Life Sciences Commons^™

4e-Bp1 Differentially Regulates Translation Of A Subset Of Human Mrnas, Mehreen Mahbub

Dissertations, Theses, and Capstone Projects

Elevated levels of eukaryotic initiation factor 4E-binding protein 1 (4E-BP1) influence cap-independent translation by forming a complex with eukaryotic initiation factor 4E (eIF4E) (eIF4E•4E-BP1). Certain mRNAs—including those encoding hypoxia-inducible factor-1α (HIF-1α), fibroblast growth factor-9 (FGF-9), and two isoforms of tumor suppressors, p53 (p53_A, and p53_B)—contain structured 5’untranslated regions (UTRs) that enable translation either via cap-independent translation enhancer (CITE)-like or internal ribosomal entry site (IRES)-like mechanisms. However, how 4E-BP1 modulates these mechanisms remains unclear. Using fluorescence-based anisotropy assays, we showed that the eIF4E•4E-BP1 binds more tightly to the 5’ m⁷G-cap of these mRNAs than eIF4E …

Less Self, Less Fear: Manipulation Of The Self Using Virtual Out-Of-Body Experiences To Alter The Conscious And Unconscious Experience Of Emotion, Dillon Freed

Dissertations, Theses, and Capstone Projects

This study investigated whether adopting an out-of-body perspective in virtual reality (VR) reduces subjective and physiological emotional responses to vicarious pain stimuli compared to inhabiting a first-person embodied avatar. Twenty-four participants experienced two counterbalanced VR conditions: (1) Avatar Embodiment (AV), in which they inhabited a photorealistic avatar from a first-person perspective, and (2) a Virtual Out-of-Body Experience (vOBE), in which they observed their avatar from a displaced third-person perspective. In both conditions, participants viewed a standardized series of vicarious pain images while electrodermal activity was recorded and self-report measures of embodiment (AV) and disembodiment (the vOBE state), emotional intensity (a …

Protein Allostery Probed By Ligands Across Sites, Virgil A. Woods

Dissertations, Theses, and Capstone Projects

Allostery is a pervasive regulatory principle throughout biology, yet the structural pathways by which distal inputs alter active‑site chemistry within protein structures remain incompletely defined and exploited. This dissertation uses protein tyrosine phosphatase 1B (PTP1B) as a tractable model to map those pathways with complementary experimental and computational tools. I integrate high‑resolution hydrogen-deuterium exchange mass spectrometry (HDX-MS), room-temperature crystallography, NMR, steady-state kinetics, crystallographic pseudo-ensembles, and machine-learning-guided ligand discovery. The working premise is that regulation reflects redistribution within a conformational ensemble rather than a binary switch. That orthogonal perturbations by small molecules, mutations, and protein partners can be used to both …

How To Search For The Engram: Optogenetics And Network Dynamics, Claudia Garcia Jou

Dissertations, Theses, and Capstone Projects

Memories are thought to be encoded by ensembles of neurons called "engram cells", because their artificial activation with optogenetics leads to the behavioral expression of a memory. However, the physiological mechanisms that mediate this process remain unknown. In this thesis, I investigate how optogenetic stimulation of memory-tagged cells changes neuronal firing, spatial coding, and the geometry of neural manifolds. I used an active place avoidance task and a foraging task to label engram cells in the dorsal hippocampus with Channelrhodopsin2 (ChR2). I then recorded the hippocampal activity response to optogenetic stimulation in mice under anesthesia, head-fixed, or freely moving. I …

Monosaccharide Binding To Synthetic Carbohydrate Receptor Microarrays, Milan A. Shlain

