Engineering Commons^™

Identification And Engineering Of Nonribosomal Peptide Biosynthetic Systems, Fuchao Xu

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

This research focuses on the understanding and engineering of nonribosomal peptide biosynthetic pathways in Streptomyces coelicolor CH999, Escherichia coli BAP1 and Saccharomyces cerevisiae BJ5464-NpgA. The biosynthetic systems of indigoidine from bacteria and beauvericin/bassianolide from fungi were studied in this research. The production of these valuble products was significantly increased by enhancing their synthetic pathway with metabolic engineering approaches.

Indigoidine is a bacterial natural product with antioxidant and antimicrobial activities. Its bright blue color resembles the industrial dye indigo, thus representing a new natural blue dye that may find uses in industry. Indigo is a dark blue crystalline powder and has …

Production And Biocompatibility Of Spider Silk Proteins In Goat Milk, Richard E. Decker Jr

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Due to its strength, flexibility, and biocompatibility, spider silk is a highly appealing material for applications in the medical field. Unfortunately, natural spider silk is difficult to obtain in large quantities because spiders are territorial and cannibalistic, making them impractical to farm. Synthetic spider silk proteins produced by transgenic hosts such as bacteria and goats have made it possible to obtain the quantities of spider silk needed to study it more fully and to investigate its potential uses. The spider silk proteins produced in our laboratory do not have an optimal purification method to remove all of the non-biocompatible contaminants …

Identification And Heterologous Reconstitution Of A 5-Alk(En)Ylresorcinol Synthase From Endophytic Fungus Shiraia Sp. Slf14, Huiwen Yan, Lei Sun, Jinge Huang, Yixing Qiu, Fuchao Xu, Riming Yan, Du Zhu, Wei Wang, Jixun Zhan

Biological Engineering Faculty Publications

A new type III polyketide synthase gene (Ssars) was discovered from the genome of Shiraia sp. Slf14, an endophytic fungal strain from Huperzia serrata. The intron-free gene was cloned from the cDNA and ligated to two expression vectors pET28a and YEpADH2p-URA3 for expression in Escherichia coli BL21(DE3) and Saccharomyces cerevisiae BJ5464, respectively. SsARS was efficiently expressed in E. coli BL21(DE3), leading to the synthesis of a series of polyketide products. Six major products were isolated from the engineered E. coli and characterized as 1,3-dihydroxyphenyl-5-undecane, 1,3-dihydroxyphenyl-5-cis-6'-tridecene,1,3-dihydroxyphenyl-5-tridecane, 1,3-dihydroxyphenyl-5-cis-8'-pentadecene, 1,3-dihydroxyphenyl-5-pentadecane and 1,3-dihydroxyphenyl-5-cis-10'-heptadecene, respectively, …

Novel Devices For Studying Acute And Chronic Mechanical Stress In Retinal Pigment Epithelial Cells, Farhad Farjood, Elizabeth Vargis

Biological Engineering Faculty Publications

Choroidal neovascularization (CNV) is a major cause of blindness in patients with age-related macular degeneration (AMD). Overexpression of vascular endothelial growth factor (VEGF), a potent angiogenic protein, by retinal pigment epithelial (RPE) cells is a key stimulator of CNV. Mechanical stress occurs during different stages of AMD and is a possible inducer of VEGF expression in RPE cells. However, robust and realistic approaches to studying acute and chronic mechanical stress under various AMD stages do not exist.The majority of previous work has studied cyclic stretching of RPE cells grown on flexible substrates, but an ideal model must be able to …

Hydrodeoxygenation Of Aqueous Phase Catalytic Pyrolysis Oil To Liquid Hydrocarbons Using Multi-Functional Nickel Catalyst, Hossein Jahromi, Foster A. Agblevor

Biological Engineering Faculty Publications

Herein we investigated the hydrodeoxygenation (HDO) of aqueous phase pinyon-juniper catalytic pyrolysis oil (APPJCPO) using a new multifunctional red mud-supported nickel (Ni/RM) catalyst. The organic liquid yield after HDO of APPJCPO using 30 wt. % Ni/RM at reaction temperature of 350 °C was 47.8 wt. % with oxygen content of 1.14 wt. %. The organic liquid fraction consisted of aliphatics, aromatics, and alkylated aromatic hydrocarbons as well as small amounts of oxygenates. The RM support catalyzed ketonization of carboxylic acids. The Ni metal catalyzed partial reduction of oxygenates that underwent carbonyl alkylation with aldehydes and ketones on the RM. Catalyst …

