Biotechnology Commons^™

Data Curation And Integration For Cancer Cell Line Pharmacogenomics Analysis, Meric Kinali

Graduate Masters Theses

Cancer cell lines are essential resources for connecting genomic and molecular features with drug response and identifying biomarkers. Therefore, large-scale cancer cell line resources have been growing, but this introduces challenges such as data standardization, consistent annotation, matching identifiers, cross-database integration, and a reproducible computational framework. CellMiner Cross Database (CellMinerCDB) integrates pharmacogenomic datasets from multiple resources and provides a standardized analysis of cell lines across datasets. This thesis examines cancer cell line cross-databases and their importance in pharmacogenomics, with a particular focus on CellMinerCDB. As part of this work, I developed an R package for the gCSI (Genentech Cell Line …

Discovery Of Bmi-Associated Gut Microbiome Signatures In The Awi-Gen 2 Cohort, Meriem Yagoubi

Theses and Dissertations

Obesity is increasing across sub-Saharan Africa amid rapid dietary, environmental, and urbanization transitions, yet the gut microbiome features associated with adiposity in African populations remain under-characterized. This study investigated whether species-level gut microbiome composition is associated with body mass index (BMI) in the AWI-Gen 2 cohort, and whether BMI-associated microbial signals remain detectable after accounting for the dominant geographic structure of the microbiome. Gut microbiome community structure and diversity were characterized across 1,665 participants, and differential abundance analysis was used to identify taxa associated with BMI after controlling for study site. Machine learning models were then trained to assess how …

Virus-Like Particle Peptoid Conjugate As A Triple-Negative Breast Cancer Targeting Delivery System, Ricky Zhu

Chemistry Theses

Triple-negative breast cancer (TNBC), an aggressive form of breast cancer, characterized by its lack of estrogen receptors (ER), progesterone receptors (PR), and human epidermal growth factor receptors (HER2) poses a therapeutic challenge as common treatment options are rendered ineffective. Here is a strategy to develop a drug delivery system utilizing poly-glycinated LC129 8, a TNBC targeting peptoid, covalently attached to HK97 virus-like particles (VLP) containing a C-terminal LPETG sequence via a sortase mediated reaction. Using the properties of the cage-like structure of VLPs and the TNBC specificity of the LC129-8, high doses of chemotherapy can be efficiently loaded into the …

Interpretable Deep Learning Models For Trustworthy Prediction Of Enzyme Functions, Louis Dumontet

UNLV Theses, Dissertations, Professional Papers, and Capstones

Trustworthy prediction of enzyme function from protein sequences remains a central challenge in computational biology, particularly when annotated data are limited, imbalanced, or incomplete. This dissertation develops interpretable deep learning methods for enzyme discovery and enzyme function prediction from amino acid sequences. First, it introduces PEPIC, an interpretable convolutional neural network for substrate-level prediction of hydrolytic plastic-degrading enzymes. Using curated and expanded sequence datasets, PEPIC improved predictive performance over benchmark methods, identified sequence regions aligned with catalytic and substrate-binding residues, and supported the discovery and experimental validation of a previously uncharacterized PET-degrading enzyme. Second, this dissertation investigates the integration of …

Thrombin-Induced Myofibroblast Differentiation Is Regulated By Myocardin And Novel Effector Genes In Ipf Fibroblasts, Christiana Okeke

Biotechnology Theses

Idiopathic pulmonary fibrosis (IPF) is a progressive interstitial lung disease characterized by fibroblast activation, excessive extracellular matrix (ECM) deposition, and irreversible respiratory decline. In this study, we investigated the role of myocardin and its downstream effectors, RGS5, DLGAP5, and TAGLN, in thrombin-induced myofibroblast differentiation and ECM remodeling using primary human IPF fibroblasts. Myocardin knockdown significantly attenuated thrombin-induced expression of profibrotic genes, including FN1, COL1A1, PAI-1, ACTA2, and CNN1, as well as the novel effectors RGS5, DLGAP5, and TAGLN, confirming myocardin as a central regulator of fibrotic signaling. Silencing RGS5 produced minimal effects on gene and protein expression despite minor downward …