Dissertations, Theses, and Capstone Projects

Chapter 1: A glycan detection platform comprised of synthetic carbohydrate receptors (SCRs) immobilized onto polymer brushes was prepared. SCR043, an alkene-containing SCR, was incorporated into grafted-from polymer brushes using hypersurface photolithography, resulting in microarrays of SCR043-functionalized polymer brushes, where brush height (h) and SCR grafting density (Γ) is controlled precisely at each feature in the array. The influence of h and Γ on the binding to five fluorescently labelled monosaccharides – α-glucose (α-Gluc-FL), α-galactose (α-Gal-FL), α-mannose (α-Man-FL), β-glucose (β-Gluc-FL), and β-galactose (β-Gal-FL) – in aqueous buffer …

Somatosensory Cortex Responses To Illusory Touch In A Visual-Tactile Integration Task, Aditi Surendra Pawar

Dissertations, Theses, and Capstone Projects

Perceptual illusions arising from multisensory integration reveal how the brain constructs subjective experience from sensory input, and provide a powerful means of allowing the investigation of neural processes that track perceptual interpretation rather than physical stimulation alone. While visual illusions induced by auditory or tactile stimuli have been fairly well studied, the neural mechanisms underlying visually-induced illusory touch remain unclear. This study investigated whether illusory tactile perception engages the somatosensory cortex in a manner similar to veridical touch. Twenty healthy adults participated in an event-related functional magnetic resonance imaging (fMRI) study while performing a tactile numerosity judgment task. Each trial …

The Role Of Exotic Plants In The Diet Of Black-And-White Colobus Monkeys (Colobus Guereza) In Kibale National Park, Uganda, Michelle Gaykov

Theses and Dissertations

Exotic plants have both positive and negative impacts on their environment. They may act as additional food sources for the local fauna or as competition for local flora or leading to changes within a landscape or ecosystem. To considere the role of exotics in primate diet, this study focused on the dietary role of exotic plant species in the diet of a leaf-eating foregut fermenting monkey, the black-and-white colobus monkeys (Colobus guereza) in Kibale National Park, Uganda. Int this study, I followed individuals in two groups of black-and-white colobus monkeys for 21 days recording their food intake (0700-1900). I also …

Structural Characterization Of Peptide Nanoaggregates At Varying Concentrations And Their Impact On Cellular Responses, Malika Rozmetova

Theses and Dissertations

Peptide nano-assemblies can regulate cellular pathways in a structure-dependent manner. Here, we show that the enzyme-responsive peptide NapFFK(NBD)Yp forms distinct nanoscale assemblies at different concentrations, triggering differential ER stress and extracellular vesicle release in MDA-MB231 cells. These results highlight the importance of supramolecular organization in peptide–cell interactions.

Hybridization And Introgression In Marine Invertebrates: Population Genomics Of Phymactis Papillosa And Asterias Sea Stars, Christopher J. Dookie

Dissertations and Theses

Hybridization and introgression are evolutionary significant processes in marine invertebrates (Sanford & Kelly,2011) yet genome-wide investigations of gene flow in these taxa remain limited relative to vertebrate systems (Marchi et al., 2021). This thesis presents genomic analyses of hybridization and introgression in two marine invertebrates occupying contrasting oceanographic settings and characterized by contrasting genomic datasets: restriction-site associated DNA sequencing (RADseq) SNP data for the eastern Pacific sea anemone Phymactis papillosa and whole genome sequencing (WGS) data for the North Atlantic sea stars Asterias rubens and Asterias forbesi. For each system, I applied coalescent-based species tree inference using CASTER (Zhang …

Hidden In The Mist: Three New Species Of Salamanders Of The Genus Pseudoeurycea (Amphibia: Plethodontidae) From Oaxaca, Mexico, Eduardo A. Aguilar-Herrera, Salomón Sanabria-Urbán, Dulce L. Flores-Martínez, José David Gómez-Tapia, Misael Seba-Chacha, Leopoldo D. Vázquez-Reyes, Francisco A. Rivera-Ortíz, Patricia Ramírez-Bastida, Bruno Cortés-Ortiz, R. Alejandro Calzada-Arciniega, Etienne U. Avila-Ortega, Dónovan I. Víquez-Vega, Omar Hernández-Ordoñez, Christopher Blair, Víctor H. Jiménez-Arcos

