Alumni Dissertations

 

Alumni Dissertations

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  • Dissecting the role of human PPR motif proteins in mitochondrial gene expression

    Author:
    Catherine Bangeranye
    Year of Dissertation:
    2010
    Program:
    Biochemistry
    Advisor:
    Serafin Piñol-Roma
    Abstract:

    Pentatricopeptide repeat (PPR) motif proteins constitute a growing superfamily of proteins that are broadly defined by the presence of one or more copies of a conserved 35 amino acid sequence, the PPR motif. They are particularly abundant in plants, and those whose function has been characterized have been implicated in several aspects of RNA metabolism in mitochondria and chloroplasts. In humans, PPR motif proteins are fewer in number. They include LRPPRC (Leucine-Rich PPR-motif -Containing protein), an RNA-binding protein that is a component of nuclear ribonucleoprotein (RNP) complexes that contain spliced mRNAs. Most of the LRPPRC, however, localizes predominantly to mitochondria, where it binds polyadenylated RNAs. Mutations in the lrpprc gene cause cytochrome c oxidase deficiency in Leigh Syndrome (LSFC), which is accompanied by a decrease in COXI and COXIII mitochondrial mRNAs. Our hypothesis is that LRPPRC is an essential trans-acting factor in mitochondrial mRNA metabolism. In order to address the function of LRPPRC in mitochondria, we isolated LRPPRC-associated mitochondrial RNP complexes (mtRNPs). Analysis of isolated mtRNPs shows that the mitochondrially-encoded mRNAs associate with LRPPRC. A reduction in LRPPRC levels using RNAi causes a parallel reduction in steady-state levels of mitochondrially-encoded mRNAs, but not of nuclear-encoded mRNAs. Thus, LRPPRC is an important factor for mitochondrial gene expression and is necessary for the accumulation of the mitochondrial mRNAs to which it binds. Using LRPPRC as a paradigm, we sought and analyzed other members of the PPR motif family in humans. Four other human PPR-motif proteins, PTCD1, PTCD2, PTCD3 and PTCD4, also localize in mitochondria. Moreover, some of these proteins also bind RNA and exist in the same complexes as LRPPRC. This indicates that the human PTCD proteins, as is the case with LRPPRC, are also involved in mitochondrial RNA metabolism, pointing to PPR motif proteins in humans as a novel family of trans-acting factors in mitochondrial gene expression. These findings open the way for an expanded and more detailed understanding of human mitochondrial gene expression, and for an exploration of the potential involvement of human PPR motif proteins in mitochondrial diseases, as has already been determined for LRPPRC.

  • Continuum and Molecular Dynamics Simulations of the Growth of a Vapor Bubble on a Heating Surface: Exploring the Mechanism of Nucleate Boiling Heat Transfer

    Author:
    Jinyong Bao
    Year of Dissertation:
    2011
    Program:
    Engineering
    Advisor:
    David Rumschitzki
    Abstract:

    Starting with a completely rewritten code for the conductively-driven quasi-static vapor bubble growth in an axisymmetric, cylindrical cell comprised of solid and liquid phase of finite thicknesses under small Reynolds, Peclet, Capillary and Bond numbers to verify L. Huang's (our prior Ph.D. student) earlier results, we couple the solution of the quasi-static problem with three simple, somewhat ad hoc models of contact line motion and relax the assumption of small Bond number to simulate the growth of an incipient bubble until gravity begins to slowly deform the vapor bubble and then to detach it from the solid heater surface. A simple physical theory is developed to explain that when the bubble density is not too high, the bubble volume vs time approaches a 3/2 power before gravity begins to deform its shape, independent of contact line motion models and system parameters such as the conductivity ratio of the liquid to solid and degree of wall superheat. On the other hand, contact line motion does have a significant effect on bubble deformation and detachment. Molecular dynamics (MD) is employed to determine the contact line motion in a nano-scale version of our three-phase system because MD not only includes heat transfer, but also fluid flow, which can remove many restrictions of the earlier continuum calculation in our nano-size system. Instead of nucleating a bubble by cavitation, we nucleate a vapor bubble by heating the bottom of the solid upon which the fluid sits at constant pressure. Under a uniform body force that, due to the scale of MD is far larger than terrestrial gravity, we then track the bubble's growth driven by heat transfer from the conducting heated solid until detachment. Its contact line motion is monitored and the effects of wettability of solid surface, temperature-slip of fluid-solid interface and the choice of the interaction between the solid and the fluid have also been discussed. Unfortunately, this temperature slip mitigates some of the effects of the contact line that the continuum modeling (without temperature slip) finds so crucial at macroscopic scales.

