Life Sciences Commons^™

The Cranial Nerves And Electrical Stimulation, Devin K. P. Adair

Dissertations, Theses, and Capstone Projects

Cranial nerves provide afferent pathways that enable bottom-up modulation of central autonomic and cognitive neural pathways. Because these pathways project to brainstem nuclei such as the nucleus tractus solitarius and engage neuromodulatory systems, including the locus coeruleus, electrical stimulation offers a mechanistically grounded approach to influencing brain function. This thesis tested whether active transcutaneous auricular vagus nerve stimulation (taVNS) produces physiological responses indicative of parasympathetic engagement, defined as decreases in heart rate, increases in heart rate variability, and decreases in respiration relative to a dose-matched earlobe control condition. Using cardiac and respiratory measures as physiological markers, taVNS at the tragus …

Signal And Substance: Why Methodological Sophistication Fails To Guarantee Inference, Aamir Rashid, Rizwana Rasheed

Publications and Research

Despite increasing analytical sophistication, empirical research in organization studies continues to suffer from fragile inference, uneven theoretical accumulation, and contested credibility. This paper seeks to explain why these problems persist by shifting attention from authors’ methodological choices to the evaluative dynamics of peer review. Adopting a conceptual and theory-analytic approach, the paper theorizes peer review as an inferential gatekeeping system. Drawing on research design, theory evaluation, and philosophy-of-science literatures, this study develops an analytical framework to examine how evaluative routines shape what constitutes empirical rigor during the review process. The analysis identifies five recurring reviewer blind spots: inferential scope inflation, …

The Double Attraction Paradox, Rem Jaen D. Krafft

Publications and Research

The Double Attraction Paradox is a podcast series that teaches adolescents how to navigate attraction through body language, limerence, and mirroring while understanding the psychology behind emotional connection. It is a manuscript that combines personal experience, observations, and research, inspired by Rem Jaen D. Krafft's high school crush. Not only does it provide a guide for teenagers and young adults, but it also encourages readers to better understand attraction, communication, and emotional development. The final chapter examines how peer pressure, traditional high school cliques, fear of rejection, and fear of intimacy may influence societal norms, emotional contagion, and relationship formation …

How Temporal Integration And Complexity Drive Musical Enjoyment, August Miller

Dissertations, Theses, and Capstone Projects

Music is a type of aesthetic stimulus that unfolds dynamically over time. Combining approaches from previous research on musical preferences and research on spatial integration as a driver of visual aesthetic appreciation, we investigated how the integration of musical percepts over time influences listener enjoyment and the level of agreement between the enjoyment ratings of each listener. We used a DNN tool to quantify temporal dependencies in 32 music clips and also computed complexity scores for them. Subjects listened to each music clip while using a rotating dial to provide a continuous enjoyment rating, changing the dial’s position at the …

A Predictive Coding Account Of Spatial Working Memory Following Prophylactic Levetiracetam Administration Prior To Traumatic Brain Injury, Omeima Mutwali

Dissertations, Theses, and Capstone Projects

Traumatic brain injury (TBI) symptom prevention and remediation is an important area of research that would benefit vulnerable groups, including active-duty and veteran soldiers. These patients can sustain penetrative forces in fields of combat or in training, which result in focal lesions that trigger inflammatory and degenerative processes in the brain. Both primary and secondary injuries are associated with changes to cognition, behavior and affective state. This disease poses increased risk of epileptogenesis, as well. Given these outcomes, prior research has evaluated levetiracetam (LEV) as a prophylactic treatment for seizures, cognitive deficits and negative emotionality. LEV acts as a presynaptic …

Computational Insights Into Nucleosome Dynamics In Epigenetics Using Molecular Dynamics Simulations, Rutika Patel

Dissertations, Theses, and Capstone Projects

Nucleosome core particles (NCP) are the building blocks that form a highly organized and compact chromatin structure. Nucleosomes package DNA in the nucleus of eukaryotic cells. The NCP consists of about 147 base pairs of DNA wrapped around the histone octamer, with 1.65 superhelical turns in a left-handed manner. The histone octamer is composed of two copies of H3, H4, H2A, and H2B. Together with histone H1 and linker DNA, they further assemble into a higher-order chromatin structure. The nucleosome complex is stabilized by electrostatic interactions between positively charged histone residues and the negatively charged DNA backbone. To effectively access …

