Biotechnology Senior Capstone Projects
Students in the KU Edwards Campus biotechnology program conduct a senior capstone project that challenges them to apply their technical and research skills gained through their studies. Read below to learn more about the Biotechnology students’ capstone projects.
Biotech Seniors 2020-2021
Biotherapeutics: Characterizing the impact IL-13 treatment has on mucus production of cultured human adenocarcinoma cells.
Every year between 30,000 and 40,000 people are newly diagnosed with ulcerative colitis (UC) in the United States. UC is the most prevalent disease in the category of inflammatory bowel disease (IBD), it is disruptive to life, painful, and in severe cases it can be deadly. UC is caused by a thinning of the mucus layers that protect the lining of the digestive system from enteric bacteria and other materials. Enteric bacteria are typically harmless and even beneficial, but with the absence of a mucus barrier they can infiltrate the lining of the digestive system and cause a severe immune reaction and ulceration. IL-13 is a protein used by the immune system primarily to regulate the response to parasites. However, it has also been implicated in other immune responses: the mediation of allergic inflammation and airway hyper-responsiveness in asthma. Recently, increased levels of IL-13 have been observed in severe cases of SARS-CoV-2. IL-13 regulates, among other responses, goblet cell metaplasia and subsequent mucus secretion. My research aims to observe the effects of IL-13 treatment on a simulated intestinal epithelium (HT29 cells grown in culture) and its ability to induce goblet cell metaplasia and enhancement of mucus production. This work could be the foundation for treatments of UC that address the root cause of the disease, rather than current treatments of long-term immunosuppressants.
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Andy Cardona Orellana
Drug Metabolism & Pharmacokinetics: Assessing the influence glycosylation plays in protecting antibodies from lysosome-based proteolytic degradation.
Antibody therapeutics have recently become a valuable tool in the treatment of disease. Their ability to bind specifically to one target affords them exquisite selectivity, which can dramatically reduce off-target drug effects. Antibodies are important endogenous biomolecules that play a critical role in fighting disease. As such, our bodies have evolved mechanisms to protect antibodies from premature degradation and therefore tend to have highly favorable pharmacokinetic properties. Antibodies, such as IgG, can be taken up by cells such as monocytes, but are kept from lysosomal degradation by their interaction with the FcRn receptor. The FcRn receptor binds to the constant region of the IgG to protect them from degradation by exocytosing the IgG back into the serum. Studies have shown that glycans found in the constant region of IgG influence its interaction with the FcRn receptor. Therefore, the design of therapeutic antibodies must also consider lysosomal recycling pathways. Without the proper engagement of the FcRn, these therapeutics would have a greatly diminished half-life within the body, which would reduce their effectiveness. My research project aims to study the influence that glycosylation has on protecting IgG antibodies from lysosomal degradation in cultured THP-1 cells, a model for monocytes. Using fluorescent tags and live-cell dyes, I will evaluate the degree of antibody-lysosomal colocalization and assess proteolytic degradation of the antibodies using western blot analysis. These studies will compare results between antibodies with native glycosylation vs. deglycosylated antibodies. The results of this study will improve our understanding of antibody glycosylation and its influence in protecting them from proteolytic degradation.
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Neurodegenerative Diseases: Assessing the impact that variable expression of the SOD-1 protein has on the abundance of intracellular reactive oxidative species in cultured human cells.
