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 …

Phytochemical Analysis And Safety Assessment Of Watercress Nasturtium Officinale: Antioxidant Capacity, Heavy Metal Profiling, And Toxicity Using Brine Shrimp Model, Qurrota A’Yunin, Chamini Kasun Hemachandra, Muhaimin Rifa’I, Yoga Dwi Jatmiko, Maftuch Maftuch, Rizky Fadilla Agustin Rangkuti, Cucun Herlina, Zulfa Mahdiatur Rasyida, Moh Dliyauddin

Karbala International Journal of Modern Science

Medicinal plants have attracted growing attention as sources of natural bioactive compounds for sustainable aquaculture and health. This study evaluated the phytochemical composition, antioxidant activity, heavy metal profile, and acute toxicity of watercress (Nasturtium officinale W.T. Aiton) methanol extract using maceration, qualitative and quantitative (TPC, TFC, antioxidant DPPH) phytochemical assay, XRF, and BSLA. Phytochemical screening of plant extracts showed the existence of flavonoids, alkaloids, phenols, tannins, triterpenoids, and saponins, but not steroidal. The TPC and TFC were 20.6 mg GAE/g and 10.8 mg QE/g, respectively. The extract displayed significant antioxidant activity (IC₅₀ = 64.78 µg/mL in DPPH assay). …

The Risk Of Bpa In B Lymphocyte-Mediated Autoimmunity, Mario J. Palacios

Senior Honors Theses

Autoimmune disorders disproportionately affect females, a bias largely attributed to estrogen's modulation of B lymphocyte development and tolerance. Bisphenol A (BPA), a common plastic monomer, shows estrogenic activity and acts as an endocrine disruptor and epigenetic modifier. This thesis examines how BPA may increase autoimmune risk by mimicking estrogen such that it can excite estrogen receptors which rescue autoreactive B lymphocytes from apoptosis. While direct research linking BPA to B lymphocyte-mediated autoimmunity is limited, understanding BPA’s course of action in B lymphocytes is critical for addressing the rising prevalence of autoimmune diseases and its possible link to the increased and …

Developing Antibodies Against Galectin-3 And Galectin-9 To Target Endometriosis, Ashleigh Burger, Noah Farnsworth, Jared J. Reisnouer, Cheyenne Vue

2026 Symposium

Endometriosis is a disease characterized by pelvic pain and the formation of endometrial-like tissue on the outside of the uterine lining. This condition affects nearly 10% of women across the globe and confirming whether someone has endometriosis requires visualization in surgery. While the specific causes of this disease remain unclear, the over-expression of the Galectins 3 and 9 in ectopic endometrial tissues suggests a role in the development and maintenance of the condition. Monoclonal antibodies (mAbs) are highly specific proteins with potential as diagnostic or treatment tools. The goal of this study is to generate antibodies against Gal3 and Gal9. …

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, …

Biofunctional Characterization Of A Polyherbal Formulation, Muhammad Ameer Qarib Naqvi, Iqra Saleem, Fatma Hussain

Journal of Bioresource Management

Polyherbal formulations (PHFs) have greater medicinal importance due to their enhanced bioactivities. To check whether a combination of several plants enhances bioactivities, the current study was designed. Methanol, aqueous and n-hexane solvents were used to prepare PHF of Syzgium cumini, Origanum vulgare, Aloe vera barbadensis Miller and Gymnema sylvestre. DPPH (2, 2-diphenyl-1-picrylhydrazyl scavenging) assay was used to analyze antioxidant activity. The total phenolic content (TPC) and total flavonoid content (TFC) estimations were done by Folin-Ciocalteu reagent and AlCl₃ colourimetric techniques, respectively. Bactericidal activity was measured by agar well diffusion method, anti-diabetic profile was assessed by …

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 …

Direct Synthesis Of Cerium Oxide Nanoparticles In Reducing Sugars: Enhanced Ce3+ Surface Density For Biological Application, Balaashwin Babu, Elayaraja Kolanthai, Craig J. Neal, Samarah V. Harb, Udit Kumar, Yifei Fu, Sudipta Seal

