Biochemical and Biomolecular Engineering Commons^™

Bioengineering Extracellular Matrix Scaffolds For Volumetric Muscle Loss, Kevin Roberts

Graduate Theses and Dissertations

Volumetric muscle loss overwhelms skeletal muscle’s ordinarily capable regenerative machinery, resulting in fibrosis and severe functional deficits which have defied clinical repair strategies. My work spans the design and preclinical evaluation of implants intended to drive the cell community of injured muscle toward a regenerative state, as well as the development of an understanding of the molecular responses of this cell community to biomaterial interventions. I demonstrate a new class of biomaterial by leveraging the productive capacity of sacrificial hollow fiber membrane cell culture; I show specifically that unique threads of whole extracellular matrix can be isolated by solvent degradation …

The Synthesis, Purification, And Characterization Of The P3 Peptoid, Myles Joyce

Chemical Engineering Undergraduate Honors Theses

The relatively young field of nano-systems has vast applications over various different fields. Peptoids (peptide analogues) and their uses are consistently investigated components of these nano-studies. A particularly interesting group of peptoids are able to self-assemble into secondary structures under the right conditions. The P3 peptoid is able to form microspheres if properly synthesized and purified. Microspheres are frequently studied due to their low surface area to volume ratios. This unique aspect of microspheres makes them an excellent candidate for drug delivery systems; however, these systems must also be robust so that the desired compound can be encapsulated within the …

Self-Assembled Nanoantenna Enhance Optical Activity And Transport In Scalable Thin Films And Interfaces, Keith Richard Berry Jr.

Graduate Theses and Dissertations

Continued population growth and the decrease of existing energy platforms demands long-term solutions for development and implementation of scalable plasmonic metamaterials for energy and agricultural applications. Self-assembled nanoantenna into random and ordered arrangements are advanced herein for optical and thermal enhancements in scalable thin film. An analytical approach to estimating the thermal dynamics of random arrangements of nanoantenna resulted in estimates within 30% across a range of geometric parameters, nanoantenna-containing media, and thermal parameters. Multimodal thermal dynamics of polymer thin films containing gold nanoparticles (AuNPs) were observed through the natural log of the dimensionless temperature driving force plotted versus time …

Wafer Enhanced Electrodeionization For Conversion Of Co2 Into Bicarbonate Feed For Algae Cultured Photobioreactors, Kayvan Afrasiabi

Chemical Engineering Undergraduate Honors Theses

The world has acknowledged climate change as a global crisis that demands considerable attention, with one of the largest culprit being carbon emissions from industrial processing and power generation. While reduction in carbon emissions is the principal action towards mitigating the effects of climate change, scientists and engineers have given increased attention to alternative sources of energy as well as methods of carbon sequestration to coax traditional manufactory and industry into environmentally friendly and sustainable practices. One technology of this nature is the use of wafer-enhanced electrodeionization (WE-EDI) membranes to convert gaseous carbon dioxide (CO₂) from industrial flue …

Development Of An In Vitro Platform For The Exploration Of Skeletal Muscle Cell Mechanobiology, Sydney Spradlin

Biomedical Engineering Undergraduate Honors Theses

Muscles have the natural ability to regenerate when damaged. This works to keep the body functioning, unless this ability is overwhelmed. Volumetric muscle loss (VML) occurs when a substantial amount of a muscles mass is lost. This leads to the development of scar tissue, and often a loss of function. In order to find a solution for this condition, in vitro models are needed to explore the mechanobiology of skeletal muscle cells. Two platforms were developed in this study, to explore 3 factors: orientation, strain, and supporting structure. One platform used fibronectin stamped lanes on PDMS to encourage cell growth …

Removal Of Carbamazepine From Drinking Water, Paola Marrero-Rivera, Adam Johnson, Jordan Alex Gadberry, Juan Rodriguez, Thomas Krumpolc, Zach Wiese

