Biochemical and Biomolecular Engineering Commons^™

Cationic Poly(Glucosamine)-Based Polymers Bind To Glycans With Varying Affinity Facilitating Transport Across The Glycocalyx Of Endothelial Cells, Claire Bridges, Lu Fu, Dan Wang, James D. Sterling, Susanna Liang, Shenda M. Baker, Jonathan Yeow, Megan S. Lord

Business and Information Technology Faculty Research & Creative Works

Natural polysaccharides, such as chitosan, offer promising avenues for drug delivery due to their cytocompatibility and ability to interact with cell surfaces. However, the endothelial glycocalyx, a glycan-rich extracellular matrix, presents a barrier that must be navigated for effective intracellular delivery. This study investigates how cationic poly(glucosamine)-based polymers, functionalized with guanidinium or ammonium groups, interact with key glycocalyx components including hyaluronan (HA) and heparan sulfate (HS). We demonstrate that these cationic polymers form tunable biomolecular condensates with glycans, with stronger binding observed for sulfated glycans, HS and heparin, than unsulfated HA. Derivatized chitosan polymers with varied cationic side chains exhibit …

Molecular Survival Strategies Against Kidney Filtration: Implications For Therapeutic Protein Engineering, William Heaps, Anna Elise Packard, Kristina M. Mccammon, Tyler P. Green, Joseph P. Talley, Bradley C. Bundy, Dennis Della Corte

Faculty Publications

The glomerular filtration barrier poses a significant challenge for circulating proteins, with molecules below ~60–70 kDa facing rapid renal clearance. Endogenous proteins have evolved sophisticated evasion mechanisms including oligomerization, carrier binding, electrostatic repulsion, and FcRn-mediated recycling. Understanding these natural strategies provides blueprints for engineering therapeutic proteins with improved pharmacokinetics. This review examines how endogenous proteins resist filtration, evaluates their application in protein engineering, and discusses clinical translation including established technologies (PEGylation, Fc-fusion) and emerging strategies (albumin-binding domains, glycoengineering). We address critical challenges of balancing half-life extension with tissue penetration, biological activity, and immunogenicity—essential considerations for the rational design of next-generation …

C. Difficile Detection Method For First Responder Glove Application, Alli N. Senedak

Williams Honors College, Honors Research Projects

Clostridioides Difficile (C. diff) is a Anaerobic Gram-positive bacillus that is capable of spore formation, making it difficult to control its spread and duration in clinical environments. This phenomenon can provide danger to first responders, healthcare workers, and patients. The goal of this project is to create a biosensor capable of detecting C. diff in a clinical setting that can be applied to a glove apparatus. The project will involve the use of C. diff aptamers activated on the surface of an electrode. Once surface activation has been verified via surface analysis, the electrodes will be exposed to C. diff …

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 …

The Interplay Between Endothelial Glycocalyx Maturity And Both The Toxicity And Intracellular Uptake Of Charged Nanoparticles, Claire A. Bridges, Lu Fu, Jonathan Yeow, Xiaojing Huang, Miriam Jackson, Rhiannon P. Kuchel, James D. Sterling, Shenda M. Baker, Megan S. Lord

Business and Information Technology Faculty Research & Creative Works

Nanoparticles are widely studied for delivering treatments to target tissues, but few have reached clinical use. Most nanoparticles encounter blood vessels on their way to target tissues. The inner surface of these vessels is lined with endothelial cells covered by a glycocalyx, an extracellular matrix rich in anionic glycans. The role of the glycocalyx in nanoparticle interactions is not well understood. Here, we demonstrate that endothelial cells need extended culture times to synthesize a mature glycocalyx. Our research shows that branched polyethyleneimine functionalized gold nanoparticles bind to endothelial cells expressing either a developing or mature glycocalyx, with the interaction involving …

The Interplay Between Endothelial Glycocalyx Maturity And Both The Toxicity And Intracellular Uptake Of Charged Nanoparticles, Claire A. Bridges, Lu D. Fu, Jonathan A. Yeow, Xiaojing D. Huang, Miriam D. Jackson, Rhiannon P. Kuchel, James D. Sterling, Shenda M. Baker, Megan S. Lord

