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Elucidation of the mechanisms of RNA binding by the Escherichia coli ProQ N-terminal domain: a molecular genetic approach
No full textProQ is a global RNA-binding protein that is present in many bacterial organisms and helps control gene expression by binding to numerous RNA partners including sRNAs and mRNA UTRs. Although Escherichia coli ProQ’s structure has been solved with NMR spectroscopy, there is still no co-structure of ProQ bound to its RNA partners, so we do not have a full understanding of ProQ’s mechanism of interaction with RNA.
In order to probe this mechanism, we have used a bacterial three-hybrid assay with a genetic lacZ reporter. With this tool, we can use molecular genetics to test many mutant proteins in a relatively short amount of time. Here, I discuss a dissection of ProQ’s RNA-binding mechanisms focusing on its FinO-like domain which is the N-terminal domain (NTD) of Escherichia coli ProQ.
This study includes (1) the exploration of two surface-exposed aspartate residues on the concave face of ProQ’s NTD, as described in a previously published study. Three more recent projects focusing on (2) probing the contributions to RNA binding of potential hydrogen-bonding residues on the convex face of ProQ’s NTD; (3) using double substitutions to detect more subtle or redundant effects of residues; and (4) using an RNA substrate with an extended single stranded poly(uridine) tail to determine RNA-specificity of these effects. We demonstrate that the convex face of ProQ’s NTD does interact with RNA and that there may be some RNA-specific dependence on certain convex residues.Biochemistr
Developing an Analytical Model for Charge Transport in Organic Solar Cells through Simulation of Photocurrent
No full textIn order to develop next-generation solar cells with higher efficiency, it is important to use charge transport mechanism in a Current-Voltage (IV) model of solar cells. Therefore, we are working on developing an analytical model for current in solar cells in which the charge transport is typically governed by traps. The devices we focus on are planar bilayer organic semiconductor solar cells, and aspects of our model have the possibility of extending to other general devices with bilayer semiconductors, including diodes and transistors.
The analytical model was previously developed based on experimental work, focusing on the dark current of the solar cell. This thesis will present how we use simulation to further validate and improve our analytical model. I will introduce the basic principles of the simulation software, GPVDM, which allows us to simulate current and extract useful parameters of solar cells. Through simulation, we determine methods of correcting for series resistance and extracting the compensation voltage. We then create a new analytical equation for photocurrent, allowing us to fit the photocurrent and extract the compensation voltage. We show that this compensation voltage is proportional to the energy difference at the donor/acceptor interface. While we extended our analytical model to include photocurrent, we also identified a number of open questions and next steps to follow to continue improving and validating the model.Physic
A Literature Review of Unisexual Ambystoma and Related Polyploid Hybrid Survival and Development
No full textThe Ambystoma laterale-jeffersonianum complex is a collection of salamander populations inhabiting a significant portion of New England, including western Massachusetts. This complex consists of two groups, sexuals and unisexuals. Sexual A. laterale and A. jeffersonianum are diploid and reproduce sexually. Unisexuals, conversely, range from haploid to pentaploid, and are simply classified as Ambystoma, having no true species identity. This population of unisexual salamanders consists entirely of females which can reproduce both sexually and asexually (Bogart et al, 2007). Within this complex, unisexuals can sexually reproduce only with sexual males, often resulting in hybrid offspring (Charney et al., 2014). Due to the incongruence of ploidy between sexuals and unisexuals, hybrid offspring range in ploidy from haploid to pentaploid as well. While hybrids can develop into completely healthy, phenotypically normal adults, they face an extremely high mortality rate as embryos prior to the first cleavage event (Avis, 2019; Charney et al., 2019).
