Biomedical Engineering and Bioengineering Commons^™

Nanoparticle Properties And Synthesis Effects On Surface-Enhanced Raman Scattering (Sers) Enhancement Factor: An Introduction, Nathan D. Israelsen, Cynthia Hanson, Elizabeth Vargis

Biological Engineering Faculty Publications

Raman spectroscopy has enabled researchers to map the specific chemical makeup of surfaces, solutions, and even cells. However, the inherent insensitivity of the technique makes it difficult to use and statistically complicated. When Raman active molecules are near gold or silver nanoparticles, the Raman intensity is significantly amplified. This phenomenon is referred to as surface-enhanced Raman spectroscopy (SERS). The extent of SERS enhancement is due to a variety of factors such as nanoparticle size, shape, material, and configuration. The choice of Raman reporters and protective coatings will also influence SERS enhancement. This review provides an introduction to how these factors …

Transitioning The Benefits Of Algal Growth To The Byproducts Of Oil And Natural Gas Production, Alan Hodges, Tyler Gladwin, Cody Maxfield, Jonathan Wood

Research on Capitol Hill

No abstract provided.

Targeted Drug Delivery System For Kidney And/Or Liver Failure Patients Using Human Serum Albumin, Sean Bedingfield

Undergraduate Honors Capstone Projects

Compromised liver and/or kidney function reduces the acceptable dosage of a variety of medications that can be administered to patients. These patients still have a need for drugs such as nonsteroidal anti-inflammatory drugs (NSAIDs), antivirals, and antibiotics. The project goal is to provide a drug delivery system to accommodate these reduced dosage limits with added therapeutic benefits to address symptoms of liver or kidney failure. Localized drug delivery allows for a smaller, concentrated dose rather than inundating the patient's system with the drug of interest. Human serum albumin (HSA) is a researched candidate for drug delivery with therapeutic properties. HSA …

Effect Of Poultry Litter Biochar On Saccharomyces Cerevisiae Growth And Ethanol Production From Steam-Exploded Poplar And Corn Stover, Oumou Diallo

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The use of ethanol produced from lignocellulosic biomass for transportation fuel offers solutions in reducing environmental emission and the use of non-renewable fuels. However, lignocellulosic ethanol production is still hampered by economic and technical obstacles. For instance, the inhibitory effect of toxic compounds produced during biomass pretreatment was reported to inhibit the fermenting microorganisms, hence there was a decrease in ethanol yield and productivity. Thus, there is a need to improve the bioconversion of lignocellulosic biomass to ethanol in order to promote its commercialization. The research reported here investigated the use of poultry litter biochar to improve the ethanol production …

Designing An Artificial Tendon/Graft Derived From Silkworm Silk And Synthetic Spider Silk With Respect To Structure, Mechanical Properties, Biocompatibility, And Attachment, Neal Hengge

Undergraduate Honors Capstone Projects

The Achilles tendon is one of the most commonly damaged tendons in the human body (Hansen et al., 2012). Current surgical and therapeutic techniques require extended recovery time and the tendon is rarely returned to its original healthy state. For athletes in particular, strenuous rehabilitation is required to return from a serious injury like a ruptured Achilles tendon (Rosso et al., 2013).

Despite the high amount of sources for grafts to aid in surgical repair, all of the options have drawbacks such as availability, immune response, or poor mechanical properties. Spider silk has the potential to enhance current Achilles tendon …

Excimer-Monomer Switching Molecular Beacon: The Study On Synthetic Cryptosporidium Dna Detection, Thermodynamics, And Magnesium Effects, Michael L. Davis

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The purpose of this study is to quantify and determine the binding of a molecular DNA probe or molecular beacon used in the detection of a known waterborne pathogen Cryptosporidium parvum. The objectives of this study are to determine the stability, sensitivity, and selectivity of the molecular beacon in detecting synthesized Cryptosporidium DNA sequences. The designed probe is based on a two-fluorophore system that is different than similar molecular beacons that utilize a fluorophore and quencher detection method. A comparative study between the two probes was also performed to demonstrate enhanced selectivity of the fluorophore based molecular beacon. Magnesium …

Mechanical And Physical Properties Of Spider Silk Films Made From Organic And Water-Based Dopes, Chauncey Lewis Tucker

