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Pursuing the Bacillus subtilis ZnuABC Complex
No full texthttps://rdc.reed.edu/v1/resources/7c0f6f98-9547-4258-a4a0-b334d78013eb/thumb/128.jpgVaried metal ions are incorporated into a large number of proteins critical to survival in prokaryotes and eukaryotes alike. Homeostasis, i.e. maintaining a steady intracellular concentration of these ions, is therefore of critical importance, as both excess and scarcity are detrimental to growth and survival. To this end, humans—and other eukaryotic hosts to pathogenic infection—employ an arsenal of tools to disrupt bacterial metal homeostasis and clear said infection. In the face of such an onslaught, bacteria have developed an extensive array of ion transporters, both for influx and efflux, in order to be able to maintain tight homeostatic regulation and survive in so hostile an environment. A large family of these transporters are the ATP-binding cassette (ABC) transporters. Several of these transporters are deemed essential for pathogenesis, including ZnuABC, a high-affinity uptake pump for divalent zinc. No structure has been published, however, detailing the construction, selectivity, or mechanistic action of ZnuABC.In this study we demonstrate that the binding site of the extracellular metal chaperone ZnuA is highly selective for zinc over manganese, providing some insight into the mechanism for substrate specificity of the complex. We also tentatively observe that zinc is required for the ZnuABC complex to form. Should this prove to be the case, it would be a big step towards structural characterisation and 3D reconstruction of ZnuABC
Got Milkweed? A Study on Smoke Water and Monarch Butterfly Habitat
No full texthttps://rdc.reed.edu/v1/resources/64ba4068-65ba-4534-bfef-01f93306f2de/thumb/128.jpgThe iconic pollinator, Danaus plexippus (or monarch butterfly) has the ability to connect people from across the country through the nature of their unique migration patterns and by bringing ecology to people of all ages and experiences, making a citizen scientist out of anyone. However, decreasing breeding habitats are contributing to rapid population declines. These issues may be compounded for the western US populations, which are far less numerous, understudied, and where recent trends in wildfire activity may exacerbate habitat losses compared to eastern US populations. Though they are virtually genetically indistinguishable, they differ phenotypically in their migration and overwintering behavior. D. plexippus relies exclusively on milkweeds from the genus Asclepias for oviposition and larval consumption; thus, increased data collection and information on the composition of adequate habitat and D. plexippus migration is imperative for conservation. Extreme fire suppression efforts that started during World War II led to the increase in frequency and intensity of wildfires in California – effectively altering the fire season from Fall to almost year-round. Studies in the eastern monarch habitats showed that fire and burning caused an increase of milkweed density, meaning that prescribed burning and regular wildfires can be used as conservation tools to strategically increase milkweed presence in the monarch butterfly migration route. Recent studies have found that Asclepias. syriaca seeds exhibit a higher germination percentage when treated with smoke water during cold stratification. Based on previous results and the knowledge of the changing fire season in the west, I explored how smoke water would affect the germination of Asclepias speciosa a related species to A. syriaca but less well studied milkweed species. I found that A. speciosa has a much different response to smoke than the reported response of A. syriaca, suggesting that A. speciosa exhibits a facultative response with fire events with important implications for management of monarch butterfly habitat along the west coast of the United States
Restoring and Updating the Reed Rubidium Magneto-Optical Trap
No full texthttps://rdc.reed.edu/v1/resources/ffc9302f-d15a-4046-9712-64a59a39d715/thumb/128.jpgThis thesis focuses on the theory and experimental aspects of Magneto-Optical Traps (MOTs) for rubidium (Rb) atoms. The first part of the thesis covers the electronic structure, fine structure, and hyperfine structure of Rb atoms, as well as laser cooling techniques using radiation pressure. The second part discusses laser tuning and spectroscopy of Rb atoms, specifically 87Rb, using laser saturated absorption spectroscopy. The concept of Doppler linewidth, crossover transitions, and the structure and absorption lines of 87Rb are explored in detail. The current laser locking regime for frequency stabilization during experiments is also discussed. The final part of the thesis focuses on experimental developments and results related to the acousto-optical modulator (AOM), a device that uses sound waves to diffract light and shift its frequency used for detuning in our setup. This includes characterizing its efficiency, implementing a double pass technique to increase frequency detuning range and allow frequency adjustments without beam angle changes, and peak locking using frequency modulation. The proposed solutions to the problems encountered in previous methods are also discussed. Overall, this thesis provides a comprehensive understanding of MOTs, laser spectroscopy, and AOM techniques in the context of Rb atoms
Striking Gold: An Atomic Force Microscopy Study of Gold Nanoparticle- Polymer Interfaces
No full texthttps://rdc.reed.edu/v1/resources/704d44e5-1244-4eb2-bfc2-f7fb64cc137d/thumb/128.jpgNanoscale morphology and conductivity of composite Au nanoparticle and PEDOT:PSS (poly(3,4-ethylenedioxythiophene) polystyrene sulfonate) thermoelectric materials were characterized using tapping and conductive atomic force microscopy. Topographic and conductive images revealed nanoparticle clusters and indications of polymer coatings on some nanoparticles. Localized current-voltage (I-V) curves were used to characterize these coatings from which conductivity estimations consistent with PEDOT:PSS (PEDOT:PSS ( ≈ 0.1-1 S/cm) were found. Various components of imaging and I-V measurements were explored, including optimization of imaging methodology, I-V curve nonlinearity, and I-V curve dependence on voltage frequency. This work provides a multifaceted approach to investigating nanoscale interface effects in organic-inorganic hybrid materials. Results presented here help elucidate the structure of interfaces and their engineering possibilities in scalable, solution- processed nanocomposites that could revolutionize waste heat recovery
