Life Sciences Commons^™

Taming Biological Complexity Through The Use Of Symmetries, Luis A. Álvarez-García

Dissertations, Theses, and Capstone Projects

The study of biological systems is, inherently, the study of very complex systems. This is essentially due to the fact that they are made up of numerous, often very complicated, interactions between an extensive number of components. Often necessitating an abundance of quantitative parameters and details for a precise description. The human brain for ex- ample, consisting of ∼ 80 billion neurons with ∼ 800 to 100 trillion connections between them, each of them depending on a large set of parameters. Even simpler examples such as bacterial organisms, such as E. coli and B. subtilis, which we focus on …

How Eye See, Now I See, Michael Anthony Simon

Theses and Dissertations

Michael Anthony Simon’s paper addresses ideas surrounding the fluid nature of perception, time, and ideas of control, or lack there-of. Creating a symbolic relationship between paintings and sculpture. Simon both embraces and confuses the notion that understanding is never truly stable or secure.

Identifying Personality In Reptiles And Assessing Welfare Implications For Their Roles As Ambassador Animals In An Educational Setting, Valery Gonzalez

Theses and Dissertations

This study examined behavioral variability and personality in 13 reptiles used as ambassador animals at the American Museum of Natural History. Observations across seasons and novel object tests revealed individual differences, behavioral components, and correlations. Findings emphasize reptilian complexity, highlighting welfare implications while underscoring the need for further research.

Forest Above-Ground Biomass Estimation Using Nasa Gedi Lidar Waveforms And Global Tree Allometry, Ian Grant

Theses and Dissertations

Above-ground forest biomass plays a crucial role in global carbon cycles, yet accurately estimating biomass at global scales remains challenging. This thesis addresses two key challenges in processing NASA’s Global Ecosystem Dynamics Investigation (GEDI) space-borne lidar data to estimate above-ground biomass density (AGBD): accounting for global variation in forest structure and developing robust physical interpretations of lidar returns. The first component of the thesis analyzes global patterns of tree allometry using the Tallo tree allometry dataset, examining relationships between tree dimensions across biomes, continents, and plant functional types. This analysis reveals consistent allometry across continents for some biomes (e.g., tropical …

Social Networks And Behavioral Adaptation Of Serrano Horses In A Rewilding Initiative In Spain, Ashley Bruno

Theses and Dissertations

Rewilding is a conservation measure that involves actively relocating species or restricting human land use to improve ecosystem sustainability. However, critics raise concerns that rewilding privileges ecosystem function over endangered species. Due to a lack of monitoring around species’ relocations, uncertainty lies in ecological outcomes and psychological, social, cultural impacts on affected animals. For this project, we collaborated with the non-profit Rewilding Europe that sought to conserve Serrano horses (Equus caballus), an ancient and under-studied breed of Spanish horse by relocating 11 individuals to a protected site in Guadalajara, Spain in June 2022. Our research aimed to address …

Optimizing Biofilm Assay Reproducibility And Characterizing The 12-Hydroxystearic Acid On Escherichia Coli, Khilola Khusanova

Theses and Dissertations

Biofilm formation in Escherichia coli plays a critical role in microbial chemical communication and surface-associated persistence. This study investigates the antibiofilm activity of 12-hydroxystearic acid (12-HSA), evaluating its R and S enantiomers as well as a racemic mixture. E. coli BL21, biofilms were grown under standardized laboratory conditions and quantified using the Crystal Violet staining assay. Treatment with 12-HSA resulted in a measurable reduction in biofilm biomass, with differences observed between the individual enantiomers and the mixture. These findings suggest that 12-HSA influences early adhesion and biofilm development, supporting its potential as a small-molecule modulator of bacterial surface behavior. This …

Estimating The Amount Of Carbon Dioxide Gas Removed From The Atmosphere By The Bryant Park Tree Population, Edimarlyn Gonzalez

Open Educational Resources

No abstract provided.