Throughout my research, I have amassed information regarding the Ambystoma complex’s embryogenesis, genetics, and environment in an attempt to consolidate much of what is currently known about them in the literature. In addition, I here propose multiple experiments that could be completed by future thesis students and other researchers in order to determine what factors play a role in causing this high mortality rate in early hybrid embryos.Biological Science
Magnetic Iron Oxide Nanocubes - The Effect of Substrate Modification, and Post Assembly Manipulation on the Formation of a Monolayer
No full textOver the last decade, nanoparticles have become particles of great research interest because of their inherent chemical compositions such as size, shape, ability to be coated by other molecules, and control over their magnetic properties. The Assembly of these particles into a monolayer allows their unique properties to be harnessed and applied in various fields of study. The goal of this study was to use various surface modification techniques to assemble magnetic iron oxide (Fe3O4) nanocubes suspended in a 3:1 chloroform: methanol dispersing agent, into a monolayer. By exploring literature on how changing different factors such as plasma cleaning, Langmuir-Blodgett (LB) technique, and annealing, the conditions optimal for the monolayer formation were characterized and verified using transmission electron microscopy (TEM) imaging and subsequent analysis.
For the primary objective of nanoparticle assembly into monolayer films, the techniques of spin coating onto a carbon TEM substrate was used. The role of TEM grid modification using plasma cleaning and LB technique was explored to see the effect on the even distribution of the nanoparticles. Post-modification annealing on spin-coated nanoparticles was also explored and was projected to play a vital role in morphological stability and even particle distribution on the carbon TEM substrate. After annealing, the grids are imaged under TEM at different magnifications.
Using the Java-based program, Image J, it was found that the nanocubes maintained their shape and the mean cubic length of 15.50 nm at temperatures ranging from 100 – 150 oC. The TEM grids with no surface modification, annealed at 100 oC showed the highest area coverage of 80%. The results so far indicate that plasma cleaning of TEM grids can hinder the formation of a uniform monolayer. This could be due to the unfavorable interaction between the hydrophobic decanoic acid coating of nanocubes and the hydrophilic TEM grid. The TEM grids coated with heptadecanoic acid (HDA) had a more evenly dispersed layer of nanocubes. This could be due to the favorable hydrophobic interactions between hydrocarbon chains of HDA and decanoic acid. The study reveals how different surface modification techniques affect the assembly of nanocubes into a monolayer formation. Further investigation is needed to confirm if the annealing of nanocubes at 100 ̊ C on a hydrophobic substrate is the best modification to promote the formation of a uniform monolayer.Chemistr
"I've all the world in thee": Lesbian Poetics and Discourses of Sexuality in the Long Eighteenth Century
No full textPosthumously appointed the “English Sappho” by her contemporaries after her tragically early death, Katherine Philips was only the first in a line of several women poets (including Anne Killigrew, Anne Finch, and Elizabeth Singer Rowe) living in the late seventeenth and early eighteenth centuries who wrote passionate verses describing other women—what, today, we might identify as lesbian poetry. Decades later, Charlotte Charke penned an autobiography detailing her life, including a time during which she assumed the name “Charles Brown” and lived with a woman she called “Mrs. Brown.”
At the same time, public discourse was constructing a sort of spectre of the “tribade,” as lesbians were termed at the time. As outlined in both pseudo-medical pamphlets speculating on lesbian bodies and short stories detailing lesbians who wore men’s clothing in order to marry women, this dangerous and lascivious tribade would teach other woman how to pleasure themselves and that sex could be pleasure-driven, thereby upsetting heteropatriarchy and solidifying women’s sexual autonomy. How did lesbian writers articulate their feelings against a wider perception of them as monstrous and predatory? How did they code these feelings into their writings in order to avoid public shame, while at the same time, reaching women who were like them? In my project, I draw patterns from the evident discourses in order to answer these questions. Using both poetry and prose works by lesbians as well as fiction and anatomical texts written by outsiders, I work to understand how lesbians were responding in writing to an exaggerated social caricature.Englis
From Protest Permits to Pepper Spray: Examining Repressive Police Response to Black Lives Matter Demonstrations
No full textIn summer 2020, the United States witnessed protests that began in Minneapolis in response to
the death of George Floyd and spread to cities across the world. Some police responded
positively to these demonstrations, while in other places, they responded with violence, making
mass arrests and using pepper spray or rubber bullets for crowd dispersal. This research
addresses the question, how and why does police response to protest vary? How do police tasked
with public order and citizen protection act when they themselves are the target of
demonstrations? Or, when demonstrators are protesting them? I draw on social movement
literature and theories of policing to explore the interactions between police and activist groups,
and how each group responds to the actions of the other. I propose a series of factors to predict
when police show up at protests and what kinds of action they take, including political
environment, protest tactics, and the physical, situational threat posed to police.