Amyotrophic Lateral Sclerosis (ALS), though relatively rare, is a debilitating and fatal condition for which there currently is no cure. ALS is a degenerative neuromuscular disorder in which neural cells are damaged, leading to loss of function, and eventually affecting all muscles in the body. Mutation of the SOD-1 gene, a gene encoding a superoxide dismutase, has been identified as a significant contributor to the debilitating effects of ALS. Dysfunction of the SOD-1 gene can lead to a toxic, free radical-ladened environment inside neural cells leading to cell damage and death. This study aims to determine the influence variable expression levels of the SOD-1 enzyme have on the intracellular abundance of free radicals in human cells. To test this, HeLa cells will be used as a model human cell line in which we will vary SOD-1 expression levels: unmodified wild-type HeLa cells representing normal SOD-1 expression, HeLa cells overexpressing SOD-1 (via a transient transfection), and HeLa cells under-expressing SOD-1 (via an siRNA knock-down). The abundance of intracellular free radicals will be assessed using a fluorescent reporter system in a microplate assay format and fluorescence micrograph format. These results are expected to strengthen our understanding of the relationship between SOD-1 expression and its role in mitigating the intracellular abundance of free radicals in human cells. This knowledge could guide therapies to counter the debilitating effects of ALS and improve quality of life for these patients.
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Pharmacogenomics: Assessing the genotype-phenotype relationship of the drug metabolizing enzyme CYP1A2 allele A vs allele C on caffeine metabolism in a human subject.
Caffeine is the world's most widely consumed psychoactive drug. Caffeine can be found in food, drinks, and supplements. Many of us ingest caffeine every day to wake up for the day or throughout the day as an energy supplement. Some individuals can consume a large amount of caffeine on a daily basis but not suffer the negative consequences of insomnia despite the stimulant effects of the drug, while others experience these adverse effects even with only moderate amounts of caffeine. In large part, this is attributable to the enzyme responsible for breaking caffeine down, CYP1A2. Furthermore, it has shown that there is a link between increased risk of cardiac arrest depending on which variant of CYP1A2 with the consumption of caffeine. The human population exhibits a wide variability in the genetic sequence for drug-metabolizing enzymes (i.e., genotype) that can lead to alterations in the body’s ability to remove the drug from the body (i.e., observed phenotype). Understanding this relationship is critical for scientists seeking to characterize drug dosages for the human population. My research seeks to characterize a genotype-phenotype relationship in a human subject using caffeine as a model drug. To accomplish this goal, I will identify the genotype of the subject by PCR across a variable region of the enzyme involved in caffeine metabolism (genes: CYP1A2 AA/C and enzyme CYP1A2). To identify the phenotype, I will design a quantitative method using HPLC to perform a PK study and determine drug half-life. These data sets will be combined to assess the individual’s genotype and phenotype relationship.
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Nutraceuticals: Assessing the antimicrobial potency and chemical composition of oregano essential oil: A scientific approach to test a supplement company’s therapeutic claim.
The increased prevalence of antibiotic-resistant bacteria has generated growing interest in alternative/accessory antimicrobial agents. To meet this demand, many supplement companies market “essential oils” which are concentrated extracts from plants. These companies claim that their marketed essential oils have many health promoting properties such as antibacterial, antifungal, and anti-inflammatory effects, among others. My research aims to study the antimicrobial potency of oregano essential oil on Staphylococcus epidermis, Escherichia coli, Pseudomonas aeruginosa, and Candida albicans. Additionally, we will specifically evaluate the antimicrobial potency of carvacrol, a compound found in high concentrations within the essential oil and suspected to be its active ingredient. Using the optical density at 600nm, this study will characterize the growth vs time curves of the selected microbes to determine the antimicrobial potency of the essential oil and carvacrol. Using HPLC, we will also measure the endogenous concentration of carvacrol within the essential oil. The results of this study will allow an evidence-based approach to scientifically evaluate the supplement company’s claim that their oregano oil possesses antibacterial and antifungal properties. Overall, this work serves as a standard by which supplement companies can make a claim regarding the antibiotic activity of this and other similar nutraceuticals.
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Pharmacognosy: Assessing the anticancer potency and selectivity of mushroom-extracts in model cell culture-based systems.
