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- All Subjects: Genetics
- Creators: School of Life Sciences
Description
Colorimetric assays are an important tool in point-of-care testing that offers several advantages to traditional testing methods such as rapid response times and inexpensive costs. A factor that currently limits the portability and accessibility of these assays are methods that can objectively determine the results of these assays. Current solutions consist of creating a test reader that standardizes the conditions the strip is under before being measured in some way. However, this increases the cost and decreases the portability of these assays. The focus of this study is to create a machine learning algorithm that can objectively determine results of colorimetric assays under varying conditions. To ensure the flexibility of a model to several types of colorimetric assays, three models were trained on the same convolutional neural network with different datasets. The images these models are trained on consist of positive and negative images of ETG, fentanyl, and HPV Antibodies test strips taken under different lighting and background conditions. A fourth model is trained on an image set composed of all three strip types. The results from these models show it is able to predict positive and negative results to a high level of accuracy.
ContributorsFisher, Rachel (Author) / Blain Christen, Jennifer (Thesis director) / Anderson, Karen (Committee member) / School of Life Sciences (Contributor) / Harrington Bioengineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description
The Dorrance Center for Rare Childhood Disorders is a unique research division at TGen (The Translational Genomics Research Institute) that provides personalized care to children and young adults facing rare, undiagnosed diseases. TGen scientists believe that the answers to these enigmatic disorders can often be found in a person's genetic code. They aim to solve these genetic mysteries using whole exome sequencing, a method that prioritizes the protein-coding portion of the genome in the search for disease-causing variants. Unfortunately, a communication gap sometimes exists between the TGen scientists and the patients they serve. I have seen, first hand, the kind of confusion that this study elicits in the families of its participants. Therefore, for my thesis, I decided to create a booklet that is meant to provide some clarity as to what exactly The Dorrance Center for Rare Childhood Disorders does to help diagnose children with rare disorders. The purpose of the booklet is to dispel any confusion regarding the study by providing a general review of genetics and an application of these lessons to the relevant sequencing technology as well as a discussion of the causes and effects of genetic mutations that often times are linked to rare childhood disorders.
ContributorsCambron, Julia Claire (Author) / LaBelle, Jeffrey (Thesis director) / Huentelman, Matt (Committee member) / Barrett, The Honors College (Contributor) / Department of Chemistry and Biochemistry (Contributor) / School of Life Sciences (Contributor)
Created2015-05
Description
Duchenne Muscular Dystrophy (DMD) is an X-linked recessive disease characterized by progressive muscle loss and weakness. This disease arises from a mutation that occurs on a gene that encodes for dystrophin, which results in observable muscle death and inflammation; however, the genetic changes that result from dystrophin's dysfunctionality remain unknown. Current DMD research uses mdx mice as a model, and while very useful, does not allow the study of cell-autonomous transcriptome changes during the progression of DMD due to the strong inflammatory response, perhaps hiding important therapeutic targets. C. elegans, which has a very weak inflammatory response compared to mdx mice and humans, has been used in the past to study DMD with some success. The worm ortholog of the dystrophin gene has been identified as dys-1 since its mutation phenocopies the progression of the disease and a portion of the human dystrophin gene alleviates symptoms. Importantly, the extracted RNA transcriptome from dys-1 worms showed significant change in gene expression, which needs to be further investigated with the development of a more robust model. Our lab previously published a method to isolate high-quality muscle-specific RNA from worms, which could be used to study such changes at higher resolution. We crossed the dys-1 worms with our muscle-specific strain and demonstrated that the chimeric strain exhibits similar behavioral symptoms as DMD patients as characterized by a shortened lifespan, difficulty in movement, and a decrease in speed. The presence of dys-1 and other members of the dystrophin complex in the body muscle were supported by the development of a resulting phenotype due to RNAi knockdown of each component in the body muscle; however, further experimentation is needed to reinforce this conclusion. Thus, the constructed chimeric C. elegans strain possesses unique characteristics that will allow the study of genetic changes, such as transcriptome rearrangements and dysregulation of miRNA, and how they affect the progression of DMD.