Myocardin-Dependent Regulation Of Adam12 And Adam19 Promotes Fibronectin Fibrillogenesis During Pleural Fibrosis, Uday Siva Naga Sankar Allamneni

Biotechnology Theses

Pleural fibrosis involves excessive extracellular matrix (ECM) deposition driven by chronic injury and inflammation. Transforming growth factor-β (TGF-β) induces mesothelial–mesenchymal transition (MesoMT), promoting a myofibroblast phenotype. Our laboratory identified myocardin (Myocd), a transcriptional coactivator, as a key mediator of MesoMT that regulates ECM-remodeling proteases. RNA-seq and qPCR analyses showed that ADAM12 and ADAM19 are upregulated by TGF-β but suppressed by Myocd knockdown in Human pleural mesothelial and IPF-derived cells. Silencing ADAM12 reduced fibrotic markers, including fibronectin and smooth muscle actin (α-SMA), whereas ADAM19 showed relatively minor effects. ADAM12 knockdown also impaired fibronectin fibrillogenesis and insoluble matrix assembly, as confirmed by …

Role Of Kif4a In The Fxa-Induced Phenotypic Modulation Of Pleural Mesothelial Cells, Sudishna Khanal

Biotechnology Theses

Pleural injuries can disrupt the organization of the pleural surface, leading to pleural remodeling and fibrosis (PF), characterized by the proliferation of myofibroblasts expressing alpha-smooth muscle actin (α-SMA) and the deposition of extracellular matrix proteins, primarily due to the mesenchymal transition of pleural mesothelial cells (PMCs) (MesoMT). It is well established that various external stimuli, such as TGF-β, thrombin, and factor Xa (FXa), induce MesoMT. Our laboratory found that myocardin, a transcriptional co-activator, was dramatically up-regulated during MesoMT, and that gene silencing of myocardin (MyoCD) diminished MesoMT. RNA sequencing data showed that FXa activated a set of genes not upregulated …

Ellie - Exteroceptive Light Locomotion In Eukaryote-Fungi, Brandon Etwarroo

Doctoral Dissertations and Master's Theses

Over the past decade, fungal research and its technological applications have expanded across multiple disciplines, including the emerging field of biohybrid systems. This thesis develops and evaluates a wireless, untethered mobile robot controlled by the action potential-like activity generated by Pleurotus ostreatus sporocarps under red, green, and blue optical stimulation. Light is applied to the sporocarps, the resulting electrical responses are recorded, and these signals are transmitted wirelessly to actuate the mobile robot. Both the action potential-like activity patterns and the robot’s movement trajectories were analyzed. The results demonstrate that wireless robotic control mediated by fungal electrophysiology is feasible. Overall, …

Cultivation Of Arthrospira Platensis (Spirulina) In Food-Based Industrial Wastewater For High-Yield Phycocyanin Extraction, Pavithira Sathinathan

Student Works (2020-2029)

Arthrospira platensis (Spirulina) is a filamentous cyanobacterium valued for its nutritional profile, particularly the pigment–protein phycocyanin, with potent antioxidant and anti-inflammatory properties. Despite its industrial significance, large-scale commercialization remains constrained by high cultivation costs and inefficient extraction methods. This study investigated the use of food-based industrial wastewater as an alternative nutrient medium for Spirulina cultivation, aiming to reduce production costs, enhance phycocyanin yield, and support sustainable wastewater remediation. Three types of food-based wastewater with different nutrient composition (WW1, WW2, WW3) was diluted with Kosaric medium (1:1) and used for Spirulina cultivation. The highest biomass concentration was achieved in WW2 (1.93 …

Metagenomic Profiling Of Gut Microbiome Signatures Across Liver Disease Stages And Hcv-Related Hepatocellular Carcinoma In Egyptian Patients, Marwa A. Zahra