Supramolecular Assembly In Short Peptide Systems For Selective Metabolite Recognition And Drug Nanoencapsulation, Maithreyi Ramakrishnan

Dissertations, Theses, and Capstone Projects

Short peptides can form adaptive supramolecular assemblies, and understanding how minimal sequences organize around neurometabolites or hydrophobic cancer drugs enables the rational design of functional materials. This thesis combines molecular dynamics with experimental validation to establish design rules linking peptide sequence to emergent structure and function. Chapter 1 outlines the molecular determinants governing peptide assembly. Chapter 2 reviews computational workflows that reveal sequence-dependent conformations and supramolecular organization. Chapter 3 applies these principles to Dynamic Peptide Libraries which identify tetrapeptides that selectively interact with neurometabolites. Chapter 4 extends the same interaction-driven framework to design tryptophan-rich pentapeptides that co-assemble with kinase inhibitors …

Neural Correlates Of Recognition Memory And Metamemory In Breast Cancer Survivors: An Event-Related Potential Study, Dishari Zaman Azad

Dissertations, Theses, and Capstone Projects

Breast cancer survivors (BCS) often report noticeable cognitive difficulties despite showing limited impairment on standardized neuropsychological tests. Some have theorized that this is simply an insensitivity of standardized testing to subtle cognitive changes (test-insensitivity hypothesis), whereas others have suggested there are early neural changes that are detected by patients but precede detection by these tests (early signal hypothesis) or that when they achieve normal performance, it is through saliently effortful compensatory processes (compensation hypothesis). The present study tested these theories by assessing metamemory and recognition memory retrieval in BCS and non-cancer controls (NCC) using both behavioral and event-related potential (ERP) …

Reducing The Complexity Of The Experimental Design Attenuates Trait-Level Effects In Threat Safety Discrimination Learning, Justin M. Lazzarino

Dissertations, Theses, and Capstone Projects

Trait measures of negative emotionality have sometimes been shown to play a role in shaping threat learning, but findings are mixed. For example, Johnson et al (2023) showed that the inhibitory and prospective subscales of the Intolerance for Uncertainty Scale (IUS) were associated with diminished and enhanced threat-safety discrimination, respectively, during the acquisition phase of a Pavlovian fear conditioning task. This finding was subsequently replicated in an independent sample (Kinney-Petrucha, 2024, unpublished). However, these findings and other trait-level fear acquisition effects have not been consistently observed in the broader fear learning literature. Variation in the complexity of or uncertainty inherent …

Immunomodulatory And Signaling Molecules From Plant-Associated Bacteria: Toll-Like Receptor 4 Agonist Adjuvants And Diketopiperazine-Mediated Communication, Marian Romaine

Dissertations, Theses, and Capstone Projects

Medicinal plants and their associated microbiomes constitute a rich source of bioactive natural products with applications in immunotherapy and microbial ecology. Herbal formulations have long been valued for safe immune enhancement, while bacterial signaling molecules govern community behaviors critical to pathogenesis, symbiosis, and environmental processes. Bacterial lipopolysaccharides (LPS) from plant-associated Gram-negative bacteria have emerged as potent TLR4 agonists, yet their endotoxic potential limits direct use, and diketopiperazines (DKPs) serve as versatile quorum-sensing mediators capable of modulating biofilms in mixed microbial systems.

The work in this thesis comprises two independent but complementary research strands. The first strand pursued the engineering of …

Profiling Nucleolin Phosphorylation During Dna Damage Response And Cell Cycle Arrest, Hanjun Jeon

Dissertations, Theses, and Capstone Projects

This dissertation examines site-specific and global phosphorylation dynamics of nucleolin (NCL) in response to DNA damage and cell-cycle perturbations. By combining phospho-specific immunoblotting with Phos-tag SDS-PAGE analysis, distinct phosphorylation patterns were identified across experimental conditions. The results define reproducible, condition-dependent phosphorylation states of NCL and provide a framework for studying its regulation under cellular stress.

