Biochemical and Biomolecular Engineering Commons^™

De Novo Protein Binding To Zinc Oxide Through Biomineralization Pathways, Jean-Mark A. Francis

Theses and Dissertations

De novo proteins are structurally distinct from proteins found in nature and thus capable of having their amino acid sequence modified to accomplish tasks such as increasing protein-nanoparticle binding without unfolding or decomposing. Zinc Oxide nanoparticles are functionally distinct from their bulk counterparts and are widely used as semiconductors in a variety of fields such as medicine and agriculture. With demand for these nanoparticles increasing, environmentally sustainable methods of Zinc Oxide nanoparticle synthesis are being investigated as an eco-friendly alternative to currently utilized but environmentally hazardous chemical and physical techniques. This research investigates the binding characteristics between Zinc Oxide nanoparticles …

Coumarin/Nitrogen-Bearing Heterocyclic Hybridloaded Electrospun Pmma/Pvp Nanofibrous Scaffolds For Accelerating Topical Wound Healing Rates: Synthesis And In Vitro Bio-Evaluation, Samar A. Salim, Mohamed Ali, Tasneem Abed, El Badawy Kamoun

Nanotechnology Research Centre

Coumarin-nitrogen heterocyclic compounds (e.g. quinoline, acridine, and phthalazine) were synthesized by facile reactions and elucidated by FTIR, 1H, and 13C-NMR analyses, which showed consistency with the expected structures. Coumarin-quinoline (drug A)- and coumarin-acridine (drug B)-loaded electrospun PMMA/PVP nanofibrous scaffolds were fabricated using electrospinning techniques. Results showed a successful PMMA/PVP blend, which formed the matrix that was used as the main scaffold for drug loading/release. The drugs (A and B) were encapsulated within the matrix as verified by IR and SEM results. Bio-evaluation through cytotoxicity and anticancer screening was conducted using the MTT assay against lung fibroblast (Wi-38), colon carcinoma (Caco-2), …

Impact Of Cysteine And Tyrosine Dipeptides On Cho Cell Performance In A Perfusion Mimic, Corrin L. Pruitt

All Theses

Perfusion cell cultures typically achieve higher cell densities and generate higher volumetric productivities than fed-batch cultures due to continuous nutrient supply and spent media removal. Despite these advantages, perfusion cell cultures remain underutilized for licensed product manufacturing, primarily due to the lack of small-scale perfusion models for high-throughput process development and the complexities involved in media formulation capable of supporting high cell densities during long-term continuous operation. To avoid nutrient limitation at high cell densities, current perfusion processes rely on using higher perfusion rates, which results in significant media wastage and downstream product dilution. Therefore, there has been an effort …

Development Of Translational Microscale Systems To Interrogate How Biophysical And Biochemical Cues Alter The Phenotype Of Hormone Positive Breast Cancer, Braulio Ortega Quesada

All Dissertations

Cancer is a complicated disease and one in every three diagnoses are women with breast cancer. Recent research shows that the progression of cancer depends strongly on interactions with other non-cancerous cells and non-cellular components. Metastasis, the spread of cancer to other parts of the body, is a key step in cancer progression and makes treatment harder, leading to poor response to treatments culminating in death in ~90% of patients. This dissertation focused on creating a series of microdevices as novel pre-clinical models of breast cancer. Two different devices were fabricated to (1) study how exposing cancer cells to the …

Metabolite Analysis To Understand Factors Limiting Microbial Fermentation At High Substrate Concentrations, Bishal D. Sharma

Dartmouth College Ph.D Dissertations

Clostridium thermocellum, a thermophilic anaerobic bacterium, holds promise as a biocatalyst for conversion of lignocellulosic biomass into biofuels. This microbe has been subjected to various metabolic engineering strategies, including the deletion of genes encoding secondary fermentation products such as H₂, formate, acetate, and lactate, as well as the expression of heterologous genes to redirect carbon flux toward ethanol production. Despite these efforts, achieving economically viable ethanol titers remains a challenge. We hypothesized that studying how intracellular metabolite concentrations change as fermentation stops could reveal metabolic bottlenecks or regulatory mechanisms limiting ethanol production at high titers. However, metabolomics studies at …

