Alumni Dissertations and Theses

 
 

Alumni Dissertations and Theses

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  • COMPUTATIONAL INSIGHTS INTO THE OXYGEN EVOLVING COMPLEX OF PHOTOSYSTEM ΙΙ

    Author:
    Muhamed Amin
    Year of Dissertation:
    2014
    Program:
    Physics
    Advisor:
    Marilyn Gunner
    Abstract:

    The Oxygen Evolving Complex (OEC) of Photosystem II (PSII) is a unique Mn4O5Ca2+ cluster that catalyzes the photoactivated water splitting reaction. The OEC is a model system for bio-inspired artificial systems to use solar energy to pull electrons from water to produce fuel. The OEC goes through a cycle of 5 S states storing 4 holes, via electron transfer to P680+, the primary electron donor in PSII to generate a high valence S4 state that oxidizes water. The key questions are what controls the order of oxidation and deprotonation of the OEC complex and how does the PSII protein modulate the cluster behavior. Here, we present a classical electrostatics Monte Carlo (MC) technique, with input from density functional theory (DFT) and molecular dynamics (MD) to study the thermodynamics of the S0 to S3 states in a cluster embedded in the whole PSII. The model is tested against model complexes and yields a very good agreement with the experiment. In the simulation, the electrochemical potential (Eh) is varied to oxidize the OEC. The MC sampling allows the µ-oxo-bridges, terminal waters and amino acid residues to change their protonation states and/or their rotamer position to respond to the Mn oxidation. In addition, chloride is allowed to move during the cycle. The order of Mn oxidation found here is Mn2, Mn3, Mn4 and finally Mn1 as the system goes from the S0 to S3 states. In the S-1 state O1 and O4 are protonated as are the terminal waters on Mn4 and the Ca2+. O4 and O1 are deprotonated when S0 and S1 are formed respectively. The formation of S2 includes proton transfer from W2 to the nearby D61, reducing the release of protons to the media, consistent with experimental measurements. Protons are also lost from H337 and E329. The proton-release pattern is compared fixing the protonation states for H337, D61, terminal waters and with chloride-depleted PSII. The calculated midpoint potential of each Mn and their dependence on pH is discussed.

  • The diet and foraging ecology of gray seals, Halichoerus grypus, in United States waters

    Author:
    Kristen Ampela
    Year of Dissertation:
    2009
    Program:
    Biology
    Advisor:
    Richard Veit
    Abstract:

    Once extinct in U.S. waters, there are now more than 7,000 gray seals (Halichoerus grypus) that breed and forage in the waters of Maine and Massachusetts. This is the first long-term study of the diet and foraging behavior of this species in its U.S. range. I used hard parts in 305 seal scats and 49 stomachs, and fatty acid profiles in 45 seal blubber cores, to 1) reconstruct the diet of gray seals in U.S. waters, and 2) investigate regional, temporal, and intraspecific variation in the diet. I compared species in the diet with those most abundant in the seals' range, as measured by bottom trawl surveys. I analyzed the tracks of 6 satellite-tagged seals, and asked which prey species were most abundant in areas where foraging activity occurred. I recovered a total of 3,798 otoliths, and 7,005 prey individuals from 34 prey taxa. Sand lance (Ammodytes spp.) dominated the diet by weight (53.3% of total) and number (66.3% of total). Sand lance, winter flounder (Pseudopleuronectes americanus), red/white hake (Urophycis spp.) and Atlantic cod (Gadus morhua) together made up 82% of the diet by weight. Cod comprised 6.4% of the diet by weight, although this varied seasonally. Fatty acid profiles were best able to classify seals by age (young-of-the-year pups vs. yearlings, Wilks-Lambda = 0.27, F25,19 = 2.07, p <0.054), suggesting that diet differences were most pronounced between these two groups. Consistent 2:1 ratios of 22:6n3 and 20:5n3 fatty acids occurred in seal blubber (10.12/5.00 = 2.02). These ratios are similar to those in smooth skate (Malacoraja senta, 20.87/10.02 = 2.08) and alewife (Alosa pseudoharengus, 15.04/7.48 = 2.01), indicating that these species were important in the diet. Seals consumed abundant species, and tracked interannual trends in sand lance abundance, but the diet could not be predicted from prey availability alone. Satellite telemetry of seals revealed area restricted search behavior and central place foraging activity in areas with high abundance of sand lance and winter flounder, and these taxa comprised over 72% of the diet estimated from scats.

