Methodological advances have made it possible to generate predictions of brain activity using functional magnetic resonance imaging (fMRI) for cognitive architectures, such as Adaptive Control of Thought—Rational (ACT-R), thus expanding the range of model predictions and making it possible to distinguish between alternative models that produce otherwise identical behavioral patterns. However, for tasks associated with relatively brief response times, fMRI predictions are often not sufficient to compare alternative models. Presently, we outline a method based on effective connectivity, which significantly augments the amount of information that can be extracted from fMRI data to distinguish between models. We show the application of this method in the case of two competing ACT-R models of the Stroop task. Although the models make, predictably, identical behavioral and fMRI predictions, patterns of functional connectivity favor one model over the other. Finally, we show that the same data indicates, provided reasonable task constraints, that we may be able to automatically generate modifications to our models using measures of effective connectivity, further increasing the validity of our models and opening new avenues for model development. We see this an exciting opportunity for future research.

Inflammasomes are multimeric protein complexes involved in innate immune responses. Inflammasomes include a protein sensor, such as NLRP3 or pyrin, linked to the enzyme caspase-1 via the adaptor protein, ASC. Active caspase-1 is responsible for release of the cytokine interleukin (IL)-1ß and triggering inflammatory cell death. Inflammasomes are crucial in defense against pathogens. However, excess inflammasome activation is linked to diseases such as Alzheimer's, atherosclerosis, and other inflammatory conditions. Although inflammasomes are linked to several diseases, we do not fully understand how inflammasomes are activated. We are researching the role that potassium plays in inflammasome activation. To detect inflammasome activation, I measured released IL-1ß using enzyme-linked immunosorbent assays (ELISAs). I determined whether inflammasome activation requires potassium efflux by measuring IL-1ß released from cells stimulated in high extracellular potassium, which prevents potassium efflux. I found that IL-1ß release triggered by NLRP3 inflammasome activators is prevented when cells are stimulated in high extracellular potassium. However, IL-1ß release triggered by the pyrin inflammasome was not affected by high extracellular potassium. From these results, we conclude that the NLRP3 inflammasome is dependent on potassium efflux from the cell, whereas the pryin inflammasome is not. The implications of our research are two-fold. First, our findings argue against a long-standing hypothesis that high extracellular potassium blocks ASC binding. Both NLRP3 and pyrin need ASC, but our data show that only NLRP3 is affected by potassium concentration. This suggests that potassium affects NLRP3 activation at an unknown point. Second, understanding the role of potassium in regulating inflammasome activity provides a potential therapeutic target. There are drugs that regulate ion concentrations by controlling ion channel activity. Knowing whether an inflammasome pathway is potassium efflux dependent could be beneficial in limiting excess inflammasome activation that is linked to a variety of human diseases.

With regards to most tissues, humans lack the ability to regenerate, instead scarring in response to injury. This often leads to poor patient outcomes, especially in the event of spinal cord damage. Xenopus tropicalis are capable of avoiding this scarring response as tadpoles but not as adults. They instead fully regenerate tail tissue and are thus an excellent model system for the investigation of how regenerative and non-regenerative organisms differ in their response to injury. Due to the complexity of this process, many transcription factors have been implicated to have a role in regeneration, though the precise roles of many such transcription factors remain unknown. Here, we focus on the transcription factor Hif1α, which is canonically involved in responses to hypoxia and oxidative stress. Using an Assay for Transposase-Accessible Chromatin (ATAC-Seq) we have found that over the course of regeneration, Hif1α response elements (HREs) increase in accessibility. To understand the role of Hif1α during regeneration, I have used echinomycin, a small molecule known to inhibit binding of Hif1α to HREs. Tadpoles treated with echinomycin fail to regenerate, indicating the necessity of Hif1α in regeneration. In order to determine the effects of Hif1α on gene expression, I have queried several genes known to be differentially expressed during regeneration through the use of quantitative polymerase chain reaction. I have shown that inhibition of Hif1α transcriptional activity via echinomycin significantly alters Wnt target gene expression, indicating that Hif1α regulates Wnt target genes. This provides an improved understanding of the regulatory processes that enable regeneration.

