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A Structural Perspective On Neutralizing Antibodies To Flaviviruses And Coronaviruses, John Michael Errico

Arts & Sciences Graduate Student Theses and Dissertations

The presence of neutralizing antibodies typically correlates strongly with protection from infection, particularly for RNA viruses; elicitation of neutralizing antibody responses is thus the primary goal of most vaccines, and monoclonal antibodies (mAbs) can be leveraged as potent therapeutics. Thus, understanding the properties of individual antibodies that comprise polyclonal antibody responses and their epitopes is essential for countermeasure design. In this dissertation, I explore the epitopes and functional properties of monoclonal antibodies targeting the structural proteins of two families of RNA viruses, flaviviruses and coronaviruses.Flaviviruses are globally distributed arthropod-borne positive-sense RNA viruses transmitted primarily by either mosquitos or ticks. Symptomatic …

Uneasy Attachments: Postcolonial Anglophilia And Identity Formation In Twentieth-Century Anglophone Autobiographies, Anwesha Kundu

Arts & Sciences Graduate Student Theses and Dissertations

This dissertation focuses on the impact of anglophilia on identity formation in the British empire. Since Britishness was an identity unavailable to non-white citizens of the empire, this attachment was necessarily unrequited. Analyzing works by Cornelia Sorabji, E.R. Braithwaite, V.S. Naipaul, and Tsitsi Dangarembga, I argue that the critical significance of anglophilia does not lie in the postcolonial subject’s success or failure in achieving a British-coded identity, but in the ways in which an affiliation to Britishness can be mobilized to accomplish a variety of personal, political, and social ends. I use a range of autobiographical literature—travel narratives, autobiographical novels, …

Using Proteomics To Discover New Connections In The Arabidopsis Circadian Clock, Maria Lynn Sorkin

Arts & Sciences Graduate Student Theses and Dissertations

The plant circadian clock is an endogenous timekeeping mechanism that uses daylength and temperature cycles to synchronize internal physiology with the external environment. Much of our understanding of the clock in the model plant Arabidopsis thaliana comes from genetic approaches. In this thesis, I use affinity purification coupled with mass spectrometry (APMS) to identify protein-protein interactions for core clock components on a proteomic scale. I developed and optimized a protocol to perform APMS on a core set of circadian clock proteins: CIRCADIAN CLOCK ASSOCIATED 1 (CCA1), LATE ELONGATED HYPOCOTYL (LHY), PSEUDORESPONSE REGULATOR 5 (PRR5), PRR7, PRR9, TIMING OF CAB 1 …

Local Spectroscopy Data Infrastructure: Solid State Nmr Crystallography With Experiment, First-Principal Analysis And Machine Learning, He Sun

Arts & Sciences Graduate Student Theses and Dissertations

Solid-state magnetic resonance (SSNMR) spectroscopy is a powerful tool for obtaining precise information about the local bonding and morphology of materials. The detailed local structure of crystalline materials cannot be easily solved by traditional experimental methods such as X-ray diffraction (XRD). SSNMR combined with first principal calculation methods such as density functional theory (DFT) can be of great use in this research area. The methodology that is called “NMR crystallography” today has been widely applied to the determination of a wide range of solid materials with an increasing amount of computationally simulated NMR spectra. The construction of a well-established computational …

Connections Between Mechanosensitive Ion Channel Msl10 And Er-Plasma Membrane Contact Sites, Jennette Marie Codjoe

Arts & Sciences Graduate Student Theses and Dissertations

Mechanosensitive (MS) ion channels are an evolutionarily conserved way for cells to sense mechanical forces and transduce them into ionic signals. A plasma membrane-localized MS channel from Arabidopsis thaliana, MscS-Like (MSL)10, senses cell swelling and initiates a signaling cascade that triggers programmed cell death. Whereas the channel properties of MSL10 have been well studied, how MSL10 signals remains largely unknown. I worked collaboratively to show that important lesions for cell death signaling in the cytosolic N- and C-terminal domains of MSL10 interact genetically. I also helped show that ionic flux through MSL10 is dispensable for signaling, which suggested that MSL10 …

The Physics Of Associative Polymers And Applications To Biomolecular Condensates, Furqan Dar