  • Continuum and Molecular Dynamics Simulations of the Growth of a Vapor Bubble on a Heating Surface: Exploring the Mechanism of Nucleate Boiling Heat Transfer

    Author:
    Jinyong Bao
    Year of Dissertation:
    2011
    Program:
    Engineering
    Advisor:
    David Rumschitzki
    Abstract:

    Starting with a completely rewritten code for the conductively-driven quasi-static vapor bubble growth in an axisymmetric, cylindrical cell comprised of solid and liquid phase of finite thicknesses under small Reynolds, Peclet, Capillary and Bond numbers to verify L. Huang's (our prior Ph.D. student) earlier results, we couple the solution of the quasi-static problem with three simple, somewhat ad hoc models of contact line motion and relax the assumption of small Bond number to simulate the growth of an incipient bubble until gravity begins to slowly deform the vapor bubble and then to detach it from the solid heater surface. A simple physical theory is developed to explain that when the bubble density is not too high, the bubble volume vs time approaches a 3/2 power before gravity begins to deform its shape, independent of contact line motion models and system parameters such as the conductivity ratio of the liquid to solid and degree of wall superheat. On the other hand, contact line motion does have a significant effect on bubble deformation and detachment. Molecular dynamics (MD) is employed to determine the contact line motion in a nano-scale version of our three-phase system because MD not only includes heat transfer, but also fluid flow, which can remove many restrictions of the earlier continuum calculation in our nano-size system. Instead of nucleating a bubble by cavitation, we nucleate a vapor bubble by heating the bottom of the solid upon which the fluid sits at constant pressure. Under a uniform body force that, due to the scale of MD is far larger than terrestrial gravity, we then track the bubble's growth driven by heat transfer from the conducting heated solid until detachment. Its contact line motion is monitored and the effects of wettability of solid surface, temperature-slip of fluid-solid interface and the choice of the interaction between the solid and the fluid have also been discussed. Unfortunately, this temperature slip mitigates some of the effects of the contact line that the continuum modeling (without temperature slip) finds so crucial at macroscopic scales.

  • Neocontradictions: The Politics and Ideology of American Welfare State Decline

    Author:
    Darren Barany
    Year of Dissertation:
    2009
    Program:
    Sociology
    Advisor:
    Stanley Aronowitz
    Abstract:

    This study historically investigates the circumstances - economic, political, and ideological - out of which the American political culture would shift to the right and become hostile to welfare. It is in part a genealogy of contemporary welfare reform discourse, which is comprised by the synthesis of varied and contradictory components of conservative philosophy about family, work, responsibility, and the role of government. This study also contextualizes that discourse within the development of a conservative politico-ideological apparatus. Today's conservative movement in the United States is the fusion of other sub-strands of conservatism and has successfully defined the parameters of acceptable discourse around the issue of welfare. It has developed a large pool of resources, become adept in the arena of activist and electoral politics, built a vast infrastructure for the production and deployment of ideas, and established a resilient presence in the everyday lives of Americans. Therefore a study of the erosion of the American welfare state must trace the development of these ideas and the means by which they became policy orthodoxy. Argued here is that the conservative movement's success in affecting welfare reform can be attributed to two factors. Firstly, it can be attributed to the consolidation and organization of libertarian and traditionalist conservatism and to the mastery of ideological production by a conservative politico-ideological apparatus or policy planning network. Secondly, it can be attributed to the emergence of varied conservative ideas on work, family, equality, and personal responsibility as a new policy consensus which was itself a consequence of important transformations in social and economic conditions. The post-war conservative movement has been dynamic and has managed its own ideological tensions by continually refining its argument and perfecting its methods of framing issues. It has contributed to altering the political culture in relation to the welfare state and related issues The subjection of welfare state programs to ongoing critique has enabled the social safety net to become vulnerable to reforms which have gradually altered them to be more consistent with the shifting requirements of the economic system and elite preferences.