Mapping Nucleosome Stability: Linking Oncogenic Structural Alterations To Long-Range Allosteric Communication, Augustine C. Onyema

Dissertations, Theses, and Capstone Projects

The nucleosome core particle (NCP) is essential for chromatin structure and function, serving as the fundamental unit of eukaryotic chromatin. Oncogenic mutations in core histones disrupt chromatin dynamics, altering DNA repair and transcription processes. How DNA communicates with histones, and how this information propagates through the histone, has been suggested to be a cooperative process. Here, I investigate the molecular consequences of two mutations, H2BE76K and H4R92T, using 36 µs of all-atom molecular dynamics simulations on Anton2. I also characterize the kinetic correlation within histone/DNA domains via conditional activity (CONDACT) using the dihedral angle as our degrees of …

Identifying Textual Predictors Of Early Termination In Clinical Trials In Medicine: An Explainable Machine-Learning Study, Rohan Ramnarain

Dissertations, Theses, and Capstone Projects

About one in five clinical trials in medicine ends early, wasting valuable resources and reducing the evidence available for developing life-saving medical treatments. This project uses a method called Trial2Vec, which is a self-supervised machine-learning method that converts clinical trial documents into dense numerical representations that capture their key design and clinical characteristics, to turn each proposed clinical trial’s written protocol into a compact numerical profile (a process referred to as embedding). These profiles are then paired with a predictive machine learning models to identify the words and phrases in the trial documents that can signal a higher risk of …

Popgenhelpr: An R Package To Streamline And Facilitate Informed Population Genomic Analyses And Visualization Of Genetic Ancestry, Diversity And Differentiation, Keaka Farleigh, Mason O. Murphy, Christopher Marie Blair, Tereza Jezkova

Publications and Research

Analysing large population genomic datasets requires an interdisciplinary skillset. Beyond a knowledge base in genetics and population biology, population genomic analyses involve computer science and statistics, representing a barrier for researchers without experience in those fields. PopGenHelpR seeks to lower this barrier by enabling researchers to perform population genomic analyses and generate near-publication quality figures in a streamlined and informed fashion. PopGenHelpR allows users to estimate genetic diversity within populations as well as differentiation among populations and individuals from single nucleotide polymorphism data. PopGenHelpR includes commonly used measures such as observed heterozygosity and FST. PopGenHelpR also provides five …

Exploring Biogeographical Ancestry Inference Of New York Residents Using A 45 Indel Panel, Amanda Martinez

Student Theses

Biogeographical ancestry (BGA) inference is an important tool in forensic science, providing supplemental information when comparison/reference DNA is not available for traditional DNA analyses. Insertion/deletion polymorphisms (INDELs) have been used in the last decade as ancestry-informative markers (AIMs) for BGA inference because they can be easily adapted to forensic-type samples and are determined using low cost and easy processing methods. Limited research has attempted to estimate ancestry and admixture in United States (U.S.) populations. This study evaluated the effectiveness of a 45- and 21- INDEL panel to measure population admixture proportions of four different origins (African, European, East Asian and …

Microtubules In Breast Cancer: Exploring The Α/Β-Tubulin Toggle Switch And Its Implications In Human Breast Cancer, Annemarie Ianos

Student Theses and Dissertations

Microtubules, composed of a/b-tubulin heterodimers, play a central role in breast cancer tumor growth by polymerizing, leading to metastasis and depolymerizing, contributing to proliferation. Human enzymes protein kinase Ca (PKC-a) and cyclin-dependent kinase 1 (Cdk-1) mediate phosphorylation at sites a:Ser165 and b:Ser172, respectively, influencing the growth of microtubules. It is possible that alternating phosphorylation at these sites contribute to an a/b-tubulin “toggle switch” that mediates microtubule instability and tumor growth.

The project investigates the influence of the toggle switch model on microtubule stability by determining the impact of mutants (a:S165D, a:S165N, a:S165S_P, b:S172S_P and a:S165S_P/b:S172S …

Genomics And Bioinformatics Student Companion Workbook (First Edition), Na Xu, Tina Hu

Open Educational Resources

This Genomics and Bioinformatics Student Companion Workbook provides an integrated, hands-on introduction to the principles and applications of modern genomics and bioinformatics. Designed for undergraduate students, the workbook guides learners from foundational concepts of genome structure and sequencing technologies to advanced topics including variant analysis, comparative genomics, and multi-omics integration. Emphasizing the interplay between experimental biology and computational analysis, it introduces key analytical tools and biological databases that support genome interpretation and data-driven discovery.

