Matching Items (151)
Description
The purpose of this thesis creative project was to create an educational video to present research findings on the increasingly important issue of human biospecimen preanalytic variables. When a human biospecimen, such as blood, urine, or tissue, is removed from the body, it is subjected to a plethora of variables that are not recorded or regulated in a vast majority of cases. Frequently, these samples arrive at the research or pathology lab with an unknown history, then undergo analysis for translational research purposes, or to guide clinical management decisions. Thus, compromised specimen quality caused by preanalytic variables has substantial, and potentially devastating, downstream effects. To identify the preanalytic variables with the greatest impact on blood and tissue specimen quality, 45 articles were gathered using PubMed and Google Scholar databases and cited. Based on the articles, the top five variables with the most detrimental effects were identified for both blood and tissue samples. Multiple sets of parameters ensuring specimen fitness were compared for each of the five variables for each specimen type. Then, specific parameters guaranteeing the fitness of the greatest number of analytes were verified. To present the research findings in greater detail, a paper was written that focused on identifying the top variables and key parameters to ensure analyte fitness. To present the overall issue in an easy-to-digest format, a storyboard and script were created as a guideline for a final video project. Ultimately, two alternate versions of the video were created to pertain to the audience of choice (one version for patients, one version for professionals). It is the hope that these videos will be used as educational tools to continue efforts to standardize and enforce human biospecimen preanalytic variable parameters. This is a necessary step to improve the accuracy of our biomedical research data and the healthcare of patients worldwide.
ContributorsAzcarate, Heather (Author) / Compton, Carolyn (Thesis director) / LaBaer, Joshua (Committee member) / Borges, Chad (Committee member) / Barrett, The Honors College (Contributor) / Department of Psychology (Contributor)
Created2018-12
Description
Cleavage and polyadenylation is a step in mRNA processing in which the 3’UTR is cleaved and a polyA tail is added to create a final mature transcript. This process relies on RNA sequence elements that guide a large multimeric protein complex named the Cleavage and Polyadenylation Complex to dock on the 3’UTR and execute the cleavage reaction. Interactions of the complex with the RNA and specific dynamics of complex recruitment and formation still remain largely uncharacterized. In our lab we have identified an Adenosine residue as the nucleotide most often present at the cleavage site, although it is unclear whether this specific element is a required instructor of cleavage and polyadenylation. To address whether the Adenosine residue is necessary and sufficient for the cleavage and polyadenylation reaction, we mutated this nucleotide at the cleavage site in three C. elegans protein coding genes, forcing the expression of these wt and mutant 3’UTRs, and studied how the cleavage and polyadenylation machinery process these genes in vivo. We found that interrupting the wt sequence elements found at the cleavage site interferes with the cleavage and polyadenylation reaction, suggesting that the sequence close to the end of the transcript plays a role in modulating the site of the RNA cleavage. This activity is also gene-specific. Genes such as ges-1 showed little disruption in the cleavage of the transcript, with similar location occurring in both the wt and mutant 3’UTRs. On the other hand, mutation of the cleavage site in genes such as Y106G6H.9 caused the activation of new cryptic cleavage sites within the transcript. Taken together, my experiments suggest that the sequence elements at the cleavage site somehow participate in the reaction to guide the cleavage reaction to occur at an exact site. This work will help to better understand the mechanisms of transcription termination in vivo and will push forward research aimed to study post-transcriptional gene regulation in eukaryotes.
ContributorsSteber, Hannah Suzanne (Author) / Mangone, Marco (Thesis director) / Harris, Robin (Committee member) / LaBaer, Joshua (Committee member) / School of Life Sciences (Contributor, Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
Cancer is one of the leading causes of death globally according to the World Health Organization. Although improved treatments and early diagnoses have reduced cancer related mortalities, metastatic disease remains a major clinical challenge. The local tumor microenvironment plays a significant role in cancer metastasis, where tumor cells respond and adapt to a plethora of biochemical and biophysical signals from stromal cells and extracellular matrix (ECM) proteins. Due to these complexities, there is a critical need to understand molecular mechanisms underlying cancer metastasis to facilitate the discovery of more effective therapies. In the past few years, the integration of advanced biomaterials and microengineering approaches has initiated the development of innovative platform technologies for cancer research. These technologies enable the creation of biomimetic in vitro models with physiologically relevant (i.e. in vivo-like) characteristics to conduct studies ranging from fundamental cancer biology to high-throughput drug screening. In this review article, we discuss the biological significance of each step of the metastatic cascade and provide a broad overview on recent progress to recapitulate these stages using advanced biomaterials and microengineered technologies. In each section, we will highlight the advantages and shortcomings of each approach and provide our perspectives on future directions.