Fungi are everywhere. They are in your food, in your house and even in your body. Fungi are neither plant nor animal but a kingdom all their own. Over time, people have found increasingly creative ways to exploit the many uses of fungi. Throughout history, fungi have been used as a food source, a tool to enhance biodegradation of organic material and as a medicine. As they relates to medicine, mushrooms have been reported to contain compounds that exhibit powerful anticancer activity. To evaluate these claims, these compounds will be extracted from the mushrooms using solvents such as water or methanol and then tested on the cervical carcinoma cells line, HeLa, grown in culture. If the extracts show anticancer activity, further downstream purification will be performed to identify the specific active components. This project focuses on extracting hydrophobic compounds from different species of mushrooms, examining their chemical fingerprint, and testing their anticancer potency and selectivity in model cell culture-based systems.
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Richard T. Oliver
Aging Research: Assessing the influence CSB, a gene associated with premature aging in Cockayne syndrome, has on the induction of premature cellular senescence in a model cell culture-based system.
Cockayne Syndrome (CS) is a rare, fatal condition characterized by cognitive delays, stunted growth, and precocious aging. The molecular basis of CS is a disorder of the ERCC6 gene which codes for protein, CSA, involved in DNA repair. The accumulation of DNA damage over time contributes to cellular senescence and premature aging. Cellular senescence, defined as the irreversible arrest of cell proliferation following oncogenic stress such as DNA damage, is thought to be a major contributor to aging. The gold standard biomarker for measuring senescence is the hydrolysis of beta-galactosides into monosaccharides, which occurs only in senescent cells. My research aims to explore the influence that the CSB protein has on controlling senescence in human cells grown in culture. CRISPR will be used to knock out the ERCC6 gene in HeLa cells and verified by confirmation by PCR. To characterize any subsequent transformation of cells to a senescent phenotype, a beta-galactosidase activity assay will be developed using Fluorescein di(β-D-galactopyranoside), a fluorescent substrate for Senescent-Associated Beta-Galactosidase activity. The results of this study will further our understanding of the link between precocious aging-related disease states, cellular senescence, and the role of the CSB protein.
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Antiviral Therapies (Coronavirus): Evaluating the in vitro safety and potential antiviral activity of chloroquine and ivermectin on cultured human lung cells infected with coronavirus.
The outbreak of SARS-CoV-2 in 2019-2020 has resulted in a global pandemic infecting millions of people worldwide. As cases continue to surge and death rates climb, the race to find safe and effective coronavirus therapies is more important than ever. The mechanisms of infection and proliferation of coronavirus have been thoroughly studied and this knowledge can be exploited to develop therapeutics to potentially treat those infected with the virus. In previous studies, chloroquine has been shown to disrupt endocytosis and exocytosis processes involved in coronavirus infection, while ivermectin has been shown to inhibit coronavirus’ effect on the host cell’s anti-viral response. This research study examines chloroquine’s and ivermectin’s potential to inhibit coronavirus proliferation in a model human cell line grown in culture. Specifically, this study evaluates the in vitro safety, time- and dose-dependent anti-viral activity of these drugs, and the potential for synergic effects that might enhance antiviral activity of these two drugs. While the world continues to race for effective treatments and potential cures for SARS-CoV-2, the data collected in this study could provide insight into chloroquine’s and ivermectin’s potential to disrupt coronavirus infection.
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Forensic Science: Employing short tandem repeat (STR) analysis to develop a cheap and reliable assay to verify human cell lines.
Over the years, DNA analysis has vastly increased the power of forensics, and has become an invaluable tool in law enforcement. DNA evidence is key to linking suspects to various crimes such as robbery, rape, murder, as well as serving as a tool for paternity testing and disease screening. However, these technologies are also applicable to questions outside of forensics. One such question arises in the laboratory when researchers are culturing a number of different cell types in close proximity. Because many cell types can look the same microscopically, it becomes possible to confuse, mislabel, or even cross-contaminate cell cultures. This research project aims to develop an assay that utilizes short tandem repeat (STR) analysis as a tool to verify human cell lines grown in culture in an affordable and reliable fashion. A small number of STRs will be analyzed by polymerase chain reaction to produce DNA products of variable sizes, as determined by the cell’s alleles, which will make up a fingerprint identifying each of several cell types. As these are human STRs, they can also be used to identify human DNA samples, which will further demonstrate the flexibility and reliability this test.