An Efficient Process For Co-Production Of Γ-Aminobutyric Acid And Probiotic Bacillus Subtilis Cells, Hongbo Wang, Jinge Huang, Lei Sun, Fuchao Xu, Wei Zhang, Jixun Zhan

Biological Engineering Faculty Publications

This study was to establish an integrated process for the co-production of γ-aminobutyric acid (GABA) and live probiotics. Six probiotic bacteria were screened and Bacillus subtilis ATCC 6051 showed the highest GABA-producing capacity. The optimal temperature and initial pH value for GABA production in B. subtilis were found to be 30 °C and 8.0, respectively. A variety of carbon and nitrogen sources were tested, and potato starch and peptone were the preferred carbon and nitrogen sources for GABA production, respectively. The concentrations of carbon source, nitrogen source and substrate (sodium L-glutamate) were then optimized using the response surface methodology. The …

Development And Characterization Of Aqueous-Based Recombinant Spider Silk Protein Biomaterials With Investigations Into Potential Applications, Thomas I. Harris

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Spider silks are incredible natural materials that possess desirable combinations of strength, elasticity, weight, and robustness. Other properties such as biocompatibility and biodegradability further increase the worth of these materials. The possibility of farming spiders is impractical due to spiders’ natural behaviors. Modern biotechnologies have allowed for recombinant spider silk proteins (rSSps) to be produced without the use of spiders. However, the features responsible for spider silks impressive properties can cause difficulties with producing silk materials. A recently developed water-based and biomimetic solvation method has provided a solution to such difficulties and has also led to novel silk biomaterials. Most …

Biomass And Phycocyanin From Oil And Natural Gas Extraction Produced Water Utilizing A Cyanobacteria Dominated Rotating Algal Biofilm Reactor (Rabr), Jonathan L. Wood

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The production of cyanobacterial biofilm biomass and phycocyanin from Rotating Algal Biofilm Reactors utilizing undiluted produced water from oil and natural gas extraction as a culture medium was investigated in this study. Produced water is the largest waste stream generated by the oil and natural gas industries and represents a large volume of non-potable water that may be available for algae culture with minimal impact on freshwater resources. Combining the use of produced wastewater as culture medium with the production of high value algal pigments, such as phycocyanin, may increase the economic viability of algae culture and wastewater purification. High …

Development And Optimization Of A Produced Water, Biofilm Based Microalgae Cultivation System For Biocrude Conversion With Hydrothermal Liquefaction, Benjamin L. Peterson

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Extraction of oil and gas in Utah’s Uintah Basin results in large quantities of wastewater, or produced water, with nutrients and residual organic chemical that represent a significant resource for producing energy-related and value-added products. Produced water was obtained as a biomass producing nutrient source from industries operating in Utah’s Uintah Basin. Within the Uintah Basin (defined as Uintah and Duchesne Counties within Utah) approximately 93 million barrels of water were produced in 2013 while only 11% of the water was disposed of through evaporation, with the national average at 2%. The rest is reinjected into the subsurface.

The goal …

Novel Methods To Produce Large Recombinant Spider Silk Proteins Via Polymerization, Nathan L. Hebert

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Spider silk has long been a subject of scientific research due to its remarkable mechanical properties. Until recently, there has been no way to effectively obtain spider silk except by harvesting it from individual spiders. With advances in technology, the genes that code for the individual spider silk proteins have been isolated and genetically engineered into other hosts to produce recombinant spider silk proteins (rSSp) of varying sizes, Larger rSSp have correspondingly greater mechanical properties in any resulting materials. Using current production methods, larger rSSp cannot be produced in commercially viable quantities while simultaneously being economically viable. The current production …

Whole Cell Cross-Linking To Discover Host-Microbe Protein Cognate Receptor/Ligand Pairs, Bart C. Weimer, Poyin Chen, Prerak T. Desai, Dong Chen, Jigna Shah

Biological Engineering Faculty Publications

Bacterial surface ligands mediate interactions with the host cell during association that determines the specific outcome for the host–microbe association. The association begins with receptors on the host cell binding ligands on the microbial cell to form a partnership that initiates responses in both cells. Methods to determine the specific cognate partnerships are lacking. Determining these molecular interactions between the host and microbial surfaces are difficult, yet crucial in defining biologically important events that are triggered during association of the microbiome, and critical in defining the initiating signal from the host membrane that results in pathology or commensal association. In …

Hydrotreating Of Guaiacol: A Comparative Study Of Red Mud-Supported Nickel And Commercial Ni/Sio2-Al2o3 Catalysts, Hossein Jahromi, Foster Agblevor