Arts & Sciences Graduate Student Theses and Dissertations

Biomolecular condensates represent a new and ubiquitous class of membraneless organelles (MLOs) that are essential for healthy cellular functioning. The constituent molecules of such condensates span a vast bio-macromolecular gamut from intrinsically disordered regions and proteins (IDPs/IDRs), to RNA and RNA-binding proteins (RNPs), to polymerases and DNA etc. Apart from being part of the regular healthy cell cycle, these condensates are also implicated in many diseases, most notably progressive neurodegenerative diseases like Amyotropic Lateral Sclerosis (ALS) and Huntingtin's Disease (HD). Since the constituent molecules of these condensates span a broad range of length scales and modes of interaction, uncovering a …

Extensive Behavioral Phenotyping Of Williams Syndrome Locus Relevant Mouse Models To Assess Contributions Of Oxytocin And Gtf2ird1, Kayla Rose Nygaard

Arts & Sciences Graduate Student Theses and Dissertations

The Williams Syndrome Critical Region (WSCR) at chromosome 7q11.23 provides a unique opportunity to untangle the relationship between genotype and phenotype in complex behaviors, from fear and anxiety to sociability and sensorimotor processing. Copy number variations (CNVs) in this region result in two syndromes, Williams Syndrome (WS) and Duplication 7q11.23 Syndrome (Dup7), which display phenotypes that may align, indicating a common disruption of a system, or diverge, reflecting an underlying gene dosage-dependent effect. While case studies of atypical deletions resulting in WS have implicated telomeric genes Gtf2ird1 and Gtf2i in the cognitive and behavioral profiles of WS, proving causation requires …

The Role Of The Neurodevelopmental Disorder Gene Myt1l In Mammalian Brain Development, Jiayang Chen

Arts & Sciences Graduate Student Theses and Dissertations

Recent human genetic studies have associated mutations in a gene called Myelin Transcription Factor 1 Like (MYT1L) with neurodevelopmental disorders (NDDs). Patients with MYT1L loss of function (LoF) mutations (MYT1L Syndrome patients) demonstrate shared symptoms such as microcephaly, attention deficit and hyperactivity disorder (ADHD), and obesity. Despite prior studies showing MYT1L overexpression facilitates neuronal differentiation in vitro, its functions in vivo, especially in the mammalian brain, and how its mutation leads to human disease pathology remains poorly understood. Here, I established the first mouse model of MYT1L Syndrome mimicking a patient specific LoF mutation. I found mice with Myt1l heterozygous …

Tissue Resident Macrophages Drive Fibrosis During Pancreas Inflammatory Injury And Pancreatic Ductal Adenocarcinoma, John Baer

Arts & Sciences Graduate Student Theses and Dissertations

The immune system, and especially macrophages, are central in responding to infections, as well as providing a wide array of functions in other pathologies, especially in responding to inflammation. It is established that macrophages will accumulate within tissues during inflammation, many times secreting cytokines and chemokines central to the inflammatory response. This is particularly true during pancreatitis, or inflammation of the pancreas, where it has been shown that macrophages and monocytes accumulate in the pancreas to have various roles in further promoting inflammation. It is not well established, however, whether there are divergent roles for the distinct macrophage subsets that …

Cooperation And Conflict In The Social Amoeba Dictyostelium Discoideum And Its Paraburkholderia Endosymbionts, James Medina

Arts & Sciences Graduate Student Theses and Dissertations

A big question in biology is how organisms compete in an environment of competitors for scarce resources. Part of the answer lies in distinguishing friend from foe and in forging cooperative bonds in the face of cheaters. The social amoeba – bacteria system I have studied here is an excellent place to explore these tensions. The first part of my thesis research involves a review of cooperation and conflict in the social amoeba Dictyostelium discoideum and a study of the limits on obligate social cheating in this species. The second part focuses on the benefits of associating with D. discoideum …

A Universal Mechanism Of G Protein Inhibition, Tyson Daniel Todd

Arts & Sciences Graduate Student Theses and Dissertations

G protein coupled receptors transduce a truly staggering number of diverse extracellular signals including chemical messengers, physical force, and even photons into specific cellular responses through their coupling to heterotrimeric G proteins. G proteins amplify the originating signal through their binding to downstream effectors, activating a complex network of overlapping responses that allow the cell to respond perfectly to that specific stimulus. It is critical to the cell that this process is carried out faithfully in order to respond to the myriad environmental cues and avoid injury, exhaustion, and death for the individual cell or the development of pathology if …