Atorvastatin Alters Neuronal Morphology Data Set, Carolyn L. Pytte

Publications and Research

Statins are highly effective and widely prescribed cholesterol lowering drugs. However, statins cross the blood-brain barrier and decrease neural cholesterol in animal models, raising concern that long-term statin use may impact cholesterol-dependent structures and functions in the brain. Cholesterol is a fundamental component of cell membranes and experimentally decreasing membrane cholesterol has been shown to alter cell morphology in vitro. In addition, brain regions that undergo adult neurogenesis rely on local brain cholesterol for the manufacture of new neuronal membranes. Thus neurogenesis may be particularly vulnerable to long-term statin use. Here we asked whether oral statin treatment impacts neurogenesis …

Adaptation For Whom? Understanding The Impacts Of Dyke Policies On Small-Scale Farmers In Ca Mau Province Of Vietnam, Nguyen Minh Quang, Nguyen Van Minh, Nguyen Vo Chau Ngan, Martha B. Lerski

Publications and Research

Low-lying deltas worldwide are extremely vulnerable to sea-level rise. As the risks of climate-induced flooding become increasingly clear, the thirst for infrastructure-driven adaptation increases. This highlights a patent need to understand the impacts of engineering adaptation solutions, especially those targeting built structures such as dykes and sluices, on farmers from a bottom-up, farmer-centred perspective. The study addresses this call by examining cases where dyke policies, while successful in some dimensions, have undermined small-scale farmer livelihoods in Ca Mau ― Vietnam’s southernmost rural province. It identifies areas in need of attention and adds empirical data related to this group of farmers. …

Identifying Intangible And Biocultural Heritage Elements Toward Environmental Understanding: Engaging Stakeholders Through Art, Martha B. Lerski

Publications and Research

Grounded in a case study in Barbuda in the Caribbean, this research examines sustainability from the perspective of what arts and heritage can contribute to community engagement and local and broader understandings about the environment. This article documents a growing body of literature recognizing the role of arts and culture, including local knowledge and traditional ecological knowledge (TEK), in climate change endeavors. Art and TEK present expansive world views. Contextual information situates research done on the island of Barbuda pre- and post-Hurricane Irma. Visual arts workshops engaged community members in mixed methods research. Results documented cultural elements, particularly intangible and …

Karyotyping As A Method To Verify Phylogenetic Relationships Among The Enneacanthus Species, Ophelia A. Anderson

Theses and Dissertations

The Enneacanthus genus consists of three species of freshwater fish endemic to eastern North America: E. obesus (Banded Sunfish), E. gloriosus (Blue Spotted Sunfish), and E. chaetodon (Black Banded Sunfish). Previous studies using molecular data suggest that E. obesus and E. gloriosus are more closely related, with E. chaetodon as the most distantly related species in the genus. This study investigates the phylogenetic relationship among the Enneacanthus species, using karyotype characteristics - chromosome number, morphology and fundamental number - as comparative metrics. Chromosome spreads were obtained from scale and gill epithelium samples collected between 1993 and 1994. Prepared slides …

Caspases Protect Against Hyperglycemia Induced Necroptosis-Like Cell Death In Brain Endothelial Cells, Aleena S. Mathew

Theses and Dissertations

Acute diabetes characterized by high spikes in blood glucose levels in association with severe hyperglycemia can lead to an increased risk of ischemic stroke in the brain. To better understand high blood glucose levels, hyperglycemia, in the brain we explored its effects on endothelial cells. Endothelial cells line the inner walls of blood vessels and are directly impacted in hyperglycemia. Brain endothelial cells are a major component of the blood brain barrier (BBB) which tightly regulates the brain’s microenvironment. The type of cell death such as apoptosis, caspase dependent, or necroptosis, caspase independent, can exacerbate diabetes associated complications. There is …

Investigation Of Rna-Binding Protein Expression Changes In The Hippocampus Following Doxorubicin And Cyclophosphamide Treatment, Lijie Chen

Dissertations and Theses

This study investigated the molecular mechanisms underlying chemotherapy-induced cognitive impairment (CICI) following doxorubicin and cyclophosphamide treatment in a rat model, revealing three significant alterations in hippocampal tissue: selective downregulation of heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1) (21% decrease, p=0.0298), compromised astrocytic network integrity evidenced by reduced GFAP-positive area in cornu ammonis 3 (CA3) (24%, pB=0.026) and dentate gyrus (DG) (19%, pB=0.027) regions, and elevated cellular senescence marker p19Arf specifically in DG (69%, pB=0.033) and CA3 (27%, pB=0.024). The inverse relationship between hnRNPA1 reduction and p19Arf elevation suggests a potential mechanistic link between RNA dysregulation and senescence induction, with pronounced vulnerability in …