ContributorsNguyen, Thuy-Duyen Cao (Author) / Mangone, Marco (Thesis director) / Newbern, Jason (Committee member) / Duchaine, Thomas (Committee member) / School of Social Transformation (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
ContributorsSavarese, Erica (Author) / Robert, Jason (Thesis director) / Hurlbut, Ben (Committee member) / Verrelli, Brian (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2013-05
Description
It is important to consider factors that contribute to successful fertilization and the development of viable offspring. Better understanding the factors that contribute to infertility can be used to assist in the development of viable offspring, especially for human beings looking to successfully reproduce. Identifying paternal effect genes, genes that come from the father, introduces more targets that can be manipulated to produce specific reproductive effects. Use of Drosophila melanogaster as a model to study reproduction has increased, in part, due to the use of the GAL4 system. In this system, the GAL4 gene encodes an 881 amino acid protein that binds to the 4-site Upstream Activating Sequence (UAS) to induce transcription of the gene of interest. These sequences constitute the two components of the system: the driver (GAL4) and the responder (gene of interest) \u2014 each of which is maintained as a separate parental line. Effects of the GAL4 driver line "driving" transcription of the responder can be assessed by examining the offspring. One of the more common uses of the GAL4 system involves analyzing phenotypic effects of reducing or eliminating expression of a target gene through the induction of RNAi transcription, which often results in toxicity, lethality, or reduced viability. Utilizing these principles, we strove to demonstrate the effect of knocking down the expression of testis-specific sperm-leucyl-aminopeptidases gene CG13340 on progeny by inducing expression of RNAi with two distinct GAL4 driver lines - one with a nonspecific actin-binding activation sequence and the other with a testis-specific activation sequence. Comparison of both GAL4 driver lines to crosses using N01 wild type ("wt") flies verify that inducing RNAi transcription using the GAL4 system results in reduction of proper offspring development. Further studies using D. melanogaster and the GAL4 system can improve knowledge of factors contributing to male fertility and also be applied to better understand mammalian, specifically human, fertility.
ContributorsEvans, Donna Marie (Author) / Karr, Timothy L. (Thesis director) / Roland, Kenneth (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor) / Department of English (Contributor)
Created2014-05
Description
Amyotrophic lateral sclerosis (ALS), also known as Lou Gehrig's disease, is a devastating illness that causes the degeneration of both upper and lower motor neurons, leading to eventual muscle atrophy. ALS rapidly progresses into paralysis, with patients typically dying due to respiratory complications within three to five years from the onset of their symptoms. Even after many years of research and drug trials, there is still no cure, and current therapies only succeed in increasing life-span by approximately three months. With such limited options available for patients, there is a pressing need to not only find a cure, but also make new treatments available in order to ameliorate disease symptoms. In a genome-wide association study previously conducted by the Translational Genomics Research Institute (TGen), several single-nucleotide polymorphisms (SNPs) upstream of a novel gene, FLJ10968, were found to significantly alter risk for ALS. This novel gene acquired the name FGGY after publication of the paper. FGGY exhibits altered levels of protein expression throughout ALS disease progression in human subjects, and detectable protein and mRNA expression changes in a mouse model of ALS. We performed co-immunoprecipitation experiments coupled with mass spectrometry in order to determine which proteins are associated with FGGY. Some of these potential binding partners have been linked to RNA regulation, including regulators of the splicesomal complex such as SMN, Gemin, and hnRNP C. To further validate these findings, we have verified co-localization of these proteins with one another. We hypothesize that FGGY plays an important role in ALS pathogenesis, and we will continue to examine its biological function.
ContributorsTerzic, Barbara (Author) / Jensen, Kendall (Thesis director) / Francisco, Wilson (Committee member) / Barrett, The Honors College (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Department of Chemistry and Biochemistry (Contributor) / School of Life Sciences (Contributor)
Created2014-05
Description
The NCAA recently declared sickle cell trait (SCT) to be a risk factor for sudden illness and death among student athletes. Fetal hemoglobin (HbF) concentration in adults is negatively correlated with disease severity in sickle cell anemia, although its effect on SCT is not fully understood and the concentration is found to have high variability across populations. Two single nucleotide polymorphisms (SNPs) at the human beta globin gene cluster, rs7482144 and rs10128556, contribute to the heritable variation in HbF levels and are associated with increased HbF concentrations in adults. A sample population of NCAA football student athletes was genotyped for these two polymorphisms, and their allele frequencies were compared to those of other populations. The minor allele of both polymorphisms had allele frequencies of 0.091 in the sample population, which compared closely with other populations of recent African heritage but was significantly different from European populations. The results of this study will be included in a larger study to predict whether these among other polymorphisms can be used as markers to predict susceptibility to heat-related emergencies in NCAA student athletes with SCT, although the small sample size will delay this process until participation in the study increases. Since both rs7482144 and rs10128556 exhibit high levels of linkage disequilibrium, and as their contributions to the heritable variability of HbF concentrations tend to differ greatly between populations of different ancestry, further investigations should be aimed at distinguishing between the effects of each SNP in African American, European, and other populations represented in NCAA football before conclusions can be drawn as to their practical use as genetic markers of heat susceptibility in student athletes with SCT.