Rowan-Virtua Research Day

Cerium oxide nanoparticles (CNPs) are recognized for their ability to scavenge reactive oxygen species (ROS), making them promising candidates for mitigating oxidative damage in biomedical applications. However, many conventional synthesis methods limit the formation of Ce³⁺ states, which are critical for this antioxidant function. Building upon previous findings that glucose can promote Ce³⁺ formation, this study investigates the broader impact of both reducing (glucose, fructose, galactose) and non-reducing (dextran, sucrose, cyclodextrin) natural sugars on CNP synthesis. CNPs were synthesized in the presence of these sugars, and the surface densities of Ce³⁺ were measured. Results showed that reducing sugars significantly increased …

Immuno-Bioinformatics Study Of Secondary Metabolites From Watercress Nasturtium Officinale As Immunostimulant In Whiteleg Shrimp Litopenaeus Vannamei By Targeting Peroxinectin And Scavenger Receptor Class B, Qurrota A’Yunin, Muhaimin Rifa’I, Maftuch Maftuch, Yoga Dwi Jatmiko, Muhammad Hermawan Widyananda, Triyanto Triyanto, Muhammad Tegar Handrianto

Karbala International Journal of Modern Science

The viral disease affects the whiteleg shrimp (Litopenaeus vannamei) and causes losses. Immunostimulants are recognized as a more environmentally friendly approach to disease management and antimicrobial properties of aquatic organisms. Watercress (Nasturtium officinale) is an aquatic plant species that contains antioxidant properties that can protect the organism from disease and boost the immune system. Shrimp rely heavily on innate immunity to combat infectious agents due to their absence of adaptive immunity. Peroxinectin and scavenger receptor class B (SRB) play essential roles in the shrimp defense system. This research employs a bioinformatic to assess the immunostimulatory potential …

An Economic And Production Analysis Of Seaweed Farms In California And The Pacific Northwest, Brian Donovan

Cal Poly Humboldt theses and projects

Since the early 2010s, the seaweed aquaculture industry has steadily expanded in the United States, with states like Alaska, Maine, Hawaii, and Connecticut leading the way in the development of this emerging sector. However, information gaps remain concerning certain aspects of the domestic seaweed aquaculture industry. The purpose of this study was to examine the status of the seaweed aquaculture industry along the West Coast of the United States; specifically in the states of California, Oregon, and Washington. Seaweed farmers in these states were invited to voluntarily complete surveys asking important production, economic, and commercial questions regarding their operations. Data …

Evaluation Of The Dnazyme Gr5 For The Determination Of Lead Speciation In Natural Waters, Gaganprit Gill

Theses and Dissertations (Comprehensive)

This thesis explores the development and application of a DNAzyme-based biosensor designed to detect labile metal species in environmental samples. Real time and on-site monitoring of labile metal fractions would make a valuable contribution to environmental management, as these fractions are the most bioavailable and pose significant toxicity risks to aquatic organisms. Conventional methods for detecting labile metals, while effective, are often burdened by high costs, complexity, and lengthy processing times, making them less ideal for rapid and widespread environmental assessments.

The first manuscript of this thesis (chapter 2) establishes the fundamental capabilities of the Pb²⁺-specific DNAzyme GR5 …

Activities Of Cellulolytic, Amylolytic, And Secondary Metabolites From Thermophilic Actinomycetes Collected From The Heated Soil Around Cisolok Geyser, Dhian Chitra Ayu Fitria Sari, Fitria Ningsih, Mazytha Kinanti Rachmania, Akira Yokota, Wellyzar Sjamsuridzal

Makara Journal of Science

This study investigated the antimicrobial activity, cellulolytic, and amylolytic abilities of eight thermophilic Actinomy-cetes isolated from the heated soil around the Cisolok geyser, West Java, Indonesia. Cellulolytic and amylolytic abili-ties were screened for on media by adding 1% (w/v) soluble starch and carboxymethylcellulose (CMC), respectively. Antimicrobial activity was screened for using the agar-plug diffusion method by cultivating strains on various growth media. Growth at various temperatures showed that six strains could grow up to 50 °C. Seven out of eight strains showed amylolytic ability at 40 °C and 45 °C, and only four strains did so at 50 °C. Screening …

