Biomedical Engineering and Bioengineering Commons^™

Production Of Genetically Engineered Golden Syrian Hamsters By Pronuclear Injection Of The Crispr/Cas9 Complex, Rong Li, Jinxin Miao, Seokhwan Song, Il-Keun Kong, Yaohe Wang, Zhongde Wang

Animal, Dairy, and Veterinary Science Faculty Publications

The pronuclear (PN) injection technique was first established in mice to introduce foreign genetic materials into the pronuclei of one-cell stage embryos. The introduced genetic material may integrate into the embryonic genome and generate transgenic animals with foreign genetic information following transfer of the injected embryos to foster mothers. Following the success in mice, PN injection has been applied successfully in many other animal species. Recently, PN injection has been successfully employed to introduce reagents with gene-modifying activities, such as the CRISPR/Cas9 system, to achieve site-specific genetic modifications in several laboratory and farm animal species. In addition to mastering the …

Bioproducts From Bacteria: A Synthetic Biology Approach, Andrew Walters, Ron Sims, Charles Miller

Research on Capitol Hill

What can synthetic biology do?

Synthetic biology can solve many of Utah's problems:

1. Health: generate better medicines and treatments

- Insulin, Artemisinin (anti-malaria drug), Cancer

2. Fuel: augment petroleum with biofuels and biogas

3. Electricity: directly generate electricity from waste

4. Food: engineer more nutritious food with higher yields

- Golden rice, Arctic Apples, Corn, Soybeans, Cotton

5. Products: generate necessary products renewably

- Bioplastics, Spider silk, Adhesives, Pigments, Perfumes

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 …

Hydrodeoxygenation Of Acetic Acid As A Model Compound For The Aqueous Phase Catalytic Pyrolysis Oils, Hossein Jahromi, Foster Agblevor

Biological Engineering Faculty Publications

Catalytic pyrolysis of biomass generates organic, aqueous, gaseous and solid fractions. The organic fraction can be easily hydrotreated to produce hydrocarbons, but the aqueous phase that contains between 10 to 25% soluble organics can pose challenges in wastewater treatment. The aqueous fraction from the catalytic pyrolysis of Pinyon Juniper wood was characterized for its organic content. The fraction contained about 15 wt% organic compounds determined from Karl Fischer analysis. The organic fractions were further characterized using gas chromatography and mass selective detection (GC/MS). The analysis showed that the dissolved organics were composed of acetic acid, ketones, aldehydes, and phenolic compounds. …

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 …

Physical Disruption Of Cell-Cell Contact Induces Vegf Expression In Rpe Cells, Fahrad Farjood, Elizabeth Vargis

Biological Engineering Faculty Publications

PURPOSE: To investigate the role of RPE cell-cell contact in vascular endothelial growth factor (VEGF) protein expression in cultures of primary human RPE (hRPE) cells and a human RPE cell line (ARPE-19). METHODS: Two in vitro methods, scratching and micropatterning, were used to control the physical dissociation of RPE cell-cell junctions. Scratching was performed by scoring monolayers of RPE cells with a cell scraper. Micropatterning was achieved by using a stencil patterning method. Extracellular VEGF expression was assessed by using an enzyme-linked immunosorbent assay (ELISA) kit. Immunocytochemistry (ICC) was performed to visualize the expression and localization of VEGF and intercellular …

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 …

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 …

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 …

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 …

Exploiting Self-Organization In Bioengineered Systems: A Computational Approach, Delin Davis, Anna Doloman, Gregory J. Podgorski, Elizabeth Vargis, Nicholas S. Flann

Biological Engineering Faculty Publications

The productivity of bioengineered cell factories is limited by inefficiencies in nutrient delivery and waste and product removal. Current solution approaches explore changes in the physical configurations of the bioreactors. This work investigates the possibilities of exploiting self-organizing vascular networks to support producer cells within the factory. A computational model simulates de novo vascular development of endothelial-like cells and the resultant network functioning to deliver nutrients and extract product and waste from the cell culture. Microbial factories with vascular networks are evaluated for their scalability, robustness, and productivity compared to the cell factories without a vascular network. Initial studies demonstrate …