  • Neocontradictions: The Politics and Ideology of American Welfare State Decline

    Author:
    Darren Barany
    Year of Dissertation:
    2009
    Program:
    Sociology
    Advisor:
    Stanley Aronowitz
    Abstract:

    This study historically investigates the circumstances - economic, political, and ideological - out of which the American political culture would shift to the right and become hostile to welfare. It is in part a genealogy of contemporary welfare reform discourse, which is comprised by the synthesis of varied and contradictory components of conservative philosophy about family, work, responsibility, and the role of government. This study also contextualizes that discourse within the development of a conservative politico-ideological apparatus. Today's conservative movement in the United States is the fusion of other sub-strands of conservatism and has successfully defined the parameters of acceptable discourse around the issue of welfare. It has developed a large pool of resources, become adept in the arena of activist and electoral politics, built a vast infrastructure for the production and deployment of ideas, and established a resilient presence in the everyday lives of Americans. Therefore a study of the erosion of the American welfare state must trace the development of these ideas and the means by which they became policy orthodoxy. Argued here is that the conservative movement's success in affecting welfare reform can be attributed to two factors. Firstly, it can be attributed to the consolidation and organization of libertarian and traditionalist conservatism and to the mastery of ideological production by a conservative politico-ideological apparatus or policy planning network. Secondly, it can be attributed to the emergence of varied conservative ideas on work, family, equality, and personal responsibility as a new policy consensus which was itself a consequence of important transformations in social and economic conditions. The post-war conservative movement has been dynamic and has managed its own ideological tensions by continually refining its argument and perfecting its methods of framing issues. It has contributed to altering the political culture in relation to the welfare state and related issues The subjection of welfare state programs to ongoing critique has enabled the social safety net to become vulnerable to reforms which have gradually altered them to be more consistent with the shifting requirements of the economic system and elite preferences.

  • An Examination of Predictive Variables of Success in Mental Health Diversion Programs.

    Author:
    Virginia Barber Rioja
    Year of Dissertation:
    2009
    Program:
    Psychology
    Advisor:
    Thomas Kucharski
    Abstract:

    Diversion programs were developed to ease the overrepresentation of individuals with psychiatric disorders in the criminal justice system. These programs divert individuals with mental illnesses out of jails into community treatment. Despite the increased popularity of these programs, little is known about the psychosocial, psychiatric and psychological characteristics of the diverted individuals. In addition, despite the importance of using standardized assessment instruments pre-diversion, no published study has attempted to evaluate the utility of risk assessment instruments or measures of malingering, personality or psychopathology in diverted offenders. This investigation attempted to address this gap in the literature through three different studies that (1) described a sample of 61 defendants released from jail in terms of demographical, clinical, and criminological characteristics; (2) determined the utility of the HCR-20 violence risk assessment scheme and the Psychopathy Checklist: Screening Version (PCL: SV) in the prediction of diversion non-compliance, and recidivism in a sample of 120 defendants, and (3) identified alternative factors that help defendants succeed in diversion through a multiple case-study design. Results revealed that this sample consisted primarily of minority male defendants with extensive histories of prior arrests, significant histories of physical abuse, homelessness and suicidality, and co-morbid substance abuse and psychiatric disorders. The findings provided preliminary validation of the predictive validity of the HCR-20 and PCL: SV with defendants diverted to community treatment. The HCR-20 was found to be superior to the PCL: SV in predicting both non-compliance and recidivism, and the PCL: SV proved to be more useful in predicting recidivism than non-compliance. Results of multiple case-studies found a pattern of characteristics shared by participants who failed diversion regardless of HCR-20 results. These variables included history of physical abuse, family history of substance abuse or criminal behavior, levels of social support, and level of responsibility taken for the instant offence.