Biological Engineering Faculty Publications

Upgrading of bio-oil through catalytic hydrotreating was investigated with guaiacol as a model compound. A nickel supported on red mud (Ni/RM) hydrotreating catalyst was developed and compared to the standard Ni/SiO₂-Al₂O₃ catalysts under similar experimental conditions. The Ni/RM catalyst was characterized by inductively coupled plasma atomic emission spectrometry (ICP-AES), X-ray diffraction analysis (XRD), scanning electron microscopy (SEM), BET specific surface area, and temperature programmed reduction (TPR). The effects of reaction temperature (300, 350, 400 °C) and initial hydrogen pressure (4.83 MPa (700 psi), 5.52 MPa (800 psi), and 6.21 MPa (900 psi)) on products distribution …

Designing A Synthetic Spider Silk Based Coating For Urinary Catheters To Reduce The Risk Of Cautis, Tess Marie Armbrust

Undergraduate Honors Capstone Projects

Catheter associated urinary tract infections (CAUTis) are a leading cause of morbidity and mortality in patients with life-threatening conditions. Foley catheters are the most common catheter used when a patient requires hospitalization but can become burdened with microbes which lead to CAUTis, the most common source of hospital acquired infection (HAI). The attached bacteria can form biofilms on the catheter which are difficult to treat using oral antibiotics and can lead to chronic infections. Synthetic spider silk as a catheter coating shows great promise because of demonstrated strength, biocompatibility, and antimicrobial properties. In addition, the antiseptic chlorhexidine can enhance the …

Investigations Of Polyhydroxyalkanoate Secretion And Production Using Sustainable Carbon Sources, Chad L. Nielsen

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Polyhydroxyalkanoates (PHAs) are a type of biologically-produced plastic known for their biocompatibility and biodegradability. They have the potential to replace petroleum-based plastics as an environmentally-friendly alternative. This is beneficial because the release of plastics into environments such as the ocean and the buildup of plastics in landfills are major concerns facing society today. Currently, however, PHAs are significantly more expensive than their petroleum-based counterparts. This is largely due to the cost of carbon sources and of extracting the bioplastics from bacteria. The goal of these studies was to examine replacing traditional carbon sources used in PHA production like sugar and …

Designing A Synthetic Spider Silk-Based Coating For Urinary Catheters To Reduce The Risk Of Cautis, Alexander Cook

Undergraduate Honors Capstone Projects

Urinary and Intravenous (IV) catheters are two of the most commonly used medical devices for administering vital drugs and obtaining diagnostic samples from patients. Unfortunately, hospital acquired infections (HAIs) occur at alarming rates due to catheter usage. The aim of this project was to design a urinary catheter that would decrease the occurrence of these infections with a catheter coating that utilizes the antimicrobial properties of synthetic spider silk in combination with the antiseptic chlorhexidine. This synthetic spider silk catheter will introduce a novel approach to catheterization in the medical industry.

Silane Modulation Of Protein Conformation And Self-Assembly, Abul Bashar Mohammad Giasuddin

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

This research focused on development of nanoparticle- based therapeutics against amyloid fibrils. Amyloid fibrils are associated with various diseases such as Parkinson’s, Huntington’s, mad cow disease, Alzheimer’s, and cataracts. Amyloid fibrils develop when proteins change their shape from a native form to a pathogenic “misfolded” form. The misfolded proteins have the ability to recruit more native proteins into the pathogenic forms, which self-assemble into amyloid fibrils that are hallmarks of the various protein-misfolding diseases listed above. Amyloid fibrils are highly resistant to degradation, which may contribute to the symptoms of amyloid diseases. Synthetic drugs, natural compounds, and antibodies are widely …

The Use Of Microfluidics And Dielectrophoresis For Separation, Concentration, And Identification Of Bacteria, Cynthia Hanson

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Typical bacterial analysis involves culturing and visualizing colonies on an array of agar plates. The growth patterns and colors among the array are used to identify the bacteria. For fast growing bacteria such as Escherichia coli, analysis will take one to two days. However, slow growing bacteria such as mycobacteria can take weeks to identify. In addition, there are some species of bacteria that are viable but nonculturable. This lengthy analysis time is unacceptable for life-threatening infections and emergency situations. It is clear that to decrease the analysis of the bacteria, the culturing and growth steps must be avoided. …

Microfluidic Chip For Non-Invasive Analysis Of Tumor Cells Interaction With Anti-Cancer Drug Doxorubicin By Afm And Raman Spectroscopy, Han Zhang, Lifu Xiao, Qifei Li, Xiaojun Qi, Anhong Zhou