Chemical Engineering Undergraduate Honors Theses

Due to the increasing prevalence of prescription medication over the past few decades, pharmaceuticals have accumulated in various water sources. This has become a public health concern because many pharmaceuticals have limited research on the effects of chronic low-level exposure.One pharmaceutical of interest that has been detected in water sources is carbamazepine. Carbamazepine (CBZ) is a common pharmaceutical prescribed for the treatment of seizure disorders, neuropathic pain, and various psychological disorders. It’s mechanism of action is “sodium channel blocking,” which is the impairment of conduction of sodium ions in sodium channels. This, in effect, reduces nervous-system conductivity in key areas …

Cross-Linking Amyloid Forming Proteins For Improved Understanding Of Early Aggregation, Gram Booth

Chemical Engineering Undergraduate Honors Theses

Alzheimer’s disease is the only disease in the ten leading causes of death in the United states that cannot be slowed, prevented, or cured. Alzheimer’s dementia and type II diabetes are the top two diseases caused by improper protein folding, aggregation, and deposition of fibrillar plaques in tissues. These plaques, originally thought to be the cause of these diseases, have been discovered to be mostly benign and representative of the later stages of the disease. The smaller, more soluble oligomeric aggregates are responsible for the death of pancreatic and neural cells. Many oligomeric species are unstable and exist only for …

Peptoid-Modified Bicelles As Surrogate Cell Membranes For Membrane Protein Sensors And Analytics, Helya Najafi

Graduate Theses and Dissertations

Membrane-affiliated interactions are significant in understanding cell function, detecting biomarkers to diagnose disease, and in testing the efficiency of new therapeutic targets. Model membrane systems have been developed to study membrane proteins, allowing for stable protein structure and maintaining native activity. Bicelles, disc-shaped lipid bilayers created by combining long- and short-chain phospholipids, are the model membrane system of focus in this study. Bicelles are accessible from both sides and have a wide size range, which make them attractive for studying membrane proteins without affecting function. In this work, bicelles were functionalized with two peptoids to alter the edge and face …

Effects Of Filtration Conditions On Clearance Of Bacteriophage, Rigen Te

Graduate Theses and Dissertations

Virus Clearance is one of the major challenges in biopharmaceutical industry, especially in the manufacturing of drugs. U.S. Food and Drug Administration (FDA) recommends using several model bacteriophages as surrogates of pathogenic mammalian virus for process validation. In this work, two bacteriophages were tested against 30 kDa, 100 kDa, 300 kDa polyethersulfone (PES) membranes to investigate the effects of pore size on virus clearance. Virus particles were spiked into the protein feed solutions containing bovine serum albumin (BSA) or lysozyme at different concentrations. Besides protein concentration, the effects of feed pH on the filtration performance and virus rejection were also …

Peptoid-Based Microsphere Coatings For Use As Tunable Biocompatible Interfaces, German Raul Perez Bakovic

Graduate Theses and Dissertations

The pursuit of sensitive, non-invasive, and cost efficient diagnostic tools for early stage disease detection have led to the development of sophisticated biosensor technologies for proteomic studies. As these markers increase in complexity, the role of support substrates grows increasingly important. Limitations in existing support substrates include the potential for increased sensitivity, binding specificity, and bio-stability. Ideal support substrates need to provide biocompatible and bioresistant surfaces, that offer high surface areas for binding, and enables the incorporation of diverse chemistries. The use of peptoids as the basis for the deposition of uniform microsphere coatings offers a mean to the attainment …

Membrane Chromatography For Bioseparations: Ligand Design And Optimization, Zizhao Liu