Theses and Dissertations

Dysbiosis in the gut microbiome, particularly concerning the synchronous crosstalk between the gut and the liver, has been associated with various diseases. This study profiles the gut microbiome in liver diseases among Egyptian patients, with a focus on the hepatitis C virus (HCV) and hepatocellular carcinoma (HCC), both of which are highly prevalent in Egypt. Utilizing shotgun metagenomic sequencing, we analyzed microbial gene catalogs and taxonomic profiles from 46 Egyptian patients categorized into five groups: healthy individuals, liver disease patients of different etiologies, post-HCV, treated HCV, and HCV-HCC patients. Healthy and treated HCV patients exhibited distinct microbial profiles characterized by …

Metabolic Syndrome Beyond Diagnostic Criteria: Population-Scale Integrative Metabolomics Characterization, Marwa Talal

Theses and Dissertations

Background: Metabolic syndrome (MetS) is a complex cluster of interrelated metabolic abnormalities associated with elevated cardiometabolic risk. While diagnosis is based on well-established five clinical criteria, these may overlook early or atypical metabolic alterations. Large-scale metabolomic profiling offers an opportunity to identify biochemical signatures of MetS beyond diagnostic bias and to evaluate their relative importance across different presentations of the syndrome.

Methods: Data from 117,147 UK Biobank participants were analyzed in a cross-sectional design. High-throughput NMR quantified 75 circulating metabolites, for. Univariate analyses, MetS subtype stratification, and elastic net models with SHAP interpretation were applied to assess feature …

A Framework For Characterizing The Peripheral Immune Isonome Using Long-Read Single-Cell Rna Sequencing And Its Relevance To Neurological Disease, Patricia Hayes Doyle

Theses and Dissertations--Neuroscience

Long-read single-cell RNA sequencing provides an opportunity to understand human health and disease at isoform resolution, revealing cellular diversity and disease mechanisms difficult to resolve with bulk or short-read methodologies.

Using a modified PIPseq workflow and computational pipeline adapted for Oxford Nanopore (ONT) sequencing, we profiled isoform usage across immune cells, integrating marker expression and isoform discovery, generating the largest long-read single-cell dataset of human immune cells from a single individual to date. We identified non-canonical protein-coding variants of GZMB and CD3G enriched in unexpected cell types. We also discovered novel transcripts from CMC1 and LYAR with cell-type-specific signatures that …

Design And Advancement Of Analytical Frameworks For In Vivo Single-Photon Calcium Imaging To Characterize Temporal- And Treatment-Dependent Neural Adaptations To Opioid Exposure And Withdrawal In The Medial Prefrontal Cortex, Alexia R. Alsum Dr.

Theses and Dissertations--Pharmacy

Despite the availability of several approved medications for opioid use disorder (OUD), it remains a significant public health concern characterized by persistent neurobiological adaptations that drive relapse and impede successful recovery. The medial prefrontal cortex (mPFC), a region critical for executive control and decision-making, undergoes pronounced functional changes during chronic opioid exposure and withdrawal, yet the cellular mechanisms underlying these adaptations remain poorly understood. This dissertation aims to investigate longitudinal alterations in mPFC neural activity across opioid exposure and withdrawal using in vivo single-photon calcium imaging and newly developed computational frameworks.

Following standard preprocessing to extract and normalize calcium traces, …

Lead Biosorption By Oceanobacillus Profundus Kbz 3-2: Strategies For Bioremediation Systems In Kabwe, Danielle S. Desmarteau

Scripps Senior Theses

Lead contamination remains a significant global public health concern, particularly in Kabwe, Zambia, the site of a former lead mining operation. Bioremediation, which utilizes biological materials and processes to remove environmental contaminants, represents a promising approach for addressing lead pollution. However, the development of effective bioremediation systems requires a detailed understanding of the mechanisms underlying metal removal and the feasibility of implementation in low-resource settings. Oceanobacillus profundus KBZ 3-2, a bacterium isolated from Kabwe mine waste, has demonstrated the ability to remove lead from aqueous environments. This study proposes to investigate the mechanism of lead biosorption by this organism, …