ContributorsPeela, Nitish (Author) / Nikkhah, Mehdi (Thesis director) / LaBaer, Joshua (Committee member) / Harrington Bioengineering Program (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2017-05
Description
Glioblastoma is the most aggressive and lethal brain tumor, due to its resistance to current conventional therapy. The resistance to chemo- and radiotherapy has been attributed to a special population of cells known as glioma stem cells. Previous literature has shown the importance of a Central Nervous System-restricted transcription factor OLIG2 in maintaining the tumor-propagating potential of these glioma stem cells. OLIG2's function was further elucidated, with its pro-mitogenic function due to its ability to negatively regulate the p53 pathway by suppressing the acetylation of the p53 protein's C terminal domain. Past work in our lab has confirmed that one of OLIG2's partner proteins is Histone Deacetylase 1 (HDAC1). In vitro experiments have also shown that targeting HDAC1 using hairpin RNA in glioma stem cells negatively impacts proliferation. In a survival study using a murine glioma model, targeting Hdac1 using hairpin RNA is shown to reduce tumor burden and increase survival. In this paper, we demonstrate that silencing Hdac1 expression reduces proliferation, increases cell death, likely a result of increased acetylation of p53. Olig2 expression levels seem to be unaffected in GSCs, demonstrating that the Hdac1 protein ablation is indeed lethal to GSCs. This work builds upon previously collected results, confirming that Hdac1 is a potential surrogate target for Olig2's pro-mitotic function in regulating the p53 pathway.
ContributorsLoo, Vincent You Wei (Author) / LaBaer, Joshua (Thesis director) / Mehta, Shwetal (Committee member) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2017-05
Description
Fruit flies show a strong attraction to fruit odors. Most fruit odors, including strawberry scent, are complex multimolecular mixtures comprised of many chemically distinct constituents. How animals are able to process these mixtures and derive behaviorally relevant information is largely unknown. A new procedure was created to test odor preference for Heisenberg canton-s strain of Drosophila melanogaster. 30 flies were cold anesthetized at 4.2°C for 30 minutes and then placed in a testing arena. After acclimating for 45 minutes, the flies were exposed to two sources of air, one with ripe strawberry odor and one with only humidified air. Images were captured every minute for an hour and a preference index was calculated for every 10th image. The Drosophila had a positive average preference for the strawberry odor. Five out of six trials showed a general increase in odor preference over the course of the trial. While there was a generally positive trend for average preference over time, there was not a significant increase in average odor preference from time 1 to time 60. The data indicates that Drosophila show a preference for strawberry odor over humidified air, and we propose to extend this test to investigate how Drosophila process and react to complex odors and their chemical constituents.
ContributorsSteinmetz, Kyle J (Author) / Smith, Brian (Thesis director) / Jernigan, Chris (Committee member) / School of Life Sciences (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2017-05
Description
Recent data suggests that olfactory input is important for antennal lobe development in honey bees. Chronic association of a single odor to food resources during crucial stages of development results in delayed antennal lobe development for mature foraging bees. The antennal lobes of these bees instead closely resemble an immature network observed in young, newly emerged bees. Using an odor stimuli variance assay, learning and memory tests can be used to explore how well honey bees discriminate single odors within complex odor mixtures. Here we are validating two different odor mixtures, a Brassica rapa floral blend and a second replicate mixture composed of common molecularly dissimilar odors. Odors in each mixture are either held constant or varied in concentration over 16 conditioning trials. Subsequent memory tests are performed two hours later to observe the ability of bees to distinguish and recognize specific odor components in each mixture. So far in our assay we find high rates of generalization for both odor mixtures. In general, more bees responded to all odors in the replicate treatment group over the Brassica treatment group. Additionally, bees in the Brassica treatment group did not respond to the target odor. More data is being collected to validate this assay. In future studies, I propose to apply this behavioral assay to bees with an altered olfactory developmental in order to see the functional impacts of this chronic odor association treatment.