Biological Engineering Faculty Publications

Raman spectroscopy has been playing an increasingly significant role for cell classification. Here, we introduce a novel microfluidic chip for non-invasive Raman cell natural fingerprint collection. Traditional Raman spectroscopy measurement of the cells grown in a Polydimethylsiloxane (PDMS) based microfluidic device suffers from the background noise from the substrate materials of PDMS when intended to apply as an in vitro cell assay. To overcome this disadvantage, the current device is designed with a middle layer of PDMS layer sandwiched by two MgF2slides which minimize the PDMS background signal in Raman measurement. Three cancer cell lines, including a human lung cancer …

3d Tissue Engineering, An Emerging Technique For Pharmaceutical Research, Gregory Jensen, Christian Morrill, Yu Huang

Biological Engineering Faculty Publications

Tissue engineering and the tissue engineering model have shown promise in improving methods of drug delivery, drug action, and drug discovery in pharmaceutical research for the attenuation of the central nervous system inflammatory response. Such inflammation contributes to the lack of regenerative ability of neural cells, as well as the temporary and permanent loss of function associated with neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, and traumatic brain injury. This review is focused specifically on the recent advances in the tissue engineering model made by altering scaffold biophysical and biochemical properties for use in the treatment of neurodegenerative diseases. …

A Collaborative Solution To Harmful Algal Blooms In Utah, Kyle Hillman, Bethany Jensen, Ammon Balle

Research on Capitol Hill

Harmful algal blooms (HABs)…

• affect Utah Lake, Scofield Reservoir, Jordanelle Reservoir, Mantua Lake, and other water bodies throughout Utah
• are toxic to public health, the environment, and the economy

In Vivo Raman Spectroscopy For Biochemical Monitoring Of The Human Cervix Throughout Pregnancy, Christine M. O'Brien, Elizabeth Vargis, Amy Rudin, James C. Slaughter, Giju Thomas, J. Michael Newton, Jeff Reese, Kelly A. Bennett, Anita Mahadevan-Jansen

Biological Engineering Faculty Publications

Background

The cervix must undergo significant biochemical remodeling to allow for successful parturition. This process is not fully understood, especially in instances of spontaneous preterm birth. In vivo Raman spectroscopy is an optical technique that can be used to investigate the biochemical composition of tissue longitudinally and noninvasively in human beings, and has been utilized to measure physiology and disease states in a variety of medical applications.

Objective

The purpose of this study is to measure in vivo Raman spectra of the cervix throughout pregnancy in women, and to identify biochemical markers that change with the preparation for delivery and …

Investigation And Engineering Of Polyketide Biosynthetic Pathways, Lei Sun

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

This research is focused on investigation and engineering of natural product biosynthetic pathways for efficient production of pharmaceutically important molecules or generation of new bioactive molecules for drug development.

Natural products are an important source of therapeutics, such as chromomycin (anti-cancer), emodin (anti-inflammatory and anti-tumor) and sprolaxine (anti-Helicobacter pylori). Metabolic engineering of natural product biosynthetic pathways shows its promise for creating and producing valuable compounds with chemical diversity for drug discovery. One goal of this research is to create highly efficient strains to biosynthesize valuable natural products. The engineered Streptomyces roseiscleroticus strain constructed in this work showed higher …

Modeling De Novo Granulation Of Anaerobic Sludge, Anna Doloman, Honey Varghese, Charles D. Miller, Nicholas Flann

Computer Science Faculty and Staff Publications

Background: A unique combination of mechanical, physiochemical and biological forces influences granulation during processes of anaerobic digestion. Understanding this process requires a systems biology approach due to the need to consider not just single-cell metabolic processes, but also the multicellular organization and development of the granule.

Results: In this computational experiment, we address the role that physiochemical and biological processes play in granulation and provide a literature-validated working model of anaerobic granule de novo formation. The agent-based model developed in a cDynoMiCs simulation environment successfully demonstrated a de novo granulation in a glucose fed system, with the average specific methanogenic …

Decoding And Reprogramming Fungal Iterative Nonribosomal Peptide Synthetases, Daya Yu, Fuchao Xu, Shuwei Zhang, Jixun Zhan