Business and Information Technology Faculty Research & Creative Works

Nanoparticles are widely studied for delivering treatments to target tissues, but few have reached clinical use. Most nanoparticles encounter blood vessels on their way to target tissues. The inner surface of these vessels is lined with endothelial cells covered by a glycocalyx, an extracellular matrix rich in anionic glycans. The role of the glycocalyx in nanoparticle interactions is not well understood. Here, we demonstrate that endothelial cells need extended culture times to synthesize a mature glycocalyx. Our research shows that branched polyethyleneimine functionalized gold nanoparticles bind to endothelial cells expressing either a developing or mature glycocalyx, with the interaction involving …

Modeling Ion-Specific Effects In Polyelectrolyte Brushes: A Modified Poisson-Nernst-Planck Model, William J. Ceely, Marina Chugunova, Ali Nadim, James D. Sterling

Business and Information Technology Faculty Research & Creative Works

Polyelectrolyte brushes consist of a set of charged linear macromolecules, each tethered at one end to a surface. An example is the glycocalyx which refers to hair-like negatively charged sugar molecules that coat the outside membrane of all cells. We consider the transport and equilibrium distribution of ions and the resulting electrical potential when such a brush is immersed in a salt buffer containing monovalent cations (sodium and/or potassium). The Gouy-Chapman model for ion screening at a charged surface captures the effects of the Coulombic force that drives ion electrophoresis and diffusion but neglects non-Coulombic forces and ion pairing. By …

Determination Of The Kinetic Parameters Of Cholesterol Oxidation Using Cholesterol Oxidase From Streptomyces Sp., Meka Saima Perdani, Heri Hermansyah, Muhamad Sahlan, Dwini Normayulisa Putri, Teguh Pambudi, Anggi Khairina Hanum Hasibuan

Makara Journal of Technology

Cholesterol oxidase (CO) was successfully produced from Streptomyces sp. via the submerged fermentation method, and 69 U/mL enzyme activity was obtained. This study aimed to determine cholesterol oxidation kinetics and the production of CO as a catalyst. The enzyme was diluted to 0.15, 0.075, and 0.00375 U/mL for the oxidation reaction. The substrate was also prepared in three concentrations: 3.23, 6.46, and 12.93 mM. The optimization of conditions for enzymatic cholesterol oxidation was investigated through measurement of the effect of initial cholesterol and enzyme concentrations. Cholesterol concentration was rapidly measured via high-performance liquid chromatography (HPLC). The kinetics of CO were …

Magnetic Resonance Imaging Trackable Pathology-Triggered Polymersomes Toward Enzyme Replacement Theranostics For Gm1 Gangliosidosis, Dorian Foster

All Dissertations

This dissertation investigates the development and optimization of pathology-responsive polymersomes for simultaneous enhanced magnetic resonance imaging (MRI) and enzyme replacement therapy (ERT) in the treatment of GM1 gangliosidosis (GM1). While therapeutic strategies exist for similar, non-neuropathic lysosomal storage disorders, implementation towards GM1 faces significant challenges due to the blood-brain barrier.

Herein, we developed and characterized a range of low molecular weight hyaluronic acid-b-polylactic acid (HA-PLA) polymersomes (PSs) capable of encapsulating therapeutic enzymes in their hydrophilic core. These polymersomes exhibit pathophysiology-triggered responsiveness, degrading in the presence of acidic conditions, which is characteristic of lysosomes, and enzymes such as hexosaminidase A, which …

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 …

Integrating Galectin-3 Into A Computational Model Of Cardiac Fibrosis Progression, Adam Pieratt

Chemical Engineering Undergraduate Honors Theses

Cardiac fibrosis, a large contributor to heart failure, is the excessive accumulation of extracellular matrix in response to stress or injury. There are no approved treatments for cardiac fibrosis, and targeting specific species involved creates complex problems for drug development, so a computational model of the cardiac fibroblast signaling network can be used to observe the interactions involved in the progression of cardiac fibrosis. In this paper, a new protein called galectin-3 is integrated into this existing model, and connections are established to expand the coverage of the network. The additions are described, simulated using Netflux biological system simulation software, …

Efficient Discovery And Industrialized Manufacture Of Terpenoids, Haoming Chi, Liying Er, Tiangang Liu