ContributorsHalby, Rachael (Author) / Smith, Brian (Thesis director) / Jernigan, Christopher (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2017-05
Description
CREB3L1 has been previously shown to auto-acetylate itself when prepared from HeLa cell based in vitro protein expression lysates. To circumvent the concerns of the contamination of co-purified human proteins from HeLa lysates, the protein was purified through insect cell transfection in vitro. The objective of this study was to assay the auto-acetylation activity of CREB3L1 prepared from insect cells using the baculovirus expression vector system (BEVS). To this end, His-tagged CREB3L1 was affinity purified from Hi5 cells using an IMAC column and used for acetylation assay. Samples were taken different time points and auto-acetylation was by western using antibodies specific to acetylated lysines. Auto-acetylation activity was observed after overnight incubation. Future experiments will focus on the improvement of purification yield and the identification of the substrates and interacting proteins of CREB3L1 to better understand the biological functions of this novel acetyltransferase.
ContributorsSchwab, Anna (Author) / LaBaer, Joshua (Thesis director) / Qiu, Ji (Committee member) / Barrett, The Honors College (Contributor)
Created2017-05
Description
Asperger's syndrome is a high-functioning subset of Autism Spectrum Disorders (ASD). Diagnosed patients often lack refined social skills but possess a normal level of cognitive skills without delay in language development. These deficient social skills can impact the ability to find and maintain a job, which can be burdensome for all individuals involved in the patient's life. Although the causes of this condition are largely unknown, a wide variety of social and cognitive therapies have been used to reduce symptom severity, one of which is Mindfulness-Based Stress Reduction (MBSR). Mindfulness is the act of being aware on purpose to whatever is being experienced in the present moment with non-judgment and receptivity. MBSR has been used to bring greater awareness to sensations, thoughts and emotions with the result being reduced reactivity and increased purposeful responsiveness. It is therefore the aim of this study to address the use of an 8-week Mindfulness-Based Stress Reduction in adolescents with clinical Asperger's Syndrome to reduce reactive tendencies. This study will utilize a randomized control group of waitlisted participants given MBSR informational material and a practicing MBSR group. Post-MBSR Parent Global Impressions-III (PGI-III) and Social Responsiveness Scale scores are hypothesized to be improved in MBSR group and unaffected in the control for behavioral markers with no change in core autistic symptoms. Daily average cortisol response is also expected to decrease in the experimental group with unaffected levels in the control.
ContributorsBrzezinski, Molly Alexandra (Author) / Smith, Brian (Thesis director) / Sebren, Ann (Committee member) / School of Music (Contributor) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2017-05
Description
The mammalian olfactory system is commonly studied by using the mouse as a model system. Odor habituation is used to investigate odor perception and learning processes. Most previous experimental preparations have been tedious, requiring a researcher to manually change odorants, record investigation time and duration at each odorant, or physical alteration on the mice to enable video tracking. These limitations were overcame by creating an odorized hole-board to allow for systematic and automatic recording of olfactory behavior in mice. A cohort of five male mice were utilized in these experiments and the responses to the odor of strawberries, a diet staple of wile mice, were examined. Experiment 1 showed that free-feeding mice exhibit a preference to locations with strawberry (over control locations), even when these locations can only be identified using olfaction. This preference habituates within a trial but not across days. Experiment 2 showed that strawberry odor without reward causes habituation or extinction to the odor both within trials and across days. From these experiments, it can be concluded that mice innately explore strawberry odor and this can be exploited to the study odor habituation using an odorized hole-board.
ContributorsMa, Jason (Author) / Smith, Brian (Thesis director) / Gerkin, Richard (Committee member) / Oddo, Salvatore (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
Description
Animals must learn to ignore stimuli that are irrelevant to survival, a process referred to as latent inhibition. The Amtyr1 gene has been shown through quantitative trait loci mapping to be linked to strong latent inhibition in honey bees. Here we implicate this G-protein coupled receptor for the biogenic amine tyramine as an important factor underlying this form of learning in honey bees. We show that dsRNA targeted to disrupt the tyramine receptors, specifically affects latent inhibition but not excitatory associative conditioning. Our results therefore identify a distinct reinforcement pathway for latent inhibition in insects.
ContributorsPetersen, Mary Margaret (Author) / Smith, Brian (Thesis director) / Wang, Ying (Committee member) / Sinakevitch, Irina (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12