress. The effect of SS-31 on muscle function, mitochondrial quality, and redox homeostasis has exciting potential as a translational therapeutic treatment for human sarcopenia.

Pacific sand lance (Ammodytes personatus) are an important forage fish in the Salish Sea that spend large portions of their time buried in sediment. Five important A. personatus habitats, including San Juan Channel (SJC), Sucia Island (SI), North Peapod Island (NPI), Salmon Bank (SBnk), and Iceberg Point (IP), have been documented by students in the Pelagic Ecosystem Function apprenticeship at Friday Harbor Labs since 2010. Continued sampling efforts have led to extension of an important time series at these sand wave fields throughout the San Juan Archipelago, as well as three new sites. New sites include Hein Bank (HB), North Waldron Island (NWI), and Puffin Island (PI). Both HB and NWI had A. personatus present, while PI did not. A synthesis of data from previous years showed sediment type at Sucia Island and North Peapod Island are most similar to each other, while San Juan Channel and Salmon Bank both have a large variation in sediment type. Shell hash is a prominent portion of many A. personatus habitats. Previous studies of these wave fields have treated shell hash as analogous to typical geologic sediments, however this study aimed to examine the divergence of shell hash physical dynamics from what is generally expected. The irregular shape of these biologically-derived sediments leads to a relationship between diameter and minimum settling velocity that is the opposite of what is expected for geologically-derived sediment particles. Of the shell hash tested (n=70), the maximum velocity was relatively consistent, and differences in settling velocity between diameters was seen in minimum velocities. These results have implications for understanding net transport throughout the system where different sediment types are present, understanding how sorting and packing of shell hash impact the habitat quality for A. personatus, and how differing amounts of these materials may distinguish these important benthic habitats.

Spinal cord injury (SCI) is often a life changing and debilitating condition, where the loss of sensory and motor capabilities can be accompanied with bladder, bowel, respiratory and other dysfunctions. It is known that traumatic SCI causes an almost a complete loss of blood flow at the site of injury, as well as significant hypoperfused regions surrounding the injury, resulting in progressive cell death referred to as secondary injury. Counteracting secondary injury of spinal cord tissue, referred to as "rescue-able" tissue, is an active area of neuroprotective research. Surprisingly, there are no existing techniques to detect and assess contused spinal cord tissue at risk for secondary injury clinically or pre-clinically. In this work, we present an approach to visualize and quantify the blood flow changes after SCI by imaging microbubbles, an intravascular contrasting agent, with ultrasound following intra-venous injection. Nonlinear Doppler sequences were programmed on a research platform where Doppler processing separates microbubbles in the vasculature from background tissue signals. Our preliminary data demonstrate the ability to visualize changes in blood flow resulting from SCI in a rodent model. We will present results characterizing differences in blood flow associated from different injury severities. The nonlinear Doppler sequences are used to quantify the different characteristics of low velocity blood flow changes in the smaller vasculature and higher velocity blood flow changes in the larger vasculature. In addition, the passage of a bolus injection of microbubbles also highlights differences in blood flow in the contused and surrounding spinal cord tissue. Once translated, this ultrasound imaging technique could assist in detecting and monitoring local tissue perfusion at the injury site, ultimately improving SCI patient outcomes.

The use of targeted microbubbles to image the molecular expression of vascular factors is an active area of ultrasound research. Combining the imaging advantages of ultrasound (e.g. cost, ease of use, availability) with the potential of molecular imaging makes targeted microbubbles especially attractive for studying the expression of vascular factors. During imaging, signals from molecularly attached microbubbles need to be separated from signals of non-attached free-flowing microbubbles in the vasculature. Thus far, different indirect approaches have been used to isolate stationary microbubbles. In this work, we present a direct approach to classify bound microbubbles in the presence of free-flowing microbubbles by processing nonlinear Doppler acquisitions. Nonlinear Doppler sequences are programmed on a research platform where Doppler processing separates low frequency stationary microbubbles signals from high frequency flowing microbubbles signals. In-vitro experiments are conducted by imaging stationary microbubbles surrounded by free-flowing microbubbles in a dialysis tube. In-vivo experiments are conducted by applying this approach to image the extent of inflammation associated with spinal cord injury (SCI), which plays a critical role in progressive tissue loss after injury. Both targeted and non-targeted microbubbles have been imaged in a rat SCI model. Targeted microbubbles were made for the inflammation marker p-selectin. Our in vivo results show successful separation of a limited number of non-targeted microbubbles adhering around spinal cord contusions. We believe this may be due to interactions between microbubbles and activated leukocytes. We expect to observe increases in bubble adherence and differences in the spatial distribution in using targeted bubbles, hopefully elucidating the extent of inflammation due to SCI. This work demonstrates the potential to separate bound targeted microbubbles from of free-flowing microbubbles to image a vascular factor for inflammation, which demonstrates practical pre-clinical ultrasound molecular imaging and opportunities for broader applications.