Bulletin of Chinese Academy of Sciences (Chinese Version)

Terpenoids, a class of chemical entities with diverse biological activities in nature, demonstrate significant potential for applications in fields such as drug discovery, flavor industry, and agriculture. However, traditional methods face challenges, including inefficiency and high costs, in the discovery and industrialization of terpenoids. The rapid development of synthetic biology, genomics, artificial intelligence, and automation provides new opportunities for efficient terpenoid discovery and industrialization. This study comprehensively analyzes how these technologies synergistically contribute to the discovery, optimization, and large-scale production of terpenoids, and summarizes the current high-yield situations of terpenoids. The aim is to propose innovative strategies to accelerate technological …

Synthetic Approaches Of Carbohydrate Based Self-Assembling Systems, Guijun Wang, Anji Chen, Pramod Aryal, Jonathan Bietsch

Chemistry & Biochemistry Faculty Publications

Carbohydrate-based self-assembling systems are essential for the formation of advanced biocompatible materials via a bottom-up approach. The self-assembling of sugar-based small molecules has applications encompassing many research fields and has been studied extensively. In this focused review, we will discuss the synthetic approaches for carbohydrate-based self-assembling (SA) systems, the mechanisms of the assembly, as well as the main properties and applications. This review will mainly cover recent publications in the last four years from January 2020 to December 2023. We will essentially focus on small molecule self-assembly, excluding polymer-based systems, which include various derivatives of monosaccharides, disaccharides, and oligosaccharides. Glycolipids, …

Effects Of Energy Drink Additives On Crayfish Metabolism, Katherine Paltz

Williams Honors College, Honors Research Projects

The effects of caffeine and additives commonly found in energy drinks were tested on crayfish to record changes, if any, in their metabolism. Three experimental groups were studied: 1. Caffeine; 2. Caffeine + Glucuronolactone; 3.) Caffeine + Glucuronolactone + Taurine. Caffeine is a common stimulant used to improve mental awareness, headaches, memory, and athletic performance. Glucuronolactone is connected with cardiovascular issues and aggressive behavior. Taurine is said to improve mood and focus. The experiment was performed at two different caffeine levels: 600mg and 1200mg for an initial 1 hour of exposure and 10 hours after exposure used as a pseudo-baseline. …

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.

Triphlapan: Predicting Hla Molecules Binding Peptides Based On Triple Coding Matrix And Transfer Learning, Meng Wang, Chuqi Lei, Jianxin Wang, Yaohang Li, Min Li

Computer Science Faculty Publications

Human leukocyte antigen (HLA) recognizes foreign threats and triggers immune responses by presenting peptides to T cells. Computationally modeling the binding patterns between peptide and HLA is very important for the development of tumor vaccines. However, it is still a big challenge to accurately predict HLA molecules binding peptides. In this paper, we develop a new model TripHLApan for predicting HLA molecules binding peptides by integrating triple coding matrix, BiGRU + Attention models, and transfer learning strategy. We have found the main interaction site regions between HLA molecules and peptides, as well as the correlation between HLA encoding and binding …

Continuous, Platform Purification Of Viral Products Using Aqueous Two-Phase Extraction, Natalie M. Nold

Dissertations, Master's Theses and Master's Reports

Cell and gene therapies, a ground-breaking class of drugs that can heal genetic diseases and cure cancer, often have treatment costs over $1 million. Most cell and gene therapies are delivered using virus-based delivery vectors, which are incredibly expensive to manufacture. Liquid chromatography is the favored method of viral vector purification since it is easily scalable and can be functionalized to purify by biospecificity, charge, hydrophobicity, or size. However, chromatography-based purification processes are highly expensive and usually only recover 20-50% of the viral vectors. There is currently no platform purification strategy for viral vectors due to differences in their surface …

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 …

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 …

Mathematical Modeling Of Microscale Biology: Ion Pairing, Spatially Varying Permittivity, And Born Energy In Glycosaminoglycan Brushes, William J. Ceely, Marina Chugunova, Ali Nadim, James D. Sterling