Examining The Effects Of Artemisia Annua On Neuro2a Cells, Wesley Lim

Honors Undergraduate Theses

Artemisia annua L. is a well-known medicinal herb used in Traditional Chinese Medicine for many centuries and contains artemisinin, which exhibits antimalarial properties [1] and is a potential treatment for SARS-CoV-2 [2]. However, the neurological effect of A. annua and its compounds are poorly understood. We hypothesize that A. annua extracts and artemisinin will provide protection against oxidative stress in mouse neuronal Neuro2A cells. Superoxide dismutase 1 (SOD1) is an anti-oxidant enzyme that protects against oxidative damage [3]. Growth Arrest and DNA Damage-inducible 45 alpha (Gadd45a) is involved in DNA repair and is a common biomarker for DNA damage[4]. SOD1 …

Reducing Food Scarcity: The Benefits Of Urban Farming, S.A. Claudell, Emilio Mejia

Journal of Nonprofit Innovation

Urban farming can enhance the lives of communities and help reduce food scarcity. This paper presents a conceptual prototype of an efficient urban farming community that can be scaled for a single apartment building or an entire community across all global geoeconomics regions, including densely populated cities and rural, developing towns and communities. When deployed in coordination with smart crop choices, local farm support, and efficient transportation then the result isn’t just sustainability, but also increasing fresh produce accessibility, optimizing nutritional value, eliminating the use of ‘forever chemicals’, reducing transportation costs, and fostering global environmental benefits.

Imagine Doris, who is …

Chemical Composition, Mineral Profile, Anti-Bacterial, And Wound Healing Properties Of Snail Slime Of Helix Aspersa Müller, Marouane Aouji, Amine Rkhaila, Bouchra Bouhaddioui, Malak Zirari, Hala Harifi, Youness Taboz, Lalla Aicha Lrhorfi, Rachid Bengueddour

BioMedicine

Mucus is a substance made by snails that serves a variety of purposes and is increasingly employed in the medical and cosmetic industries. It includes bioactive compounds with a range of biological characteristics that could be useful in the treatment of particular issues. This study assessed the wound-healing efficiency, antibacterial activity, chemical and mineral composition of Helix aspersa Müller slime. Inductively Coupled Argon Plasma Atomic Emission Spectrometry (ICP-OES) was used for mineral analysis, while Gas chromatography coupled to mass spectrometry (GC-MS) analysis was used for chemical characterization. The findings showed that the H. aspersa Müller slime had inhibitory activity on …

Piperine Encourages Apoptosis In Human Cervical Adenocarcinoma Cells Through Ros Generation, Dna Fragmentation, Caspase-3 Activation And Cell Cycle Arrest, Asif Jafri, Juhi Rais, Sudhir Kumar, Md Arshad

Research Symposium

Background: Cancer is one of the most common destructive diseases and the second leading cause of death in humans. Among cancer, cervical cancer is the second most common malignancy among women globally. Thus, there is a continuous need to search for chemotherapeutic chemicals or naturally occurring drugs to resolve this global health problem. Piperine (1-piperoylpeperdine) is present in the fruits of black pepper (Piper nigrum Linn.) and long pepper (Piper longum Linn.). It possesses several pharmacological properties and in the present study we have evaluated its anti-cancer potential on human cervical adenocarcinoma (HeLa) cells.

Methods: The anti-proliferative effect …

Rapid & Sensitive Detection Of Antibiotic Resistance Genes By Utilizing New Diagnostic Probe Tales With 2d-Nanosheet Graphene Oxide, Jihye Kang

Masters Theses & Specialist Projects

As antibiotic resistance is one of the major health concerns in infectious diseases because of reducing the efficacy of antibiotics, rapid and sensitive detection of antibiotic resistance genes is critical for the effective treatment of infectious diseases. Polymerase chain reaction (PCR) is widely used to detect nucleic acids, but it requires additional steps involved in DNA denaturation and subsequent hybridization. A new class of DNA-binding domains called transcriptional activator-like effectors (TALEs) provide a novel scaffold for designing versatile DNA-binding proteins due to their modularity and predictability. Here, we developed a simple, rapid, and sensitive system for detecting antibiotic resistance genes …

Leveraging Bio-Inspired Molecules For Cancer Theranostics, Douglas S. Macpherson

Dissertations, Theses, and Capstone Projects

A variety of molecules can be radiolabeled and delivered to a cancer site for the purposes of diagnostics and therapy. Among the most promising of tumor targeting molecules are peptides and antibodies. These bio-inspired molecules can be designed and synthesized to target and respond to cancer cells based on the properties of those cells. Matrix metalloproteinase (MMP) enzymes are over-expressed by some metastatic cancers, in which they are responsible for the degradation and remodeling of the extracellular matrix. In recent years, MMPs have emerged as promising targets for enzyme-responsive diagnostic probes because oligopeptides can be designed to be selectively hydrolyzed …