Roles Of Behavioral Novelty And Organismal Energetics In The Evolution Of Extreme Encephalization, Erika Laurie Schumacher

Arts & Sciences Graduate Student Theses and Dissertations

Brains and their component brain regions vary widely in size and structure across vertebrates. However, extreme increases in total brain size relative to body size (extreme encephalization) and increases in specific major brain region sizes independent of other brain regions (mosaic brain evolution) are relatively rare. There are several hypotheses as to why, but the energetic cost of increased brain tissue and the regional interconnectedness in both brain development and function likely constrain how brains are able to change in response to selection. In this dissertation, I sought to address both how behavioral novelty relates to evolutionary changes in brain …

Cultivating Life: Skill, Sovereignty, And The Nature Of Knowledge, Bradley Jones

Arts & Sciences Graduate Student Theses and Dissertations

This dissertation examines the cultivation of knowledge, nature, and farmers in U.S. alternative agriculture. Based on ethnographic fieldwork in the Hudson Valley of New York and Central Appalachia, I trace the movement of knowledge across prominent training guides, educational workshops, and apprenticeship programs designed to train the next generation of sustainable farmers. I argue that the knowledge communities of alternative agriculture (strive to) transmit not only technical capacity—the ability to productively farm sustainability—but also holistic ways of understanding the natural world and the human place in it. In doing so practitioners of alternative agriculture gain autonomy from the political-economic and …

The Bidirectional Relationship Between The Circadian Clock And Alzheimer’S Disease, Patrick Sheehan

Arts & Sciences Graduate Student Theses and Dissertations

The circadian clock and inflammation have a well-described bidirectional relationship in the peripheral immune system: the circadian clock regulates inflammatory responses, but inflammation also impacts oscillatory gene transcription controlled by the clock. The purpose of this thesis work is to understand if manipulation of the circadian clock can impact Alzheimer’s disease pathology, and if pathology itself can alter the circadian clock and its outputs. Here, I show that astrocyte-specific disruption of the circadian clock via deletion of the clock gene Bmal1 surprisingly decreased intra-neuronal protein pathologies. Further investigation found that deletion of the circadian clock resulted in a transcriptomic profile …

Single-Cell Massively Parallel Reporter Assays, Siqi Zhao

Arts & Sciences Graduate Student Theses and Dissertations

Our understanding of gene regulation needs to be generalizable as well as specific. A generalizable understanding enables us to transfer our knowledge of one gene to another, and the specificity allows us to understand the precise regulation of gene expression through development. One framework that confers generalizability and specificity is the hierarchical and modular model of gene regulation. To test whether gene regulation is hierarchical and modular requires methods to systematically analyze how different factors collectively control gene expression. This thesis describes the development of two functional genomics methods at single-cell resolution. These methods systematically examined how cellular contexts, chromatin …

The Montclarion, December 15, 2022, The Montclarion

The Montclarion

Student Newspaper of Montclair State University

Jews And Science, Sander L. Gilman

The Jewish Role in American Life: An Annual Review

Jews and Science examines the complicated relationship between Jewish identities and the evolving meanings of science throughout the history of Western academic culture. Jews have been not only the agents for study of things Jewish, but also the subject of examination by “scientists” across a range of disciplines, from biology and bioethics to anthropology and genetics. Even the most recent iteration of Jewish studies as an academic discipline—Israel studies—stresses the global cultural, economic, and social impact of Israeli science and medicine.