Publications and Research

We describe three new species of lungless salamanders (Plethodontidae) in the genus Pseudoeurycea from Cerro Rabon, located on the eastern slopes of the Sierra Mazateca, Oaxaca, Mexico. This mid-elevation mountain, largely surrounded by warmer lowlands, remains relatively understudied. We present molecular and morphological evidence distinguishing the three new species from their congeners. According to our phylogenetic analysis, one of the new species belongs to the P. leprosa group, while the other two are members of the P. juarezi group. Notably, one of the new species represents the fourth worm salamander known from west of the Isthmus of Tehuantepec, and another …

Building A Cell Specific System For In Vivo Rna Imaging Of The Endogenous Actin Gene In C. Elegans, Jasmine A. Huerta Canete

Theses and Dissertations

Messenger RNA (mRNA) plays a crucial role in protein synthesis and cellular processes, important for the development of cells such as neurons. When dysregulation occurs, it can lead to outcomes such as aberrant translation, causing neurodegenerative conditions to arise. Unfortunately, the localization of mRNA in an in vivo cell specific manner is still not understood. To address this, we decided to develop a cell-specific system to image RNA in vivo, within the organism known as C. elegans with a focus on the actin gene. The Actin gene encodes for an important cytoskeleton protein expressed ubiquitously, vital for the cell …

A Review Of Mockingbird Song, Jacqueline Milander

Student Theses

The northern mockingbird (Mimus polyglottos) is known for its large repertoire and highly versatile song patterns.  It is a frequent mimic that is thought to continue learning sounds from its environment for the duration of its life.  Utilizing available song studies, this is a comprehensive review of northern mockingbird song, including learning, mimicry, repertoires, song dependence on seasonal cyclicity, and song function, particularly interspecific territoriality. While much discussion has surrounded the idea that northern mockingbirds engage in interspecific territoriality and that vocal mimicry functions in intersexual selection, this review provides new insight into the possibility that latitudinal differences among populations …

Will Technology Help Us Understand Animals?, Frances I. Sacks

Capstones

New technologies allow scientists to study animal communication like never before. Advanced surveillance devices ornament forests and oceans, recording animals over great stretches of distance and time. Artificial intelligence can absorb these enormous datasets, sorting tangled abstractions into coherent patterns. With a sufficiently robust library of analyzed data, some researchers believe that large language models will soon learn to translate whale communication systems.

https://docs.google.com/document/d/1ky6mPFjc-lNJFVK8CHebUa5zCSFUoMgkCB560pqxwfo/edit?tab=t.0

Two Major Ontario Hospital Labs Bought Research Dogs From U.S. Breeder With Troubled Pastdogs Bred For Scientific And Medical Testing Suffer Abuse As The Scientific Industry Increasingly Turns To Alternatives For Research., Allison Hunter, Mary Beech, Sami Marshak, Kate Morano

Capstones

The purpose-bred dog breeding industry for research is little known. Each year, thousands of dogs are bred for scientific and medical testing, supplied to research facilities by a handful of major commercial breeders. But gaps in enforcement and regulation have allowed abuses to persist, even as the industry increasingly turns to alternatives to animal testing. Animal rights advocates have been decrying the treatment of these dogs. A federal Inspector General report found lax oversight of the industry, raising further concerns about how dogs are treated. This story was reported in collaboration with the Investigative Journalism Bureau, based in Toronto, and …

Method Development And Optimization For The Detection Of Synthetic Cannabinoids In Hair Using Lc-Msms, Linda K. Obeng

Student Theses

Synthetic cannabinoids represent one of the most prevalent and high-risk classes of New Psychoactive Substances (NPS), continuously evolving in structure and potency. Their widespread presence in seized materials and toxicology casework underscores the growing need for reliable analytical methods capable of detecting these compounds in biological matrices. Hair offers several advantages for drug testing, including a long detection window, minimal invasiveness, and resistance to adulteration; however, detecting synthetic cannabinoids in hair remains challenging due to their low incorporation levels and structural diversity. This study focuses on the method development and optimization of an LC-MS/MS technique for the detection of selected …

A Halloween Decoration’S Scary Implications For Real Bats, Coralie Carlson

Capstones

This investigative article examines the online illegal trade of taxidermied bats and how the sales are threatening one particularly showy species: the painted woolly bat.

