Digital Commons Network^™

Elucidating Mechanisms Of Biofluorescence And Bioluminescence In Marine Organisms, Andrew M. Guarnaccia

Dissertations, Theses, and Capstone Projects

Biofluorescence and bioluminescence are two methods of light emission that entail separate mechanisms of action but end at the same process: a colorful display that have tremendous ecological and behavioral benefits, whether it be used to communicate with conspecifics, camouflage into a multicolored background, attract unsuspecting prey, or alert others to a predator. In biofluorescence, higher-energy, shorter wavelength light is absorbed then re-emitted as lower-energy, longer-wavelength light. Bioluminescence on the other hand entails a chemical reaction in which a small molecule is oxidized by an enzyme, creating a high-energy intermediate that sheds the excess energy in the form of visible …

Symmetry-Inspired Analysis Of Biological Networks, Ian Leifer

Dissertations, Theses, and Capstone Projects

The description of a complex system like gene regulation of a cell or a brain of an animal in terms of the dynamics of each individual element is an insurmountable task due to the complexity of interactions and the scores of associated parameters. Recent decades brought about the description of these systems that employs network models. In such models the entire system is represented by a graph encapsulating a set of independently functioning objects and their interactions. This creates a level of abstraction that makes the analysis of such large scale system possible. Common practice is to draw conclusions about …

Cdc6 Is Sequentially Regulated By Pp2a-Cdc55, Cdc14, And Sic1 For Origin Licensing In S. Cerevisiae, Jasmin Philip

Dissertations, Theses, and Capstone Projects

Control of DNA replication is critical for progression of the cell cycle and genomic stability. Cyclin-dependent kinases (CDKs) coordinate numerous phosphorylation events to accomplish two biological tasks for all living organisms: DNA replication and cell division. One CDK, Cyclin-Cdc28, is responsible for cell cycle progression in budding yeast. DNA replication requires a stepwise assembly of the pre-replicative complex on DNA, including Orc1-6, Cdc6, Cdt1 and Mcm2-7, during M-G1 phase. Cdc6 contains eight Cdc28 consensus sites, SP or TP motifs. Clb5-Cdc28 phosphorylates Cdc6-T7 to recruit Cks1, the Cdc28 phospho-adaptor, for subsequent multisite phosphorylation during S phase. There are two phospho-degrons at …

Robert Rosen And Relational System Theory: An Overview, James Lennox

Dissertations, Theses, and Capstone Projects

Relational system theory is the science of organization and function. It is the study of how systems are organized which is based on their functions and the relations between their functions. The science was originally developed by Nicolas Rashevsky, and further developed by Rashevsky’s student Robert Rosen, and continues to be developed by Rosen’s student A. H. Louie amongst others. Due to its revolutionary character, it is often misunderstood, and to some, controversial. We will mainly be focusing on Rosen’s contributions to this science. The formal and conceptual setting for Rosen’s relational system theory is category theory. Rosen was the …

Testing An Overtraining Protocol For Fear Learning In Humans, Gordon M. Haskell

Dissertations, Theses, and Capstone Projects

Successful regulation of fear memories is a fundamental tenet to the exposure-based therapies often employed by mental health professionals for individuals with PTSD, phobias, and other anxiety disorders. Consequently, the efficacy of these treatment methodologies is largely dependent on the strength of the fear memory, as stronger memories are often characterized by an increased resistance to extinction and heightened fear recovery. However, there is little consensus within the scientific community regarding how to effectively maximize fear memory strength in human studies, and the literature exploring the impact of variability in acquisition parameters on memory strength is sparse. Here, we tested …

Genetic Impacts Of Deforestation On Mouse Lemurs, Darice Westphal

Dissertations, Theses, and Capstone Projects

The impact of deforestation on the genetic structure of mouse lemurs is poorly understood. In this project, I assess deforestation of Madagascar’s terrestrial protected regions, quantify genomic wide genetic variation in two sympatric mouse lemurs, and evaluate the role of landscape structure in genetic relatedness patterns within two sympatric mouse lemur species. Overall deforestation rates across the 98 terrestrial protected areas in Madagascar are increasing, resulting in an average annual deforestation rate of 0.68% per year, with approximately 10,600 km² lost between 2000 and 2019. In a comparison of relatedness patterns between the sympatric gray mouse lemur (Microcebus …