The 2022 volume of the Casden Institute’s Jewish Role in American Life series tackles a range of issues that …

"Because I'M Black": A Qualitative Case Study Of Black Male Middle School Students Raised By Single Mothers, Whitney Hodge

Graduate Theses, Dissertations, and Capstones

Despite there being increased dialogue and attention focused upon the experience of Black males in K-12 education, there is a still a disparity between the academic and behavioral performance of Black males compared to that of their White counterparts, and it is clear that more can be done to support their success in the educational system (Cholewa et al., 2018; Morris & Perry, 2016). The purpose of this study is to examine the Black male middle school experience and take a closer look at how Black males view themselves, how they believe their teachers perceive them, what they have specifically …

Finding “A Self To Speak Of”: Affective Enactments Of The Self In Black And White Victorian Women’S Elegies, Kellie-Sue Martinucci

Theses - ALL

This thesis explores the genre of sentimental elegy within Antebellum Victorian America, drawing on affect studies, American religious history, and Black critical theory in order to contextualize the particular socio-political and religious influences that shaped the medium of the sentimental elegy and its role within Victorian America. This is punctuated by a close reading of six personal elegies written by Black and white women in the years 1855-1865. By attending to the differential application of sentimental norms about human bodies and their capacities for thought and feeling, this paper identifies the personal sentimental elegy as a technology of the self …

Growing Up With Popular Culture In The Time Of Title Ix, Christine A. Corcos

Louisiana Law Review

No abstract provided.

Countering Terrorism On Tomorrow’S Battlefield: Critical Infrastructure Security And Resiliency (Nato Coe-Dat Handbook 2), Sarah J. Lohmann, Lucas M. Cox, Denise Feldner, Trevor P. Helmy, Frank J. Kuzminski, Marcus Mohlin, Aleksander Olech, Wuraola Oyewusi, Gabriel T. Raicu, Silke Ruhl, Sabrina Schulz, Máté Tóth, Megan A. Ward

Books, Monographs & Collaborative Studies

Every day, malicious actors target emerging technologies and medical resilience or seek to wreak havoc in the wake of disasters brought on by climate change, energy insecurity, and supply-chain disruptions. Countering Terrorism on Tomorrow’s Battlefield is a handbook on how to strengthen critical infrastructure resilience in an era of emerging threats. The counterterrorism research produced for this volume is in alignment with NATO’s Warfighting Capstone Concept, which details how NATO Allies can transform and maintain their advantage despite new threats for the next two decades. The topics are rooted in NATO’s Seven Baseline requirements, which set the standard for enhancing …

Insights Into The Biotechnology Potential Of Methanosarcina, Sean Carr, Nicole R. Buan

Department of Biochemistry: Faculty Publications

Methanogens are anaerobic archaea which conserve energy by producing methane. Found in nearly every anaerobic environment on earth, methanogens serve important roles in ecology as key organisms of the global carbon cycle, and in industry as a source of renewable biofuels. Environmentally, methanogenic archaea play an essential role in the reintroducing unavailable carbon to the carbon cycle by anaerobically converting low-energy, terminal metabolic degradation products such as one and two-carbon molecules into methane which then returns to the aerobic portion of the carbon cycle. In industry, methanogens are commonly used as an inexpensive source of renewable biofuels as well as …

Financial Analysis Of Surmodics, Inc., Denver Colgrove

Dissertations, Theses, and Projects

This report aims to provide a financial analysis built from qualitative and quantitative data on Surmodics, Inc., a medical device manufacturer headquartered in Eden Prairie. I will discuss how the firm is performing and compare its financial results to a competitor in the industry, Cardiovascular Systems, Inc. Surmodics has been awaiting approval for various new devices, none more important than the SurVeil DCB. The delays in regulatory approval for these products have delayed millions in revenue for Surmodics, and any further delay increases the company’s level of risk. Throughout the various sections of this report, it will become clear that …

Host Development And Microbiota Influences On Norovirus Infection, Elizabeth Alexandra Kennedy

Arts & Sciences Graduate Student Theses and Dissertations

The mammalian gut is a complex organ which changes over the course of development and is influenced by the presence of a dense community of gut-resident microbes. Enteric viruses infect the gastrointestinal tract in the context of the commensal microbiota and host immunity. Here, we dissect the influence of host developmental stage and the gut microbiota in norovirus infection. From this work, we determine that murine norovirus (MNoV) infection in early life is restricted by an absence of the target MNoV cell tuft cells and intact interferon (IFN) signaling. However, viral inoculum taken up by non-specific endocytosis in the neonatal …

Understanding Gene Regulation With High-Throughput Genome-Integrated Reporter Assays, Clarice Hong