My OSINT research shows where the bats are still sold – from Amazon to independent websites offering bulk orders – and tracks the sellers and buyers, while weaving in the scientific and cultural history this little-known colorful bat and the conservationists’ race against time to protect them.

The very existence of the painted woolly bat is threatened by Americans who want to display the dead bats in their homes as spooky decorations. Researchers (including a …

What’S That Smell? It’S Climate Change!, Perry Gregory

Capstones

Climate change is going to make New York City smell worse. Reporter Perry Gregory breaks down the process of olfaction and explains how heat affects what we smell. The piece features a collage of voices of New Yorkers describing the current smell profile of the city. The report features insight from several Atmospheric Scientists into why New York City is getting hotter and more humid, and how those climate changes will make the existing smells of the city stronger, and worse. The most economically vulnerable New Yorkers, who cannot afford air conditioning to buffer them from heat, will be the …

Modeling Mineral Redistribution In Biological Tissue Using Apple As An In Vitro Analogue, Daler Djuraev, Ali Algemsh, Halima Alazeb, Zeenia Ahmed

Publications and Research

This project aims to model mineral (ion) redistribution that occurs in human soft tissue after injury or mechanical/thermal stress. Because direct, repeatable in vivo measurements are difficult, we use apples as an in vitro analogue: their mineral content is relatively uniform and the tissue can be cut, dried, and repeatedly imaged under controlled conditions. Using X-ray imaging, we tracked how minerals in apple tissue move toward damaged regions immediately after cutting, and how subsequent drying at room temperature drives a redistribution toward the central core. We also observed that biological degradation (decay) alters mineral density over time, indicating that even …

Grapes Cure Cancer: My First Molecular Docking Analysis Of Resveratrol Binding To Anti-Apoptotic Protein Bcl-2: In Silico, Sydni Ann Kolokoltsev, Vishwas Joshi

Publications and Research

B-cell lymphoma 2 (BCL-2) is an anti-apoptotic protein frequently overexpressed in cancer, enabling tumor cells to evade programmed death. Resveratrol, a grape-derived polyphenol, has reported anticancer properties. Here we performed in silico docking of resveratrol to human BCL-2 using AutoDock Vina. The best-ranked pose exhibited a predicted binding free energy of 8.0 kcal/mol and formed at least one short hydrogen bond (~1.8 Å) with pocket residues. These results support further evaluation of resveratrol as a potential modulator of BCL-2-mediated apoptosis.

Pfos And Lung Injury: A Review Of Human And Experimental Evidence, Farzana Hakim

Theses and Dissertations

Human epidemiological research has shown the adverse health consequences of long-term accumulation of per- and polyfluoroalkyl substances (PFAS) in human tissue. Specifically, this review will examine the relationship between PFAS exposure, impaired immune system functioning, and an elevated risk of respiratory disease using both human and experimental data. Research on human populations indicates that children exposed to PFAS have lower levels of antibodies to vaccines; those children prenatally exposed to PFAS are more susceptible to upper respiratory infections; and that adult humans have a higher incidence of chronic obstructive pulmonary disease (COPD). Additionally, experimental studies demonstrate that PFOS and PFOA …

Fast & Forensic: Rapid Detection & Quantitation Of 30 + Emerging Novel Psychoactive Substances In Hair Using Lc-Ms/Ms, Seokjin Hwang

Student Theses

The continuous emergence of novel psychoactive substances (NPS) poses a significant challenge for forensic and clinical toxicologists, due to their structural diversity, rapid turnover on the illicit drug market, and limited toxicological information. Hair is a powerful matrix for retrospective drug exposure assessment and monitoring NPS worldwide. Not only does it provide a broad window of detection but also a simple sample exchange amongst laboratories. However, the extraction of multi-class NPS in a single method remains an analytical challenge. Therefore, there is an urgent need for extraction techniques and analytical methods that are both rapid and capable of multi-class quantitation …

