Capstone 2021 Biological Engineering

Mike Machado, Corbin Schichtl
Faculty Advisor: David Simpson

Heavy metal pollution is a serious problem throughout the world, so we attempted to biologically engineer a plant to glow in the presence of heavy metals. To this end we sought to introduce a set of genes that confer glowing (auto-luminescence) into the mother of thousands succulent. The necessary genes were inserted into the A. tumefaciens bacteria, which would then be used to insert the genes into our plants of interest.

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Jason Dufresne, Tinatini Kapanadze
Faculty Advisor: David Simpson

Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2) is responsible for the current COVID-19 pandemic, which has resulted in over 190 million cases and 4 million deaths worldwide. An effective treatment that significantly reduces or eliminates the symptoms of COVID-19 is still not available. Due to lack of effective treatments, this study set out determine a strategy to prevent SARS-CoV-2 infection via an engineered nanobody (EN) inhibitor that targets the SARS-CoV-2 spike protein in comparison to small molecule inhibitors (SMIs) identified computationally.

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Colin Nash, Eric Offerman
Faculty Advisor: David Simpson

Lead poisoning is a significant health concern accounted for 1.06 million deaths and 24.4 million years of healthy life lost due to its debilitating and sometimes fatal effects. As a common environmental pollutant present in water, soil, food, and consumer goods, the prevention of lead exposure would require broad infrastructural changes which remain out of reach for the most vulnerable populations. Chelation therapy is the only clinically recognized treatment for metal poisoning, requiring repeated IV infusions which can total thousands of dollars and confer no future protection against metal poisoning. In our project we propose the use of a native bacteria of the human microbiome as a lead poisoning treatment and preventative measure. Using a naturally lead resistant bacteria Ralstonia Metalliduranswe intend to confer an enhanced lead uptake ability to the human gut bacteria Lactobacillus Plantarum. In this project the lead resistant genes from R. Metalliduranswill be transferred to L. Plantarum using traditional techniques of bacterial cloning.

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Tyler Coles, Peter Dudko, Mathew Esquivel, Jak Knox
Faculty Advisor: David Simpson

The world has benefitted from the invention of plastics because they are cheap to make, revolutionized packaging and storing, and are easily mass-produced. These plastics, however, are a double-edged sword in that they are not easily degradable and are pollutants to the environment and all organisms living on Earth. Polyethylene terephthalate (PET) is the most common type of plastic used and can be found in fabrics for clothing and lightweight plastic materials like food packaging. PETase is a known enzyme that can break down PET plastics into a main carbon and energy source. Unfortunately, the rate of degradation of PET is too small to be considered a logical option. That is why this group aimed to increase the rate of PETase in E. coli, thus increasing the rate of PET degradation and making it a viable solution to plastic removal from the environment. And through our experiments, we can conclude that with a stronger PETase enzyme present, there will be more plastic degradation. Furthermore, we plan to investigate manipulating the PETase enzyme even further, to achieve maximum plastic consumption that will ultimately have a positive impact on the environment and offer an alternative to current plastic disposal methods.

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Hannah Erickson, Cassidy Hayes, Emerson Moore
Faculty Advisor: David Simpson

More than 10 million people worldwide are living with Parkinson's Disease (PD). PD is the second most common neurodegenerative disease with no cure. PD causes loss of dopaminergic neurons which leads to locomotive dysfunction. Genetically engineered Drosophila Melanogaster (fruit flies) were used to model a common genetic mutation found in many PD patients. To study the impact of diet on the progression of PD, the model Drosophila were raised on standard, high-sugar, and whey protein-supplemented diets. Changes in spontaneous movement and gene expression of molecular targets linked to PD were measured and compared to wild-type flies. Mitochondrial stress, inflammation, and dopamine transportation gene expression will be measured with qPCR. It is hypothesized that high-sugar diets will progress the disease faster than flies on a standard diet by increasing reactive oxygen species which play a role in the degeneration of dopaminergic neurons. The whey protein-supplemented PD flies were predicted to have reduced disease progression by promoting production of natural antioxidants.

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CiCi Deakin, Ryan McBride
Faculty Advisor: David Simpson

Healing of an adult wound is a complex process that requires the collaborative effort of many biological components. Different cell lineages and tissues express different behaviors that contribute to the regeneration of the wound site. We have established a 3D culture of pluripotent stem cell derived skin organoids that produces regenerative properties when inflicted with an injury. The derivation of a homogenous population of mouse pluripotent stem cells has been shown previously to produce skin organoids that compose of an epidermis and dermis layer and also produces hair follicles that mimic normal embryonic hair folliculogenesis. We show that after infliction of a wound within our skin organoid model, a regenerative response occurs. We also provide a wound healing assay that utilizes a GeneQuery™ Human Skin Wound Healing qPCR Array Kit. This kit includes 88 known genes that are critical to the regeneration of a wound in each of the four stages of the wound healing process. This in vitro model of skin regeneration will be useful to test experimental drugs and model degenerative diseases in human patients.

View the PDF for Understanding wound healing and regenerative processes using stem cell-derived skin organoids