Biological Engineering Faculty Publications

Nonribosomal peptide synthetases (NRPSs) assemble a large group of structurally and functionally diverse natural products. While the iterative catalytic mechanism of bacterial NRPSs is known, it remains unclear how fungal NRPSs create products of desired length. Here we show that fungal iterative NRPSs adopt an alternate incorporation strategy. Beauvericin and bassianolide synthetases have the same C₁-A₁-T₁-C₂-A₂-MT-T_2a-T_2b-C₃ domain organization. During catalysis, C₃ and C₂ take turns to incorporate the two biosynthetic precursors into the growing depsipeptide chain that swings between T₁ and T …

Production Of Phenol-Formaldehyde Adhesives From Catalytic Pyrolysis Oil, Angela M. Akude

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Phenol-formaldehyde adhesives conventionally synthesized from fossil fuel resources pose two major concerns: sustainability issues and environmental concerns. The sustainability issues arise from the inevitable depletion of fossil fuel resources while
the environmental concerns, primarily, stem from the emission of volatile organic compounds. Thus, opting for alternative raw materials from renewable resources reduces the dependence on fossil fuels as well as promote the production of environmentally-friendly products.

The successful commercialization of bio-adhesives requires that the substitution of phenol with bio-oil during resin synthesis should be above 40%. In this study, catalytic pyrolysis oil produced from pinyon-juniper biomass and red mud alumina …

Anaerobic Digestion Of Wastewater: Effects Of Inoculants And Nutrient Management On Biomethane Production And Treatment, Jason Peterson

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Due to population expiation and the increased awareness of the impact on the environment by wastewater treatment, improved wastewater treatment systems are needed to treat municipal and agricultural wastewater. Treating wastewater with oxygen decreases carbon compounds at the expense of energy to move carbon and oxygen to be in contact with each other. Anaerobic digestion of wastewater can reduce the cost by utilizing microbes to treat high amounts of carbon in wastewater without the need for extensive oxygen requirement. With a proper balance of nutrients, microbes also produce methane, a renewable energy source.

It has been suggested that microalgae be …

Alternative Treatment Technologies For Low-Cost Industrial And Municipal Wastewater Management, Alan J. Hodges

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Roughly the same volume of water that rushes over the Niagara Falls is produced as wastewater in North America. This wastewater is treated through a variety of means to ensure that it can be safely returned to the natural ecosystem. This thesis examines two novel means for this treatment, one biological and one physical-chemical in nature, namely, Rotating Algae Biofilm Reactor treatment and expanded shale augmented coagulation-flocculation.

Rotating algae biofilm reactors (RABRs) support biofilm algae growth, and in turn, the algae take up harmful contaminants from the wastewater. This system was tested in wastewater from petroleum refining operations. The efficacy …

Algae-Based Biofilm Productivity And Treatment Of Dairy Wastewater: Effects Of Temperature And Organic Carbon Concentration, Zachary T. Fica

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Production of dairy and associated products is a source of millions of gallons of wastewater every year. Water used in cleaning feeding stalls as well as the liquid component of the animal waste are two of the major volumetric components of this wastewater. This water is nutrient rich, often limiting the viability as a land applied fertilizer. However, these same nutrients could be used as an inexpensive feedstock for the cultivation of algae, which can then be used to produce downstream products including animal feed and aquaculture.

As part of this study, algal biomass was cultivated on dairy wastewater from …

Pairing Of Anaerobic And Aerobic Treatment Of Petroleum Wastewater, Zachary Fica

Undergraduate Honors Capstone Projects

The objective of this project was to treat petroleum refinery wastewater using a combination of anaerobic and aerobic processes, namely an Up-flow Anaerobic Sludge Blanket (UASB) reactor paired with a Rotation Algae Biofilm Reactor (RABR), respectively, to produce a treated effluent. The treatment method developed needed to produce a cost-effective and efficient way to decrease nitrogen, phosphorous, total suspended solids (TSS), and COD concentrations to below State of Utah limitations. It was demonstrated that RABR treatment was capable of reducing effluent concentrations of nitrogen, phosphorus, and TSS to State of Utah limitations. RABR treatment did not significantly reduce COD from …

Electrospun Spiderskin Bandage For Epidermal Protection And Recovery, Michael David Paskett

Undergraduate Honors Capstone Projects

Spider silk is one of nature's most promising biomaterial s for a variety of applications, however, due to the inability to farm spiders, transgenic hosts are required for large-scale production. With the unique combination of strength, elasticity, and biocompatibility, spider silk has an incredible potential for use in the human body. This study was conducted to merge two major applications of spider silk for the creation of a novel bandaging product. Electrospinning technology was utilized to create a spider silk/polymer bandage matrix to be applied with an aqueous spider silk skin adhesive.

In designing the bandaging matrix , the mechanical …