Undergraduate Research Day Projects
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Organized by the University of Houston Office of Undergraduate Research and Major Awards, Undergraduate Research Day is an annual event showcasing exceptional scholarship undertaken by the UH undergraduate community.
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Browsing Undergraduate Research Day Projects by Subject "Biochemical and Biophysical Sciences"
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Item A computational investigation of folding free energy surfaces and structural characterization of Staphylococcal Protein A(2023-04-13) Nguyen, Minh NgocInvasive plants disrupt native ecosystems and decrease native plant diversity. Under strong selection pressure, native plants sometimes adapt to better compete with an invasive species. My research investigates two variants of the annual forb Coreopsis that co-occur with the invasive forb Verbena brasiliensis. The objective of my research is to answer three questions: (1) Is an observed phenotypic variant Coreopsis more competitive than the wild type C. tinctoria? (2) If so, what traits potentially make it more competitive?, (3) Is it an adapted variety of C. tinctoria or a related species? Whether or not it is a separate species, the existence of a more competitive variant may provide an effective replacement for the wild-type C. tinctoria in native restoration projects within the range of V. brasiliensis. Results suggest that the invasive V. brasiliensis does not significantly suppress the biomass of the phenotypic variant C. tinctoria as much as that of the wild-type C. tinctoria. Furthermore, the variant produces significantly more flowers than the wild type suggesting it would be more competitive with the invasive plant than the wild type. The stark difference in growth habits between the two varieties of C. tinctoria suggests the variant may be a closely related species that converge in appearance at maturity.Item Dual Cross-Linking Improves Ability to Map Chromatin Loops(2023-04-13) Pasha, ShaizaHi-C is a method that maps the 3D architecture and folding pattern of the genome generating annotations of features, like DNA loops and domains, that bring distal elements in proximity and influence their regulation. Cross-linking samples is the first step in Hi-C and can greatly affect the quality of contacts observed in the Hi-C data. Here we are testing the quality of data processed with formaldehyde cross-linking versus formaldehyde plus DSG dual cross-linking in cell lines and human tissues, using standard Intact Hi-C protocol and Juicer 2 pipeline. We found that dual cross-linking improves noise statistics and DNA yield that can be attributed to heightened chromatin stability from the addition of DSG. Furthermore, we can see that looping signal, regulatory, and architectural features present are enhanced with dual cross-linking. After further investigation for robustness, dual cross-linking can be adopted as a new standard protocol for Hi-C tissue processing.Item ELISA Validation of Novel Urine Biomarkers of Lupus Nephritis Discovered Using O-link Proximity Extension Assay(2023-04-13) Thai, NgaBackground: Lupus nephritis (LN) is the inflammation of the kidneys, leading to reduced function. A renal biopsy is currently the preferred diagnosis method, but it cannot be serially repeated for monitoring disease progression and is not optimal for early diagnosis. Urine biomarkers can be used to determine the state of the kidney, diagnose the disease, and monitor disease progression noninvasively. Objective: To determine whether urinary biomarkers discovered using O-link Proximity Extension Assay (O-link) are reliable and reproducible using enzyme-linked immunosorbent assays (ELISA). Methods: Urine from the Hong Kong cohort was interrogated using the O-link technology for the levels of proteins that were significantly different in each step of lupus progression. On the basis of these screens, Human CXCL16, Human IGFBP-2, Human IL-1 RII, Human ICAM-2/CD102, Human FABP4/A-FABP, Human BAFF/BLyS/TNFSF13B, and Human E-selectin were selected for ELISA-based validation in an independent cohort from the University of Texas Southwestern. Results: After the determination of whether the standard proteins worked and the optimal sample dilution factor for each kit, significant differences in the protein levels of the healthy control and active renal samples. Conclusion: It has been demonstrated that O-link is a reliable method of discovering novel biomarkers of LN and the results are reproducible using ELISA screens. Through this study, we hope to find a biomarker that is an accurate and reliable measure for LN patients, with the potential of use in the necessary early detection and diagnosis of renal involvement, regular monitoring of disease activity, and long-term projections for LN.