ContributorsGrieger, Ryan Wayne (Author) / Stone, Anne C. (Thesis director) / Rosenberg, Michael (Committee member) / Madrigal, Lorena (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2014-05
Description
The knowledge of medical genetics is currently used with prenatal testing, and the advancements in the field of behavioral genetics may someday allow for its use with prenatal testing as well. The use of prenatal procedures for medical phenotypes has its own implications and should these techniques be used for behavioral phenotypes, such implications can also apply. The complexity of behavior in terms of the factors that may affect it, along with the way it is conceptualized and perceived, adds further implications for prenatal testing of it. In this thesis, I discuss the qualitative, quantitative, and historical facets of prenatal testing for medical and behavioral phenotypes and the undercurrent of eugenics. I do so by presenting an example of the medical phenotype (cystic fibrosis) as a case for envisioning the implications of medical phenotypes before delving into examples of behavioral phenotypes (aggression, impulsivity, extraversion, and neuroticism) in order to explore the implications shared with those for medical phenotypes as well as those unique to it. These implications then set the foundation for a discussion of eugenics, and the considerations for how behavioral genetics with prenatal testing may give way to a modern form of it.
ContributorsMinai, Mandana (Author) / Maienschein, Jane (Thesis director) / Robert, Jason (Committee member) / Magnus, David (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor) / Department of Psychology (Contributor)
Created2014-05
Description
Esophageal adenocarcinoma (EAC) is one of the most lethal and fastest growing cancers in the United States. Its onset is commonly triggered by metaplastic transformation of normal squamous esophageal epithelial cells to Barrett's esophagus (BE) cells in response to acid reflux. BE patients are believed to progress through non-dysplastic metaplasia and increasing grades of dysplasia prior to EAC. Conventional cancer diagnostic tools rely on bulk-cell analyses that are incapable of identifying intratumoral heterogeneity or rare driver cells that play important roles in cancer progression. An improved single-cell method of cancer diagnosis would overcome this challenge by detecting cancer initiating cells before they progress into untreatable stages. In this study, using EAC as a model, we attempted to identify a more effective method of cancer diagnosis. We quantified the single- and bulk-cell mRNA expression of genes that have been proposed to be instrumental in the progression of EAC through BE. Quantitative Reverse Transcription Polymerase Chain Reaction (qRT-PCR) analysis was performed on human primary cells to measure the mRNA expression levels of BE- and EAC-associated genes. Our results showed high levels of heterogeneity of CDX2 and TFF3 at the single-cell resolution in human BE and EAC samples. Additionally, while expression of VEGF is generally low at the bulk-cell level, our results showed that a few, rare cells had significantly higher VEGF expression levels than the majority of cells in the EAC sample. In conclusion, we have affirmed that EAC cancer cells, as well as BE cells, show high levels of heterogeneity. Based on the VEGF gene expression pattern, single-cell analysis could potentially be more effective for identifying rare, but essential cells for cancer progression, which could then be targeted for treatment. Future studies will focus on analyzing human samples from thousands of normal and cancer subjects to validate the use of single-cell profiling in cancer.
ContributorsHaeuser, Kelsey Lynn (Author) / Tran, Thai (Thesis director) / Kelbauskas, Laimonas (Committee member) / Gao, Weimin (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2013-12
Description
Alternative polyadenylation (APA) is the biological mechanism in which the same gene can have multiple 3'untranslated region (3'UTR) isoforms due to the presence of multiple polyadenylation signal (PAS) elements within the pre mRNAs. Because APA produces mRNA transcripts that have different 3'UTR isoforms, certain transcripts may be subject to post-transcriptional regulation by regulatory non-coding RNAs, such as microRNAs or RNA binding proteins defects of which have been implicated in diseases such as cancer. Despite the increasing level of information, functional understanding of the molecular mechanisms involved in transcription is still poorly understood, nor is it clear why APA is necessary at a cell or tissue-specific level. To address these questions I wanted to develop a set of sensor strain plasmids capable of detecting cleavage and polyadenylation in vivo, inject the complete sensor strain plasmid into C. elegans and prepare stable transgenic lines, and perform proof-of-principle RNAi feeding experiments targeting genes associated with the cleavage and polyadenylation complex machinery. I demonstrated that it was possible to create a plasmid capable of detecting cleavage and polyadenylation in C. elegans; however, issues arose during the RNAi assays indicating the sensor strain plasmid was not sensitive enough to the RNAi to effectively detect in the worms. Once the problems involved with sensitivity and variability in the RNAi effects are resolved, the plasmid would be able to better address questions regarding the functional understanding of molecular mechanisms involved in transcription termination.
ContributorsWilky, Henry Patrick (Author) / Mangone, Marco (Thesis director) / Newbern, Jason (Committee member) / Blazie, Stephen (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2015-05