Graduate Theses and Dissertations

Membrane chromatography, or membrane adsorber, represents an attractive alternative to conventional packed bed chromatography used in downstream processing. Membrane chromatography has many advantages, including high productivity, low buffer consumption and ease to scale up. This doctoral dissertation focuses on developing novel polymeric ligands for protein separations using membrane chromatography. Atom transfer radical polymerization (ATRP), known as a controlled radical polymerization technique, has been used to control the architecture of grafted polymeric ligands. The center theme of this dissertation is to develop new polymeric ligands and investigate how the polymer’s property (e.g. flexibility, hydrophobicity) and architecture (e.g. chain density, chain length) …

Local Delivery Of Ctla-4 Blockade Inhibits Growth Of Pancreatic Tumors, Jack Baltz

Biomedical Engineering Undergraduate Honors Theses

Immune checkpoint blockade has demonstrated great potential in activating antitumor immunity. Ipilimumab is a monoclonal antibody which targets cytotoxic T-lymphocyte antigen-4. CTLA-4 belongs to the CD28 class of receptors and is found on the surface of CD4⁺ and CD8⁺ T cells. CTLA-4 acts to suppress the immune system when bound to CD80 and CD86 receptors on antigen presenting cells. Ipilimumab, or anti-CTLA-4, has shown to be effective in significantly extending the survival of patients with metastatic melanoma. However, systemic delivery of Ipilimumab also induces significant side effects such as: colitis, dermatitis, uveitis, and hypophysitis. In order to minimize …

Development Of A Simple Handheld Biosensor For Waterborne Pathogens, Bryce C. Jones

Chemical Engineering Undergraduate Honors Theses

Current methods of detecting waterborne pathogens involve testing strips which take 24-48 hours to yield results, or require expensive equipment in order to function. In minimalist environments, these two technologies are not always applicable to test water quality. With the emergence of a new method of PCR, named LAMP PCR, it is possible to quickly and accurately detect pathogen DNA in a water sample. In order to scale this technique into a simple device, the aspects of the reaction must be accommodated, and a visual detection method chosen. A handheld device which keeps the isothermal LAMP PCR stable for the …

Targeted Drug Delivery Using Peptoid Based Nanospheres, Kaylee J. Smith

Chemical Engineering Undergraduate Honors Theses

While medicine has improved greatly in the last couple of decades, there are negative side effects that accompany many drugs. Undesirable side effects could be greatly reduced if non-systemic drug delivery systems were used because the medicine would harm diseased cells at a much higher rate than it does healthy cells. One possible non-systemic drug delivery system is peptoid nanospheres. These nanospheres will then be linked to another peptoid that is engineered to attach almost exclusively to diseased cells.

This research project is focused on designing peptoids that will form nanospheres in solution. Four specific peptoids were synthesized and tested …

Investigating The Modulation Of Aggregating Amyloid Beta 40, Marlee J. Motes

Chemical Engineering Undergraduate Honors Theses

Amyloid beta protein has been linked to the formation of Alzheimer’s disease in patients.¹ Plaques form from amyloid beta fibrils. The formation of these plaques between neural connections in the brain are associated with Alzheimer’s disease.² The reduction of the formation of fibrils can be linked to utilizing protein mimics. The protocols that are used to reproduce the simulation of amyloid beta in the brain can be very important. Also, the structure of the protein mimic that is being used to inhibit the formation of fibrils can determine how the amyloid beta plaques are reduced.

The structure of sequence KLLFFLFFLLK …

Cloning, Fed-Batch Expression And Purification Of A Novel Anti-Candida Peptide And Development Of A Cleavage Resistant Variant Of Green Fluorescence Protein, Rudra Palash Mukherjee

Graduate Theses and Dissertations

This work illustrates that the intelligent design of a bioprocess for the production of peptides of various length is possible by having a prior knowledge of desired product, cell line, fermentation conditions, and choices for downstream recovery. Cloning, expression, and recovery of a novel 12-mer anti-Candida peptide served as an illustrative case for a proposed Escherichia coli platform. The antifungal peptide, expressed as a fusion to GFPUV during high call density fed-batch, was recovered from cell lysate, concentrated using ion exchange chromatography, and finally cleaved with cyanogen bromide. The platform was capable of producing active peptide capable of arresting the …