Untargeted Metabolomics Reveals Organ-Specific And Extraction-Dependent Metabolite Profiles In Endemic Tajik Species Ferula Violacea Korovin, Sylhiya Mavlonazarova, Kenneth Acosta, Rinat Abzalimov, Saidbeg Satorov, Vyacheslav Dushenkov

Publications and Research

Ferula violacea Korovin, an endemic Tajikistani plant with purported medicinal properties, remains understudied. This study employs untargeted metabolomics to characterize the metabolite profiles of ethanol extracts and juices from F. violacea roots and seeds. In total, 540 distinct metabolites are putatively identified, 419 of which are previously unreported in the Ferula genus, representing a substantial expansion of its known chemical diversity. The most abundant metabolites are terpenoids, amino acid derivatives, and alkaloids. A particularly abundant group of daucane sesquiterpenoids, sharing a common (6-methyl-azulen-4-yl) cyclohexanecarboxylate substructure, is identified, including known metabolites such as ferutidin and ferutinin. Comparative analysis reveals organ-specific metabolic …

Zero Textbook Cost Syllabus For Env 3070 (Agroecology), Benjamin Iuliano

Open Educational Resources

Our relationships with the food we eat are deeply personal, but also connect us to a wide array of people, plants, animals, and landscapes around the world. Encompassing a diversity of scholarly approaches, the field of agroecology seeks to understand the interactions among these components, draw attention to the consequences of our present industrial food system, and create the conditions for more sustainable and just futures. In this course, students will learn about the science, practice, and social movement of agroecology through lectures, course discussions, field trips, and hands-on activities.

Characterization Of Mannosidases (Man) In Tetrahymena Thermophila Using Bioinformatics Tools, Cynthia Wen

Publications and Research

Mannosidases are a type of glycoside hydrolase (glycosidase) that facilitate the hydrolysis of glycosidic bonds in mannose-containing polysaccharides and glycans, including those found in glycoproteins. Their main role is to cleave specific linkages involving D-mannose residues, effectively trimming or degrading mannose-rich oligosaccharides. These enzymes are crucial in N-glycosylation pathways, which are essential for proper protein folding, glycoprotein maturation, and the regulation of carbohydrate metabolism in eukaryotic cells.

There are two main types of mannosidases: alpha-mannosidases and beta-mannosidases. In humans, several of these enzymes exist, including those found in the endoplasmic reticulum (alpha-mannosidase I), those in the Golgi apparatus (alpha-mannosidase II), …

Beneficial Effects Of Performlytetm, A Prodosomed Phytonutrient-Enriched Electrolyte Formulation, In Enhancing Neuro-Muscular Synergy, Immune Competence, Cellular Aerobic Glycolysis And Sports Performance, Bernard William Downs, Samudra P. Banik, Bruce S. Morrison, Tandra Chakraborty, Manashi Bagchi, Sanjoy Chakraborty, Steve Kushner, Debasis Bagchi

Publications and Research

An optimised sports nutrition formulation achieving the correct blend of electrolytes with antioxidants and vitamins is integral towards meeting the demanding performance in professional sports arena. In this work, we describe a pilot study carried out to understand the effect of a novel phytonutrient- and electrolyte-fortified sports nutrition composition, PerformLyte^TM, developed in our laboratories, in boosting the performance of trained male cyclists. PerformLyte^TM is a unique fortified formulation comprising of polyphenolic antioxidants, flavonoids, and anthocyanins, as well as carotenoids, sulforaphanes, exotic spices, sea water-derived electrolytes, and vitamin C, encapsulated in proprietary patent-pending Prodosome absorption technology, enabling sustained …