  • An Examination of Predictive Variables of Success in Mental Health Diversion Programs.

    Author:
    Virginia Barber Rioja
    Year of Dissertation:
    2009
    Program:
    Psychology
    Advisor:
    Thomas Kucharski
    Abstract:

    Diversion programs were developed to ease the overrepresentation of individuals with psychiatric disorders in the criminal justice system. These programs divert individuals with mental illnesses out of jails into community treatment. Despite the increased popularity of these programs, little is known about the psychosocial, psychiatric and psychological characteristics of the diverted individuals. In addition, despite the importance of using standardized assessment instruments pre-diversion, no published study has attempted to evaluate the utility of risk assessment instruments or measures of malingering, personality or psychopathology in diverted offenders. This investigation attempted to address this gap in the literature through three different studies that (1) described a sample of 61 defendants released from jail in terms of demographical, clinical, and criminological characteristics; (2) determined the utility of the HCR-20 violence risk assessment scheme and the Psychopathy Checklist: Screening Version (PCL: SV) in the prediction of diversion non-compliance, and recidivism in a sample of 120 defendants, and (3) identified alternative factors that help defendants succeed in diversion through a multiple case-study design. Results revealed that this sample consisted primarily of minority male defendants with extensive histories of prior arrests, significant histories of physical abuse, homelessness and suicidality, and co-morbid substance abuse and psychiatric disorders. The findings provided preliminary validation of the predictive validity of the HCR-20 and PCL: SV with defendants diverted to community treatment. The HCR-20 was found to be superior to the PCL: SV in predicting both non-compliance and recidivism, and the PCL: SV proved to be more useful in predicting recidivism than non-compliance. Results of multiple case-studies found a pattern of characteristics shared by participants who failed diversion regardless of HCR-20 results. These variables included history of physical abuse, family history of substance abuse or criminal behavior, levels of social support, and level of responsibility taken for the instant offence.

  • El modernismo desde dentro: Discurso de la "gente nueva" y campo literario en la prensa modernista madrileña (1897-1907)

    Author:
    MARIA SUSANA BARDAVIO ESTEVAN
    Year of Dissertation:
    2010
    Program:
    Hispanic & Luso Brazilian Literatures & Languages
    Advisor:
    William Sherzer
    Abstract:

    This dissertation examines the trajectory of modernist discourse between 1897 and 1907 and its impact on the process toward autonomy of Madrid's literary field. In the late nineteenth century, the failure of the liberal project and of positivism plunged European thought into what has been called the fin de siècle crisis. Spain participated fully in this process, generating a series of protest discourses that rejected the prevailing system. In the arts and literature in particular, this led to a number of trends aesthetically or ideologically opposed to the political system of the Restoration, to bourgeois values, to radical positivism and to realist aesthetics. The material and social conditioning factors greatly hindered the development of the new aesthetics. This caused the young writers to come together as a community of discourse conjoining the plurality of perspectives that characterized them under two basic principles: the defense of literary renewal and the rejection of the established powers. The constant struggle for these two assumptions laid the foundations for a symbolic revolution in the literary field. I understand modernism as the collective discourse that in the late nineteenth century started to make its way into the literary field and whose impact on it would be crucial in the process of autonomization. My study focuses on the public sphere of modernist discourse. I have examined mainly the modernist magazines published in Madrid between 1897 and 1907 because, compared to the consecrated press, they were the means by which the gente nueva could freely express and disseminate their opinions. Throughout the dissertation I explore the development of modernist discourse to show that it was not immutable, but that it was changing within the literary field. As it was gaining recognition, the modernist writers adopted literary positions that caused confrontations among themselves, leading to the breakup of the original community of discourse. However, they were still sharing the defense of the aforementioned principles, and when they finally imposed them and their discourse was perceived as legitimate by the whole field, a degree of autonomy hitherto nonexistent in the literary world was eventually reached.