Overview And Methods Of Molecular Paleontology: A Review, Shelby Touchstone

Williams Honors College, Honors Research Projects

Molecular paleontology—the study of ancient biomolecules preserved in fossils and sediments, including ancient DNA, lipids, and proteins—has motivated researchers since the 1950s, inspiring both scientific inquiry and broader cultural imagination. Think Jurassic Park. This honors thesis presents a comprehensive review of the history, current state, and methods of the field of molecular paleontology. Drawing on peer-reviewed literature and scholarly resources accessed through databases such as EBSCO and Bierce library, this review examines key techniques such as Next Generation Sequencing and amino acid racemization and will go over limitations and controversies in the field. It will also explore potential new …

Combining Crispr And Nanoasv To Uncover The Rare Bacterial Communities Of The Human Oral Microbiome, Gilma Ruth Sevilla Alvarez

Master's Projects

Studying the oral microbiome is vital because its health implications are not contained to the mouth. Cariogenic bacteria cause tooth demineralization and oral microbes that translocate to extra-oral organ systems are linked to conditions like Alzheimer’s disease, heart disease, diabetes, and cancer. Some of these pathogens belong to the most abundant phyla in the oral cavity: Bacillota, Pseudomonadota, Bacteroidota, Actinomycetota, Spirochaetota, and Fusobacteriota, which together comprise 94% of the oral microbiome. This project uses CRISPR-Cas9 to deplete sequences from highly abundant phyla and the Eubacteria domain, enriching the remaining 6% of rarer taxa. Paired with NanoASV for single-nucleotide resolution, this …

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 …

Dna Barcoding Complements Citizen Science Identifications In An Arthropod Survey At Governors Island, New York, Malky Gestetner

Dissertations and Theses

Arthropods are declining worldwide, threatened by habitat loss, climate change, and growing urbanization. Efforts to monitor arthropod biodiversity are crucial for conservation policies and for maintaining the ecosystem services provided by these animals in urban environments. Surveys of arthropods have been attempted in many New York neighborhoods, but no formal assessment has been conducted on Governors Island, which harbors 72-acres of parkland within a short boat ride away from Manhattan. This is a deficiency which this study helps to address. Following student-led collection efforts within four Governors Island sites, DNA barcoding was employed to complement specimen identification based on morphology …

Hyperglycemia Detection From Sigle - Lead Ecg Using A Hybrid Cnn & Transformer Model, Adam Ayomikun Ogunjembola

Graduate Theses, Dissertations, and Problem Reports (ETD)

Abstract
Hyperglycemia Detection from Single-Lead ECG using a Hybrid CNN & Transformer Model
Adam Ogunjembola

Diabetes Mellitus is known as high blood glucose. This high blood glucose level happens when the body has a problem with producing or using insulin. Insulin is a very important hormone that the pancreas makes to control how much glucose gets into the bloodstream and cells. Diabetes Mellitus has an effect on the body if it is not treated, such as damaging the blood vessels and nerves which can lead to stroke, kidney failure, heart attack and permanent loss of vision. Since people with diabetes …

Physicochemical Characterization Of Small Extracellular Vesicles: Effects Of Immobilization, Isolation, And Disease State, Bianca M. Mercado Velez

Dissertations, Master's Theses and Master's Reports

Cancer treatments and survival outcomes have improved significantly in the last couple of decades, with survival rates increasing in the U.S. Despite improvements in treatment outcomes, early detection and treatment are crucial for improving cancer prognosis and survival rates. The standard cancer diagnostic procedure of tissue biopsy is highly invasive, leading to the further spread of cancer in some cases. Alternatively, the extraction of biofluids from cancer patients, also called a liquid biopsy, is increasingly popular because it is less invasive and more representative of the tumor microenvironment, which contains cancer cells, tumor genetic material, and extracellular vesicles, including small …

Identifying Controls On The Biodegradation Of Dissolved Organic Matter To Inform Microbial Fuel Cell Applications, Lily N. O'Hagan