Toxin-Like Proteins In The Venom Of Drosophila Parasitoids, Lady V. Cardenas

Dissertations and Theses

The figitid parasitoid wasps of Drosophila are gaining importance in agriculture due to their ability to kill the resilient soft-fruit pest Drosophila suzukii. Their success and infection strategies vary, and the mechanisms underlying these differences are largely unknown. Some of their venom proteins have been shown to be important in suppressing host defense. Here, we report that Ganaspis brasiliensis, a parasitoid of D. suzukii survives well on Drosophila yakuba, a host species with a strong cellular immunity, and infected flies are unable to mount a strong immune response. To predict possible toxin-like proteins in Ganaspis venoms that might suppress cellular …

Multimodal Imaging Of Protein-Based Biomaterials For Delivering Chemo-Agent Cargo For Glioblastoma Treatment In A Murine Model, Orin Mishkit

Dissertations and Theses

Protein-based self-assembling biomaterials, known as Thermo-Responsive Assembled Proteins (TRAP), present meaningful potential as drug delivery carriers. These materials enable the controlled, slow release of poorly soluble chemotherapeutic agents, such as doxorubicin (Dox), while potentially reducing systemic off-target effects. In collaboration with multiple NYU labs, this study evaluated the efficacy of two TRAP variants—TRAP and F-TRAP—as drug delivery carriers in a xenograft mouse model of glioblastoma multiforme (GBM).

The primary objective was to compare the effectiveness of TRAP-loaded Dox (TRAP-DOX) to free Dox in achieving tumor extravasation and accumulation, facilitating sustained drug release. We hypothesized that the leaky vasculature of GBM …

Explorations Of Dna-Single-Walled Carbon Nanotube Interactions To Develop Multiplexed Molecularly Specific Biosensors For Inflammation, Amelia K. Ryan

Dissertations and Theses

Inflammatory cytokines such as interleukin-6 (IL-6) and interleukin-12 (IL-12) are central regulators of immune signaling and key biomarkers of disease, yet existing assays for their detection remain slow, invasive, and lack multiplexing ability. This dissertation advances the development of single-walled carbon nanotube (SWCNT) optical nanosensors capable of real-time, multiplexed, and molecularly specific cytokine detection through innovative use of single-stranded DNA (ssDNA) interfaces.

First, an IL-6-specific DNA aptamer was employed as both a dispersing agent and recognition probe for SWCNT fluorescence sensing. Sequence modifications, including anchor domains, truncations, and thermally induced refolding, were systematically tested to optimize sensitivity and selectivity. The …

Assembly Of Ppsu-Oligomers, Mariam Nesterov

Student Theses and Dissertations

The development of nanostructures for delivering multiple proteins to targeted antibodies has become a promising avenue in biotechnology, driven by advancements in synthetic polymers like poly(propylene sulfone), PPSU. However, the PPSU polymer faces a major limitation - its high insolubility. To address this challenge, this study investigates whether PPSU oligomers can enhance both the solubility and stability of lysozyme, a model protein that is cost-effective and widely accessible. Using dimer, trimer, tetramer, and hexamer configurations, we analyzed the interactions between PPSU oligomer and lysozyme under varying conditions. Our results show that the dimer and trimer are water soluble (no aggregate …

Comparison Of Methods For Amphetamine Enantiomer Analysis Using Hplc And 1h-Nmr, Martin Mai

Student Theses

A molecule is chiral if it cannot be superimposed on its mirror image. Chiral drugs exist as these mirror image enantiomers, which can differ in their pharmacological effects. When a drug’s active molecule exists as a pair of enantiomers, the relative ratio of each enantiomer in the final product can provide information about the source of production for this drug, i.e., whether the drug was legally or illegally produced. However, typical detection methods may not differentiate between enantiomers of a chiral molecule. This thesis study compares three different methods for enantiomer detection of amphetamine, which is a drug often prescribed …

Developing Coexpression Systems To Introduce Hydroxyproline Into Protein Engineered Collagen Peptides Utilizing Hydroxylase From Acanthamoeba Polyphaga Mimivirus, Jennifer Soldatich

Theses and Dissertations

A major challenge of developing collagen mimetic peptides (CMPs) by bacterial expression is to include hydroxyproline for biomedical applications. Coexpression of Prolyl-4-hydroxylase from A.mimivirus with CMPs was investigated. Additionally, four expression designs were created for potential applications in mammalian cells to utilize their natural ability of proline-hydroxylation by post-translational modification.