  • El modernismo desde dentro: Discurso de la "gente nueva" y campo literario en la prensa modernista madrileña (1897-1907)

    Author:
    MARIA SUSANA BARDAVIO ESTEVAN
    Year of Dissertation:
    2010
    Program:
    Hispanic & Luso Brazilian Literatures & Languages
    Advisor:
    William Sherzer
    Abstract:

    This dissertation examines the trajectory of modernist discourse between 1897 and 1907 and its impact on the process toward autonomy of Madrid's literary field. In the late nineteenth century, the failure of the liberal project and of positivism plunged European thought into what has been called the fin de siècle crisis. Spain participated fully in this process, generating a series of protest discourses that rejected the prevailing system. In the arts and literature in particular, this led to a number of trends aesthetically or ideologically opposed to the political system of the Restoration, to bourgeois values, to radical positivism and to realist aesthetics. The material and social conditioning factors greatly hindered the development of the new aesthetics. This caused the young writers to come together as a community of discourse conjoining the plurality of perspectives that characterized them under two basic principles: the defense of literary renewal and the rejection of the established powers. The constant struggle for these two assumptions laid the foundations for a symbolic revolution in the literary field. I understand modernism as the collective discourse that in the late nineteenth century started to make its way into the literary field and whose impact on it would be crucial in the process of autonomization. My study focuses on the public sphere of modernist discourse. I have examined mainly the modernist magazines published in Madrid between 1897 and 1907 because, compared to the consecrated press, they were the means by which the gente nueva could freely express and disseminate their opinions. Throughout the dissertation I explore the development of modernist discourse to show that it was not immutable, but that it was changing within the literary field. As it was gaining recognition, the modernist writers adopted literary positions that caused confrontations among themselves, leading to the breakup of the original community of discourse. However, they were still sharing the defense of the aforementioned principles, and when they finally imposed them and their discourse was perceived as legitimate by the whole field, a degree of autonomy hitherto nonexistent in the literary world was eventually reached.

  • The Role of Sleep in Odor Memory Consolidation Within the Piriform Cortex

    Author:
    Dylan Barnes
    Year of Dissertation:
    2014
    Program:
    Psychology
    Advisor:
    Donald Wilson
    Abstract:

    Sleep is important for memory consolidation. One potential mechanism of memory consolidation is replay, where recently formed memories are repeated during post-learning sleep. For example, the firing sequences evoked in hippocampus during learning are spontaneously replayed during bouts of slow wave sleep (SWS). The phenomenon of replay during SWS is common in many neocortical systems. Odor memory may also rely on sleep-dependent consolidation, even though olfaction is not a neocortical system. The primary olfactory (piriform) cortex is a three-layered archicortex receiving direct input from the olfactory bulb. Piriform cortical activity during slow-wave sleep-like states is modified by recent odor experiences and becomes highly coherent with the amygdala and hippocampus, suggesting a possibility of replay in the olfactory system. The goal of this research was to describe the role post-training sleep had in odor memory consolidation. The initial study utilized two different types of conditioning: standard odor fear conditioning and differential fear conditioning to examine how olfactory training can affect perceptual odor discrimination. Results from this study showed that animals that undergo differential odor fear conditioning are better able to discriminate similar odors following conditioning compared to animals that undergo standard conditioning. Furthermore, this change in perception is possible through changes in the receptive fields of individual units within the piriform cortex. The next study examined how SWS in the anterior piriform cortex is involved in olfactory memory consolidation following odor fear conditioning. The amount of time animals spent in SWS following conditioning significantly increased compared to baseline habituation days and the amount of time animals spent in SWS following learning predicted how much time they froze to the odor during testing. Finally, the last study assessed changes in both the strength and precision of olfactory memory following modifications made during post-training SWS. Imposing replay of the learned odor during post-training SWS enhanced the strength of the odor memory, while imposing replay of another odor stimulus caused animals to generalize their fear response to multiple olfactory stimuli. Taken together, these results underlie the importance of sleep in the consolidation of both the strength and precision of odor memory.