Business and Information Technology Faculty Research & Creative Works

Biological macromolecules including nucleic acids, proteins, and glycosaminoglycans are typically anionic and can span domains of up to hundreds of nanometers and even micron length scales. The structures exist in crowded environments that are dominated by multivalent electrostatic interactions that can be modeled using mean-field continuum approaches that represent underlying molecular nanoscale biophysics. We develop such models for glycosaminoglycan brushes using steady state modified Poisson-Boltzmann models that incorporate important ion-specific (Hofmeister) effects. The results quantify how electroneutrality is attained through ion electrophoresis, spatially varying permittivity hydration forces, and ion-specific pairing. Brush-salt interfacial profiles of the electrostatic potential as well as …

Salt Doping Of Hyaluronic Acid Glycopolymer Biocondensates, James D. Sterling, Lu Fu, Kenisha Pudun, Shenda Baker, Megan Lord, Henry E. Riggs

Business and Information Technology Faculty Research & Creative Works

Biocondensates are largely studied with regard to intracellular components, while recognition of the formation of extracellular biocondensates are emerging, such as for cell surface heparan sulfate binding with basic fibroblast growth factor. This study analyzed the formation of biocondensates in vitro between the ubiquitous extracellular component, hyaluronan an anionic glycosaminoglycan, and cationic derivitized polyglucosamines known to bind to mucosal interfaces. The effect of molecular weight and net charge ratio was studied using a combination of microscopy, turbidity, laser diffraction particle sizing and zeta potential measurements. These analyses revealed that molecular weight affected the ability to form biocondensates while the surface …

Leveraging Cell-Substrate Adhesion And Cell Migratory Properties In Skeletal Muscle Constructs And Cancer Metastasis Assays, Lauren E. Mehanna

Theses and Dissertations--Chemical and Materials Engineering

Volumetric muscle loss (VML) remains one of the few skeletal muscle injuries without a reliable and repeatable treatment. In large volume muscle injuries, muscle fibers as well as the surrounding connective tissue are damaged, preventing therapeutic muscle stem cells, called myogenic progenitor cells (MPCs), from reaching the injury site and initiating repair. There is a clinical need to rapidly fabricate in vitro muscle tissue constructs that mimic the native tissue organization, with aligned myotubes, for insertion and integration at the patient’s injury site. In this dissertation, we utilize the MPC’s natural propensity to close gaps across an injury site to …

Drug-Facilitated Sexual Assault At The University Of Arkansas, Barrett Weidman

Chemical Engineering Undergraduate Honors Theses

This work was written to fulfill two main purposes. First, to help survivors of Drug-Facilitated Sexual Assault (DFSA) process their experience by compiling the toxicological, pharmacological, and distribution of the three most used date-rape drugs. Second, to gauge the knowledge and interest of University of Arkansas students regarding drug impairments, sexual assault education, and bystander intervention training. A survey was conducted for the latter and revealed that 91.6% of students believe the University’s existing sexual assault prevention education and bystander intervention training have room for improvement. Also, 37.1% of students who have received this education report that the programming does …

Discovery Of Phosphotyrosine-Binding Oligopeptides With Supramolecular Target Selectivity, Ana S. Pina, Leonor Morgado, Krystyna L. Duncan, Sara Carvalho, Henrique F. Carvalho, Armenio J. M. Barbosa, Beatriz De P. Mariz, Ines P. Moreira, Daniela Kalafatovic, Bruno M. Morais Faustino, Vishal Narang, Tong Wang, Charalampos G. Pappas, Isabel Ferreira, A. Cecılia A. Roque, Rein V. Ulijn

Advanced Science Research Center

We demonstrate phage-display screening on self-assembled ligands that enables the identification of oligopeptides that selectively bind dynamic supramolecular targets over their unassembled counterparts. The concept is demonstrated through panning of a phage-display oligopeptide library against supramolecular tyrosine-phosphate ligands using 9-fluorenylmethoxycarbonyl-phenylalanine-tyrosine-phosphate (Fmoc-FpY) micellar aggregates as targets. The 14 selected peptides showed no sequence consensus but were enriched in cationic and proline residues. The lead peptide, KVYFSIPWRVPM-NH2 (P7) was found to bind to the Fmoc-FpY ligand exclusively in its self-assembled state with KD = 74 ± 3 μM. Circular dichroism, NMR and molecular dynamics simulations revealed that the peptide interacts with Fmoc-FpY …

Continuous Liquid-Liquid Extraction Of Lomustine Synthesis, Devna Grover

The Journal of Purdue Undergraduate Research

No abstract provided.