Thermophysical Properties Of Aqueous Amine Salts For Closed Air Cabin Revitalization, Mahmud R. Yusuf, Isabela Flores, Ben Hines, Li Hua Zhang, Seth Christa, Brooks D. Rabideau, Kevin West, Breanna Dobyns, James Davis

Shelby Hall Graduate Research Forum Posters

Carbon dioxide (CO2) capture plays a crucial role in closed cabin air revitalization, however current CO2 capture technologies pose several issues. Traditional amine solutions, such as monoethanolamine, are commonly used in CO2 capture on the International Space Station but face drawbacks including high volatility, thermal degradation, and unpleasant odor. To overcome these challenges, amine salt solutions have emerged as promising alternatives. Amine salt solutions have reduced environmental impact, lower corrosion potential, and improved CO2 loading capacity, making them a more efficient and sustainable replacement. Knowing these physical properties are critical for modeling and optimizing a scrubbing process that employs these …

Influence Of Fused Deposition Modeling Process Parameters On The Constitutive Model Of Hyperelastic Thermoplastic Polyurethane, Lucas Gallup, Mohamed Trabia, Brendan O'Toole, Youssef Fahmy

Mechanical Engineering Faculty Research

Thermoplastic polyurethanes (TPUs) are suited for fused deposition modeling (FDM) of parts that require high levels of flexibility and strength. Predicting the deformation of TPU parts produced using FDM may be difficult, especially under large deformations, as their constitutive models depend on the printing process parameters. The lack of understanding led to the absence of constitutive models for TPU parts produced using FDM. This work aims to identify accurate hyperelastic constitutive models. Six groups of uniaxial tensile specimens were produced using FDM. These groups were made with variations in two process parameters, which were infill geometry and extrusion nozzle temperature. …

Targeted Drug Delivery: Investigating Protein Corona Behavior, Atharva Markale

Theses

Due to high specificity and less toxicity, nanoparticles have become promising for targeted drug delivery against cancer, although they face challenges when they enter the bloodstream, making their behavior unpredictable. The deposition of proteins on nanoparticles, the protein corona, changes their biosignature, affecting their circulation, drug release potency, targeting ability, and immunogenicity. The continuous exchange of protein layers on a nanoscale is complex to analyze.

Nanoparticle tracking analysis (NTA) is a method to characterize nanoparticles in blood plasma by combining principles of light scattering microscopy and Brownian motion. In this work, time-dependent experiments with plasma were conducted to analyze the …

Investigating The Role Of Fluid Shear Stress During Metastasis On Enhanced Breast Cancer Extravasation, Alejandra M. Ham

LSU Master's Theses

In 2022, ~288,000 American women were diagnosed with metastatic breast cancer which was the leading cause of patient mortality with ~43,000 American women succumbing to the disease. Women can be diagnosed with four different molecular subtypes of breast cancer: luminal A, luminal B, human epithelial growth receptor type 2 enriched (HER2+), and triple-negative breast cancer (TNBC). TNBC accounts for ~12% of all breast cancers, yet it has the worst outcomes. TNBC is highly invasive, with ~46% of TNBC patients developing metastatic disease. A further understanding of metastatic TNBC is needed to provide a greater understanding of how to treat this …

Aphid-Ant Relationships: The Role Of Cuticular Hydrocarbons And Different Chemical Stimuli In Triggeringmutualistic Behavior, Amged El-Harairy, Ahmed El-Harairy, Alaa Mahfouz

Department of Chemical and Biomolecular Engineering: Faculty Publications

In ant-aphid interactions, various aphid species offer honeydew to the ant partner and increase their density by ant attendance, whilst others never attend ant species, in which case ants tend to treat them as prey. In this regard, ants should have the ability to distinguish myrmecophile aphid species from non-mutualistic species, so that mutualistic aphids will be accepted as partners rather than prey. Although ant-aphid interactions are now the focus of chemical ecology studies, the role of the different chemical stimuli in determining mutualistic interactions has not been completely clarified. Therefore, we have investigated the cuticular hydrocarbon profile of four …