Through a structured progression of chapters, students explore genome organization across diverse biological systems, from prokaryotes and viruses to complex eukaryotic genomes, and examine how genomic …

Scb252 Fundamentals Of Biotechniques Laboratory Manual, Na Xu, Hanqi Ye

Open Educational Resources

This laboratory manual for SCB252: Fundamentals of Biotechniques provides an integrated, hands-on introduction to core concepts and methods in modern biological research using Drosophila melanogaster as a model organism. The manual emphasizes laboratory safety, research integrity, and responsible conduct of research, alongside foundational experimental skills. Students are guided through key biological techniques including fly husbandry, genetic crosses, mutant analysis, microscopy, DNA extraction, polymerase chain reaction (PCR), gel electrophoresis, sequencing technologies, and bioinformatics tools such as BLAST and genome databases. Advanced modules introduce gene structure annotation, RNA-seq data analysis, and primer design, while fluorescence microscopy and protein analysis techniques further expand …

The Effects Of Cinnamaldehyde On Tetrahymena Thermophila, Sydney Kurland

Publications and Research

In addition to their common use as spices in cooking and baking, cinnamon plants, Cinnamomum zeylanicum and Cinnamomum cassia for example, have long been used in herbal remedies worldwide. Cinnamon contains many vital oils and active compounds including cinnamaldehyde (CMD). Numerous studies looking at potential therapeutic effects of cinnamon have demonstrated its antioxidant, anti-inflammatory, and antimicrobial properties (1, 2, 3).   Therefore, it is important to continue studying the efficacy, benefits, and mechanisms of action of cinnamon and CMD to have a complete understanding of its full potential. Tetrahymena thermophila is a ciliated protozoan commonly used as a model organism to …

Monitoring Biodiversity Growth In An Oyster Reef Restoration: Understanding How Oyster Reef Life Cycle May Impact Biodiversity., Gabriel A. Roses

Theses and Dissertations

Oyster reefs are vital to marine ecosystem health, improving water quality and providing food and habitat for diverse species. We assessed biodiversity changes for a proposed oyster reef restoration site to help guide management, future assessment, and deepen understanding of how oyster reefs function and their ecosystems dynamics.

Bugs, Birds, Blue: Queer Ecologies Of Embodiment, Kinship, And Survival, Celeste B. Newcomb

Theses and Dissertations

bugs, birds, blue is a multi-channel audiovisual installation that examines queer ecology as a framework for understanding transgender embodiment, kinship, and survival amid environmental crisis and ongoing political attacks on trans life (Mortimer-Sandilands and Erickson). Through sculpture, projection, sound, reflective surfaces, and biological imagery, the installation places human bodily matter alongside microbial and aquatic life forms to challenge narratives that frame trans existence as unnatural, recent, or isolated. Instead, the work proposes transness as relational, adaptive, and deeply entangled with broader ecological systems. The installation is composed of two interconnected environments. On one side of the space, three aquariums rest …

Genetic Screen For Regulators Of Pol4, A Dna Repair Polymerase In Saccharomyces Cerevisiae, Pasang Dolma Sherpa

Theses and Dissertations

In Saccharomyces cerevisiae, DNA polymerase 4 (POL4) is the beta repair polymerase, the product of the POL4 gene, and is involved in base excision repair (BER) and microhomology-mediated end joining (MMEJ). Despite its involvement in these repair pathways and its conservation across eukaryotes, deletion of POL4 shows no detectable phenotype under standard laboratory conditions. I hypothesized that unknown genes act as backup systems, providing redundant activities that allow pol4Δ cells to survive. To test this, a genetic screen for mutants showing synthetic lethality with pol4Δ was implemented. I constructed a strain lacking the POL4 gene and carrying …

Bio 23 Human Anatomy & Physiology I Syllabus, Rujin Tian

Open Educational Resources

The syllabus for BIO 23 contains a course description, course objectives, course readings divided by week and a link to an OER textbook.