Effects Of Magnetically Induced Micro-Mixing On Nanofiltration Performance, Guanghui Song

Graduate Theses and Dissertations

Nanofiltration (NF) is a relatively new membrane separation process mainly used for removing low molecular weight species from aqueous and non-aqueous solutions. NF membranes suffer from concentration polarization leading to membrane fouling thus compromised membrane performance. Magnetically responsive nanofiltration (NF) membranes functionalized with superparamagnetic nanoparticles (SPNs) attached to the chain ends of grafted polymer nanolayers have been shown to be effective in breaking concentration polarization at the membrane-liquid interface under an appropriate external oscillating magnetic field. Under an oscillating magnetic field, the movement of the polymer chains acts as micro-mixer leading to the suppression of concentration polarization and improved filtration …

Using Peptoids To Build Robust, Efficient Microarray Systems, Dhaval Sunil Shah

Graduate Theses and Dissertations

Recent studies have shown microarrays to be indispensable for various biological applications, allowing for high-throughput processing and screening of biological samples such as RNA, DNA, proteins and peptides using a small sample volume (< 1 µL). Peptoids (poly-N-substituted glycine oligomers) can be used as a substitute for antibodies as capture molecules, as well as coatings for slides in antibody microarrays. The ease of synthesis of peptoids, high customizability with desired bioactivity, and speed of synthesis allows us to build a diagnostic system with a large dynamic range that can detect biomolecules from a minimal sample size. In this study, peptoid-based antibody mimics are designed to have both structural and functional features similar to those of antibodies, including a stable constant region (scaffolding) and a variable region for protein recognition. Peptoids previously screened via combinatorial library synthesis to be specific to bind Mdm-2 (mouse double minute 2 homolog) and GST (gluthathione S-transferase), have been synthesized. The protein recognition peptoids have been conjugated to PEG (polyethylene glycol) molecules with modified end groups; an amine group on one end that allows for immobilization and orientation on the slide, and an azide group on the other end that will allow for attachment to the peptoid through “click chemistry”. The number of capture molecules printed on the slides can be increased by making the available surface area of the slide larger via coating with microspheres. We have determined that partially water soluble peptoids that are also helical, can self-assemble into microspheres. Sequences have been developed that can consistently produce uniform microsphere coatings on slides that increase the overall surface area. A high surface area corresponds to a higher number of binding sites, and therefore a more sensitive system. The work done has shown that slides may be successfully coated in order to potentially improve the detection system.

Peptoid-Based Klvff Mimics: A Unique Approach To Alzheimer's Disease, James Phillip Turner

Graduate Theses and Dissertations

Alzheimer’s disease (AD) is the leading form of dementia worldwide. AD patients experience a slow, gradual cognitive decline that includes loss of memory and behavioral stability as the disease progresses. Surprisingly, AD is the sixth leading cause of death in the United States and has had a profound impact on the U.S. economy. Though there are medications to help improve the quality of life of diagnosed patients for a period of time, there is still no cure for AD. AD is characterized by the build-up of amyloid plaques that develop from the aggregation of the amyloid beta protein (Aβ) in …

Characterization Of Novel Chitosan/Polyelectrolyte Nanoparticles, Michaela Wynne Mertz

Biomedical Engineering Undergraduate Honors Theses

Chitosan-based nanoparticles are under investigation as delivery vehicles for drugs, genes, and proteins. Due to the biocompatibility, mucoadhesive nature, and biodegradable nature of chitosan and binding qualities, anionic nature, and biocompatible qualities of heparin, chitosan/heparin nanoparticles (CHNPs) are a promising platform for the delivery of labile proteins. However, the literature lacks a definitive process to control the size, efficiency, and yield of CHNPs at higher concentrations of reagents. Additionally there is a need to improve loading efficiency of CHNPs. In this study CHNPs have been synthesized and characterized for size, yield, protein loading efficiency, and release. The CHNPs were prepared …