Many communities of color have been disenfranchised as a result of interactions with the criminal legal system. While many studies have shown that access to higher education reduces recidivism and encourages upward mobility, a very small percentage of this impacted population are actually able to access institutions of higher education. Therefore, the purpose of this research is to address the disparate representation of system-impacted individuals in higher education. This project aims to answer and begin to respond to the following questions: 1) What are the challenges and outright barriers for system-impacted students who wish to continue their education at UW? 2) What can UW do to make it a feasible destination for students who are system-impacted? This research project includes: the collection and analysis of existing data on system-impacted individuals and access to higher education; interviews with UW administrative offices that may play a role in the access to higher education for system-impacted individuals. Thereafter, a working group consisting of: system-impacted individuals; system-impacted students; students interested in criminal justice reform; and UW faculty interested in criminal justice reform; will form and implement strategies on how to lower institutional barriers and create clearer pathways to the UW for system impacted-individuals. By building partnering strategies with the UW community, the goal of the Pathways to UW project is to develop more clearer and transparent pathways for individuals who have been system-impacted to enroll on UW campuses. I want to ultimately build a community and a working network on campus that supports access and welcomes individuals impacted by the criminal and immigration system. Currently, there is no system in place on campus that supports such a marginalized population. To have such a system in place would address many racial and class disparities among the marginalized communities these impacted individuals traditionally come from.

Ion Mobility-Mass Spectrometry (IM-MS) is an analytical technique that is useful for analyzing large biomolecules with minimal disruption to their natural structure. One of the most common methods of introducing proteins to the gas phase in IM-MS is electrospray ionization (ESI), whereby a large voltage applied to a sample induces a spray of droplets that quickly evaporate and leave the desired analyte as a gas-phase ion. It is established that the high voltages of this process lead to a buildup of charge via electrochemistry in the sample solution, which may cause changes to the pH of the solution. However, this phenomenon has primarily been characterized in systems with continuously replenishing samples that form a steady state between excess charge formation and incoming sample flow. This work establishes a method to identify these changes in small, non-replenishing systems, which have not yet been characterized and are the standard practice for IM-MS analysis of proteins. Using SNARF-4F, a pH-sensitive fluorescent dye; a series of filters and a camera; and Python scripts for image processing; the rates and spatial position of pH changes under non-equilibrium conditions were determined with high accuracy. Additionally, several methods of preventing or slowing pH changes are examined. These include the use of buffers such as ammonium dihydrogen phosphate and ammonium bicarbonate, or periodic cycling between positive and negative electrospray. Preliminary findings indicate that these buffers can affect pH change, but at high enough concentrations, may also reduce the quality of mass spectra.

For many globular proteins, the sequence and native structure are known. However, less is understood about how a string of amino acids folds into a functional protein. Experimental study of folding presents challenges due to the transience and variability of folding/unfolding transition states and intermediates. Alternatively, computational study of unfolding can provide significant insight into folding. Here, molecular dynamics simulations have been used to study the unfolding pathways of the SH3 domain structural family and to investigate the factors that determine the path and outcome. To separate folding determinants from amino acid sequence, 17 SH3 proteins were chosen with an average sequence identity of only 27%. Six unfolding simulations were performed for each protein, and the unfolding transition state ensemble was identified by locating the large, rapid conformational changes that signal the start of unfolding. Contact analysis was used to characterize the structure of the transition states ensembles. Two general pathways at the transition state were identified, distinguished based on the specific β-sheet structure lost at the transition state. In the first, more populated pathway contacts in the β-sheet containing the N- and C- terminal β-strands were lost while the second pathway was defined by structure loss in the other β-sheet. Though many of the investigated proteins went through both pathways in different simulations, most showed a clear bias towards one pathway. This work demonstrates that similar protein structures can fold through different pathways. The bias of many SH3 proteins towards one folding pathway also suggests the presence of some elements of primary structure that direct folding. Further investigation of the SH3 domain may yield ‘rules’ that determine the structure and folding pathway of the domain, and these rules may inform the study of other, similar proteins.