Harnessing Neural Activity To Prevent Non-Apoptotic Spinal Neurons From Microglial Phagocytosis After Motor System Injury, Jasmine L. Pathan

Dissertations, Theses, and Capstone Projects

Producing skilled, voluntary movements in humans and many animals requires the corticospinal tract, the direct motor pathway connecting the cerebral cortex with spinal cord interneurons and motor neurons in humans and many non-human primates. Spinal cord injury (SCI) typically results in corticospinal tract damage, leading to transneuronal degeneration of its interneuron targets. Complement protein C1q triggers this degenerative process and induces microglia, the innate immune cells of the central nervous system, to phagocytose non-apoptotic interneurons. We examined two classes of premotor interneurons, cholinergic (ChAT) and glutamatergic (Chx10), essential to the spinal motor circuit as they receive direct corticospinal tract inputs …

Regulation Of P21 Function By A Sense Long Non-Coding Rna Generated By Alternative Polyadenylation, Anthony Ramadei

Dissertations, Theses, and Capstone Projects

As cells are continually undergoing damage to the genome, a coordinated change in gene expression across thousands of genes is required for the progression of the DNA damage response (DDR). After initial sensing of DNA damage, the transcription factor p53 induces expression of target genes to halt the cell-cycle to allow DNA repair and induce either senescence or apoptosis. One of the p53 target genes is CDKN1A which encodes the cyclin dependent kinase inhibitor p21. p21 halts cell-cycle progression in response to DNA damage and can also induce senescence. However, p21 expression in cancer cells undergoing chemotherapy allows survival by …

The Influence Of Environmental Change On Genetic Diversity Across Spatial And Taxonomic Scales, Connor M. French

Dissertations, Theses, and Capstone Projects

The spatial distribution of genetic diversity is of interest to biodiversity scientists and conservationists and is a fundamental metric of biodiversity. Genetic diversity patterns across spatial and taxonomic scales contain information about population and assemblage dynamics that can convey their resilience to environmental change. Ectotherms are especially linked to their environments and may be especially sensitive to fluctuations in the environment over time. Herein, I investigate global and regional patterns of genetic diversity in two groups of ectotherms, insects and lizards, to understand the relationship between environmental change and genetic diversity, from populations to assemblages. Overall, my research aims to …

Incorporating Solvation Thermodynamic Mapping In Computer-Aided Drug Design, Yeonji Ji

Dissertations, Theses, and Capstone Projects

Advancements in computational techniques have revolutionized structure-based drug design, substantially improving the efficiency and effectiveness of the drug discovery process by reducing time, costs, and labor requirements. These advancements include various methods, such as investigating small molecule ligands binding to proteins, exploring alternative protein conformations, and solvation mapping on the protein surfaces. Among these methods, understanding the correlation between protein-ligand binding and the role of solvation is important.

A fundamental concept in protein-ligand binding is shape and electrostatic complementarity, which is complicated by the inherent flexibility of proteins. In the absence of small molecule ligands, proteins are complementary to surface …

Repurposing Bt-11 To Treat Alzheimer’S Disease: Exploring The Glutathione-S-Transferase Lancl2 As A Target, Emily Birnbaum

Dissertations, Theses, and Capstone Projects

Approximately 99.6% of potential Alzheimer’s drugs fail, thus developing successful drugs is a high priority. The failure at developing successful drugs relates to the complex nature of the disease itself. Many components act together to trigger a cascade that ultimately results in neurodegeneration and cognitive dysfunction associated with the disease. In building a multiplex model of Alzheimer’s it is important to understand its specific biological mechanisms. One of these key pathological mechanisms is neuroinflammation. Understanding the pathways involved in neuroinflammation in Alzheimer’s is an urgent need, as it poses a promising avenue for future effective therapeutics. Specifically, as many investigational …

Retinoblastoma Malignance And Exosome Mechanisms Facilitating Optic Nerve Head Metastatic Niche Formation, Cui Shi