Influence Of Alkali Metal Cations On The Oxygen Reduction Activity Of Pt5Y And Pt5Gd Alloys, Kun-Ting Song, Alexandra Zagalskaya, Christian M. Schott, Peter M. Schneider, Batyr Garlyyev, Vitaly Alexandrov, Aliaksandr S. Bandarenka

Department of Chemical and Biomolecular Engineering: Faculty Publications

Electrolyte species can significantly influence the electrocatalytic performance. In this work, we investigate the impact of alkali metal cations on the oxygen reduction reaction (ORR) on active Pt₅Gd and Pt₅Y polycrystalline electrodes. Due to the strain effects, Pt alloys exhibit a higher kinetic current density of ORR than pure Pt electrodes in acidic media. In alkaline solutions, the kinetic current density of ORR for Pt alloys decreases linearly with the decreasing hydration energy in the order of Li⁺ > Na⁺ > K⁺ > Rb⁺ > Cs⁺, whereas Pt shows the opposite trend. To gain …

A Review Of Proton Exchange Membrane Degradation Pathways, Mechanisms, And Mitigation Strategies In A Fuel Cell, Dharmjeet Madhav, Junru Wang, Rajesh Keloth, Jorben Mus, Frank Buysschaert, Veerle Vandeginste

Department of Chemical and Biomolecular Engineering: Faculty Publications

Proton exchange membrane fuel cells (PEMFCs) have the potential to tackle major challenges associated with fossil fuel-sourced energy consumption. Nafion, a perfluorosulfonic acid (PFSA) membrane that has high proton conductivity and good chemical stability, is a standard proton exchange membrane (PEM) used in PEMFCs. However, PEM degradation is one of the significant issues in the long-term operation of PEMFCs. Membrane degradation can lead to a decrease in the performance and the lifespan of PEMFCs. The membrane can degrade through chemical, mechanical, and thermal pathways. This paper reviews the different causes of all three routes of PFSA degradation, underlying mechanisms, their …

Strain-Dependent Activity-Stability Relations In Ruo2 And Iro2 Oxygen Evolution Catalysts, Payal Chaudhary, Alexandra Zagalskaya, Herbert Over, Vitaly Alexandrov

Department of Chemical and Biomolecular Engineering: Faculty Publications

Strain engineering is an effective strategy in modulating activity of electrocatalysts, but the effect of strain on electrochemical stability of catalysts remains poorly understood. In this work, we combine ab initio thermodynamics and molecular dynamics simulations to examine the role of compressive and tensile strain in the interplay between activity and stability of metal oxides considering RuO₂ and IrO₂ as exemplary catalysts. We reveal that although compressive strain leads to improved activity via the adsorbate-evolving mechanism of the oxygen evolution reaction, even small strains should substantially destabilize these catalysts promoting dissolution of transition metals. In contrast, our results …

Engineering Mussel Foot Protein 5 (Mfp5) For Enhanced Adhesive Performance In Tendon And Bone Repair, Ziyue Zhu

McKelvey School of Engineering Graduate Student Theses & Dissertations

This study explores the development of Mussel Foot Protein 5 (MFP5) bioadhesives to improve tendon-to-tendon and tendon-to-bone adhesive outcomes. MFP5, known for its underwater adhesive properties, was synthesized using recombinant techniques and optimized through coacervation and cross-linking. Adhesion tests demonstrated the superior performance of the optimized MFP5 adhesive on the tendon and bone samples. Improved protein concentration testing and purification methods enhanced MFP5 yield and consistency. Future research will focus on further standardization, exploring alternative purification methods, and evaluating the adhesive's performance in animal models. This study lays a foundation for developing robust MFP5-based bioadhesives, potentially revolutionizing surgical repair techniques …

Aggregation-Induced Emission Probe For Alzheimer's Detection And Treatment Screening, Gemini Ramlo

Williams Honors College, Honors Research Projects

The proposed project is to research if ROF-2, an aggregation-induced emitter, can be used to screen medications for Alzheimer's Disease and to accurately detect this disease, along with its progression. This will be done through multiple incubation periods using different identifiers that have already been solidified within Alzheimer's research to prove its ability and accuracy within screening and detection regarding this disease.