Development Of A Chemical Biology Approach To Uncover The Influence Of Sequence Variations On Ces1 Activity In Live Cells, Samuel James Knebel

Masters Theses

Drug metabolism is the biochemical process of modifying drugs to detoxify and remove them through enzymatic transformations. These biotransformation’s occur primarily in the liver and are critical to understanding how pharmaceutical compounds are chemically altered inside the human body. Human carboxylesterases (CESs) catalyze the hydrolysis of esters, amides, thioesters, and carbamates. CES-mediated hydrolysis plays an important role in the metabolism of many drugs including the first FDA approved antiviral treatment for COVID-19, remdesivir (Veklury), the seizure control medication rufinamide (Banzel), and the flu antiviral drug oseltamivir (Tamiflu). CES activity is known to be influenced by a variety of factors including …

Nanoparticle Conjugated Photosensitizer For Targeted Photodynamic Inactivation Of Cancer Cells, Symone D. Crowder

Honors College Theses

Photodynamic therapy (PDT) is considered to be a potential replacement for traditional methods of chemotherapy. It includes the administration of photosensitizing agents (PS), which generate reactive oxygen species (ROS) upon excitation at a specific wavelength. With new outlooks and techniques, cancer research is advancing each day. It has allowed the progress of several theranostic drug delivery systems (DDS) exploring the area of nanomedicine.2 In the present work, a Rhodamine derivative, Rhodamine 6G (R6G) was used as the PS. In general, rhodamine compounds undergo cytotoxic reactions on photoexcitation by electron transfer reactions with folic acid within cells, making them a favorable …

In Silico Screening Of Violacein As An Epidermal Growth Factor Receptor Inhibitor, Smitha S Bhat, Sindhu R, Shashanka K Prasad

International Journal of Health and Allied Sciences

EGFR is a key player in the signalling cascades of various kinds of cancers and tyrosine kinase inhibitors block EGFR signalling. Natural products have long been used as candidates for therapy in the management of cancer. Violacein, a bacterial pigment, has been known for its numerous biological applications such as antimicrobial, antileishmanial, antiviral, as well as antitumoral. Computational studies have concluded that it may have activity against cancers like pancreatic cancer, thyroid cancer, colorectal cancer, and endometrial cancer indicating its potential application as a broad range of anti-cancerous drug. This study aimed to perform the molecular docking of violacein with …

Identifying A Glucocorticoid-Activated Gpcr That Rapidly And Non-Genomically Increases Camp Levels In Mammalian Cells, Francisco Nunez

Pharmaceutical Sciences (PhD) Dissertations

Glucocorticoids (GCs) are steroid hormones that regulate diverse physiological processes. Synthetic versions of GCs are commonly used to treat inflammatory diseases such as asthma by modulating gene expression to suppressing several inflammatory activities. However, it is estimated that 5-10% of asthmatics are unresponsive to GCs, which may be explained by receptor desensitization and/or the presence of a neutrophilic endotype. One understudied phenomenon of GCs is their ability to induce rapid, non-genomic actions. For example, GCs can acutely modulate calcium concentrations levels, induce smooth muscle relaxation and modulate nitric oxide synthase activity, within minutes and sometimes seconds, which is too rapid …

Biowill - Characterising Willow Bark Bio-Actives For Skin Therapies, Arnold Marisa

ORBioM (Open Research BioSciences Meeting)

Willow bark is considered as a disposable by-product when processing willow for biomass. Willow (Salix) is known to contain high value bioactive compounds which include salicin and its derivatives, and other phytochemicals of interest such as polyphenols and flavonoids. The plant is historically known as the primary source of salicylates to which the well-known drug aspirin is derived from. The work forms part of the Interreg project BioWILL, which is focused on integrated “Zero Waste” biorefinery utilising all fractions of willow feedstock for the production of biochemicals and renewable energy. This project aims to investigate the crude and …

