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Activation Of The Sonic Hedgehog Effector Smoothened Counteracts L-Dopa Induced Dyskinesia By Restoring Cholinergic Interneuron Function, Lauren Malave Feb 2020

Activation Of The Sonic Hedgehog Effector Smoothened Counteracts L-Dopa Induced Dyskinesia By Restoring Cholinergic Interneuron Function, Lauren Malave

All Dissertations, Theses, and Capstone Projects

Many types of neurons act as multimodal signaling centers. Yet, we have only limited insight into the regulation and functional consequences of neuronal co-transmission. For example, dopamine (DA) neurons, whose degeneration causes motor deficits characteristic of Parkinson’s Diseases (PD), communicate with all their targets by DA but only a selective subset of their targets using GABA, Glutamate, and the secreted cell signaling protein Sonic Hedgehog (Shh). It is unknown whether Levo-dopamine (L-Dopa) induced dyskinesia (LIDs), a severely debilitating side effect of DA supplementation in PD, might appear because DA neuron targets are exposed to high DA- but low Shh- ...


Blocking Visual Awareness With Continuous Flash Suppression Prevents Cognitive Control, Jonathan Lovoi Feb 2020

Blocking Visual Awareness With Continuous Flash Suppression Prevents Cognitive Control, Jonathan Lovoi

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Cognitive control refers to a set of functions that allow for the execution of goal-directed behavior while remaining flexible to changes in task demands. Findings addressing whether or not awareness is necessary to elicit cognitive control are inconsistent, possibly stemming from the short stimulus presentation times employed in most masking paradigms, which could prevent sufficient processing time in some cases or provide a gist of the masked stimulus in other cases. The present study examined the necessity of awareness in cognitive control using Continuous Flash Suppression (CFS) to suppress stimulus awareness for periods of time longer than possible with other ...


Experience-Dependent Changes In Nucleus Accumbens Activity Predict Cued Approach Learning: Contribution Of Nmda Receptors, Mercedes Vega Villar Feb 2020

Experience-Dependent Changes In Nucleus Accumbens Activity Predict Cued Approach Learning: Contribution Of Nmda Receptors, Mercedes Vega Villar

All Dissertations, Theses, and Capstone Projects

Animals learn associations between environmental cues and the natural rewards they predict (e.g., food, water, sex). As a result, reward-predictive cues come to trigger vigorous reward-seeking responses. Many neurons in the nucleus accumbens (NAc) become excited upon presentation of an already-learned reward-predictive cue. These NAc responses encode the motivational value of the cue and are necessary for the expression of the subsequent approach behavior. However, the precise temporal relationship between the emergence of cue-evoked excitations in the NAc and the acquisition of cued approach behavior remains unknown. In Experiment 1, NAc activity was recorded as rats learned to approach ...


On The Distribution Of Genetic Variation In Ecological Communities, Isaac Overcast Feb 2020

On The Distribution Of Genetic Variation In Ecological Communities, Isaac Overcast

All Dissertations, Theses, and Capstone Projects

Biodiversity in ecological communities is structured hierarchically across spatial and temporal scales. Many open questions remain as to how this structure accumulates. For example, what are the relative contributions of dispersal versus in situ speciation? Or, how important are stochastic drift versus deterministic processes? Up to this point, these questions have been investigated by isolated disciplines (e.g. macroecology, comparative phylogeography, macroevolution) using tools and data that tend to focus on only one axis of community scale data (e.g. phylogenies, relative abundances, and/or trait information). Yet we know that there are feedbacks among processes that respond on short ...


Neurogenesis Is Altered Between And Across Brain Regions After Neurodegeneration And Injury, Alice Perez Sep 2019

Neurogenesis Is Altered Between And Across Brain Regions After Neurodegeneration And Injury, Alice Perez

All Dissertations, Theses, and Capstone Projects

Adult neurogenesis is the addition of new neurons in the adult brain. In mammals, neurogenesis is largely restricted to the hippocampus and olfactory bulb, which underlie learning, memory, and olfaction. In songbirds, new neurons are incorporated into telencephalic regions that subserve the production, perception, and maintenance of song. Studies of the regulation of neurogenesis have exclusively focused on a single brain region and within a single hemisphere. Interestingly, it has yet to be investigated whether there are correlations between numbers of new neurons across regions and hemispheres within the same animal. Here we examined these differences in a rat model ...