Evaluating The Viability Of Graphene Oxide For The Removal Of Ni(Ii) Ions From Waste Water, Cale M. White

Biomedical Engineering Undergraduate Honors Theses

When levels of heavy metal ions such as nickel (Ni), copper (Cu), lead (Pb), Zinc (Zn), and Cobalt (Co) exceed the tolerance values for industrial wastewater, it can devastate the environment as well as the health of the individuals consuming the water. Heavy metal ions are not biodegradable and will accumulate in organic matter.(1) This accumulation leads to toxic levels in the blood and hence damage to nerve tissue, kidneys, the liver, and other vital organs. (2) Effective removal processes of these heavy metals from water must be developed. This study explores a method to adsorb nickel from water with …

Fractionation Of Chitosan Using A Novel Precipitation Method, Davis J. Ward

Biomedical Engineering Undergraduate Honors Theses

Chitosan is a derivative of chitin, a biopolymer found in the exoskeletons of crustaceans. Chitosan is under heavy investigation in the field of drug delivery due to its wide versatility. One such delivery mechanism is the use of hydrogels in cancer immunotherapy delivery. The viscosity of chitosan in its use as a hydrogel depends on the length of chitosan’s N-acetyl D-glucosamine chains, which in turn determines the molecular weight of chitosan. Because there is such a wide range of viscosity in a typical sample of chitosan, there is a need for a simple technique to fractionate the chitosan based on …

The Investigation Of Chitosan-Based Hydrogels For Intratumoral Delivery Of Immunotherapeutic Cytokines, Ethan Drew Lowry

Biomedical Engineering Undergraduate Honors Theses

Controlled and localized delivery of Interleukin 12 (IL-12) is critical to effective and non-toxic cancer immunotherapy. Current delivery protocols for pre-clinical anti-tumor trials utilize solutions of chitosan, a mucoadhesive and bioeliminable biopolymer, to slow the release of IL- 12 into the tumor microenvironment. In order to further increase IL-12 retention, we have developed and characterized two chitosan-based in situ gelling hydrogels for IL-12 immunotherapy. One hydrogel, composed of heparin and chitosan, is herein described from initial conception through multiple stages of characterization including isolation of a range of suitable hydrogel formulations and observational physical and chemical properties. A second hydrogel …

Fluorescent Imaging On A Microfluidics Chip For Quantification Of Leukocyte Count, Aneeka Majid

Biomedical Engineering Undergraduate Honors Theses

We have demonstrated a method for conducting a leukocyte count in whole blood using a microfluidics chip and epi-fluorescence setup. Leukocyte counts provide physicians with a wealth of information about a patient’s medical condition and as such are routinely completed for many hospital visits. Miniaturization of this diagnostic tool may enable physicians to provide healthcare in resource-limited settings, where patients would otherwise not receive this test. The microfluidics chip was fabricated in polydimethylsiloxane (PDMS) using soft-film lithography. Following further processing and cleaning, the PDMS mold is exposed to UV-ozone for surface activation, and then sealed with a glass coverslip to …

Monitoring The Effects Of Mmp Inhibitors On Extracellular Matrix Degradation For Use In Implant Protection, Jake D. Jones

Biomedical Engineering Undergraduate Honors Theses

In order to lengthen the functional time of implantable ECM, the mechanism of degradation must be inhibited. The matrix metalloproteases are the primary method by which ECM is broken down, and the TIMP family of proteins exists as proof that inhibition of these proteases is possible naturally. In particular, the glycoprotein TIMP-1 plays an inhibitory role with most of the MMPs including the collagenases. Furthermore, there exist synthetic or chemical molecules that likewise inhibit the catalytic actions of MMPs. One such molecule is Batimastat (BB-94) which has been proven to be a dose dependent inhibitor of MMPs during the inflammatory …