Medicinal Plant Use For Type-2 Diabetes Treatment In The Traditional Vietnamese Medicine System Of Southern Vietnam, Lan Truong

Dissertations, Theses, and Capstone Projects

This ethnobotanical study examines the traditional health care system of the Mekong River Delta in Vietnam. The basic inquiry focuses on how the healers in the traditional Vietnamese medicine (TVM) system are treating a disease relatively new in Vietnam, type-2 diabetes (T2D). The study includes a description of the system in which the healers work. The research design compares two locations, one on the mainland (Rạch Giá City) and the other on a nearby island (Phú Quốc Island).

There are six chapters. The first chapter establishes foundational information about the region, population, and the traditional medical system. The results of …

Molecular Mechanism Of Rapamycin Resistance In Cancer Cells, Sohag Chakraborty

Dissertations, Theses, and Capstone Projects

The mammalian target of rapamycin (mTOR) acts as the central regulator of multiple cellular processes including cell growth, proliferation, and survival by integrating signals via nutrients, growth factors, hormones, and energy sensing. In cancer cells, the mTOR pathway is highly dysregulated providing survival signals to the cells for their uncontrolled growth. Hence, mTOR has evolved to be a potential therapeutic target for cancer treatment for the past two decades. Application of micro-molar doses of Rapamycin in vitro has been found to successfully inhibit mTOR complex 1 (mTORC1) by blocking the phosphorylation of its downstream substrates- a) ribosomal protein p70 S6 …

The Effects Of Near-Threshold Color Manipulation On Perceptual Decision-Making And Confidence Report, Trevor Caruso

Dissertations, Theses, and Capstone Projects

Confidence measures are sometimes used to index awareness below a participant’s criterion for what counts as being subjectively aware of a stimulus or stimulus property. If confidence ratings index awareness below subjective thresholds, then one might be tempted to use confidence ratings in place of subjective reports of whether a stimulus/stimulus property was “seen” or “unseen”. As such, a dissociation of confidence from performance may be construed as a dissociation of subjective awareness from objective task performance. This methodology has been used as supporting evidence for blindsight in typical observers (Balsdon and Azzopardi 2015; Peters and Lau 2015; Peters et …

Histone Post-Translational Modification Dysregulation Contributes To Toxicity In Amyotrophic Lateral Sclerosis Proteinopathy Models, Seth A. Bennett

Dissertations, Theses, and Capstone Projects

Amyotrophic Lateral Sclerosis (ALS) is the third most common adult onset neurodegenerative disorder worldwide. It is generally characterized by progressive paralysis starting at the limbs ultimately leading to death caused by respiratory failure. There is no cure and current treatments fail to slow the progression of the disease. As such, new treatment options are desperately needed. Epigenetic targets are an attractive possibility because they are reversible. Epigenetics refers to heritable changes in gene expression unrelated to changes in DNA sequence. Histone modifications, a main epigenetic mechanism, occur in many amino acid residues and include phosphorylation, acetylation, methylation as well as …

Molecular Mechanisms Of Microrna-1205 In Aggressive Prostate Cancer, Michelle K. Naidoo

Dissertations, Theses, and Capstone Projects

Prostate cancer (PCa) is one of the most commonly diagnosed cancers among men in the United States. High mortality rates of PCa are associated with metastatic castration-resistant prostate cancer (mCRPC) due to the maintenance of androgen receptor (AR) signaling despite androgen deprivation therapies (ADTs). Resistance to second generation ADTs leads to the progression of AR-independent treatment related-neuroendocrine PCa (t-NEPC), which is observed in nearly 1 in 5 men with mCRPC and is associated with very poor outcomes. The 8q24 chromosomal locus is a region of very high PCa susceptibility that carries genetic variants associated with PCa aggressiveness. Located at this …

Understanding Species Interactions And Their Impacts In Restored Communities, Jennifer Zhu

Dissertations, Theses, and Capstone Projects

Species interactions may mediate the ability of organisms to survive in a community and provide valued services but are rarely fully considered in restoration planning. To address this, I considered how service provisioning will change as restored marsh communities mature and the value of incorporating antipredator training into captive-rearing programs.