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Spider silk has become a popular material due to its exceptional mechanical and biocompatibility properties. The project team has developed methods of producing and improving the properties of synthetic spider silk films. Other groups have been able to produce similar films having less than impressive mechanical properties using a toxic solvent. The spider silk team here at Utah State University has developed a new way of processing these films to more than triple their mechanical properties and has created a novel form of spider silk films produced from a water-based liquid, making it less expensive, more environmentally friendly, and more …

Optimization Of Wastewater Microalgae Pretreatment For Acetone, Butanol, And Ethanol Fermentation, Yessica A. Castro

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Acetone-butanol-ethanol (ABE) fermentation from wastewater microalgae by Clostridium saccharoperbutylacetonicum N1-4 is a novel bioprocess that utilizes waste substrate to generate valuable solvents. Butanol, the most abundant product resulting from ABE fermentation, is an environmentally safe and high performing fuel that can be utilized as a drop-in-fuel; however, high operational costs and low ABE yield present challenge in scale-up of the process. The utilization of algae as a substrate requires pretreatment prior to fermentation to increase the bioavailability of the algal fermentable sugars and to improve the conditions of the pre-fermentation medium. The purpose of this thesis was to optimize wastewater …

Sustainable Production Of Novel Biomaterials In Escherichia Coli, Asif Rahman

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The biotechnology revenues in the United States exceeded $100 billion in 2010 and the potential impact of synthetic biological engineering has been identified nationally as an emerging technology to further expand the national bioeconomy. Synthetic biological engineering approaches biology from an engineering perspective to make biology easier to engineer. The potential to engineer microorganisms for novel applications can have far-reaching implications and benefits for society. Some of the potential applications range from biosensors, biofuels, therapeutics, and biomaterials.

In this study two biomaterials were produced in genetically engineered Escherichia coli: polyhydroxybutyrates (PHBs) and spider silk. PHBs are bioplastics that have …

Alkaloid Production By Hairy Root Cultures, Bo Zhao

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

In the present research, nicotine alkaloid production by Nicotiana tabacum (tobacco) hairy roots and tropane alkaloid production by Hyoscyamus niger hairy roots were investigated. The first objective of this research was to improve the oxygen mass transfer in hairy root cultures with microbubbles. Oxygen was shown as a critical nutrient for the growth of tobacco and H. niger hairy roots. In a 1-liter fermentor, microbubble dispersion improved the oxygen mass transfer, tobacco hairy root growth, and nicotine production in the medium. In a novel ground-joint column bioreactor, microbubbles enhanced the oxygen mass transfer and the growth of H. niger hairy …

Metabolic Modeling Of Spider Silk Production In E. Coli, Sarah Allred

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Spider silk has the potential to be a useful biomaterial due to its high tensile strength and elasticity. It is also biocompatible and biodegradable, making it useful for wound dressings and sutures, tissue and bone scaffolds, vessels for drug delivery, and ligament and tendon replacements. In some studies where spider silk has been used to grow cells, the silk has promoted more cell growth than the control. However, it is difficult to obtain the high volume of silk needed for these undertakings on a large scale. Spiders are territorial and cannibalistic, so they cannot be easily farmed. Therefore, spider silk …

Distribution Of Heavy Metals From Flue Gas In Algal Bioreactor, Katerine Napan

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Algae are microscopic organisms with a great potential to produce biomass and lipids at productivities several times higher than terrestrial crops. To grow, these organisms consume carbon dioxide (CO₂), a greenhouse gas. This gas, emitted primarily by power plants after coal burning, can be effectively used for algae production, thus resulting in CO₂ remediation and biomass beneficial utilization as feedstuff, industrial filler and biodiesel feedstock. However, since coal is a fuel mined from the earth’s crust, it contains heavy metals that are released during coal burning and inevitably enter the algal cultivation system, contaminating the water were …

Friction Coefficients For Dried Distillers Grains On Eight Structural Surfaces, G. C. Nyendu, S. Pflum, P. Schumacher, C. J. Bern, T. J. Brumm

Biological Engineering Faculty Publications

Static and dynamic coefficients of friction on structural surfaces play important roles in the power requirements and material selection for equipment used in handling and storing agricultural commodities. However, friction data on dried distillers grains with solubles (DDGS) is limited. Further, lack of a standardized method for determining friction coefficient on grain handling materials presents a challenge. This article describes studies carried out to determine the static coefficient of friction (•_s) and dynamic coefficient of friction (•_d) for corn DDGS at 10%, 8.2%, and 6.5% moisture content (all moistures are % wet basis) on eight structural surfaces: High-Density Polyethylene (HDPE), …