Diversity Of Bacteriophage In Burkholderia Species, Abigail Price

Honors Projects

Bacteriophages are viruses that infect and replicate within bacteria and offer the potential of a therapeutic alternative to chronic infections that do not respond to antibiotic-based therapies. B. vietnamiensis is one of a number of Burkholderia species involved with chronic drug resistant infections in the lungs of individuals with compromised respiratory systems, as found in those with chronic obstructive pulmonary disease and, most especially, are of particular significance in patients with cystic fibrosis. The diversity of the Burkholderia species is explored by using online databases and looking at bacteriophage or phage-encoding viruses found in B. vietnamiensis. The open reading frames …

Effect Of Rehmannia Glutinosa Libosch Extract On Proliferation And Cardiogenic Pre-Differentiation Of Human Mesenchymal Stem Cells, Huu Dat Nguyen, Len Ho Thi, Xuan Bach Ho, Van Anh Cao, Duy Minh Le Hoang

BioMedicine

Background: Vietnamese medicine tried and tested certain bioactive compounds from plants to increase the rate of tissue immunomodulation, regeneration, and differentiation. Although there are many research papers discovered about phytochemicals of Rehmannia glutinosa Libosch and differentiation induction potential of some substances purified from this herbal, it finds difficult to seek research that investigated the effect of Rehmannia glutinosa Libosch extract on proliferation and cardiogenic differentiation of mesenchymal stem cells, even though it has commonly been used for a long time because of its function as a restorative and as a critical role in cardiovascular treatment in traditional.

Results: Our …

Selective Gsk3Β Inhibition Mediates An Nrf2-Independent Anti-Inflammatory Microglial Response, Mohamed H. Yousef

Theses and Dissertations

Glycogen Synthase Kinase 3 (GSK3) is associated with the proinflammatory phenotype of microglia and has been shown to act in concert with Nuclear factor kappa B (NF-κB). . GSK3 is also a suppressor of Nuclear factor erythroid 2-related factor 2 (Nrf2), the principal regulator of redox homeostasis. Agreeing with the oxidative paradigm of aging, Nrf2 is often deregulated in parainflammatory and neurodegenerative diseases. In this study, we aimed to explore a multimodal disease-modifying utility of GSK3 inhibition, beyond neuronal proteopathologies, Furthermore, we aimed to underscore the difference in therapeutic value between the two GSK3 paralogs by isoform-selective chemical inhibition.

The …

Building Tools For Improved Modulation Of The Human Gabaa Receptor, A Central Nervous System Target For The Treatment Of Anxiety, Garrett Edward Zinck

Theses and Dissertations--Pharmacy

In the U.S., anxiety is recognized as an increasing range of mentally and physically debilitating psychiatric health disorders with significant economic repercussions. Over the last 20 years, several novel anti-anxiety therapies have entered the drug development pipeline, but none have made it to market.

The work in this dissertation focused on structurally modifying valerenic acid (VA), a structurally unique carboxylated sesquiterpene acid found in Valeriana officinalis. VA is putatively reported to have allosteric modulatory activity of the human GABA_A receptor, a ligand-gated ion channel responsible for attenuating neurotransmissions. Structural modeling of VA’s GABA_A receptor interaction suggests that …

Comparison Of Free Versus Encapsulated Drugs On 3t3 Differentiation, Simon H. Friedrich, Gabriel Volpe

UROP Posters

The scope of this project was to design, synthesize and test targeted nanoparticles containing hydrophobic and hydrophilic drugs that promote browning in adipose tissue. For hydrophilic drugs the use of liposomes and their hydrophilic core is more useful than the PLGA nanoparticles which have hydrophobic cores. The inhibition of the FOXO1 pathway and modulation of autophagy in adipose tissue can promote browning of white adipose tissue, or an energy burning state where excess energy is burned as heat instead of stored in the cell. If successful, these drugs would offer an alternative treatment for obesity where changes to the patient's …

Real-Time Monitoring Of Cell Death Progress Using Capacitance Spectroscopy, Suyang Wu

Electronic Theses and Dissertations

Biologics, including the monoclonal antibody (mAb), has experienced rapid development in the last decade. However, the price of biologics is often prohibitively high because of the low process efficiency. Delaying the inevitable cell death improves the productivity of upstream bioprocessing, whose success relies on monitoring the cell death onset that indicates the timing for preventive actions.

This study proposes to develop a real-time monitoring model that quantifies the dying cell percentage in lab-scale bioreactors using capacitance spectroscopy. The capacitance spectroscopy contains cell death-related information due to various physical properties changes during the cell death process, e.g., cytoplasmic conductivity change. The …