For chapter 1, I explored how a facultative mutualism between Atlantic ribbed mussels Geukensia demissa and cordgrass Spartina alterniflora may enhance marsh growth and nitrogen cycling in a eutrophic setting. I created experimental plots in Jamaica Bay, NY, that contained live mussels, mussel shells, or no mussels (control) and measured …

Paddling Along The Voltage Gated Sodium Channel Galaxy With Sea Anemone Toxins: Structural Studies Of The Interaction Between The Paddle Motif From Nav1.5div And Sea Anemone Toxin, Adel K. Hussein

Dissertations, Theses, and Capstone Projects

Voltage gated sodium channels (VGSC) are membrane proteins that serve an important function in the central nervous system (CNS), peripheral nervous system (PNS), and cardiac muscles amongst others. The main function of VGSC is in the propagation of electrical signals by depolarizing excitable cells. Nine mammalian VGSC subtypes have been characterized, Na_V1.1 – Na_V1.9, that are expressed in a tissue specific manner, each with unique gating properties. Numerous diseases have been linked to defects in VGSC including epilepsy, mental retardation, long QT syndrome, and Brugada disease. Furthermore, these channels are one of the primary targets of …

An In Silico Approach To Investigate The Structural And Biochemical Basis Of The Rna Binding Functions Of Nucleolin, Avdar San

Dissertations, Theses, and Capstone Projects

Nucleolin (NCL) is a stress responsive multifunctional nucleolar protein and accounts for 10% of the total nucleolar protein content. NCL belongs to the class of RNA binding proteins (RBPs) that regulate many important cellular processes through their interactions with different RNA molecules. The dysregulation of RBPs and the RNA metabolism pathways they intersect is a known driver of tumorigenesis. NCL regulates ribosome biogenesis, chromatin remodeling, microRNA processing, and gene expression on multiple levels. The RNA-protein interactions of NCL are primarily driven by its four RNA binding domains (RBDs). NCL is known to interact with a growing list of primary-miRNA (pri-miRNA) …

Role Of Metals In Human Immune System: Study Of Metal-Dependent Structural Changes Of S100a12 Protein, Aleksey Aleshintsev

Dissertations, Theses, and Capstone Projects

S100A12 protein belongs to the S100 family of calcium-binding proteins and participates in the innate immune system. Antimicrobial proteins from the S100 family of the proteins (S100A12, S100A8/A9, etc.) are secreted and expressed by neutrophils during microbial infection and perform their antimicrobial activity through metal sequestration. While most S100 proteins function intracellularly, S100A12 is highly expressed and secreted into the extracellular space by neutrophils during infection. Sequestration of Zn²⁺ by S100A12 is aided by the nanomolar zinc binding affinity of the protein at neutral pH conditions, which is further enhanced upon calcium-binding. The Zn²⁺ binding scaffold in S100A12 …

Structural And Biochemical Investigations Of The Initiation Of Dna Replication In Bacteriophage Lambda And Escherichia Coli, Jillian D. Chase

Dissertations, Theses, and Capstone Projects

Faithful transmission of genetic information is requisite for the propagation of all life. DNA replication in each of the three domains of life requires the separation of double stranded DNA (dsDNA) into single stranded DNA (ssDNA) which then serves as a template for genomic duplication of each original DNA strand. Initiation of replication events occurs by tightly regulated processes during which specialized proteins are loaded at a specific locus within the genome, termed the origin of replication, in preparation of bidirectional replication events. A replicative helicase must be loaded or assembled on both strands of DNA at the origin to …

Novel Strategies For Glutamate Clearance In The Glia-Deprived Synaptic Hub Of C. Elegans, Joyce Chan