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Biotech Seniors 2019 - 2020
Cancer Therapy: Is Ellagic Acid, a micronutrient found in fruits a vegetables, a cancer fighting agent?
Ellagic Acid is a micronutrient found in fruits and vegetables, described as a polyphenol antioxidant, with a purported ability to induce apoptosis and reduce cellular proliferation of cancer cells. My capstone project is focused on assessing the anticancer potency of Ellagic Acid. My research will characterize Ellagic Acid’s cytotoxic potency and antiproliferative effects on a cervical cancer cell line, HeLa. Additionally, I seek to determine the natural abundance of Ellagic Acid in select fruits and beverages. Ultimately, this research could provide evidence that supports further investigation into Ellagic Acid’s potential as a cancer fighting therapy.
Animal Health: Is CBD an effective therapeutic treatment for reducing anxiety in dogs?
Like humans, many dogs suffer from debilitating anxiety. Recent hype surrounding cannabidiol (CBD) and its therapeutic potential for treating anxiety has inspired me to design a study to test this claim. My research focuses on developing an assay capable of detecting cortisol, a physiological biomarker of stress/anxiety, in the saliva of dogs. Once this assay is validated, a single-animal crossover study will be performed in which baseline values of anxiety will be assessed using both observational data and quantitative cortisol levels found in saliva. Following baseline assessment of anxiety, a veterinarian-prescribed regimen of CBD will be administered and assessment of anxiety will continue to the end of the study. Ultimately, this data could provide evidence to support further investigation into CBD as a routine and effective treatment for managing anxiety in canines.
Cancer Therapy: Can the sweet drinks we enjoy also fight cancer?
Sweeteners are commonly added to our food and drinks. What if some of these sweeteners also had cancer-fighting properties? Monk fruit is a common sweetener that naturally contains mogroside V which has been suggested to have anticancer properties. Although mogroside V’s mechanism of action is not fully understood, it is thought to limit cancer cell growth by increase the expression of p53, a tumor suppressor. My capstone project aims to measure two key aspects of mogroside V’s impact on a cervical cancer cell line (HeLa): its cytotoxic potency and its impact on p53 expression-levels. Ultimately, this research will provide evidence to support further investigation into mogroside V and its potential to serve as an anticancer therapy.
Environmental Biology:Induction of Escherichia Coli (E. Coli) to Degrade PET Plastic, an environmental pollutant.
Accumulation of plastic waste in our natural environment is becoming a serious threat to wildlife and the health of Earth’s ecosystems. Plastics accumulate in our environment because there are limited number of organisms capable of degrading them, i.e., they are not biodegradable. Until recently, scientists were not aware of an existing natural mechanism capable of biodegrading plastics. However, a strain of bacteria was recently discovered that shows the ability to degrade polyethylene terephthalate, or PET plastic. These bacteria, named Ideonella sakaiensis (I. Sakaiensis), were found in sediments near a plastic bottle recycling facility in Sakai, Japan. Although I. Sakaiensis biodegrades PET plastic, it does so rather slowly and is only found in sediment and is therefore cannot effectively be used to degrade all plastic pollution. My project aims to exploit the genes I. Sakaiensis uses to degrade PET and insert these genes into Echerichia coli (E. Coli). Once established, these modified E. Coli could potentially be used as a tool to remediate environments polluted with plastics.
Vaccine Production: Can a toxoid-vaccine for strep throat be created from s. pyogenes toxin?
Streptococcus pyogenes is an extremely morbid bacteria, causing over 10 known diseases in humans including strep throat. A common mediator of the diseases caused by this organism is the toxin, streptolysin O. Streptolysin O is a protein secreted by streptococcal bacteria capable of directly injuring host cells and lysing red blood cells. Although widely researched, there remains no vaccine against s. pyogenes. My research aims to clone this toxin and inactivate it in order to generate a safe and effective vaccine.