Suspended sediment in the bottom boundary layer impacts both ecosystems and geomorphology. High concentrations of suspended sediment affect light attenuation, harming benthic plants, and sediment resuspension and transport can affect the distribution and size of sediment on the seafloor. The purpose of this project was to determine the variations and controls on suspended sediment in the Elwha River nearshore region and to find relationships between bed shear velocity and suspended sediment concentration. The 2011 Elwha River dam removal released a large pulse of sediment, giving us the opportunity to study a coastal environment with fine sediment deposits, and varying hydrodynamic conditions. Data collection measured near-bed turbidity and wave conditions, and sediment grab samples were collected to characterize bed conditions. Harmonic tidal analysis was used to predict tidal current velocity. Over the sampling period, on the east side of the river mouth, currents ranging from ~0 to 100 cm/s and wave heights up to 1.0 m were sufficient to resuspend sediment. Suspended sediment concentrations generally ranged from 1.5 to 25 mg/L. In Freshwater Bay, currents ranging from ~0 to 31 cm/s and wave heights up to 0.86 m were not sufficient to resuspend sediment. Instead, fine sediment settled out of the water column, resulting in near-bed sediment concentrations generally ranging from 1 mg/L to 101 mg/L. These findings show how variable the processes controlling sediment in suspension can be in a tidal environment with complex morphology.

Larval tadpoles of the frog Xenopus tropicalis exhibit a natural ability to regenerate multiple tissue types in response to injury. Unlike tadpoles, humans are incapable of regenerating a majority of their major organs and tissues following traumatic injury, often resulting in an irreversible loss of function of the affected tissues. While both non-regenerative and regenerative organisms undergo a period of wound healing in response to injury, the former then undergo scarring, whereas regenerative systems forgo scarring and ultimately regenerate the lost or damaged tissue. After tail amputation, reactivation of the cell cycle in the remaining tissue is required to promote cell proliferation in order to create the cells that will populate the regenerated tail. However, the molecular mechanisms that enable naturally occurring regeneration are not entirely understood. In order to better understand how wound healing promotes regeneration in tadpoles, I used immunofluorescent microscopy of Phospho-histone 3 (PH3) to assess the mitotic activity of Xenopus tropicalis tails during early regeneration. Over the first two hours post tail amputation, image analysis of PH3-positive cells shows that the amount and localization of mitotic activity varies greatly in the remaining tail tissue. Specifically, tissues adjacent to the amputation site transiently experience a dramatic decrease in mitotic activity beginning at 45 minutes post amputation (mpa), followed by the return of mitotic activity to these areas after 75mpa. I hypothesize that cell cycle inhibition during this 30 minute window is an important point of regulation during the regenerative process and may be a critical component of setting up a regenerative response to traumatic injury. Identifying mechanisms that enable regeneration will be critical for the development of clinical therapies that promote regeneration in humans

In humans, limb amputation and recovery post-amputation is characterized by inflammation and scarring that lead to poor clinical outcomes. In contrast, amphibians such as the frog Xenopus tropicalis are capable of healing scarlessly and can fully regenerate previously amputated appendages. Successful limb regeneration depends on precisely choreographed expression of genes, directed in part by the deposition and removal of epigenetic markers. The broad aim of this research is to identify the spatiotemporal dynamics of epigenetic modifications and how they play a role in regulating gene expression during regeneration. It is known that histone deacetylases (HDACs) and H3K27-specific methyltransferase EZH2 enzymes limit chromatin accessibility and are necessary for regeneration to occur properly. However, the precise mechanisms and genomic targets of these enzymes remain unknown. We hypothesize that inhibiting these enzymes will leave chromatin in a constitutively accessible state, disrupting the gene expression required for successful regeneration. I am utilizing the drugs Trichostatin A (TSA) and DZNep to inhibit HDACs and EZH2 respectively at differing sequential time points throughout tail regeneration. In addition to characterizing the morphological outcome of regenerating tails that have been treated with these drugs at varying intervals post-amputation, I  also use immunofluorescence to identify the targeted location relative to the injury site and tissue types as they are affected across time. For humans and other mammals with limited regenerative capability, studying these epigenetic changes and their impact on Xenopus tropicalis tadpole tail regeneration is especially significant: it has the potential to determine how changes in gene regulation may enable and facilitate a broader capacity for limb regeneration by informing future therapeutic possibilities.