Neural Correlates Of Automatic Emotional Processing And Emotion Regulation In Empathy And Psychopathy-Related Coldheartedness, Danielle Difilipo Sep 2019

Neural Correlates Of Automatic Emotional Processing And Emotion Regulation In Empathy And Psychopathy-Related Coldheartedness, Danielle Difilipo

All Dissertations, Theses, and Capstone Projects

Psychopathy is a personality disorder that is defined, in part, by a lack of empathy. Psychopathy-related empathic deficits have been associated with atypical behavioral and neural responses to emotional facial expressions. Although the mirror neuron system (MNS) has been implicated in empathy, very few studies have examined the role of MNS functioning as it pertains to empathy impairments in psychopathy. Moreover, there is very little empirical research regarding emotion regulation in psychopathy, and specifically whether emotional responses can be intentionally upregulated. The present study sought to clarify whether the MNS is functionally intact in adults with subclinical psychopathic traits, particularly ...


Murine Genetic Variance In Sugar And Fat-Conditioned Flavor Preferences: Roles Of Dopamine, Opioid And Nmda Receptors And Nutritive Sensing, Tamar T. Kraft Sep 2019

Murine Genetic Variance In Sugar And Fat-Conditioned Flavor Preferences: Roles Of Dopamine, Opioid And Nmda Receptors And Nutritive Sensing, Tamar T. Kraft

All Dissertations, Theses, and Capstone Projects

As obesity and diabetes have emerged as a severe public health crisis, understanding the mechanisms underlying the consumption of sugars and fats has become a topic of vigorous study. From a biological standpoint, genetic dispositions, neurochemical and hormonal influences, and predetermined orosensory and postingestive signals that modulate the hunger and satiety process may govern physiological aspects of the obesity puzzle. In addition to an innate appetite and attraction for simple carbohydrates and fats, learning plays an important role in modulating preferences for sugar- and fat-rich foods in rodents, including inbred mouse strains. Marked genetic variance has been observed among murine ...


Sex, Scents, And Cephalopods: Factors That Affect Social And Reproductive Behavior In Chambered Nautilus And Oval Squid, Naomi J. Lewandowski Sep 2019

Sex, Scents, And Cephalopods: Factors That Affect Social And Reproductive Behavior In Chambered Nautilus And Oval Squid, Naomi J. Lewandowski

All Dissertations, Theses, and Capstone Projects

Cephalopods are a highly specialized group of molluscs that show a wide range of behavioral patterns. Chambered nautilus (Nautilus pompilius) and oval squid (Sepioteuthis lessoniana) are two very distinct species of cephalopod that both provide unique insight into cephalopod reproductive and social behavior. In experiments utilizing both species, I aimed to fill in knowledge gaps in a range of reproductive behaviors from fundamental responses to conspecifics, to preferred mating habitat.

In Chapter 1 and 2 I tested individual nautiluses in a Y-maze where recipients were exposed to paired odors of two donor nautiluses. I collected data on both their choice ...


The Interaction Of Attention And Memory On The Reorienting Negativity, John C. Moses Sep 2019

The Interaction Of Attention And Memory On The Reorienting Negativity, John C. Moses

All Dissertations, Theses, and Capstone Projects

The three-stage model of distraction asserts that when we are presented with salient but task-irrelevant information, our sensory systems first detect the distracting stimulus by way of sensory memory buffers, which is indicated electrophysiologically by the mismatch negativity (MMN). Following detection, attentional resources are involuntarily allocated towards the processing of the distraction, as represented by the P3a. Finally, attentional resources are shifted away from the distracting stimulus and returned to the task-relevant information, as indicated by the reorienting negativity (RON). A great deal of research has focused on this last step in the model, largely centering around defining the mechanisms ...


Minimalistic Peptide-Based Supramolecular Systems Relevant To The Chemical Origin Of Life, Daniela Kroiss Sep 2019

Minimalistic Peptide-Based Supramolecular Systems Relevant To The Chemical Origin Of Life, Daniela Kroiss

All Dissertations, Theses, and Capstone Projects

All forms of life are based on biopolymers, which are made up of a selection of simple building blocks, such as amino acids, nucleotides, fatty acids and sugars. Their individual properties govern their interactions, giving rise to complex supramolecular structures with highly specialized functionality, including ligand recognition, catalysis and compartmentalization. In this thesis, we aim to answer the question whether short peptides could have acted as precursors of modern proteins during prebiotic evolution. Using a combination of experimental and computational techniques, we screened a large molecular search space for peptide sequences that are capable of forming supramolecular complexes with adenosine ...