Drug Delivery: Development and testing of novel peptides to improve drug deliver to the brain
Diseases of the brain can be difficult to treat with pharmaceuticals due to a unique anatomical barrier called the blood brain barrier (BBB). The BBB is a collection of cells that encapsulates all the capillaries entering the brain. These cells are bound together by special proteins called VE-cadherins. VE-cadherins keep the cells of the BBB tightly linked and this limits drugs’ ability to slip into the brain. One promising method of increasing drug delivery through the BBB is by modulating (reducing) the tight binding of VE-cadherins. My research seeks to test two linear peptides’ (AVAIDK and KVFRVDAETGDVFAI) ability to modulate VE-cadherin binding and thereby increase drug penetration into the brain. VE-cadherin binding will be assessed using native PAGE (polyacrylamide gel electrophoresis). While changes in endothelial cell permeability will be observed by measuring TEER (trans-electrical endothelial resistance) values. Ultimately, this work will lay the foundation for follow-up work focused on developing adjunct therapies that improve the efficacy of brain-targeting drugs.
Immunology: Cloning and characterization of an immune signaling protein
When the immune system turns against itself, a variety of disease states arise. Many of these conditions exhibit a vicious cycle leading to increased severity of symptoms. In the last two decades, a new class of immune cells has been characterized as secreting a powerful signaling protein. These cells and the protein they secrete, interleukin – 17 (IL-17), have been linked to inflammation associated with the pathogenesis of autoimmune diseases, including the skin condition, psoriasis. In order to better understand the pathology of psoriasis, my research seeks to clone and characterize IL-17 and the signals it elicits in receptive cells.
Environmental Survey: Development and validation of a rapid, onsite test-kit to detect toxic algal blooms in local bodies of water.
Harmful algal blooms (HAB) are a growing concern for water supplies in the United States and around the world. These HABs are increasing in prevalence and produce toxins that negatively impact the health of humans, pets, livestock, and wildlife. Currently, there is not a wide selection of cost-efficient, on-site methods for testing water samples for HAB toxins. My research focuses on creating a simple test kit that can detect one of Kansas City’s most prevalent HAB toxins, microcystin. The design of the test-kit will exploit the natural inhibitory effects of microcystin on protein phosphatases to create a colorimetric assay that will generates signal proportional to microcystin concentration. This kit will enable users to perform a quick, on-site test of water supplies and determine if local bodies of water are contaminated with microcystin. Ultimately, this research will provide a proof of concept study that can potentially be used to launch a startup company focused on developing test-kits for public use.
Drug Delivery: Overcoming drug delivery barriers through the use of liposomes
Drugs can only be effective if they are able to reach their intended drug target. To reach these drug targets, they must traverse biological environments. Unfortunately, these environments present many anatomical and chemical barriers that limit drugs’ access to their intended target. Liposomes are tiny lipid-containing particles that hold the promise of overcoming many drug-delivery barriers. My project focuses on producing a variety of liposomes using different formulations and then testing their effectiveness of overcoming an antibiotic drug’s limited cellular permeability. This research project will lay the foundation for me as a scientist entering the scientific field of drug delivery.
Pharmaceutical Science: Are nutraceuticals truly what they say they are?
A nutraceutical is a food, fortified food, or supplement that is purported to provide medical benefits, boost performance, or prevent/treat disease. Nutraceuticals are available over the counter and do not require any medical supervision or oversight to use. Additionally, nutraceuticals often make audacious claims that “suggest” a myriad of health benefits resulting from the active ingredient; however, the Food and Drug Administration (FDA) does not oversee the production and safety of these products. This ultimately creates a situation whereby nutraceutical company’s can sell a product without actually proving the active component is present or proving the active component is present at the stated concentration. My research project is focused on analyzing glutamine supplements, testing for both the presence and abundance of glutamine and comparing that to the specifications defined on the packaging. This project ultimately aims to raise awareness of regulatory compliance of pharmaceuticals and their role in our society.