I locate these factors in three historical case studies, and I then examine them through statistical
analysis, using a dataset of nearly 12,000 protest events in the US from May 27 through August
26, 2020. I test ordered logistic regression models to determine the statistical significance of
factors of political environment and threat on police response. I find that the situational threat of
a demonstration has the most significant role in determining how police react. The threat of a
protest’s claim—whether it is pro-Black lives—greatly increases the likelihood that police will
respond with more repression. I illustrate these findings with a case study on the Denver Police
Department in Denver, CO and their disproportionately violent response. I conclude with
questions about the feasibility of police reform and the success of the Black Lives Matter
movement.Politic
Understanding Religiosity and Mental Health through Attribution Styles: A Resiliency-Based Framework
No full textEvents such as the COVID-19 pandemic illustrate the need to examine the relationship between religiosity and mental health during stressful situations. With a recent increase in religious discrimination against the Muslim and Catholic communities, coping in response to secondary trauma becomes an important mental health variable to consider during the pandemic. Furthermore, subjective well-being, measured through happiness, was examined to understand the role of religiosity in enhancing well-being. Adopting a resiliency framework for this study, the researcher conceptualized religiosity as a protective factor against negative mental health outcomes. Thus, to understand the unique contribution of religiosity as a protective factor, resilience was added as a control variable. This study also considered attributional styles as a possible mediator for the proposed relationship between religiosity and mental health outcomes. Thus, this exploratory study aimed to understand how religion may be a resilience resource for individuals facing a global stressor, such as the COVID-19 pandemic. Results suggested that higher levels of religiosity in Catholics were related to higher levels of secondary trauma self-efficacy. While for Muslims, higher levels of religiosity were related to higher levels of happiness. Attributional styles did not mediate the relationship between religiosity and happiness. Nor did attributional styles mediate the relationship between religiosity and secondary trauma self-efficacy. However, the variable resilience, which served as a control in the modeling, related positively with religiosity, secondary trauma self-efficacy, and happiness. Implications and recommendations for future research based on the findings are discussed.Psychology & Educatio
Tau isoform-specific effects on lifespan in a Drosophila melanogaster model of glial tauopathy
No full textTauopathies are a class of neurodegenerative diseases characterized by the abnormal phosphorylation and accumulation of the protein, tau. This abnormal accumulation occurs in both neuronal and glial cells and correlates with loss of normal functioning and cell death. In the human brain, tau has six main alternatively spliced isoforms (0N3R, 0N4R, 1N3R, 1N4R, 2N3R and 2N4R) that differ in the inclusion of one or two N-terminal inserts (N) and the second of four microtubule-binding domain repeat regions (R). 4R tau has been shown to aggregate more readily and exhibit greater toxicity than 3R tau in neurons, but isoform-specific effects on glial cells have yet to be elucidated. In this study, we utilized a fruit fly, Drosophila melanogaster, model of glial tauopathy to determine tau isoform-specific effects on toxicity. 0N3R and 0N4R were overexpressed in Drosophila glia and lifespan was measured as an indicator of toxicity. We found an interaction of the isoform type - 0N3R and 0N4R - with tau toxicity. Glial tau overexpression of both isoforms reduced lifespan in comparison to control, with 0N4R tau isoform resulting in a greater decrease in fly lifespan than 0N3R tau isoform. Generally, these results suggest that isoform type has an effect on tau toxicity when expressed in Drosophila glial cells.Neuroscience and Behavio
What to Expect When You’re Existential: The Politics of Reproduction During Times of Climate Crisis
No full textClimate change represents an existential crisis demanding human response, whether it be actively preparatory or reactively passive. This thesis project is aimed at understanding and analyzing the complex intersectionalities of international movements and personal pledges through an exploratory qualitative research process that elevates the lived experiences of climate organization leaders and members. Focusing on two climate groups with reproductive themes — UK-based “Birth Strike for the Climate” and US-based “Conceivable Future” — this thesis investigates the underlying political demands and grassroots organizing that have led to group members pledging not to have children because of climate change. I use the collectivist approach of Feminist Marxism to tie together class and gender liberation, and I build on reproductive justice — an intersectional framework for reproductive advocacy and racial justice told through acknowledging the legacy of racial reproductive violence — to reject individualism for its inadequacy as a political response. Ultimately, I argue that justice cannot be achieved by working within or replicating the systems that created the problem.