Molecular Dynamics Simulations Of Supramolecular Assemblies In Biology And Bionanotechnology, Anjela Manandhar Sep 2019

Molecular Dynamics Simulations Of Supramolecular Assemblies In Biology And Bionanotechnology, Anjela Manandhar

All Dissertations, Theses, and Capstone Projects

Molecular self-assembly is an energy driven process where randomly organized building blocks interact noncovalently to form highly organized supramolecular nanostructures. In biology, the cytoskeleton is a classic example of a dynamic self-assembly, forming long filamentous structures from monomeric protein subunits. Similarly, the self-assembly process is widely exploited in nanotechnology to build bio-functional nanostructures. In this work, we studied biological (microtubule) and synthetic (peptide drug amphiphile nanotube) self-assembled systems. We utilized long time-scale molecular dynamics simulation to investigate the structural and dynamical properties of these systems.

At the molecular level, the dynamic instability (random growth and shrinkage) of the microtubule (MT ...


Anti-Cancer Effects Of Oleocanthal And Extra Virgin Olive Oil, Limor Goren Sep 2019

Anti-Cancer Effects Of Oleocanthal And Extra Virgin Olive Oil, Limor Goren

All Dissertations, Theses, and Capstone Projects

Oleocanthal is a phenolic compound found in varying concentrations in extra virgin olive oil. Oleocanthal has been shown to be active physiologically, benefiting several diseased states by conferring anti-inflammatory and neuroprotective benefits. Recently, we and other groups have demonstrated its specific and selective toxicity toward cancer cells; however, the mechanism leading to cancer cell death is still disputed. The current study demonstrates that oleocanthal induced damage to cancer cells’ lysosomes leading to cellular toxicity in vitro. Non-cancer cells were significantly less affected. Lysosomal membrane permeabilization following oleocanthal treatment in various cell lines was assayed via three complementary methods. Additionally, we ...


Hyaluronan At The Brain-Environment Interface, Donald M. Thevalingam Sep 2019

Hyaluronan At The Brain-Environment Interface, Donald M. Thevalingam

All Dissertations, Theses, and Capstone Projects

Hyaluronan (HA; Hyaluronic Acid), a primary scaffolding component of the brain extracellular matrix, serves as an integral structural component to the brain extracellular space (ECS). The fossorial African naked mole-rat (Heterocephalus glaber; NM-R), a mammal which lives in a low-oxygen environment and is capable of tolerating hypoxia and hypercapnia, has been shown to synthesize and sustain a unique high-molecular-mass variant of hyaluronan macromolecule (HMM-HA). This body of work highlights HA’s role in mediating the interplay between brain ECM composition, ECS structure, and cell viability.

Here we employ the NM-R as a unique animal model to observe the role of ...


The Role Of The Direct And Indirect Basal Ganglia Pathways In The Learning, Performance, And Goal-Directed Control Of Action Sequences, Eric Garr Sep 2019

The Role Of The Direct And Indirect Basal Ganglia Pathways In The Learning, Performance, And Goal-Directed Control Of Action Sequences, Eric Garr

All Dissertations, Theses, and Capstone Projects

Animals engage in intricately woven action sequences that are constructed from trial-and-error learning, but the mechanisms by which the brain links together individual actions which are later recalled as fluid chains of behavior are not fully understood. The aim of this dissertation is to investigate the learning and goal-directed control of action sequences in rats. Experiment 1 addresses a question that comes out of a reinforcement learning model of action sequencing: how does the extent of training change how the performance of an action sequence is impacted by reward devaluation. The data show that action sequences remain goal-directed overall regardless ...


The Evolution Of Spinosad Resistance In Colorado Potato Beetles (Leptinotarsa Decemlineata), Coby Michael Klein Sep 2019

The Evolution Of Spinosad Resistance In Colorado Potato Beetles (Leptinotarsa Decemlineata), Coby Michael Klein

All Dissertations, Theses, and Capstone Projects

Colorado potato beetles (Leptinotarsa decemlineata) are a major pest of cultivated potato plants worldwide. They are well-known for their ability to rapidly evolve resistance to all major classes of pesticides. Defoliation of potato plants by L. decemlineata can reduce potato yields by a considerable margin. The damage done by resistant beetles is steep and much research is focused on developing new chemical controls, especially those derived from naturally occurring compounds. Spinosad is a relatively new natural product insecticide, introduced approximately a decade ago, suitable for use in organic farming. Potato beetles on Long Island, NY developed very strong resistance to ...