Dissertations, Master's Theses and Master's Reports

Microbial fuel cells (MFCs) harness dissolved organic matter (DOM) biodegradation to generate power. To evaluate effects of DOM source, nutrients (nitrate and phosphate), and oxygen on DOM biodegradation, we conducted 4-day DOM biodegradation experiments with water and sediments from the Chesapeake Bay. Compared to soil-derived DOM, algal-derived DOM composition changed more and nearly doubled carbon dioxide (CO₂) production, peak CO₂ rates, and carbon removal, indicating MFC site selection should target regions with algal-rich DOM. Aerobic conditions increased CO₂ production by ca. 16%, doubled peak CO₂ rates, and reached peak rates 1 hour faster than anaerobic …

Bio-Orthogonal Chemistry-Based Strategy To Turn-On And Turn-Off Crispr-Cas9 Gene Editing In Solution And In Live Cells, Bhoomika Pandit

Electronic Theses & Dissertations (2024 - present)

The CRISPR–Cas9 system is a widely popular tool for genome engineering. There is a strong interest in developing tools for temporal control of CRISPR-Cas9 activity to address some of the challenges and to broaden the scope of potential applications. In this thesis I describe two biorthogonal based approaches to either Turn-ON and Turn-OFF CRISPR-Cas9 gene editing.

In first project work I describe a bio-orthogonal chemistry-based approach to Turn-ON Cas9 nuclease activity with temporal precision. We report a TCO-acylimidazole reagent that acylates 2′-OH groups of RNA. Poly-acylation (“cloaking”) of RNA was optimized in vitro using a model 18-nt oligonucleotide, as well …

Development Of Self-Assembled Polymeric Polyplexes For Microrna Delivery: Toward Treatment Of Alcohol-Associated Liver Disease, Marjina Akter Kalpana

Theses & Dissertations

Self-assembled polymeric polyplexes have the potential to serve as an RNA interference (RNAi) delivery platform for the combined inhibition of CXCR4 and miR-155 in the treatment of alcohol-associated liver disease (AALD). A central challenge in RNA delivery is balancing the extracellular stability of polyplexes, cellular uptake, and intracellular release of RNA cargo. We developed polymeric polyplexes using the CXCR4-antagonist polymer PAMD, designed to target CXCR4 on activated hepatic stellate cells (HSCs) and deliver therapeutic miRNA to activated Kupffer cells (KCs) in fibrotic liver. We improved the polyplexes by cholesterol modification of PAMD and by PEGylation of PAMD-Ch. The cholesterol modification …

Environmental Risk Assessment Of Textile Waste From Bio-Engineered Fibers In The Fashion Industry, Aayush Pankaj Agarwal, Harshit Soral, Irmak Aktan, Karol Montserrat Gonzalez Saad, Maria Daniela Saa Espinosa, Sheetal Suhas Dhanuka, Yi Yang

Harrisburg University Dissertations and Theses

The global fashion industry generates over 92 million tons of textile waste annually, a figure projected to increase significantly by 2030. Bio-engineered fibers, including bacterial cellulose, mycelium-based leather, and recombinant protein textiles emerge as sustainable alternatives to conventional fibers. Despite their promise, recent evidence suggests that these fibers may pose environmental risks at the end-of-life stage, such as incomplete biodegradation in landfills, microfiber shedding, and chemical leaching from dyes and coatings. The purpose of this study is to examine how these risks are represented through scientific literature, corporate sustainability reports, and policy frameworks, and to identify strategies for integrating risk …

Generating Predictive Gene Expression Signatures For Alzheimer's Disease Using Postmortem Brain Tissue, Ashley Duche

Pharmaceutical Sciences (PhD) Dissertations

Background: Alzheimer’s Disease (AD) is a progressive neurodegenerative disorder characterized by the accumulation of amyloid-beta (Aβ) plaques and tau protein aggregates. These pathological features develop in specific brain regions, but why some areas are more vulnerable to early AD-related changes remains unclear. To address this, predictive gene expression signatures were developed to explore the molecular mechanisms underlying regional susceptibility to AD pathology.