Conventional And Catalytic Pyrolysis Of Pinyon Juniper Biomass, Bhuvanesh Kumar Yathavan

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Pinyon and juniper are invasive woody species which has occupied more than 47 million acres of land in Western United States. Pinyon juniper woodlands domination decreases the herbaceous vegetation, increase bare lands which in turn increases soil erosion and nutrition loss. Thus, The US Bureau of Land Management (BLM) has focused on harvesting these woody species to make room for herbaceous vegetation. The major application of harvested pinyon-juniper (PJ) is low value firewood. Thus, there is a need to develop new high value products from this woody biomass to reduce the cost of harvesting. In this study pyrolysis was carried …

Utilizing Municipal And Industrial Wastes For The Production Of Bioproducts: From Metagenomics To Bioproducts, Joshua T. Ellis

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Developing renewable sources of energy is gaining interest due to limited supplies, rising costs, and environmental impacts of exploiting fossil fuels. Biosolvents such as acetone, butanol, and ethanol are attractive sources of fuel which can aid in replacing our dependence on foreign oil. Butanol is of particular interest due to its ability to directly replace gasoline, thus considered a drop-in-fuel. Biological hydrogen and methane gas are also attractive energy sources that can lower dependence on fossil energy.

This research focused on incorporating DNA sequencing technologies in parallel with fermentation methods for understanding and producing energy. The natural environment provides diverse …

Cationic Starch Synthesis, Development, And Evaluation For Harvesting Microalgae For Wastewater Treatment, Renil John Anthony

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Microalgae are the preferred crop for the production of biodiesel. Microalgae are microplants that have the ability to harness sunlight more efficiently than other plants and store 20-80% lipids per g of dry algae in their cells. Microalgae have the extraordinary ability to grow in brackish water or wastewater. Microalgae can be grown in municipal wastewater to uptake phosphorus and nitrogen and remediate the wastewater of these nutrients. Microalgae thus cultivated accomplishes a dual role of wastewater treatment and provides a sustainable feedstock for biofuels and other bioproducts.

This study focused on efficiently harvesting microalgae from water using modified starch. …

Functional Dissection And Module Swapping Of Fungal Cyclooligomer Depsipeptide Synthetases, Dayu Yu, Fuchao Xu, David Gage, Jixun Zhan

Biological Engineering Faculty Publications

BbBSLS and BbBEAS were dissected and reconstituted in Saccharomyces cerevisiae. The intermodular linker is essential for the reconstitution of the separate modules. Module 1 can be swapped between BbBEAS and BbBSLS, while modules 2 and 3 control the product profiles. BbBSLS is a flexible enzyme that also synthesizes beauvericins.

Optimization Of Polyhydroxybutyrate Production In Recombinant Escherichia Coli Through Metabolic Modeling And Simulation, Yoshitaro Heshiki

All Graduate Plan B and other Reports, Spring 1920 to Spring 2023

The objective of this study is to optimize the growth media and genes to maximize PHB production computer simulations, and to evaluate the simulation results through experiments. In order to achieve this objective, the metabolism of E. coli that produces PHB was modeled using the existing E. coli genome-scale metabolic networks. To identify the best additional nutrient for PHB production, carbon sources, minerals, amiano acids, nitrogen sources, and sulfur sources were examined by production potential analysis. Strain design was conducted to find the unwanted reactions to overexpress PHB synthesis pathway.

Engineered Production Of Fungal Anticancer Cyclooligomer Depsipeptides In Saccharo-Myces Cerevisiae, Dayu Yu, Fuchao Xu, Jiachen Zi, Siyuan Wang, David Gage, Jia Zeng, Jixun Zhan

Biological Engineering Faculty Publications

Two fungal cyclooligomer depsipeptide synthetases (CODSs), BbBEAS (352 kDa) and BbBSLS (348 kDa) from Beauveria bassiana ATCC 7159, were reconstituted in Saccharomyces cerevisiae BJ5464-NpgA, leading to the production of the corresponding anticancer natural products, beauvericins and bassianolide, respectively. The titers of beauvericins (33.82±1.41 mg/l) and bassianolide (21.74±0.08 mg/l) in the engineered S. cerevisiae BJ5464-NpgA strains were comparable to those in the native producer B. bassiana. Feeding D-hydroxyisovaleric acid (D-Hiv) and the corresponding L-amino acid precursors improved the production of beauvericins and bassianolide. However, the high price of D-Hiv limits its application in large-scale production of these cyclooligomer depsipeptides. Alternatively, we …