Ion Pairing And Dielectric Decrement In Glycosaminoglycan Brushes, James D. Sterling, Wenjuan Jiang, Wesley M. Botello-Smith, Yun L. Luo

Business and Information Technology Faculty Research & Creative Works

Cell−surface polysaccharides are essential to many aspects of physiology, serving as a highly conserved evolutionary feature of life and as an important part of the innate immune system in mammals. Here, as simplified biophysical models of these sugar coatings, we present results of molecular dynamics simulations of hyaluronic acid and heparin brushes that show important effects of ion pairing, water dielectric decrease, and coion exclusion. As in prior studies of macromolecular crowding under physiologically relevant salt concentrations, our results show equilibria with electroneutrality attained through screening and pairing of brush anionic charges by monovalent cations at the atomistic detail. Most …

Development Of Light Actuated Chemical Delivery Platform On A 2-D Array Of Micropore Structure, Hojjat Rostami Azmand, Hojjat Rostami Azmand

Dissertations and Theses

Localized chemical delivery plays an essential role in the fundamental information transfers within biological systems. Thus, the ability to mimic the natural chemical signal modulation would provide significant contributions to understand the functional signaling pathway of biological cells and develop new prosthetic devices for neurological disorders. In this paper, we demonstrate a light-controlled hydrogel platform that can be used for localized chemical delivery in a high spatial resolution. By utilizing the photothermal behavior of graphene-hydrogel composites confined within micron-sized fluidic channels, patterned light illumination creates the parallel and independent actuation of chemical release in a group of fluidic ports. The …

Atherosclerosis: Pathology, Role Of Sd-Ldl, Particle Size Characterization Of Sd-Ldl With Multiangle Light Scattering, Akshay Sudhakar Ukey

Masters Theses

Atherosclerosis is an inflammatory disease due to the accumulation of lipids in the inner wall of arteries. As per the report of Center of Diseases Control and Prevention (CDC), 1 in every 4 deaths is due to heart diseases each year. Atherosclerosis occurs when artery walls harden by the buildup of cholesterol, forming multiple atherosclerotic plaques within the aorta (4). Out of the modern medicines available to control cholesterol, statin is amongst the foremost widely used because it is both safe and effective in lowering high risk patients (9). However, usage of high statins dosage typically leads to some mild …

Incorporation Of Lignin In Natural And Synthetic Biomaterials To Alter Mechanical And Biochemical Properties For Enhanced Wound Healing, Jorge Alfonso Belgodere

LSU Doctoral Dissertations

It is estimated that chronic, non-healing wounds affect more than 6.5 million Americans annually, with an estimated healthcare cost beyond $14 billion. Here, we attempted to create composites of natural (collagen type I or gelatin-methacrylate) or synthetic (poly(ethylene glycol) polymers incorporating a natural plant component, lignin, to combat the costs and limitations current wound healing methods face. Three-dimensional matrices of collagen type I (Col I) are widely used in tissue engineering applications for its abundance in many tissues, bioactivity with many cell types, and excellent biocompatibility. Inspired by the structural role of lignin in plant tissue, we found that sodium …

Novel Application Of Graphene Oxide Based-Biosensor Utilizing Crispr/Dcas9 For Rapid Detection Of Antibiotic Resistance Genes, Joel Omage

Masters Theses & Specialist Projects

Antibiotic resistance is one of the biggest public health challenges globally. To combat this threat, we have designed a method for the facile and rapid detection of antibiotic resistance gene (ARG) in bacteria. We utilized an emerging tool termed the clusters of regularly interspaced short palindromic repeats (CRISPR) in complex with deactivated CRISPR associated proteins (dCas9) on conjugated 2-dimensional graphene oxide (GO) sheets. Nuclease-deactivated Cas9 in complex with customized single guided RNA (sgRNA) was used for the target DNA recognition. The sgRNA was easy to design and we demonstrated that it is complementary to its target sequence by performing a …