Development Of Glutathione-Responsive Disulfide-Containing Poly(Beta-Amino Esters) With Varied Hydrophilicity And Acrylate Functionality, Anastasiia Aronova

Theses and Dissertations--Chemical and Materials Engineering

Smart biomaterials are becoming promising for therapeutic deliveries due to their ability to respond to changes in the environment. Redox-responsive hydrogels are a promising type of smart polymer that can swell and degrade according to cellular oxidative stress levels. Glutathione, abundant in cells, is crucial in redox-responsive biomaterials, serving as a key reactive molecule. This study explored the degradation kinetics of glutathione-responsive poly(β-amino ester) (PBAE) polymers created through a single-step Michael addition. We examined how disulfide content influences the degradation kinetics of these PBAE networks. Additionally, we investigated how the hydrophilicity and functionality of acrylate affect the degradation of disulfide-containing …

Machine Learning And Metabolic Model Guided Crispri Reveals A Central Role For Phosphoglycerate Mutase In Chlamydia Trachomatis Persistence, Niaz Bahar Chowdhury, Nick Pokorzynski, Elizabeth A. Rucks, Scot P. Ouellette, Rey A. Carabeo, Rajib Saha

Department of Chemical and Biomolecular Engineering: Faculty Publications

Upon nutrient starvation, Chlamydia trachomatis serovar L2 (CTL) shifts from its normal growth to a non-replicating form, termed persistence. It is unclear if persistence is an adaptive response or lack of it. To understand that transcriptomics data were collected for nutrientsufficient and nutrient-starved CTL. Applying machine learning approaches on transcriptomics data revealed a global transcriptomic rewiring of CTL under stress conditions without having any global stress regulator. This indicated that CTL’s stress response is due to lack of an adaptive response mechanism. To investigate the impact of this on CTL metabolism, we reconstructed a genome-scale metabolic model of CTL (iCTL278) …

Air-Jet Bioprinting Of Stem Cell-Encapsulated Alginate Micro-Droplets For Organoid Biomanufacturing, Mirabella B. Stump

Electronic Theses and Dissertations

Biomanufactured 3D-organoids show promise for modeling and treating various conditions, particularly insulin-dependent diabetes mellitus (type-1 diabetes). Pancreatic islet organoids serve as sustainable sources of insulin-producing β-cells, potentially restoring insulin regulation in patients and providing a long-term solution for diabetes. Hydrogel droplet printing is an emerging technique in regenerative medicine due to its advantageous tunability and biocompatibility; however, challenges of consistency, quality control, and scalability persist. To address these issues, we developed a novel air-jetting based droplet bioprinting system for the generation of monodispersed alginate micro-droplets. The objective of this project was to incorporate human induced pluripotent stem cells (hiPSCs) into …

Vapor-Phase Synthesis Of Electrocatalytic Covalent Organic Frameworks, Syed Ibrahim Gnani Peer Mohamed, Shahriar Namvar, Tan Zhang, Hessam Shahbazi, Zhen Jiang, Andrew M. Rappe, Amin Salehi-Khojin, Siamak Nejati

Department of Chemical and Biomolecular Engineering: Faculty Publications

The inability to process many covalent organic frameworks (COFs) as thin films plagues their widespread utilization. Herein, a vapor-phase pathway for the bottom-up synthesis of a class of porphyrin-based COFs is presented. This approach allows integrating electrocatalysts made of metal-ion-containing COFs into the electrodes’ architectures in a single-step synthesis and deposition. By precisely controlling the metal sites at the atomic level, remarkable electrocatalytic performance is achieved, resulting in unprecedentedly high mass activity values. How the choice of metal atoms, i.e., cobalt and copper, can determine the catalytic activities of POR-COFs is demonstrated. The theoretical data proves that the Cu site …

Determining The Effects Of Glycocalyx Modifications On The Electrophysical Properties Of Human Mesenchymal Stem Cells, Rominna E. Valentine Ico