Systematics And Ecology Of The Andean Neotropical Schefflera (Araliaceae) With Globose Capitate Inflorescences And Use Of Niche Modeling For Iucn Red List Threat Assessment Of Plerandra Elegantissima (Araliaceae), Carlos V. Rodrigues Sep 2019

Systematics And Ecology Of The Andean Neotropical Schefflera (Araliaceae) With Globose Capitate Inflorescences And Use Of Niche Modeling For Iucn Red List Threat Assessment Of Plerandra Elegantissima (Araliaceae), Carlos V. Rodrigues

All Dissertations, Theses, and Capstone Projects

Since the end of the 19thcentury, ScheffleraJ.R. Forst. & G. Forst.has been recognized as the largest and most wide-ranging genus of Araliaceae. It can be found throughout the humid tropics and subtropics, is not particularly diverse at low elevations in the warmest regions, and a few taxa extend into warm-temperate areas. As currently circumscribed, the genus contains 605 described species and many hundreds more awaiting formal description. However, a succession of phylogenetic studies have confirmed that Schefflera, as currently circumscribed,is polyphyletic, comprising five geographically centered lineages scattered across the phylogenetic tree of Araliaceae, and informally ...


Eugenics In The 21st Century, Jessica Linn Chin Sep 2019

Eugenics In The 21st Century, Jessica Linn Chin

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Eugenics is the science of enhancing the human population through the management of breeding and hereditary traits. This thesis explores the history of eugenics and shows how eugenic practices continue in the 21st century with advancements in technology and positive eugenic goals that can result in adverse effects on the human body and society. When Sir Francis Galton coined the term eugenics in 1883, he intended to improve British society with the use of positive eugenics. Galton used positive eugenics to encourage people with good mental and physical qualities to produce more children. He avoided negative eugenics, which involved ...


Renal Specific Rnai Delivery By Fibrillar Nanoparticle Excipients, Sam Wong Sep 2019

Renal Specific Rnai Delivery By Fibrillar Nanoparticle Excipients, Sam Wong

All Dissertations, Theses, and Capstone Projects

RNA interference (RNAi) is a powerful tool to manipulate the phenotype of an organism by silencing the expression of specific genes and is viewed as a highly promising platform for treating undruggable targets and disorders where small molecule drugs and antibodies would fail. However, development of RNAi based therapies has faced major barriers including cellular and tissue-specific uptake of the Small Interfering RNA (siRNA). Utilizing different nanoparticles as RNAi excipients, cellular uptake and gene silencing potency can be greatly improved. The research in Dr. McDevitt groups has fibrillar carbon nanotubes (CNT) as carriers for siRNA for gene silencing in vitro ...


Voluntary Oral Methamphetamine Reveals Susceptibilities To Spatial Memory Deficits, Decreased Dopamine Marker Expression And Increased Neuroinflammation In The Hippocampus Of Male And Female Mice, Jorge A. Avila Sep 2019

Voluntary Oral Methamphetamine Reveals Susceptibilities To Spatial Memory Deficits, Decreased Dopamine Marker Expression And Increased Neuroinflammation In The Hippocampus Of Male And Female Mice, Jorge A. Avila

All Dissertations, Theses, and Capstone Projects

Methamphetamine is an addictive illicit psychostimulant that produces lasting neurochemical and behavioral changes. The mechanisms underlying these deficits have been characterized in animal models using extremely high doses. Currently, better translational models are needed to understand the onset and progression of these deficits that more accurately reflect the gradual and voluntary dosing parameters as chosen by an abuser. To that end, a new model of methamphetamine administration, labeled Voluntary Oral Methamphetamine Administration (VOMA), offers a means to examine the progression of neurotoxicity, behavioral deficits, and the addiction process through a voluntary consumption framework.

Female populations show consistent vulnerabilities to methamphetamine ...


Cognitive Models Of Defense Behaviors In Hosts Of Brood Parasites, Thomas J. Manna May 2019

Cognitive Models Of Defense Behaviors In Hosts Of Brood Parasites, Thomas J. Manna

All Dissertations, Theses, and Capstone Projects

Social parasites exploit the behavioral repertoire of their hosts for their own benefit, thereby reducing host reproductive success. Whether and how hosts respond to prevent, reduce, or eliminate the costs of parasitism requires the characterization of host cognitive algorithms in response to parasites. In this dissertation, I review the suite of the defense behaviors and decision rules of hosts targeted by avian and insect brood parasites, and present new experimental data on the detection of parasitism through the visual system of focal host species. In Chapter 1, I review extensive data already accumulated to isolate the cognitive mechanisms used by ...