Bio 24 Human Anatomy And Physiology Ii, Rujin Tian

Open Educational Resources

The syllabus for BIO 24 contains a course description, course objectives, course readings divided by week and a link to an OER textbook.

Autoantibody Reactivity In Hidradenitis Suppurativa: Characterizing Keratinocyte And Apocrine Gland Targets Across Disease Progression And Anti-Tnf-Α Treatment, Talla Hamouche

Student Theses and Dissertations

Hidradenitis suppurativa (HS) is a chronic, relapsing inflammatory skin disease associated with impaired quality of life, representing one of the highest burdens among dermatological conditions. This debilitating disorder primarily affects apocrine-gland-bearing and flexural skin areas, most commonly the axillae, breast, buttocks, and groin. As lesions recur and new sites emerge, surgical excision does not guarantee prevention of disease reestablishment. Despite its substantial burden, HS remains among the least understood and most treatment-resistant inflammatory diseases. The mechanisms underlying this chronicity and the frequent failure of conventional anti-inflammatory therapies remain unresolved. An underappreciated autoimmune dimension may contribute to HS pathogenesis: the clonal …

Short Lab Report- Presentation, Wroud Saleh, Yevgeniy Grigoryev

Open Educational Resources

No abstract provided.

Bio 230 - Microbiology, Sarah Moroianu

Open Educational Resources

This open educational resource (OER) syllabus is designed for BIO 230: Microbiology at Lehman College, City University of New York (CUNY), a single-semester introductory microbiology course for non-biology majors such as Nursing, Dietetics, Health Education, and Physical Education. The course reviews microbial structure, metabolism, genetics, and microbial ecology, with applied emphasis on infectious disease, antimicrobial drugs, host immune defenses, and microbial diseases. The syllabus aligns course content with the freely available OpenStax Microbiology textbook (Parker et al., CC BY 4.0) and reflects accessibility best practices consistent with CUNY guidelines.

Characterization And Advancement Of Molluscan Venom Gland Cell Model Systems, James V. Parziale

Dissertations, Theses, and Capstone Projects

Venomous mollusks, including cone snails and coleoid cephalopods, produce rich repertoires of bioactive peptides with profound effects on cellular physiology, yet there are few tractable experimental systems that exist to study their development, maintenance, and venom secretion. Although therapeutics such as the cone snail peptide Ziconotide demonstrate the biomedical potential of molluscan venoms, progress in understanding how venom glands form, function, and evolve has been hindered by the lack of reliable husbandry and the complete absence of in vitro cell models. Modern comparative genomics has revealed widespread convergent evolution across venomous lineages, but molluscan datasets remain underrepresented, limiting insights into …

Local Angiotensin Converting Enzyme 2 (Ace2) Enzymatic Activity Modulates Cholinergic Interneuron Function In The Dorsolateral Striatum, Aria R. Walls

Dissertations, Theses, and Capstone Projects

The renin angiotensin system (RAS) is an ancestrally ancient peptidergic signaling pathway best known for its role regulating blood pressure in the periphery. However, its presence and importance in the central nervous system has more recently been identified and is less well understood. Previous work shows RAS is expressed in the nigrostriatal pathway of the basal ganglia and has been implicated in basal ganglia disorders including Parkinson’s disease (PD) and levodopa-induced dyskinesia (LID). Interestingly, the canonical and noncanonical arms of the RAS pathway produce opposite effects on PD disease vulnerability and progression. The shift from the neurodegenerative canonical RAS to …

Computational And Functional Characterization Of Terebrid Venom Peptides, Favour T. Achimba

Dissertations, Theses, and Capstone Projects

Venom peptides represent a natural repertoire of bioactive compounds that are potent modulators of ion channels. Teretoxins, venom peptides from terebrid snails, remain underexplored despite their structural and functional diversity. This thesis is the first to comprehensively explore the structure and function of teretoxins using a comparative computational sequence and structure model followed by experimental assays. The majority of the functional focus has been on identifying the ion channel molecular targets of uncharacterized teretoxins. Teretoxins, like other venom peptides, are hypothesized to manipulate the cellular function of a diversity of ion channels. Dysregulation of ion channels leads to several …