Electronic Theses, Projects, and Dissertations

Human mesenchymal stem cells (hMSCs) have gained popularity in clinical trials due to their multipotent differentiation characteristics, ability to secrete bioactive molecules, migrate into diseased or damaged tissues, and their immunosuppressive properties. HMSC cultures are heterogeneous, containing stem cells, partially differentiated progenitor cells, and fully differentiated cells. One of the major challenges with hMSCs therapeutic potential is the inability to select specific cell subpopulations due to an insufficient number of biomarkers. Often the biomarkers used, like those for fluorescence-activated cell sorting, are not sufficient to define hMSCs because they overlap with other cell types. Consequently, there is a need to …

Surface Antibody Changes Protein Corona Both In Human And Mouse Serum But Not Final Opsonization And Elimination Of Targeted Polymeric Nanoparticles, Sara Capolla, Federico Colombo, Luca De Maso, Prisca Mauro, Paolo Bertoncin, Thilo Kähne, Alexander Engler, Luis Núñez, Gustavo Larsen, Et Al.

Department of Chemical and Biomolecular Engineering: Faculty Publications

Background: Nanoparticles represent one of the most important innovations in the medical field. Among nanocarriers, polymeric nanoparticles (PNPs) attracted much attention due to their biodegradability, biocompatibility, and capacity to increase efficacy and safety of encapsulated drugs. Another important improvement in the use of nanoparticles as delivery systems is the conjugation of a targeting agent that enables the nanoparticles to accumulate in a specific tissue. Despite these advantages, the clinical translation of therapeutic approaches based on nanoparticles is prevented by their interactions with blood proteins. In fact, the so-formed protein corona (PC) drastically alters the biological identity of the particles. Adsorbed …

Computational Modeling Using A Novel Continuum Approach Coupled With Pathway-Informed Neural Networks To Optimize Dynein-Mediated Centrosome Positioning In Polarized Cells, Arkaprovo Ghosal, Padmanabhan Seshaiyar Dr., Adriana Dawes Dr., General Genomics Inc.

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

A Multi-Organ Maize Metabolic Model Connects Temperature Stress With Energy Production And Reducing Power Generation, Niaz Bahar Chowdhury, Margaret Simons- Senftle, Berengere Decouard, Isabelle Quillere, Martine Rigault, Karuna Anna Sajeevan, Bibek Acharya, Ratul Chowdhury, Bertrand Hirel, Alia Dellagi, Costas Maranas, Rajib Saha

Department of Chemical and Biomolecular Engineering: Faculty Publications

Climate change has adversely affected maize productivity. Thereby, a holistic understanding of metabolic crosstalk among its organs is important to address this issue. Thus, we reconstructed the first multi-organ maize metabolicmodel, iZMA6517, and contextualized itwith heat and cold stress transcriptomics data using expression distributed reaction flux measurement (EXTREAM) algorithm. Furthermore, implementing metabolic bottleneck analysis on contextualized models revealed differences between these stresses. While both stresses had reducing power bottlenecks, heat stress had additional energy generation bottlenecks.We also performed thermodynamic driving force analysis, revealing thermodynamics-reducing power-energy generation axis dictating the nature of temperature stress responses. Thus, a temperaturetolerant maize ideotype can …

Conduction Mechanism Switching From Coulomb Blockade To Classical Critical Percolation Behavior In Disordered Nanoparticle Array, Abhijeet Prasad, Jay Min Lim, Ravi Saraf

Department of Chemical and Biomolecular Engineering: Faculty Publications

Large, open-gate transistors made from metal nanoparticle arrays offer possibilities to build new electronic devices, such as sensors. A nanoparticle necklace network (N³) of Au particles from 300 K to cryogenic temperatures exhibit a nonohmic I–V_d behavior, I ≈ (V_d–V_T)^𝜻, where V_T is a conduction gap and 𝜻 is a constant critical exponent. The conduction gap in N³, made from disordered networks of 1D chains of 10 nm diameter Au particles exhibits room temperature (RT) gating. Although the I–V_d behavior at RT is identical to Coulomb blockade, …

Physiologically Relevant Fluid Shear Stress Induced Receptor Conversion In Hormone Receptor-Positive (Hr+) Breast Cancer, Jonathan James Cuccia