Amending Phb With Algal Biomass To Enhance Biodegradability, Amanda R. Stoudt

Undergraduate Honors Capstone Projects

Pollution due to petroleum-based plastic is a growing problem all over the world. Petroleum-based plastics that fill landfills and oceans take hundreds of years to degrade. One possible solution to this growing problem is to increase the use of bioplastics. Polyhydroxybutyrate (PHB) is a widely studied bioplastic that is biodegradable in both soil and marine environments. However, PHB use is limited due to its poor mechanical properties. Past researchers have investigated the use of natural additives, primarily different types of plant fibers, to enhance both the mechanical properties and degradation rates of bioplastics. The purpose of this project was to …

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 …

Alternative Cdep Design To Facilitate Cell Isolation For Identification By Raman Spectroscopy, Cynthia Hanson, Elizabeth Vargis

Biological Engineering Faculty Publications

Dielectrophoresis (DEP) uses non-uniform electric fields to cause motion in particles due to the particles' intrinsic properties. As such, DEP is a well-suited label-free means for cell sorting. Of the various methods of implementing DEP, contactless dielectrophoresis (cDEP) is advantageous as it avoids common problems associated with DEP, such as electrode fouling and electrolysis. Unfortunately, cDEP devices can be difficult to fabricate, replicate, and reuse. In addition, the operating parameters are limited by the dielectric breakdown of polydimethylsiloxane (PDMS). This study presents an alternative way to fabricate a cDEP device allowing for higher operating voltages, improved replication, and the opportunity …

A Computational Study Of Vegf Production By Patterned Retinal Epithelial Cell Colonies As A Model For Neovascular Macular Degeneration, Qanita Bani Baker, Gregory J. Podgorski, Elizabeth Vargis, Nicholas Flann

Biology Faculty Publications

Background: The configuration of necrotic areas within the retinal pigmented epithelium is an important element in the progression of age-related macular degeneration (AMD). In the exudative (wet) and non-exudative (dry) forms of the disease, retinal pigment epithelial (RPE) cells respond to adjacent atrophied regions by secreting vascular endothelial growth factor (VEGF) that in turn recruits new blood vessels which lead to a further reduction in retinal function and vision. In vitro models exist for studying VEGF expression in wet AMD (Vargis et al., Biomaterials 35(13):3999–4004, 2014), but are limited in the patterns of necrotic and intact RPE epithelium they can …

Biomanufacturing Through Igem-An International Student Competition, Asif Rahman, Ryan J. Putman, Neal Hengge, Charles D. Miller

Biological Engineering Faculty Publications

The foundations of synthetic biology are built on molecular biology and genetic engineering. One of the purposes of synthetic biology is to make biology easier to engineer by the creation of standardized biological parts and devices. There are a wide range of potential applications for synthetic biology and a variety of approaches to constructing parts and systems. Undergraduate Science, Technology, Engineering, and Mathematics (STEM) students from around the world apply synthetic biology principles at the annual International Genetically Engineered Machine (iGEM) competition to demonstrate functioning biological systems created from standardized parts. The iGEM competition will continue to add to the …

Qualitative Analysis Of Microbial Dynamics During Anaerobic Digestion Of Microalgal Biomass In A Uasb Reactor, Anna Doloman, Yousef Soboh, Andrew J. Walters, Ronald C. Sims, Charles D. Miller

Biological Engineering Faculty Publications

Anaerobic digestion (AD) is a microbiologically coordinated process with dynamic relationships between bacterial players. Current understanding of dynamic changes in the bacterial composition during the AD process is incomplete. The objective of this research was to assess changes in bacterial community composition that coordinates with anaerobic codigestion of microalgal biomass cultivated on municipal wastewater. An upflow anaerobic sludge blanket reactor was used to achieve high rates of microalgae decomposition and biogas production. Samples of the sludge were collected throughout AD and extracted DNA was subjected to next-generation sequencing using methanogen mcrA gene specific and universal bacterial primers. Analysis of the …

Mannequin Challenge | Biological Engineering, Usu College Of Engineering

College of Engineering News

Who says that learning about the various properties of Biomaterials is boring? Clearly, they haven't taken Dr. Yu Huang's BENG 2330 Properties of Biomaterials course. Not only do these students know how to distinguish the differences between natural and synthetic biomaterials.They know how to have a good time bringing the mannequin challenge into their lab clean up.