  • ACCESS TO URBAN FOOD OUTLETS AS A PREDICTOR OF DIABETES

    Author:
    Philippe Amstislavski
    Year of Dissertation:
    2012
    Program:
    Earth & Environmental Sciences
    Advisor:
    Juliana Maantay
    Abstract:

    Background and problem statement:There is an unprecedented rise in diabetes in urban populations worldwide. A relationship between spatial concentration of other metabolic diseases and poor access to healthy foods in some underserved urban neighborhoods have been reported. Concurrently, a relationship between increased risk of developing diabetes and consumption of unhealthy foods and has been shown to exist. Neighborhood food contexts hypothesized to lead to developing diabetes need to be studied. Study goals:: The main hypothesis of this study is that the degree of access to food outlets near residences influences the outcome of diabetes. Covariates include individual-level variables of age and gender of the subjects, and neighborhood-level variables of educational attainment, percent of residents in poverty, of housing units without vehicles, and of female-headed households with children. Methods:Address, demographic, and health data extracted from medical records of black visitors to hospital emergency department were linked to geo-referenced socio-economic and food outlet data for the visitors' Census Tract (CT) of residence. Hierarchical linear modeling was used to consider the effect of variation in food and socio-economic environments on diabetes among the subjects. A cross-sectional study was designed and a multilevel logistic regression analysis was performed. Results: Spatial access to food outlets was not a significant predictor of diabetes in this study. However, subjects living in the socio-economically deprived neighborhoods had a higher probability of having diabetes. For every unit decrease in the neighborhood's socio-economic index constructed from the census variables, the subjects were 7 percent more likely to have diabetes (CI 1.03-1.12, p-value 0.0024). Female gender and older age were strongly associated with odds of having diabetes. Conclusions: Socio-economic context of neighborhood was shown to affect probability of having diabetes, while local food outlet access did not. The results indicate that there may be a critical difference between economic and spatial access to foods and the actual choices individuals make about their diets. These choices may be driven by individual cultural and social preferences. More research is needed to study these individual biosocial factors and to analyze how they affect diet and diabetes outcome.

  • Effects of Native Language on Perception and Neurophysiologic Processing of English /r/ and /l/ by Native American, Korean, and Japanese Listeners

    Author:
    LEE JUNG AN
    Year of Dissertation:
    2015
    Program:
    Speech-Language-Hearing Sciences
    Advisor:
    Brett Martin
    Abstract:

    The perception of English liquids /r/ and /l/ is challenging for native Korean and Japanese adult speakers because these sounds are not phonemic in these languages. The Korean language has a partial phonetic model that could potentially facilitate processing of English /r/ and /l/ but the Japanese language does not. The purpose of this study was to compare the effects of native language on the neurophysiologic processing of English intervocalic /r/ and /l/ by native American, Korean and Japanese listeners using several event-related evoked potentials (ACC, MMN, & P3a) along with behavioral identification and discrimination. Three specific aims were investigated. The first aim was to examine the effects of native language on the perceptual identification and discrimination of English intervocalic /r/ and /l/. The second aim was to determine the effects of native language on the neurophysiologic encoding of English intervocalic /r/ and /l/ using the acoustic change complex (ACC). The third aim was to determine the effects of native language on the pre-attentive discrimination of and related attention shifting/orienting to English intervocalic /r/ and /l/ using the mismatch negativity (MMN) and P3a. Stimuli were a synthetic vowel-consonant-vowel (VCV) continuum that generated percepts in American English listeners ranging from /iri/ to /ili/. Stimuli falling within- and across-phonetic category were presented using an oddball paradigm. The probability of occurrence of the deviant was 20%. Nine participants from each language group participated. Stimuli were presented via insert earphones at 70 dB SPL using an 1100 ms offset-to-onset interstimulus interval. The evoked potentials were recorded from surface electrodes using a Neuroscan system. Behavioral testing included a 2-alternative forced choice identification task and a 3-alternative forced choice oddity discrimination task. English medial /r/ and /l/ were perceived in a categorical manner by Americans, in a categorical-like manner by Koreans and in a non-categorical manner by Japanese. The midline-central ACC P1-N1-P2 responses did not differ significantly between language groups, suggesting little effect of native language on the primary cortical encoding of these sounds. In contrast, the lateral-temporal ACC T-complex differed across language groups, suggesting that native language influences secondary cortical processing of these sounds. The MMN also depended on native language, suggesting that native language influences automatic, pre-attentive discrimination of English medial /r/ and /l/. Both early (400-650 ms) and late (655-905 ms) responses were obtained for Americans and Koreans, whereas early responses were absent in Japanese. Early MMN responses were significantly larger for across-category pairs than for within-category pairs only in Americans and Koreans. Late MMN responses were significantly larger for across-category pairs than for within-category pairs only in Americans. Additionally, late MMN responses for the across category pairs were significantly larger in Americans compared to other language groups. The P3a had both early (600-700 ms) and late (900-1000 ms) responses, similar to MMN responses. Early P3a responses were present in Americans and Koreans and P3a latency for across-category pairs was shorter for Americans than for Koreans. Late P3a responses were obtained from all three language groups, and did not differ significantly across tokens or groups. The partial language model available to Koreans appears to facilitate both neurophysiologic processing and behavioral perception of English /r/ and /l/. The absence of such a model in Japanese results in perceptual processing difficulties and alterations of the neurophysiologic processing of these sounds. Native language influences the neurophysiologic processing, including encoding at the level of secondary auditory cortex, pre-attentive discrimination, attention-related processing, and behavioral identification and discrimination.