Arts & Sciences Graduate Student Theses and Dissertations

Proper spatiotemporal gene expression depends on specific interactions between cis-regulatory sequences (CRSs) and chromatin modifications at a genomic location. However, we do not yet understand the rules that determine how CRSs work together to influence gene expression. The goal of this thesis is to systematically assay and quantify how different genomic environments interact with CRSs to control gene expression output using a variety of genome-integrated massively parallel reporter assays (MPRAs). First, we tested the hypothesis that core promoters confer specificity by only responding to compatible enhancers and chromatin in specific genomic environments. We measured the activities of hundreds of core …

A War Of Compassion: Challenging The Species Barrier In The Works Of Céline And Léautaud, Dawn Mohrmann

Arts & Sciences Graduate Student Theses and Dissertations

Jacques Derrida, when affirming the undeniability of animal suffering in L’Animal que donc je suis, states that there is “une guerre en cours … entre d’une part, ceux qui violent non seulement la vie animale mais jusqu’à ce sentiment de compassion et d’autre part, ceux qui en appellent au témoignage irrécusable de cette pitié” (50). This study investigates the nature of this ongoing war to which Derrida referred. I investigate both the nature of human cruelty and its counterpoint, empathy, which I propose as the response to the anthropocentrism that allows this struggle to continue. Through investigating theories of empathy, …

Non-Canonical Beta-Lactam Antibiotics, Brett Wesley Virgin-Downey

Arts & Sciences Graduate Student Theses and Dissertations

In canonical β-Lactam antibiotics, such as penicillin, the strained nature of the β-Lactam ring leads to acylation of the catalytic serine in the active site of transpeptidases. In 2018, our lab reported a novel mechanism for monocyclic β-lactam antibiotics in the inhibition of glutamine synthetase (GS) by a natural product, tabtoxinine-β-lactam (TβL) using a 3-hydroxy-β-lactam pharmacophore. This work aims to generalize the β-lactam scaffold from TβL to act as a warhead against ATP-dependent carboxylate-amine ligase enzymes, with dihydrofolate synthetase (DHFS) as the test case. A pure 3-hydroxy-β-lactam warhead was synthesized and ligated both chemically and chemoenzymatically to different pteridine mimics. …

A Deep Learning-Based Model For Plant Lesion Segmentation, Subtype Identification, And Survival Probability Estimation, Muhammad Shoaib, Babar Shah, Tariq Hussain, Akhtar Ali, Asad Ullah, Fayadh Alenezi, Tsanko Gechev, Farman Ali, Ikram Syed

All Works

Plants are the primary source of food for world’s population. Diseases in plants can cause yield loss, which can be mitigated by continual monitoring. Monitoring plant diseases manually is difficult and prone to errors. Using computer vision and artificial intelligence (AI) for the early identification of plant illnesses can prevent the negative consequences of diseases at the very beginning and overcome the limitations of continuous manual monitoring. The research focuses on the development of an automatic system capable of performing the segmentation of leaf lesions and the detection of disease without requiring human intervention. To get lesion region segmentation, we …

Inferring Adaptation In Social Microbes From Experimental Evolution Under Relaxed Selection, Tyler John Larsen

Arts & Sciences Graduate Student Theses and Dissertations

Microbes exist against a backdrop of other organisms, and the interactions between microbes have major consequences on their traits, their evolution, and their impact on the world. Microbial interactions and the adaptations that enable them are extremely diverse – they can unlock abilities beyond the reach of individual cells or lead to a population’s destruction, they can be temporary or permanent, they can be between genetically identical cells or different species entirely. The first chapter of this dissertation reviews microbial interactions and the related concept of the evolution of conflict and cooperation.To be certain a trait is an adaptation at …

Working Paper No. 68, Variables Precipitating The Extermination Of The American Bison, Cameron Winterer

Working Papers in Economics

This inquiry seeks to establish that innovations in tanning technology advanced by Europeans in the late 19th century accelerated the destruction of the bison, and subsequently the downfall of bison-reliant indigenous groups of the Great Plains, especially. The North American bison is considered as a crucial natural resource in the plains region of North America. What this inquiry seeks to emphasize is that advancements in technology, coupled with a growing demand for bison hides, contributed to the demise of bison populations. Lastly, this inquiry seeks to examine the near extinction of the plains bison and some of the effects their …