Methods: This was performed using postmortem brain (PMB) tissue from participants in the Religious Orders Study and Memory and Aging Project (ROSMAP), Mayo Clinic, and Mount Sinai Brain Bank (MSBB) to generate gene expression signatures from six brain …

Synthesis Of Antibody Functionalized Polyaniline/Polystyrene/N-Gqds Composite Fibermats For Sweat Based Cortisol Biosensing Applications, Ashwin James

Honors Theses

Noninvasive, wearable biosensors capable of detecting stress biomarkers in sweat require electrodes that are flexible, conductive, insoluble in water, and highly sensitive at low concentrations of analyte. In this work, bovine serum albumin blocked and anti-cmab immobilized nitrogen doped graphene quantum dots integrated polyaniline/polystyrene composite fibermat electrodes (BSA/Anti-Cmab/N-GQDs/PANI/PS electrodes) were synthesized and evaluated as a potential platform for an electrochemical cortisol biosensor in sweat based systems. Polyaniline was utilized in order to provide electrical conductivity, while polystyrene served as a carrying polymer for mechanical support and its hydrophobicity. Composite fibermats were manufactured through Forcespinning™, followed by a secondary polyaniline graft …

Comparative Assessment Of Lower Limb Neuromusculoskeletal Activation And Joint Kinematics In Normal And Impaired Gait, Jack Ryan Schule

Theses and Dissertations

This thesis evaluates whether accessible and affordable technologies can provide clinically significant, quantifiable gait analysis comparable to traditional marker-based motion capture systems. Modern high-end systems offer excellent accuracy but remain financially and logistically inaccessible to many clinicians and researchers. To address this gap, a framework was developed using markerless pose estimation using the model, MediaPipe, inertial measurement units (IMUs) processed through an Extended Kalman Filter (EKF), and surface electromyography (sEMG) to measure joint kinematics and neuromuscular activity during gait. An experiment was performed where data was collected from participants with both normal gait and pathologies including: Osgood–Schlatter disease, Plica Band …

Assessing The Role Of Social Media As A Complementary Source In Pharmacovigilance: Insights From Faers, X (Formerly Twitter), And Askapatient Data Across Multiple Drug Classes, Nwanneka Okere

Dissertations

Background: Adverse drug reactions (ADRs) pose significant public health challenges yet remain substantially underreported in traditional pharmacovigilance systems. Social media platforms and patient-reported outcome forums have emerged as potential complementary sources for capturing real-time patient experiences with medications, but their integration with established surveillance systems remains underexplored.

Purpose: This study examined ADR reporting patterns across FDA Adverse Event Reporting System (FAERS), X (formerly Twitter), and Askapatient to evaluate whether patient-generated digital data can complement traditional pharmacovigilance systems for enhanced drug safety monitoring.

Methods: An explanatory sequential mixed-methods design analyzed 107,753 reports representing 289,740 individual ADR occurrences for …

Screening For Potential Plant Growth‐Promoting Rhizobacteria (Pgpr)-Assisted Phytoremediation To Mitigate Lead Toxicity In Uae Soils, Zeinab Mohamed Abdalla

Theses

This study investigates the potential of lead (Pb)-tolerant actinobacteria that possess 1-aminocyclopropane-1-carboxylate deaminase (ACCD) activity and plant growth-promoting (PGP) traits to serve as a biological tool for enhancing the growth of corn (Zea mays L.) under Pb stress. The primary objective of this research was to isolate and characterize novel, Pb-tolerant, rhizosphere-competent actinobacteria and to evaluate their efficacy in mitigating Pb toxicity, reducing its uptake, and promoting biomass accumulation in corn grown in contaminated soil. A total of 43 actinobacterial isolates were obtained from Pb-contaminated rhizosphere soil and screened for Pb tolerance, rhizosphere competence, ACCD activity, and PGP traits. …

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 …