Metacom: Automated Data Processing And Analysis Of Metagenomic Community Sequences, Cody A. Tramp, Charles D. Miller

Browse all Datasets

Advances in next generation sequencing technology have allowed metagenomic researchers to study the composition of bacterial communities through analysis of the vast numbers of sequence reads that these technologies generate. It is not feasible to analyze and interpret this large amount of data manually and individual research groups must create automated scripts and programs to analyze this data. Here, we present MetaCom, a program that offers a common set of analysis and organizational tools that can be used by research groups in the analysis of environmental samples. MetaCom is an open-source software tool that can process next generation sequencing output, …

Rational Reprogramming Of Fungal Polyketide First Ring Cyclization, Yuquan Xu, Tong Zhou, Zhengfu Zhou, Shiyou Su, Sue A. Roberts, William R. Montfort, Jia Zeng, Ming Chen, Wei Zhang, Min Lin, Jixun Zhan, Istvan Molnar

Biological Engineering Faculty Publications

Resorcylic acid lactones (RAL) and dihydroxyphenylacetic acid lactones (DAL) represent important pharmacophores with heat shock response and immune system modulatory activities. The biosynthesis of these fungal polyketides involves a pair of collaborating iterative polyketide synthases (iPKSs): a highly reducing iPKS (hrPKS) whose product is further elaborated by a nonreducing iPKS (nrPKS) to yield a 1,3-benzenediol moiety bridged by a macrolactone. Biosynthesis of unreduced polyketides requires the sequestration and programmed cyclization of highly reactive poly-β-ketoacyl intermediates to channel these uncommitted, pluripotent substrates towards defined subsets of the polyketide structural space. Catalyzed by product template (PT) domains of the fungal nrPKSs and …

Design And Application Of An In Vivo Reporter Assay For Phenylalanine Ammonialyase, S. Wang, S. Zhang, T. Zhou, J. Zeng, Jixun Zhan

Biological Engineering Faculty Publications

Phenylalanine ammonia-lyase (PAL) is an important enzyme that links primary metabolism to secondary metabolism. Its efficiency is often a critical factor that affects the overall flux of a related metabolic pathway, the titer of the final products, and the efficacy of PAL-based therapies. Thus, PAL is a common target for metabolic engineering and it is of significant interest to screen efficient PALs for industrial and medical applications. In this study, a novel and efficient visible reporter assay for screening of PAL efficiency in Escherichia coli was established based on a plant type III polyketide biosynthetic pathway. The candidate PALs were …

Biodiesel Production From Mixed Culture Algae Via A Wet Lipid Extraction Procedure, Ashik Sathish

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Development of renewable sources of energy has received significant interest due to the rising costs of energy and the environmental impact of using fossil fuels. Biodiesel production from renewable sources of oil has shown promise of helping to replace or reduce dependence on petroleum based diesel thereby reducing demand for crude oil. Microalgae have been considered as a strong candidate for the production of large quantities of renewable oil for biodiesel production.

Microalgae are single cell photosynthetic organisms that posses the capability to produce renewable oil at rates much faster than land based plants and crops. In addition, microalgae can …

An Indigoidine Biosynthetic Gene Cluster From Streptomyces Chromofuscus Atcc 49982 Contains An Unusual Indb Homologue, Dayu Yu, Fuchao Xu, Jonathan Valiente, Siyuan Wang, Jixun Zhan

Biological Engineering Faculty Publications

A putative indigoidine biosynthetic gene cluster was located in the genome of Streptomyces chromofuscus ATCC 49982. The silent 9.4-kb gene cluster consists of five open reading frames, named orf1, Sc-indC, Sc-indA, Sc-indB, and orf2, respectively. Sc-IndC was functionally characterized as an indigoidine synthase through heterologous expression of the enzyme in both Streptomyces coelicolor CH999 and Escherichia coli BAP1. The yield of indigoidine in E. coli BAP1 reached 2.78 g/l under the optimized conditions. The predicted protein product of Sc-indB is unusual and much larger than any other reported IndB-like protein. The N-terminal portion of this enzyme resembles IdgB and the …

Designing Predictive Mathematical Models For The Metabolic Pathways Associated With Polyhydroxybutyrate Synthesis In Escherichia Coli, Angela Dixon

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Plastics are a versatile and widely used material. However, traditional plastics are derived from petrochemicals and are not biodegradable. Polymers synthesized from microorganisms that have similar properties to plastic are potential biodegradable replacements. The objective of this project is to use mathematical modeling as a tool to engineer a strain of bacteria optimized for the production of bio-plastics.