LSU Doctoral Dissertations

Breast cancer is the most common type of cancer among all people in the United States as of 2023 and often has devastating impacts on afflicted patients. Although some treatments show great efficacy against primary breast tumors, none have been able to significantly reduce the mortality rate of breast cancer once it has metastasized to distant sites. In primary, hormone receptor-positive (HR+) breast cancers, endocrine therapies are often used as first-line treatments and are generally well-tolerated. However, as the disease progresses, these previously sensitive cancers can become resistant to endocrine therapies and continue proliferating despite them. Therefore, there is a …

Protocol To Develop A Synthetic Biology Toolkit For The Non-Model Bacterium R. Palustris, Mark Kathol, Cheryl Immethun, Rajib Saha

Department of Chemical and Biomolecular Engineering: Faculty Publications

Numerous biology tools are developed to work for model organisms, which, however, do not work effectively in non-model organisms. Here, we present a protocol for developing a synthetic biology toolkit for Rhodopseudomonas palustris CGA009, a non-model bacterium with unique metabolic properties. We describe steps for introducing and characterizing biological devices in nonmodel bacteria, such as the utilization of fluorescence markers and RT-qPCR. This protocol may also be applicable for other non-model organisms. For complete details on the use and execution of this protocol, please refer to Immethun et al..¹

The Biological Activity Of Dual-Responsive Glycopolymers For Intracellular Codelivery Of Antigen And Lipophilic Adjuvant, Micaela Shields

Honors Theses

Subunit vaccines present themselves as an attractive alternative to traditional approaches to vaccines, which utilizes whole organisms to trigger an immune response. While these traditional approaches have proven themselves reliable within the history of vaccinations, they generally deliver subpar robust cellular-mediated immunity and pose many safety risks. Composed of proteins and /or peptides, subunit vaccines are safer and more precise alternatives to traditional approaches. However, the pharmacokinetic properties of the macromolecules that make up these vaccines hinder the subunit vaccine’s level of immunogenicity [d1] Examples of this hindrance include but are not limited to aggregation at the injection site and …

Antimicrobial Activity And Mechanism Of Amyloid Proteins And Synthetic Conjugated Polyelectrolytes, Fahimeh Maghsoodi

Nanoscience and Microsystems ETDs

Although the exact cause of Alzheimer’s disease (AD) is still unknown, it is widely considered that the accumulation of amyloid plaques composed of the amyloid-β (Aβ) peptide in the brain is linked to neurodegeneration. Co-localization of viral DNA with Aβ plaques, the association of brain infection and AD, and research indicating the protective effect of Aβ against bacteria and fungi in mice and human cells have led to the hypothesis that Aβ expression and deposition may be central to its function as an antimicrobial peptide (AMP). In my thesis research, we seek to elucidate how Aβ functions as an AMP …

A Comparison Of Optical Measurement Methods For The Growth Of S. Cerevisiae, Jackson Black

Chemical Engineering Undergraduate Honors Theses

Genetic engineering of living organisms provides the opportunity to express and harvest different proteins from cell surfaces. Yeast (S. cerevisiae) is one such organism and is capable of being grown on an industrial scale. Cellular concentration is an important parameter to monitor while fermentation processes are underway, in order to control the environment inside the growth medium and maximize yields. Spectrophotometry is a conventional method for measuring concentration, but is limited by a narrow absorbance range, and the need for on-site periodic sampling. A continuous method of measurement, as provided by Bug Labs BE2100 non-invasive biomass monitor, would …

Comparing Firocoxib And Meloxicam In The Application Of Microneedle Patch For Transdermal Drug Delivery, Ruohan Li

Chemical Engineering Undergraduate Honors Theses

This thesis compares the performance of meloxicam and firocoxib in the aspects of its physical characteristic, chemical compositions, and in-vitro performances for transdermal pain management microneedle patches on farm animals. The microneedle patches are composed of polyvinyl alcohol (PVA), type I collagen (COL), and chitosan (CHI) as base material that carries NSAIDs to achieve therapeutic purposes. Scanning electron microscopy (SEM) was utilized to observe the morphological and physical characteristics of the microneedle patches. Both meloxicam and firocoxib microneedle patches were successfully prepared using the methodology, with organized microneedle distribution and sizing. And Fourier transform infrared spectroscopy (FTIR) confirmed the chemical …