Biomedical Engineering and Bioengineering Commons^™

Engineering Platforms For Advancing Plant Synthetic Biology, Tayler Marie Schimel Mcneillie

Doctoral Dissertations

This work describes research aimed at adapting advanced engineering systems for plant biotechnology. The droplet interface bilayer (DIB) is a robust and versatile platform for replicating model cell membranes, providing a bottom-up approach for synthetic cell- and tissue-like structures. In this work, a microfluidic device featuring five inlets, one for the continuous oil phase and four discrete aqueous channels for droplet generation was designed. Droplet production rates were controlled by adjusting the applied pressure of each inlet; and thus, altering the droplet sequence for capturing linear DIB networks in a downstream hydrodynamic trapping array. This microfluidic system provides a high-throughput …

Bio Circuits For Evolutionary Biotech, Camilo Toruno

ENGS 86 Independent Projects (AB Students)

The field of bioengineering has much promise for renewable chemical production, bioremediation, and of course medical applications. Developing new useful microorganisms is extremely time and capital intensive, typically taking 50 million USD and eight years. This is due in large part to the low throughput techniques that are characteristic of the field of metabolic engineering. Here we describe the modification of an existing synthetic biosensor to measure the pharmaceutical dopamine, and the use of a circuit simulator Cadence to predict improvements to the biosensor. This biosensor paired with directed evolution techniques could reach throughputs of 5 million cells per day …

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

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 …

Development Of In Vivo Systems For Detecting And Studying Ribosome Inhibition By Small Molecules, Shijie Huang

Chemistry and Chemical Biology ETDs

The ribosome is the quintessential antibacterial drug target, with many structurally and mechanistically distinct classes of antibacterial agents acting by inhibiting ribosome function. Detecting and quantifying ribosome inhibition by small molecules and investigating their binding modes and mechanisms of action are critical to antibacterial drug discovery and development efforts. To develop a ribosome inhibition assay that is operationally simple, yet provides direct information on the drug target and the mechanism of action, we have developed engineered E. coli strains harboring an orthogonal ribosome controlled green fluorescent protein reporter that produce fluorescent signal when the O-ribosome is inhibited. As a proof …

Engineering Of Polyketide Biosynthetic Pathways For Bioactive Molecules, Siyuan Wang

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

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

Plant natural products are an important source of therapeutics, such as paclitaxel (anticancer) and artemisinin (anti-malarial). Production of plant natural products relies on conventional plant cultivation and solvent extraction, which is time-consuming and cost-ineffective. This work built a biosynthetic platform in Escherichia coli using seven biosynthetic genes from plants and bacteria, which were used to make valuable compounds such as the strong antioxidant resveratrol and anti-inflammatory agent curcuminoids. Through different combinations of these …

A Roadmap To Safe And Reliable Engineered Biological Nano-Communication Networks, Justin W. Firestone

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Synthetic biology has the potential to benefit society with novel applications that can improve soil quality, produce biofuels, grow customized biological tissue, and perform intelligent drug delivery, among many other possibilities. Engineers are creating techniques to program living cells, inserting new logic, and leveraging cell-to-cell communication, which result in changes to a cell's core functionality. Using these techniques, we can now create synthetic biological organisms (SBOs) with entirely new (potentially unseen) behaviors, which, similar to silicon devices, can sense, actuate, perform computation, and interconnect with other networks at the nanoscale level. SBOs are programmable evolving entities, and can be likened …

A Novel Synthetic Yeast For Enzymatic Biodigester Pretreatment, Tianyu Tan, Mark S. Aronson, Arren Liu, Jill H. Osterhus, Melissa Robins, Suraj Mohan, Erich Leazer, Bowman Clark, Alexa Petrucciani, Katherine Lowery, James Welch, Casey Martin, Helena Lysandrou, Michael E. Scharf, Jenna Rickus

The Summer Undergraduate Research Fellowship (SURF) Symposium

Lignin, a complex organic polymer, is a major roadblock to the efficiency of biofuel conversion as it both physically blocks carbohydrate substrates and poisons biomass degrading enzymes, even if broken down to monomer units. A pretreatment process is often applied to separate the lignin from biomass prior to biofuel conversion. However, contemporary methods of pretreatment require large amounts of energy, which may be economically uncompelling or unfeasible. Taking inspiration from several genes that have been isolated from termites and fungi which translate to enzymes that degrade lignin, we want to establish a novel “enzymatic pretreatment” system where microbes secrete these …

Ex Vivo Dna Cloning, Adam B. Fisher

Theses and Dissertations

Genetic engineering of microbes has developed rapidly along with our ability to synthesize DNA de novo. Yet, even with decreasing DNA synthesis costs there remains a need for inexpensive, rapid and reliable methods for assembling synthetic DNA into larger constructs or combinatorial libraries. While technological advances have resulted in powerful techniques for in vitro and in vivo assembly of DNA, each suffers inherent disadvantages. Here, an ex vivo DNA cloning suite using crude cellular lysates derived from E. coli is demonstrated to amplify and assemble DNA containing small sequence homologies. Further, the advantages of an ex vivo approach are …

Artificial Yeast Polarization Controlled By Chemical Gradient, James K. Nolan, Bernard Tao

The Summer Undergraduate Research Fellowship (SURF) Symposium

Engineering synthetic multicellular systems will lead to new synthetic biology technological platforms, inform developmental biology through recapitulation of natural systems and possibly unveil novel morphologies with practical applications not before reached throughout natural history (Maharbiz, 2012). Creating an exogenous molecular circuit that will polarize unicellular cells into “apical” and “basal” domains relative to a substrate plane would fulfill a missing component towards fully multicellular synthetic cellular communities (Maharbiz, 2012). To this end, a PIP₃ polarization network previously designed by Chau and associates (Chau, Walter, Gerardin, Tang, Lim 2012) was coupled to the specific activation by niacin of a recombinant …

Beyond Biobricks: Synthesizing Synergistic Biochemical Systems From The Bottom-Up, Mark A. Bedau

Systems Science Friday Noon Seminar Series

Engineers who attempt to discover and optimize the behavior of complex biochemical systems face a dauntingly difficult task. This is especially true if the systems are governed by multiple qualitative and quantitative variables that have non-linear response functions and that interact synergistically. The synthetic biology community has responded to this difficulty by promoting the use of "standard biological parts" called "BioBricks", which are supposed to make biology into traditional engineering and enable engineers to "program living organisms in the same way a computer scientists can program a computer". But the BioBricks research program faces daunting hurdles, because the nonlinearity and …