Dissertations, Theses, and Capstone Projects

Retinoblastoma (RB) is a rare pediatric ocular tumor that occurs before five years of age and it is the most common intraocular cancer of childhood with more than 300 children in the United States and 8000 diagnosed globally each year. RB arises from the proliferation of cone photoreceptor precursor cells in the retina as a result of mutations in the RB1 gene. The influence of RB secreted factors on cells in the retinal environment has not been fully elucidated. Cancer cell released exosomes have been shown to transform their microenvironment through transfer of metastasis promoting molecular cargo. Cancer cell extracellular …

Variability In Associations Among Seabirds And Marine Mammals: Causes And Consequences, Samantha A. Monier

Dissertations, Theses, and Capstone Projects

Marine predators today face multifaceted stressors from changing climate to changing prey availability, and these changes are occurring at unprecedented speeds. Any alteration to a species’ environment has the potential to disrupt social networks and thus, how animals obtain and transfer information. Interspecific social interactions in the form of local enhancement and facilitation are a critical, but not yet well-understood, component of seabird foraging; of immediate concern is that anthropogenic changes may be altering the quantity and quality of positive species interactions, with consequences for the species involved.

While we know these interactions are not immutable, less is known about …

The Effects Of Environmental Changes On The Biodiversity And Macroecological Patterns Of Bird Assemblages In The United States, Marlen Acosta Alamo

Dissertations, Theses, and Capstone Projects

The current restructuring of species assemblages and global loss of biodiversity result from species-specific responses to anthropogenic changes in climate and land cover. I investigated the effect of these two drivers on the seasonal distribution and biodiversity of birds in the United States and how human-induced habitat loss impacts macroecological patterns such as the species-area and the abundance-occupancy relationships. In Chapter 1, I examined the existence of a correlation between breeding and wintering geographic distributions of birds with different migratory strategies and the effect of changes in climate and the proportion of crop-pasture and urban land cover on this correlation. …

Structural Insights Into Bacterial Helicase Loading At A Replication Origin By Cryogenic Electron Microscopy, Abhipsa Shatarupa

Dissertations, Theses, and Capstone Projects

DNA replication is a meticulously regulated and intricate process crucial for cellular viability. Replicative helicases, essential for unwinding DNA during replication, rely on helicase loader proteins for efficient loading and assembly at replication origins. In Escherichia coli, the replicative helicase DnaB forms a complex with six copies of the bacteriophage Lambda λP loader, resulting in a B₆P₆ conformation. The conformation of the BP complex, with a 6:6 stoichiometry, indicates that the isolated DnaB is initially captured by λP (B₆P₆) through its carboxy-terminal domain lassos/grappling hooks, serving as an early intermediate before transitioning …

Development Of Collagen Mimetic Mini-Fibrils With Tunable Collagenase Susceptibility, Jui Chaugule

Dissertations, Theses, and Capstone Projects

Collagen fibrils are the primary molecular scaffold of all connective tissues and provide the essential support for cell migration and differentiation. Collagen fibrils represent one of the most complex molecular hierarchies: three polypeptide chains in Gly-Xaa-Yaa repeating amino acid sequences, first form the rod-shaped collagen triple helix. These triple helices further self-assemble laterally in a specific manner to form fibrils having the characteristic 67 nm axially repeating structure known as the D-period. Enzymatic digestion of collagen fibrils by matrix metalloproteinases (MMPs) is critical for several physiological processes and is of particular consequence during wound healing. Many of the mechanisms of …

Establishing A Murine Model Of Malaria-Associated Acute Kidney Injury And Demonstrating The Contribution Of Extrinsic Apoptosis To Tubular Necrosis, Johanna Bensalel-Lyampe

Dissertations, Theses, and Capstone Projects

Malaria-associated acute kidney injury (MAKI) is a form of severe malaria (SM), which is usually caused by Plasmodium falciparum infection. Until recently, the impact of this particular complication of SM was severely underestimated and research in this area has been neglected. There is in fact a high prevalence (40-60%) of MAKI in SM patients and the associated risk of mortality and development of comorbidities is high. Furthermore, pediatric patients that recover often develop long-term complications such as chronic kidney disease or neurocognitive defects. The need for adjunctive therapies and early diagnostic biomarkers specific to this SM complication is critical but …