I approached my research process with the intention of bridging conventionally-viewed ‘objective’ academic knowledge (in the form of theoretical literature, data analysis, and historical primary sources) with feminist epistemologies. I conducted interviews with members involved on different levels of Birth Strike and Conceivable Future. Through applied thematic analysis, qualitative interviews with climate organization founders and members were coded and comparatively interpreted against official movement statements and extensive theoretical literature. I used qualitative and interpretive methods of analysis for outgoing communications of Birth Strike and Conceivable Future through their website statements and social media. These methods are integral to gaining the depth of understanding necessary for balancing personal and academic perspectives on the same theme.Politic
Hippocampal lesions prevent adjustment to reward devaluation
No full textIncentive relativity refers to a distortion in the absolute value of an incentive that results from the comparison between the present and the memory of past rewards, and it triggers frustration when this comparison indicates that an incentive has been lost. The adaptive value of frustration resides in its ability to cause a rapid change in learning and performance preventing perseveration on no-longer rewarded responses. Thus, frustration facilitates a switch from responses that no longer yield incentives to a search mode that may result in the discovery of needed resources. However, in vulnerable individuals, reward loss can also result in maladaptive persistent behaviors that can lead to neuropsychiatric disorders. A large body of evidence links reward loss experience with aversive emotion (anxiety, disappointment), negative affect (depression), and activation of the hypothalamic-pituitary-adrenal axis (stress). Animal models of frustrative nonreward provide a useful approach to study reward value, and its behavioral consequences from a psychobiological perspective because they enable a careful manipulation of physiological and environmental variables, and a systematic recording of behavioral and neural responses. While little is known about the neural circuit mechanisms of incentive relativity in rodents, there is a good indication that the hippocampus could be involved because (1) reward value needs reward representation, and (2) reward value needs memory, since it is based on reward comparisons. Because women are twice as likely as men to present the disorders that reward loss can induce (Canuto et al., 2018; Kessler & Bromet, 2013), we decided to use female rats for our experiments. Adult female rats with either a hippocampal lesion (n=7) or a sham lesion (n=6) were exposed to a reduction in the amount of expected solid food presented in one of the two goal sites of a figure-eight-maze. Response latencies and choice responses were registered before and after the incentive downshift. We found that excitotoxic lesions of the hippocampus prevented behavioral adjustment to reward devaluation. In particular, unlike control rats, hippocampal lesion rats did not change their preference and perseverated on choosing the downshifted reward, demonstrating a lack of flexibility to modify their response to the new reward conditions. Our results indicate that hippocampal reward computations are required to flexibly guide behavior at the service of obtaining biologically relevant rewards. Identifying the function of neural circuits for reward value and resilience to loss is a critical step for developing therapeutic approaches to prevent or ameliorate emotional and cognitive problems in disease.Neuroscience and Behavio