Flowers Seen Through the Fog
No full texthttps://rdc.reed.edu/v1/resources/14718711-1ab4-46df-ad7c-639ac798f436/thumb/128.jp
Spectroscopic Studies of the CuA Assembly Mechanism
No full texthttps://rdc.reed.edu/v1/resources/a5430c7c-e876-4cc2-8f8f-03c58bce8eb3/thumb/128.jpgCuA is a binuclear copper-binding site located in the Subunit II of the cytochrome c oxidase. In the copper-binding center of CuA, a pair of mixed-valence copper ions (Cu(I) and Cu(II)) are bridged by two Cys residues and form a delocalized Cu-Cu bond of 2.48 Å long, where each ion has an equal charge of +1.5. This unique structure makes it very efficient in electron transfer. To assemble the well-functioning CuA center, Cu ions must be loaded into apo-CuA, and how this process is achieved is of great interest in biochemistry. This thesis used UV-Vis spectroscopy to study various binding patterns of Cu ions to the CuA protein in Thermus thermophilus (Tt CuA), as well as the interactions between Tt CuA and two known proteins involved in proper CuA assembly: Tt Sco1 and Tt PCuAC. In this thesis, it was found that CuA was able to bind both Cu(I) and Cu(II) at the same time and form the mixed-valence complex, suggesting a possible presence of a Cu(II) chaperone protein. The binuclear Cu(II)2-CuA complex automatically reduces to the mixed-valence protein, implying a reducing site on CuA. The mononuclear Cu(II)-CuA complex was found to coexist with the binuclear mixed-valence protein. A brief procedure of setting up a glovebox is also included
"It's All About the Green”: The Tony Award's Effect on Broadway Show Demand
No full texthttps://rdc.reed.edu/v1/resources/d870ebe2-a273-43eb-a303-84364a77e925/thumb/128.jpgThis economics of information thesis explores the effect of an economic signal (Tony Award) on consumer demand (Broadway shows). It builds on a similar paper by Boyle and Chiou, who examined this relationship using data from 1996 to 2007. I use the market share variable developed by Boyle and Chiou, as well as gross revenue and average ticket price, to measure demand. Overall, the evidence suggests both Tony Award wins and nominations increase show demand. Gross revenue is expected to increase up to 14.4% after being nominated for and 22% after winning a Tony Award. For nominations, this increase can be attributed both to an increase in market share and ticket prices. For the awards themselves, market share loses its statistical significance and ticket price becomes the primary explanation for this increase. The magnitude of these effects begins to decrease over time, eventually becoming negative by the eight-to-eleven-month mark. These results provide evidence that the Tony Awards are a strong and credible quality signal for Broadway productions, but the signal's strength and quality may lessen over time
tfb: a Package for Targeted Function Balancing
No full texthttps://rdc.reed.edu/v1/resources/9d4b39f5-69de-495e-947d-f973ff83cbc5/thumb/128.jpgRetrieving causal estimates from data is a worthwhile problem, but observational studies frequently make the task more difficult. When observables confound the rela- tionship between a treatment of interest and an outcome, conditioning on the observ- ables may satisfy conditional ignorability. The assumption is relevant to the potential outcomes framework of Splawa-Neyman, Dabrowska, & Speed (1990), and allows for potentially unbiased estimation through the identification of conditional expectation functions (CEFs). One class of estimators constructed through such identification are the weighted differences in means (WDIMs). Many weighting techniques exist, and targeted function balancing (TFB) is a novel one (Wainstein, 2022). By fitting an initial regression, the method is able to find weights that minimize a worst-case scenario of imbalance in the data within a probabilistically defined subset of functions near the initial estimate that ideally contains the true CEF of the potential outcomes. TFB transforms the problem of weighting observables into a problem of specifying the CEF correctly, creating a scalable weighting method that rewards the researcher’s domain knowledge. This thesis presents a motivation of TFB for the average treat- ment effect (ATE), and introduces a package tfb for the application of the method in R, with a focus on the regression technique kernel regularized least squares (KRLS) (Hainmueller & Hazlett, 2014)
Becoming A Neuron: Visual Input Influences on the Pace of Neurogenesis in the Zebrafish Optic Tectum
No full texthttps://rdc.reed.edu/v1/resources/2a39259b-a1bc-43db-a521-8e8cf35e28c2/thumb/128.jpgBrain development is facilitated by myriad innate and experience- dependent factors. Disentangling one from the other often involves isolating genetic variables or sensory systems to examine, one by one, the impact that each has on the brain as it develops at the cellular level. In this thesis, I use an EdU pulse-chase method to examine the rate at which proliferative neural progenitor cells exit the cell cycle and become neurons in the optic tectum, the primary recipient of visual information in the brain. Data from wild-type and lakritz mutant fish, which lack optic nerves, show that optic nerve innervation promotes cell cycle exit and expands neuronal populations. Measures of total EdU+ cells over time raise the possibility that estimates are likely confounded by differential levels of cell death across WT and lakritz mutant larvae
Is It Good for the Jews? Conceptions of Modernity in American Jewish Folk Dance 1910-1990
No full texthttps://rdc.reed.edu/v1/resources/e4acbd10-6dad-491b-b8ce-c14f619f133e/thumb/128.jpgIn my thesis, I argue that Ashkenazi Jewish dance did not die with Holocaust or pre-war assimilation and was not fully displaced by Israeli dance. Instead, Yiddish dance and klezmer music were transformed throughout the decades and were part of an indirect but continuous chain of transmission from the pre-war era through to the klezmer revival. In this paper I trace the context and form of Yiddish dance in its journey from Europe to America, and then from urban immigrant neighborhoods to the suburbs, and finally to its place in the Klezmer revival