  • Neuromodulatory and cytoprotective roles of zinc in the vertebrate retina

    Author:
    Ivan Anastassov
    Year of Dissertation:
    2013
    Program:
    Biology
    Advisor:
    Richard Chappell
    Abstract:

    There is increasing evidence that the role of Zn2+ in the central nervous system is more complex and widespread than originally thought. Chelatable Zn2+ is co-localized with glutamate in the terminals of mossy fiber hippocampal and first order retinal neurons. The co-release of Zn2+ with glutamate in a stimulation-dependent manner has been shown in the hippocampus and the distal retina, while the electrophysiological effects of photoreceptor-released Zn2+ suggest a neuromodulatory role at the first visual synapse. This dissertation examines the neuromodulatory and cytoprotective roles of zinc in the vertebrate retina. When endogenous Zn2+ release is chelated in a skate eyecup preparation, the photoreceptor-generated a-wave of the electroretinogram doubles. This treatment also depolarizes horizontal cells and enhances their light response, suggesting that in the absence of Zn2+ , tonic release of glutamate from photoreceptors onto postsynaptic neurons is increased. Live cell imaging demonstrates that Zn2+ is released from photoreceptor terminals following Ca2+ entry through synaptic voltage-gated calcium channels. In isolated photoreceptors from salamander, chelation of extracellular Zn2+ significantly increases Ca2+ entry at the terminal and this effect is abolished when voltage-gated calcium channels are blocked pharmacologically. In the skate, removal of retinal Zn2+ via intraocular injections of chelators severely damages the inner retina. In the absence of Zn2+ , the retina develops classic signs of glutamate excitotoxicity; cell and tissue swelling, pyknosis and spongy appearance of the inner plexiform layer. Similar tissue characteristics are observed with injections of kainate, a well-known and potent excitotoxic agent. Additionally, neurons in the ganglion cell layer become necrotic with either kainate or chelator treatments, suggesting they are particularly sensitive to overactivation of glutamate receptors. Taken together, these experiments show the importance of Zn2+ as a neuromodulatory agent at the first visual synapse, where control of glutamate release affects the transmission of the visual message and provides broad protection of the retina from excitotoxicity. Understanding the role of Zn2+ in the retina may provide novel insights into retinal diseases and contribute to our growing knowledge of zinc's important functions elsewhere in the CNS.

  • Object Relations, Internal Resources, and HIV/AIDS Risk: A Rorschach Study

    Author:
    Virginia Andersen
    Year of Dissertation:
    2013
    Program:
    Psychology
    Advisor:
    Arietta Slade
    Abstract:

    Abstract The purpose of this study was to explore the quality of Rorschach scores of a population who self-reported sexual risk-taking behaviors that place them at increased risk for contracting HIV. It was hypothesized that this group would produce scores indicative of fewer internal resources available for impulse inhibition, specifically capacity for affect regulation and stress tolerance. It was further predicted that a measure of object relations would indicate that study participants would generally experience interpersonal interactions as imbalanced and possibly threatening. This group produced significantly lower scores with regard to affect regulation, but did not differ from the normed, non-clinical sample with regard to stress tolerance. Further, study participants produced scores in the healthy range on the measure of object relational development. The potential theoretical and clinical implications of this finding are discussed.

  • For Love and for Justice: Narratives of Lesbian Activism

    Author:
    Kelly Anderson
    Year of Dissertation:
    2014
    Program:
    History
    Advisor:
    Blanche Cook
    Abstract:

    This dissertation explores the role of lesbians in the U.S. second wave feminist movement, arguing that the history of women's liberation is more diverse, more intersectional, and more radical than previously documented. The body of this work is five oral histories conducted with lifelong activists and public intellectuals for the Voices of Feminism project at the Sophia Smith Collection: Katherine Acey, former Executive Director of the Astraea Lesbian Foundation for Justice; Dorothy Allison, author and sex radical; Suzanne Pharr, southern anti-racist organizer and author; Achebe Powell, activist and diversity trainer; and Carmen Vázquez, LGBT activist and founding director of the San Francisco Women's Building. Taken together, their stories dovetail into a new narrative about the relationship between lesbians, feminism, and queer liberation, from the late 60's to the present. In addition to the edited transcripts, this dissertation includes a new chronology of gender and sexual liberation, demonstrating the interconnectedness of late 20th century social change movements, and a chapter on oral history methodology. This work adds to our collective knowledge about lesbian lives by sharing five important life narratives, contributes to a re-imagination of the vast and intersectional scope of second wave feminism and sexual liberation, and attempts to disrupt conventional methods of documenting and sharing history by privileging oral narratives.