Stem Cell Therapy: Can insulin-producing cells be generated to treat diabetes in dogs?
Is the time for daily insulin injections for the treatment of diabetes coming to an end? Everyday thousands of pets are subjected to insulin injections to treat their diabetes. This puts a major strain on both the animals and their owners. I have the privilege to collaborate with Likarda, an animal health company seeking to find a better treatment for type 1 diabetes in companion animals. Our goal is to develop and optimize an effective and cost-efficient way of transforming stem cells into insulin producing cells that can be stably infused into animals. My project specifically examines the growth signals required to generate these cells in culture. Ultimately, this would serve as a long-term treatment for animals suffering from diabetes and thus eliminate the need for daily injections.
Biotech Seniors 2018 - 2019
Cancer Biology: Human cancer cells metabolize sugar in an aberrant way. Can this be reversed to remediate the cancer?
Cancer cells can display an array of aberrant cellular behaviors. One of these behaviors, termed the Warburg Effect, describes cancer cells that overproduce lactate through anaerobic metabolism. My research aims to design and validate a lactate quantitation assay. This assay will be used to characterize the Warburg Effect in various cancer cell lines. Additional studies will be performed to reduce the expression of Lactate Dehydrogenous, a key enzyme that produces lactate, and assess the antiproliferative effects of this modification. Ultimately, this lactate quantification assay could potentially be used by other cancer research labs to characterize metabolism of their cultured cells in an inexpensive way.
Cancer Therapy: Is Lychee fruit a cancer-slaying super food?
My project involves utilizing an extract, called kuromanin, from lychee fruit to treat breast cancer cells. The treatments have shown promise in other studies and I would like to build on those by not only testing extracts made from fresh fruit, but by also testing extracts from frozen and canned lychee because they are more widely available. From this project I hope to further investigate whether or not kuromanin could be used as a viable treatment for cancer in the future.
Antibiotic Resistance: Does Manuka Honey contain our next-generation antibiotic?
Concerns have grown rapidly about antibiotic resistance in the recent years. Scientists are working to create and discover novel antibiotic drugs to combat this resistance. My project focuses on this area of scientific inquiry. Specifically, I am fascinated by the potential antimicrobial ability of honeys, especially Manuka honey. Methylglyoxal is the major antimicrobial component found in Manuka Honey. In my project, I am going to use the Kirby-Bauer method and microbial viability assays to measure the antimicrobial effects of Methylglyoxal against gram-positive, gram-negative and multidrug-resistant bacterial strains.
Drug Delivery: Can that diet soda really affect your brain? An in vitro study of aspartame permeability across the blood-brain barrier.
My capstone focuses on the design and validation of an in vitro blood-brain barrier assay. I would like to see if aspartame can pass through the blood-brain barrier using the neutral amino acid transporter (NAAT), which is expressed in the hCMEC/D3 human endothelial blood-brain barrier cell line. I will use high pressure liquid chromatography (HPLC) to measure the permeability of the aspartame into the brain in vitro.
Gene Editing: Using CRISPR to make bacteria glow
I am doing my project on gene editing. Specifically, I will be using CRISPR-Cas9, a gene-editing tool derived from bacteria, to incorporate a fluorescence gene (GFP) into a specific region of the E. Coli genome. This experimental work will serve as a training experience as I seek to master the CRISPR-Cas9 tool. My follow-up studies will use CRISPR-Cas9 to specifically edit a gene within mammalian cells grown in culture.
Disease Biomarkers: Creating an in-home test for PSA, a protein correlated with prostate cancer
PSA (prostate-specific antigen) is used as a biomarker to screen for prostate cancer in men. For my project, I want to develop an at-home test strip to assess PSA levels. The test strip will be designed to detect blood levels of PSA that exceed 3 ng/mL (the established threshold for a positive result in clinical testing). The broader goal of this project is to make it easier and cheaper for men to screen for prostate cancer. The increased ease and accessibility of this at-home test will hopefully decrease the number of deaths caused from delayed clinical testing.