Methylotrophic bacteria have long been recognized for their metabolism of reduced single carbon (C₁) compounds. Their potential for biotechnology and the occurrence of C₁ metabolism in all organisms signify their importance on an industrial and fundamental scale. Currently, mechanisms used by methylotrophs to regulate and reset their metabolic network in response to perturbations are not well understood. Previous studies suggest abrupt shifts in nucleotide levels drastically affect growth. This project will examine how nucleotide ratios correlate with carbon flux in Methylobacterium extorquens AM1. Once C₁ compounds undergo serial oxidation to formate, carbon flux is partitioned for further oxidation or assimilation. Two reactions involved in C₁ oxidation are known to generate reducing power: (1) the dehydrogenation of methylene-dH₄MPT into methenyl-dH₄MPT catalyzed by MtdA or MtdB and (2) the oxidation of formate into CO₂ catalyzed by Fdh1 or Fdh2. Genetic studies demonstrated differential phenotypes in which mtdB fdh1 grew similarly to wild type while mtdB fdh2 grew worse relative to the mtdB mutant strain. One possible explanation is a global decrease in NADH production offsets the delicate balance of intracellular nucleotides required for an already reducing power-limited mode of growth. To explore this hypothesis, I will conduct experiments to: (1) quantify the levels of NADP⁺, NADPH, NAD⁺, and NADH in WT, mtdB, mtdB fdh1, and mtdB fdh2 and (2) manipulate nucleotide ratios with overexpression and deletion of the pntAB and udhA genes. These genes encode for membrane bound (PntAB) and soluble (UdhA) transhydrogenases capable of interconverting between NADPH and NADH. Since mechanisms exist in other bacteria to alter nucleotides pools to meet metabolic demands, a similar mechanism can be predicted to operate in M. extorquens AM1. Success in this project will lead to better understanding of how cells balance reducing power and energy for oxidation and growth, ultimately leading to improved biotechnological utilization.

Foraminifera are a diverse and extensive group of marine shelled protists that are found all over the world, including Puget Sound. Because foraminifera are relatively abundant, short-lived and susceptible to environmental change, they have the potential to be inexpensive and effective environmental monitoring tools for local estuaries. Since Puget Sound exploits its water ways for industrial profit, foraminifera could prove to be useful tools for environmental monitoring. Thus it is surprising that, to date, no one has ever catalogued and observed foraminifera in the Sound to search for any changes in structure, abundance or diversity that could indicate a change in the environment. In fact Puget Sound is the only industrialized waterway that has not done this. The purpose of this project is to assemble an atlas of the foraminifera found in Puget Sound, from Bellingham Bay to south Sound. This atlas contains photographs, and in-depth descriptions of each foraminifera species. A catalogue such as this is a useful tool because it helps to better understand the foraminifera of Puget Sound and furthers the understanding of the organisms and their ecosystem.  This atlas can also be used as a quick and easy reference to compare any changes discovered among foraminifera and their communities. Ultimately, the complete atlas will be submitted to Paleontologica Electronica for publication.

The purpose of this study is to investigate the effects of different pollutant sources in Sinclair and Dyes Inlets, both located in Puget Sound, Washington. Puget Sound is a fjord-like waterway extending from Olympia, Washington to the Canadian border. Sinclair Inlet and Dyes Inlet are connected by the Port Washington Waterway near Bremerton in Kitsap County, Washington. Bremerton is the home of Puget Sound Naval Shipyard. This naval base is a Superfund site that discharged large amounts of industrial pollution into Sinclair Inlet. In comparison, agricultural and residential pollution are deposited in Dyes Inlet from streams surrounding the perimeter of the inlet. This study aimed to analyze foraminiferal assemblages to determine if environmental changes through pollution and other factors have affected the health of the Bremerton area marine ecosystems. Foraminifera are shelled single-celled marine microorganisms that react to environmental stresses, thus they act as good indicators of environmental change. Foraminifera were collected from a total of 21 samples provided by the Washington State Department of Ecology from 1998-2009. Thirteen of these samples were taken from Dyes Inlet and 8 were taken from Sinclair Inlet. This study focused on examining the density and diversity of foraminifera from 1998-2009. Our results show that Dyes Inlet contains a low diversity of foraminifera with 7 different species found. However, 2 samples did not contain any foraminifera and several samples from more recent years only contained one species. In Sinclair Inlet, 15 species were identified in total, but diversity was nearly cut in half over the time period studied. The dominant species in both inlets was Elphidium hannai. By comparing foraminiferal assemblages from our locations with samples from less anthropogenically impacted locations in the Puget Sound, we can begin to analyze the potential effects of different types of pollution on the health of Puget Sound.

The purpose of this study was to do a temporal investigation of the benthic forminifera in northern Puget Sound, specifically Semiahmoo Bay north of Bellingham Bay, to correlate any fluctuations in species diversity or abundance with environmental parameters. Semiahmoo Bay is influenced by an influx of both sediment and water from the Fraser River as well as mixing with ocean waters that travel in through the Strait of Juan de Fuca. The area is of interest because it is less impacted by anthropogenic activity than the rest of the Puget Sound and this allows for comparisons with other areas that are more heavily industrialized. Foraminifera are single celled, marine protists with specific habitat requirements. The sensitivity of these animals to their ecosystem allows us to use them for environmental monitoring. This study examines the foraminiferal genera and species present in sediments from this region spanning twelve years; from 2001 to 2012. The samples used were collected by the Washington Department of Ecology annually in April. Results of this investigation show an average of 15 species of foraminifera were present each year with three species dominating the samples. These species are Bucella frigida, Elphidium frigidum and Elphidium hannai, which are present in every sample. There are 10 to 12 other species that occur in small numbers present in most samples. One species, Cassidulina limbata, which is intolerant to pollution, indicates that this water is clean. There are only a few agglutinated species found in Semiahmoo Bay which is in contrast to the high abundance found in Bellingham Bay. This is significant because the dominant agglutinated species in Bellingham Bay are known to be opportunistic colonizers of polluted waterways. Thus, the foraminiferal assemblage in Semiahmoo Bay corroborates the hypothesis that the area is not subject to the degree of environmental stress as other embayments of Puget Sound.

The development of best practices in instruction, defined by student learning outcomes, requires evaluation of student engagement. How can engagement be measured? Student engagement or disengagement is manifested in body language and behavior. Educational studies that employ behavior to evaluate engagement often subjectively rely on a classical perception of how an engaged student behaves; however, recent work suggests that traditional engaged-behavior patterns can fail to account for student-reported engagement, as attentiveness may have many manifestations. Our research pioneers an objective approach to identifying and evaluating student behaviors that function as accurate indicators of engagement level. Using video recordings of Biology 200 students in lecture, student behaviors were catalogued. These same students were surveyed to determine their perceived engagement. The completed catalogue indicated both the presence and frequency of behaviors unique to individual target students, allowing us to compare students’ self-reported engagement level with their corresponding behaviors. The combination of in-class engagement self-assessment and objective cataloguing of behaviors presents the opportunity for quantitative analysis of each behavior’s ability to serve as a hallmark of engagement. Analyses are in progress to determine the predictive power of classical engaged-behavior patterns, and to identify the behaviors most strongly correlated with student-reported engagement. Our purpose is to provide the educational field with a method for analyzing student behaviors as a means for quantifying engagement, and to lay the groundwork on which a widely applicable engagement evaluation tool can be developed in the future.