  • The Problem of Malawi in Western Discourse: Power, Patronage, and the Politics of Pity

    Author:
    Norma Anderson
    Year of Dissertation:
    2012
    Program:
    Sociology
    Advisor:
    Barbara Katz Rothman
    Abstract:

    While recent sociological work on African social problems tends to focus on particular areas such as HIV/AIDS, this dissertation considers relationships and links between diverse social issues to argue that western-defined African social problems are not only disconnected from what Africans themselves see as their major needs but are also rooted in an historical pattern of power and inequality. Using Malawi as a case study I compare discourse about four diverse social problems--slavery, HIV/AIDS, climate change, and homosexuality. I demonstrate how these vastly different issues are related: each is framed and funded by foreigners and each is depoliticized, often blaming Africans themselves for various negative outcomes of global inequality. But despite the blame, these social problems are presented to the western public through a frame of pity that underscores the need for immediate western intervention. Since the mid-1800s Malawi has experienced numerous and distinct cycles of western "help," interest, and involvement but each individual issue revolves around a central troublesome notion--that Malawi and Malawians are flawed and in need of western guidance and assistance to (re)achieve a more ideal state. In this way, even the most "well-meaning" attempts to address legitimate health and social problems further long-standing stereotypes of African helplessness and western superiority. Engaging theories of stratification, development, and realist constructionism, and relying on interviews, ethnography, and survey data, I interweave historical and contemporary western discourse about Malawi to analyze shifting and competing conceptions of what is wrong with the country as well as how these understandings have influenced western interventions. By contrasting western understandings and images of Malawi with Malawians' views of the same problems, this dissertation not only builds on stratification and development theories but also investigates practical reasons why western policy interventions have so often failed to create sustainable change.

  • West Side Stories: Everyday Life and the social space of West Forty-Sixth Street

    Author:
    Christian Anderson
    Year of Dissertation:
    2012
    Program:
    Earth & Environmental Sciences
    Advisor:
    Cindi Katz
    Abstract:

    This is an ethnographic study of macro-structural change from the vantage point of everyday life on a few blocks of a single street in the Hell's Kitchen/Clinton neighborhood of New York City. The study tells stories from daily life on several blocks of West Forty-Sixth Street between Eighth Avenue and the Hudson River as documented over three years of close observation. These stories show how the actions of some residents serve to lubricate outcomes like privatization, rising housing costs, discriminatory policing, displacement, and eviction. These outcomes then negatively affect others who have less power--particularly undocumented migrants, the elderly, the poor, and people of color. This finding is complicated by the fact that people here are not acting malevolently, but more often than not out of well-intentioned common sense ideas about community, quality of life, and progress. What this means, I contend, is that processes like gentrification, neoliberalization, and inequitable urban development are not simply imposed from outside by macro forces such as real estate capital or top-down urban policy. I argue that these processes are also deeply contingent on everyday life--on the daily actions, ideas, and subjectivities of ordinary people in places such as West Forty-Sixth--which act as a kind of social infrastructure. This situation presents a mash-up of spatial, political, and structural questions about hegemony and power that span the intimate and the global in scope while complicating existing understandings of urban space and everyday life.

  • Exploring the Effects of Strain on Cross-national Lethal Violence: An Integrated Model

    Author:
    Catrin Andersson
    Year of Dissertation:
    2015
    Program:
    Criminal Justice
    Advisor:
    Lila Kazemian
    Abstract:

    Lethal violence is a global problem. In 2012, the United Nations documented 437,000 homicides worldwide (United Nations Office on Drugs and Crime, 2014b), and in 2012, the World Health Organization reported that there were 800,000 suicides internationally (World Health Organization, 2015c). There is a large body of research on violence in the social sciences. Although suicide and homicide are often studied separately, they have been said to share many of the same correlates, such as inequality and divorce (e.g., inequality and divorce; Nivette, 2011; Stack, 2000). There is a need to integrate theories drawn from different disciplines to better understand macro- and micro-level predictors of homicide and suicide. Drawing on data from multiple sources, the current research aims to test some of the postulates of the frustration-aggression hypothesis, strain theory, and the stream analogy model. This dissertation utilizes a quantitative approach to investigate the effects of objective and situational strains, and potential mediating effects of micro-level negative affect (e.g., frustration) on cross-national homicide and suicide rates, while controlling for macro-level predictors (e.g., population, culture and social control indicators). It is hypothesized that macro and micro-level indicators of social support moderate the relationship between strain, frustration, and violence, potentially acting as buffers against violence. Ultimately, this dissertation seeks to investigate whether homicide and suicide are different manifestations of frustration, but emerging from the same underlying source.