Development Of An In Vitro Myogenesis Assay, Anna Arnaud

Biomedical Engineering Undergraduate Honors Theses

The objective of this study was to explore the interaction between mouse C2C12 cells and the extracellular matrix, particularly the process of myoblasts converting to myocytes. This study aimed to create a myogenesis assay that presents a process to effectively monitor the development of mouse C2C12 myoblasts into differentiated skeletal myotubes through detection of the protein MyoD. Myogenesis, the development of muscle tissue, occurs when muscle progenitor cells, myoblasts, fuse to form multinucleated myotubes, followed by cell fusion and resulting in a myofiber capable of contraction. An in vitro myogenesis assay would enable further research to efficiently test the effect …

Multiplexed Microfluidic Loop-Mediated Isothermal Amplification Of The 16s Rrna Gene For The Diagnosis Of Neonatal Sepsis In Resource-Limited Environments, Griffin Thomas Sonaty

Biomedical Engineering Undergraduate Honors Theses

Bacterial infection, or sepsis, places a disproportionately high burden on newborns in developing countries. This is due in part to a lack of diagnostic tools suitable for sustainable use in resource-limited nurseries. One potential vehicle for a new diagnostic assay is loop-mediated isothermal amplification (LAMP), a high-yield DNA amplification method. LAMP has been used to detect single genes from bacteria in blood serum samples to aid in sepsis diagnosis. While specific, this approach can only provide detection for one species at a time. LAMP could be adapted to detect a broader set of bacteria, while retaining a degree of specificity …

Intracellular Uptake Of Chitosan Nanoparticle-Based Vaccines, Katherine E. Wilson

Biomedical Engineering Undergraduate Honors Theses

Particle-based delivery systems are a promising approach to enhance antigen-specific immunity for use in vaccines. Chitosan, a natural polysaccharide derived from the exoskeletons of crustaceans, shows great potential as a vaccine carrier due to its favorable properties as a biomaterial, including biocompatibility and biodegradability. In this study, the intracellular uptake of chitosan nanoparticles is explored and compared to that of other commonly used particle-based delivery vehicles, such as poly (lactic-co-glycolic acid) (PLGA). Fluorescein isothiocyanate-labeled bovine serum albumin (FITC-BSA) was used as a model protein antigen and encapsulated in both chitosan particles via precipitation-coacervation and PLGA particles via double emulsion solvent …

The Production Of Biobutanol From Biomass Via A Hybrid Biological/Chemical Process, Thomas Melvin Potts

Graduate Theses and Dissertations

Biobutanol use as a fuel began in the late 19th century. Problems remain in economic viability. A review of the state of the art and need for technical advances is presented.

The technical potential of producing biofuel from a naturally occurring macroalgae was studied. The algae grow in Jamaica Bay, New York City, in contaminated water. The process consisted of mechanical harvesting, drying, grinding, and acid hydrolysis to form an algal sugar solution. Clostridium beijerinckii and C. saccharoperbutylacetonicum were used in an acetone butanol ethanol (ABE) fermentation to make butanol. Fermentation was followed by distillation Butanol concentrations during fermentation reached …

Application Of Membrane Processes For Concentration And Separation Of Sugar Streams In Biofuel Production, Mohammadmahdi Malmali

Graduate Theses and Dissertations

The overall objective of this study was identification and development of a sugar concentration/separation membrane filtration unit to improve the bioconversion of lignocellulosic biomass into chemicals and fuels. This thesis is divided into three main parts. The first part is about our studies on the use of nanofiltration membranes for concentration of sugars in a lignocellulosic biomass hydrolysate. In addition, the feasibility of simultaneous removal of acetic acid, 5-(hydroxymethyl)furfural and furfural from the hydrolysate has also been investigated. The results obtained indicate that both concentration of sugars and removal of hydrolysis degradation products is feasible. However, careful selection of the …