Dissertations, Theses, and Capstone Projects

As the major excitatory neurotransmitter in the mammalian brain, Glutamate (Glu) is critical for normal neuronal physiology. Disruption in Glu clearance results in hyper-stimulation of glutamatergic circuits, potentially leading to excitotoxic neurodegeneration. The canonical model of brain connectivity describes glutamatergic synapses as well insulated and enveloped by glia. These glia express Glu Transporters (GluTs) which work to clear Glu following synaptic activity. However, critical areas of the brain such as the mammalian hippocampus display poor synaptic isolation, which may result in Glu spillover between adjacent synapses and subsequent loss of circuit specificity. How accurate signal transmission is achieved in these …

Water-Based Lead Generation, Brian Olson

Dissertations, Theses, and Capstone Projects

Water-based Lead Generation. The opioid epidemic and the SARS-CoV-2 pandemic are current serious challenges whose devastating effects could be assuaged through the development of new drugs. Opioids that are functional painkillers, that are less likely to cause overdose, and small molecule drugs that could inhibit the life cycle of SARS-CoV-2 would be useful. The work herein investigated the use of water molecules for lead generation in drug development against opioid receptors and SARS-CoV-2 viral proteins. In opioid receptor binding sites, purported bridging waters were obtained from crystal waters or from molecular dynamics simulations, as Hydration Site Analysis was used to …

Eukaryotic Initiation Factor 3 Interactions With Structural Elements Of Barley Yellow Dwarf Virus Untranslated Regions Reveal Details Of A New Cap-Independent Translation Initiation Model, Paul S. Powell

Dissertations, Theses, and Capstone Projects

Barley Yellow Dwarf Virus (BYDV) is a positive strand RNA plant virus that translates without using a 5′ 7-methylguanosine cap or a 3′ poly-adenosine tail, features that are required for canonical mRNA translation. BYDV’s non-canonical translation relies on RNA structures in the 5′ and 3′ untranslated regions (UTRs) to recruit eukaryotic initiation factors (eIFs) and ribosomes. BYDV’s 3′ translation enhancer (BTE) is a cruciform structure capable of recruiting the cap-binding complex eIF4F, the large scaffolding complex eIF3, and the 40S ribosomal subunit. Together eIF3, eIF4F, and BTE influence factor binding and 40S recruitment on the 5′ UTR and play a …

Reducing Fear Overgeneralization With Safety Learning: Attention Bias As A Moderator, Boyang Fan

Dissertations, Theses, and Capstone Projects

Anxiety disorders are the most prevalent mental health condition and affect one out of nine individuals around the world. Fear generalization is a neurocognitive mechanism thought to maintain and exacerbate anxiety, and thus is an important target of therapeutic interventions. Yet, intervention research and practice place relatively little emphasis on its importance. Given that a significant proportion of individuals do not respond to extant treatments of anxiety disorders, a strengthened focus on fear generalization may inform the development and personalization of new treatment approaches. Recent notions have linked fear generalization to failures in distinguishing between signals that predict the occurrence …

Scientific Development Of An Integrated Workflow For Latent Print, Questioned Document, And Dna Processing Of Paper Evidence, Ashley Morgan

Dissertations, Theses, and Capstone Projects

Touch paper evidence could be the source of probative human DNA but recovery is challenging and forensic laboratories instead prioritize processing by the Latent Print and Questioned Document disciplines. Recent advances in DNA collection methods and the increased sensitivity of STR typing kits have improved success rates for DNA testing of paper evidence; but prior to implementing DNA collection, laboratories have to decide in which order to examine paper for the different types of forensic evidence. This thesis developed and tested a multi-discipline workflow for processing paper evidence by DNA, Latent Prints and Questioned Documents experts. Preliminary sampling studies indicated …

Conservation, Comparative Genomics And Species Delimitation Of The Reindeer Lichens (Cladonia), Jordan R. Hoffman

Dissertations, Theses, and Capstone Projects

The genus Cladonia represents one of the most speciose genera of lichenized fungi, with more than 500 known species encompassing a diverse array of morphologies and habits. These lichens form keystone species in many habitats, serving a variety of ecological roles. However, despite being among of the more well studied lichens, there is much still unknown or under-studied about them. As is the case with most lichen study systems, phylogenetic study has been limited to a small number of partial loci, while adoption of next-generation sequence methods has been slow. As a consequence, there are still knowledge gaps in Cladonia …