Production costs can be reduced by using a bacterial strain specifically optimized for bio-plastic production. By reducing production costs, bio-plastics will be able to commercially compete with traditional plastics. Society will benefit as bio-plastics replace traditional plastics. Fossil fuels will not be …

Predictive Mathematical Model For Polyhydroxybutyrate Synthesis In Escherichia Coli, Angela Dixon

Engineering Datasets

Polyhydroxybutyrate has been studied as a potential biodegradable replacement for petrochemical plastics. Polyhydroxybutyrate synthesis is not native to Escherichia coli, but the genes have successfully been inserted through plasmids. However, polyhydroxybutyrate production needs to be more cost-effective before it can be commercially produced. A mathematical model for polyhydroxybutyrate synthesis was developed to identify genes that could be altered to increase polyhydroxybutyrate production. The major metabolic pathways included in the model were glycolysis, acetyl coenzyme-A synthesis, tricarboxylic acid cycle, glyoxylate bypass, and polyhydroxybutyrate synthesis. Reactions were modeled using kinetic mechanisms identified for each enzyme. The transcriptional network was incorporated into the …

Looking Below The Surface Of Breast Tissue During Surgery, A Mahadevan-Jansen, Md Keller, Elizabeth Vargis, B Caldwell, T-Q Nguyen, Ndm Granja, M Sanders, Mc Kelley

Biological Engineering Faculty Publications

In this article, we present a method that provides prompt detection of the presence of cancer cells inside the 2-mm margin of tissue surrounding the tumor after excision using spatially offset Raman spectroscopy (SORS). SORS was developed to detect subtle changes in soft tissue spectra in the 100–2000 μm range and tested on excised breast tissues. The results display a very high specificity and sensitivity (100% and 95%, respectively) of classification between positive and negative tumor margins. SORS is a clinically feasible method, suitable for the real-time, intraoperative assessment of tumor margins at the micrometer level.

Combating Antibiotic Resistance Through Development Of A Novel Antimicrobial Delivery Vehicle, Alex Hatch

Undergraduate Honors Capstone Projects

A thermoreversible gel for antimicrobial agent delivery would provide a novel platform suitable for medical applications from persistent infections arising from localized biofilms. Thermoreversible gels could be used to coat medical implants, to inject for subdermal treatments, or to implement in topical applications. FDA approved Pluronics® form thermoreversible gels and certain Pluronics® display inherent varying degrees of antimicrobial activity. Pluronics® have been shown to affect efflux pumps, and reduce ATP levels within the bacterial cell. In combination with antibiotics and other pharmaceuticals, Pluronics® have been used to sequester drugs and act as a delivery vehicle. With advances in nanomedicine, nanoparticles …

Characterization And Application Of Dynamic In Vitro Models Of Human Airway, Hemangkumar J. Patel

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

In recent years, respiratory diseases have emerged as a leading cause of mortality across the globe. In the United States alone respiratory diseases are the fourth leading cause of deaths annually. Moreover, with the rapid increase of industrialization and urbanization, the occurrences of respiratory diseases are expected to remain high with strong chances of increasing in the future. To ameliorate the epidemic of respiratory disease, it is first important to understand its underlying mechanisms.

Respiratory research studies in animals have elucidated the chronological order of the pathological events and systemic responses inside the lung, but understanding the response of individual …

Fluoro-Silane As A Functional Monomer For Protein Conformational Imprinting, Yun Peng

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

By using the technology of molecularly imprinted polymer (MIP), we propose to synthesize a protein conformational imprint that also acts as a plastic enzyme, inducing protein structural transitions. The imprint aims at MIP-induced stabilization and / or formation of bound protein secondary structure and the applications associated with analysis and correction of misfolded proteins. The screening of polymeric functional monomers being able to induce the conformational transitions in proteins is investigated in this report.

The fluoro-silanes (3-heptafluoroisopropoxy)propalethoxysilane (7F) and 3,3,3-trifluoropropylmethoxysilane (3F) were employed as functional monomers for synthesis of this catalytic protein conformational imprint via sol-gel reactions. 3F was demonstrated …