Resisting Industrial Food Systems On The Web: How Non-Profit Organizations Use Digital Technology For Sustainability Education, Aleksandr Segal May 2019

Resisting Industrial Food Systems On The Web: How Non-Profit Organizations Use Digital Technology For Sustainability Education, Aleksandr Segal

All Dissertations, Theses, and Capstone Projects

This thesis examines the link between how community-based organizations use digital tools with the fundamentally resistance-based philosophy that these organizations have at the core of their mission. It aims to uncover how non-profit organizations (NPOs) that work in community development through food and agriculture use digital tools, and how their digital communication strategies relate to issues of resistance to neoliberalism and industrialization in the food and agriculture sectors.

Using a foundation of existing literature on food and agriculture, climate change and waste management, critical theory, and technology in pedagogy, this thesis will contextualize how non-profits resist neoliberal regimes of de-traditionalization ...


Cultural Heritage Preservation In The Context Of Climate Change Adaptation Or Relocation: Barbuda As A Case Study, Martha B. Lerski May 2019

Cultural Heritage Preservation In The Context Of Climate Change Adaptation Or Relocation: Barbuda As A Case Study, Martha B. Lerski

All Dissertations, Theses, and Capstone Projects

This case study introduces an arts camp methodology of engaging communities in identifying their key cultural heritage features, thus serving as a meta study. It presents original research based on field studies on the climate-vulnerable Caribbean island of Barbuda during 2017 and 2018. Its Valued Cultural Elements survey, enabling precise identification of key tangible and intangible art forms and biocultural practices, may serve as a basis for further studies. Such approaches may facilitate future research or planning as climate-vulnerable communities harness Local or Indigenous Knowledge for purposes of biocultural heritage preservation, or towards adaptation or relocation. I report on findings ...


A Novel Kinesin Adapter Directly Mediates Dendritic Mrna Localization During Synapse Development, Hao Wu May 2019

A Novel Kinesin Adapter Directly Mediates Dendritic Mrna Localization During Synapse Development, Hao Wu

All Dissertations, Theses, and Capstone Projects

Cytoskeleton based active transport with motor proteins is essential for mRNA localization and local protein translation in animal cells, yet how mRNA granules interact with motor proteins remains poorly understood. Using an unbiased screen for interaction between mRNA binding proteins (RBP) and motor proteins, we identified protein interacting with APP tail 1 (PAT1) as a potential direct adapter between the β-actin mRNA Zipcode-binding protein 1 (ZBP1) and Kinesin-1 motor complex.

Mouse PAT1 is similar to the Kinesin Light Chain (KLC) in amino acid sequence and binds directly to KLC. High-resolution images from structured illumination microscopy (SIM) indicates that synaptic stimulation ...


Context Dependent Roles Of Mdmx (Mdm4) And Mdm2 In Breast Cancer Proliferation And Circulating Tumor Cells, Chong Gao May 2019

Context Dependent Roles Of Mdmx (Mdm4) And Mdm2 In Breast Cancer Proliferation And Circulating Tumor Cells, Chong Gao

All Dissertations, Theses, and Capstone Projects

Many human breast cancers overexpress the E3 ubiquitin ligase MDM2 and its homolog MDMX. Expression of MDM2 and MDMX occurs in both estrogen receptor α positive (ER+) and triple negative breast cancer (TNBC). We and others have reported that estrogen activated MDM2 strongly promotes proliferation in ER+ T47D breast cancer cells in a p53-independent manner. Whether MDM2 elicits in vivo p53-independent proliferative functions in T47D breast cancer cells has not been determined. Furthermore it has been shown that ectopic expression of MDM2 targets E-Cadherin for degradation thus leading to increased cell migration and invasion. Therefore we assessed the in vivo ...


The Molecular Mechanisms Underlying The Cancer Killing Effect Of Interleukin-24, Leah Eshanie Persaud May 2019

The Molecular Mechanisms Underlying The Cancer Killing Effect Of Interleukin-24, Leah Eshanie Persaud

All Dissertations, Theses, and Capstone Projects

Interleukin-24 (IL-24) is an immunomodulatory cytokine that also displays specific anti-tumor effects across many cancer cell types. The tumor suppressor activities of IL-24 include inhibition of angiogenesis, metastasis, toxic autophagy, cancer-specific apoptosis, and sensitization to traditional cancer treatments like chemotherapy and radiation. Overexpression of IL-24 can selectively induce apoptosis in various cancer cells while having no adverse effects on normal cells. Due to this favorable killing effect, IL-24 is currently in phase II clinical trials. There is accumulating evidence that IL-24’s anti-cancer activity is primarily through the endoplasmic reticulum (ER) stress pathway but other pathways leading to cell death ...