Cellular growth and aging requires constant replication of the genome. The processes of genome replication and segregation must be carefully regulated to prevent DNA damage which can cause cell death or oncogenic transformation. Damage can arise from errors in cellular processes, as well as environmental factors such as UV radiation or chemical agents. In mammals, the protein Retinoblastoma (Rb) prevents cells from beginning the process of DNA replication for cell division if internal conditions are not suitable for replication. This function is disrupted in virtually all cancers, and mutations in Rb have been widely studied as a result. Whi5 is the functional analog to Rb in S. cerevisiae. Whi5 activity is modulated by phosphorylation at 4 different sites, triggering Whi5 export from the nucleus and allowing transcription of DNA replication genes. Previous research suggested Whi5 export initiates irreversible progression through cell division. However, using single-cell observation technology, we show that Whi5 can re-enter the nucleus prior to cellular division, arresting the cell cycle. Cells that undergo Whi5 re-entry events exhibit a longer average replicative life span, counted in number of divisions. Additionally, cells without a functional copy of Whi5 have a reduced replicative lifespan. Our results suggest Whi5 may play a role in arresting the cell cycle in response to DNA damage to prevent the cell from making fatal errors during replication and ensure healthy aging. To investigate the role of Whi5 in response to DNA damage, I am using CRISPR gene editing technology to modify the phosphorylation sites on the Whi5 gene, modulating Whi5 activity. The ability of modified Whi5 strains to recover from UV induced DNA damage and their relative replicative life spans will clarify the role of Whi5 in DNA damage response. Our results may help us better understand the interactions governing Rb dysfunction in cancer cells.

The DNA damage checkpoint (DDC) is critical for survival as it responds to damage such as mutations or chromosomal rearrangement, and prohibits the cell cycle from proceeding through a failed replication. One of the many responses DDC activates is histone degradation. When wrapped around histone proteins, DNA is blocked from repair mechanisms. By reducing histone and nucleosome density, the cell increases DNA mobility and allows the DNA to be quickly repaired via homologous recombination. The cell does this by uncoupling histone transcription from the S-phase of the cell cycle, which is normally confined to this phase. When DDC is activated outside of S-phase, the cell can no longer produce histones to replace those it consumed and ensure proper chromatin packing after the DNA is repaired. According to published literature, uncoupling histone transcription from S-phase increases lifespan but should compromise the DNA damage response. However, it is largely unknown how this uncoupling affects the DNA damage response in different mutants. Our goal is to explore how this affects mutants with reduced DNA damage responses. Our mutants of interest are 1) rad52Δ, which reduces homologous recombination, and 2) lif1Δ, which reduces non-homologous end joining (NHEJ). Our protocol involves yeast (Saccharomyces cerevisiae) spotting and exposing yeast to different durations of high-intensity UV energy. We will compare colony sizes across different strains, dilution factors, and UV-exposure degrees. We expect to see strains with rad52 or lif1 deletion to have a lower growth rate compared to the wild type. Following this experiment, we will explore how altering histone transcription interacts with, and may enhance rad52 and lif1 in DNA repair. We hope to apply our findings to mammalian and human genes, and help to decrease the onset frequency of age-related diseases such as cancer due to genomic instability.

The James Webb Space Telescope (JWST) has the power to resolve many unanswered questions in the field of astronomy. The new telescope, which has taken many years and large amounts of resources to build, will have a limited lifetime so it is imperative that it is used as efficiently as possible. The unprecedented power of the JWST means that for the first time it may be possible to detect the clustering of high-redshift galaxies, and this could help to clarify uncertain details about the early universe. The purpose of this project is to determine the ability with which the JWST will be able to detect the clustering of early galaxies and the most efficient survey strategies for realizing this capability. Using simulation data, we are able to take into account JWST detectability limits and analyze clustering at different redshifts (z=6, z=8, and z=10). By comparing the simulation galaxies to a random test case, we have come to the conclusion that the clustering of high-redshift galaxies will likely be detectable with the JWST. Simulating different survey strategies then allows us to determine how to maximize the JWST's efficiency. The amount of time that the JWST spends pointed in a specific direction determines the depth of the survey. For a given amount of time, a deeper survey will be able to pick up on dimmer galaxies, but it will cover a smaller area. Our next step is to determine an ideal combination of depth and of area for the detection of early galaxy clustering at different redshifts in order to best plan for the JWST's launch.

Prion diseases occur from the misfolding of the Prion Protein cellular form (PrP^C) under low pH conditions to the infectious scrapie species (PrP^Sc), which can aggregate further into insoluble fibrils. Previous studies have demonstrated that along with other amyloid oligomers, the prion scrapie oligomers cause neurotoxicity by disrupting the membrane, increasing its permeability and affecting calcium ion influx; however, the molecular mechanism for this effect is unknown. Molecular Dynamics simulations were performed to gain insight into the molecular mechanism of PrP^Sc-induced misfolding of PrP^C and oligomer toxicity in a membrane environment. The system was composed of the hexameric bovine PrP^Sc spiral model oligomer and the di-glycosylated human PrP^C attached to a POPC membrane via a glycophosphatidylinositol (GPI) anchor. Prior unpublished membrane simulations of this system have suggested that PrP^Sc induced PrP^C conformational changes as well as significant membrane disruption from oligomer-binding. Here we confirm and build upon these earlier studies demonstrating the reproducibility and robustness of oligomer binding affinity by varying the proximity of the oligomer to the membrane, providing key insight into infectious scrapie propagation and PrP^Sc cellular toxicity.