Unveiling The Precision Of Physiological Signals In Prediction Error During Fear Learning: Insights From Associative Strength And Generalized Uncertainty, Haja H. Jallo-Jamboria

Dissertations, Theses, and Capstone Projects

Prediction error (PE) is the discrepancy between expected and actual outcomes. It is a central mechanism in associative learning particularly within fear-conditioning paradigms. Identifying physiological markers of PE in aversive contexts has important implications for refining learning models and enhancing clinical interventions for anxiety-related disorders. This study examined skin conductance response (SCR) as a potential physiological index of PE by analyzing both anticipatory and omission-related responses across multiple learning phases. Participants completed a Pavlovian fear-conditioning paradigm in which two conditioned stimuli (CS+) signaled threat at different reinforcement probabilities: CS+100 (certain threat) and CS+50 (uncertain threat), alongside a non-reinforced safety cue …

Ai-Powered Multi-Omics Integration For Predictive Modeling Of Genotype-Environment-Phenotype Relationships, You Wu

Dissertations, Theses, and Capstone Projects

This dissertation presents a series of machine learning frameworks for modeling genotype–environment–phenotype relationships through integrative predictive modeling of multi-omics data. The work addresses three major axes of biological complexity: modeling biological information transmission cross-levels from genes to proteins to phenotypes, predicting molecular features cross-scale from cells to tissues to organisms, and translating phenotypes cross-species from model systems to humans. Each proposed method also tackles key machine learning (ML) challenges in the biomedical domain, including data scarcity, domain shift, out-of-distribution (OOD) generalization, and hierarchical modeling. Specifically, this dissertation introduces five novel deep learning algorithms: MultiDCP predicts drug-induced transcriptomic and viability responses …

Detecting Sonic Hedgehog Expression In The Adult Mouse Brain Using A Gene Expression Tracer, Kendra Stephens-Jones

Dissertations, Theses, and Capstone Projects

Sonic Hedgehog (Shh) is best known for its role in development, yet evidence supports Shh signaling plays a functional role in the adult brain. Previous work demonstrated that Shh is expressed by dopamine (DA) neurons in the ventral midbrain and that loss of Shh from these neurons leads to late-onset motor and structural abnormalities resembling Parkinson’s disease. However, the extent of Shh expression and its connectivity to the striatum in the adult mouse brain remain unclear due to the lack of reliable antibodies for Shh detection. To address this gap, the present study employed Shh ^L/L and DAT-Cre^+/- mice …

Investigation Of Motor Neuronal And Circuit Level Mechanistic Determinants Of Spinal Excitability Following Cst Injury, Thelma Bethea

Dissertations, Theses, and Capstone Projects

The corticospinal tract (CST) is the primary descending motor pathway in mammals, essential for precise, dexterous movements, especially in humans and nonhuman primates. Damage to the CST, such as from spinal cord injury (SCI), impairs skilled motor function and triggers maladaptive changes including aberrant proprioceptive afferent sprouting and increased spinal excitability. These changes are closely linked to both muscle weakness and the development of hyperreflexia, compounding the functional deficits. Animal models of SCI are valuable for investigating mechanisms of injury and recovery, though traditional models often limit the ability to isolate circuit-specific contributions. To address this, I employed selective unilateral …

From Sequence To Allostery: How Amino Acid Differences Rewire Coupled Conformational Heterogeneity In The Ptp Enzyme Family, Shivani Sharma

Dissertations, Theses, and Capstone Projects

Protein Tyrosine Phosphatases (PTPs) are critical regulators of cellular signaling, and their activity is often modulated through allosteric mechanisms. Allostery is defined as a chemical or conformational change in one site of the protein due to a binding event at another site. Although several studies have investigated aspects of allostery in PTPs, the mechanistic foundations underlying allosteric regulation remain poorly understood. Despite a highly conserved catalytic domain across PTPs, regions with low or no conservation suggest potential "rewiring" of allosteric networks. This raises key questions about the universality versus individuality of allosteric mechanisms across the PTP family.

In this work, …