Design And Application Of Matrix Metalloproteinase-9-Responsive Peptide Nanostructures, Jiye Son May 2019

Design And Application Of Matrix Metalloproteinase-9-Responsive Peptide Nanostructures, Jiye Son

All Dissertations, Theses, and Capstone Projects

Matrix metalloproteinase (MMP)-responsive materials have been investigated since the late 1990’s as scaffolds for tissue engineering and since then, have evolved into sophisticated nanomaterials for cancer-targeting therapy. In this thesis titled, “Design and Application of Matrix Metalloproteinase-9-Responsive Peptide Nanostructures,” we aim to answer the following key questions: can MMP-responsive nanomaterials improve the efficacy of anti-cancer treatments? How can we achieve specificity towards MMPs using nanomaterials? Finally, what are the advantages in using peptides as building blocks to create MMP-responsive nanostructures? Each chapter in the thesis will address one or more of the key questions and draw conclusions at ...


The 5-Ht1a-R Knockout Mouse As A Model Of Later Life Anxiety Disorders: Implications For Sex Differences, Tatyana Budylin May 2019

The 5-Ht1a-R Knockout Mouse As A Model Of Later Life Anxiety Disorders: Implications For Sex Differences, Tatyana Budylin

All Dissertations, Theses, and Capstone Projects

Anxiety affects nearly twice as many women as it affects men across all cultures and economic groups. Importantly, girls have a higher chance of inheriting anxiety disorders than boys, and many anxiety disorders appear at a very young age. However, little is known about sex differences in brain and behavioral development and how they relate to anxiety in adulthood. Serotonin 1A receptor (5-HT1A-R) mediated signaling has been implicated in depression and anxiety, however most studies that focus on the involvement of the 5-HT1A-R have been conducted in adults. Little is known about how the 5-HT1A ...


Interhemispheric Communication And Lateralization In The Mouse Hippocampus, Jake Jordan May 2019

Interhemispheric Communication And Lateralization In The Mouse Hippocampus, Jake Jordan

All Dissertations, Theses, and Capstone Projects

The hippocampus is essential for memory and spatial navigation. Many theories have been proposed to explain how the hippocampus contributes to cognition; however, none has fully explained relevant neurophysiological and behavioral data. Hemispheric lateralization of hippocampal function has been reported in humans and in rodents, and lateralization of hippocampal neural circuitry has been reported in rodents. Most theories of hippocampal function fail to consider the hippocampus as a bilateral structure with hemispheric differences. Further, proposed theories of hippocampal lateralization have their own limitations in explaining empirical data concerning left/right function. Little is known about communication between the hippocampi across ...


Getting At The Surface: A Promoter And Coding Sequence Characterization Of An Odorant Receptor, Irena G. Parvanova May 2019

Getting At The Surface: A Promoter And Coding Sequence Characterization Of An Odorant Receptor, Irena G. Parvanova

All Dissertations, Theses, and Capstone Projects

Odorant receptors (ORs) are expressed by mature olfactory sensory neurons (OSNs), in a monogenic and monoallelic fashion (singular gene choice). It has been repeatedly published that the singular expression of ORs is a consequence of epigenetic regulation. The model invokes the depositing of epigenetic marks (off marks) that reflect transcriptional inactivity on all OR genes in immature neurons followed by the activation of one OR allele in maturing neurons. OR expression has been exclusively studied via transgenic animal models, due to the lack of cell line system that can undergo singular gene choice. Here, we used chromatin immunoprecipitation-quantitative polymerase chain ...


Solvation Thermodynamic Mapping In Computer Aided Drug Design, Steven Ramsey Feb 2019

Solvation Thermodynamic Mapping In Computer Aided Drug Design, Steven Ramsey

All Dissertations, Theses, and Capstone Projects

The displacement of water from surfaces upon biomolecular recognition and association makes a significant contribution to the free energy changes of these processes. We therefore posit that accurate characterization of local structural and thermodynamic molecular water properties can improve computational model accuracy and predictivity of recognition and association processes. In this thesis, we discuss Solvation Thermodynamic Mapping (STM) methods that we have developed using inhomogeneous fluid solvation theory (IST) to better characterize active site water structural and thermodynamic properties on protein surfaces and the open source tools that we have developed, GIST-CPPTRAJ and SSTMap, which implement these methods which we ...