Measuring The Effects Of High-Altitude Flight And Upper Atmospheric Radiation On Muscle Cells, Annelise Dykes

Undergraduate Honors Capstone Projects

There are several physiological barriers to long-term space travel, including the effects of launch, landing, and microgravity on muscle cells. A payload capsule was designed to maintain cell growth during a high altitude balloon flight to model some of these physiological processes. Murine muscle cells (strain C2C12) were cultured and launched in a capsule on a balloon satellite in November 2016. Cells were monitored for changes due to temperature, flight motion, radiation, and gravity differences by quantifying cell characteristics before and after the flight using physical measurements and cell viability. Instruments were selected to monitor flight data, and a payload …

Importance Of Heat And Pressure For Solubilization Of Recombinant Spider Silk Proteins In Aqueous Solution, Justin A. Jones, Thomas I. Harris, Paula F. Oliveira, Brianne E. Bell, Abdulrahman Alhabib, Randolph V. Lewis

Biology Faculty Publications

The production of recombinant spider silk proteins continues to be a key area of interest for a number of research groups. Several key obstacles exist in their production as well as in their formulation into useable products. The original reported method to solubilize recombinant spider silk proteins (rSSp) in an aqueous solution involved using microwaves to quickly generate heat and pressure inside of a sealed vial containing rSSp and water. Fibers produced from this system are remarkable in their mechanical ability and demonstrate the ability to be stretched and recover 100 times. The microwave method dissolves the rSSPs with dissolution …

Hydrodeoxygenation Of Pinyon Juniper Catalytic Pyrolysis Oil To Hydrocarbon Fuels, Hossein Jahromi, Foster Agblevor

Biological Engineering Faculty Publications

As a renewable source, biomass is an essential option for diminishing dependence on conventional fossil fuel energy sources. Pyrolysis is a promising technology for the conversion of biomass into liquid fuels. However, several challenges associated with using pyrolysis oils such as their high acidity and low energy content inhibit their direct use as transportation fuels. We conducted a batch hydrodeoxygenation of pinyon juniper catalytic pyrolysis oil using Ni/SiO2-Al2O3 catalyst to improve the following properties of the oil: heating value, acidity, oxygen content, water content, and viscosity. During the hydrogenation process, the influence of four experimental factors; temperature, catalyst loading, residence …

Be Students Attend Bmes Conference | Biological Engineering, Usu College Of Engineering

College of Engineering News

The Biomedical Engineering Society (BMES) is a society of professionals devoted to developing and using engineering and technology to advancing human health and well-being. This year students from the Biological Engineering department at Utah State University attended the annual BMES conference. Here is what one of our students, Ian Wadsworth had to say about the conference.

Aqueous Processing Of Lignocellulosic Biomass To Advanced Biofuels | Biological Engineering, Usu College Of Engineering

College of Engineering News

An important current focus of research in biology, chemistry, engineering, agriculture, and environmental sciences is the development of clean technologies that utilize cellulosic biomass as a renewable resource to the largest extent possible in a biorefinery setting to produce sustainable liquid transportation fuels and chemicals. Of all sustainable resources, only biomass can be transformed into organic fuels and chemicals that can integrate well into our current transportation infrastructure with the inherent convenience, cost, and efficiency advantages of current fuels. Cellulosic biomass can be converted to fuels and chemicals through aqueous-phase processes involving carbohydrates-derived and lignin-derived reactive intermediates deconstructed from these …

Bd Medical Tour | Biological Engineering, Usu College Of Engineering

College of Engineering News

On October 6, 2016, 19 students, mostly from the Biological Engineering Department, traveled to Sandy, UT to tour BD Medical. Students were able to experience a medical manufacturing company first hand. They were able to see the various steps that go into the research, development, production, and quality control when producing and streamlining a product. The tour featured questions and answers about what BD Medical does, career and internship opportunities, and a walk-through of the manufacturing facility.

Angela Akude's Thesis Defense | Biological Engineering, Usu College Of Engineering

College of Engineering News

The Biological Engineering Department is pleased to annouce that Angela Akude will be presenting her thesis defense on Thursday, October 6, 2016 at 9 am in the BENG Conference Room (ENGR 402C).

Student Spotlight | Biological Engineering, Usu College Of Engineering

College of Engineering News

July 2016 - Q&A with Biological Engineering student Harsh Singh