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 "Biochemistry"
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Item A native Coreopsis variant competes more strongly against the invasive Verbena brasiliensis(2023-04-13) Nguyen, Minh KhueOrganic light- emitting diodes (OLEDs) are the top-performing technology for flat-panel color displays in smartphones and televisions. Cyclometalated iridium complexes are the most successful class of phosphorescent metal complexes used to produce light in OLEDs. Currently, blue-phosphorescent iridium complexes are the most challenging due to the requirement of the high HOMO-LUMO energy gaps. Strong s-donors are targeted as a supporting ligand for blue-emitting compounds. Acyclic diaminocarbene (ADC) and other strong s-donors ancillary ligands derived from isocyanide precursors are hypothesized to improve the phosphorescence efficiency. Understand the effects of these ancillary ligands on photophysical properties are the key to producing better blue-phosphorescent iridium complexes which are suitable for OLEDs application. Cycolometating ligands are used to control phosphorescence color and fluorinated 2-phenyl pyridine ligands are known to give blue phosphorescence. So fluorinated 2-phenyl pyridine-based cyclometalating ligands are used in this study and paired with different ancillary ligands installed by reactions between azide and isocyanides. Aryl isocyanide ligands with different electronic characteristics (CNAr-dmp, CNAr-NO2, CNAr-OMe, CNtBu) were used to produce different bis-cyclometaled iridium bis-isocyanide complexes. Then the bis-cyclometalated iridium bis-isocyanide complexes react with sodium azide (NaN3) in different solvents (CH2Cl2, CH3CN) at different conditions. This process produces new luminescent structures. These complexes have unique structures but were not obtained by the traditional synthesis route and they have unusual photophysical properties.Item Analysis of the SARS-CoV-2 nucleocapsid protein suggests multiple structures suitable for use in vaccine design(2023-04-13) Calderon-Macedo, AlfredoSARS-CoV-2 is the virus that causes the Covid-19 respiratory disease. Recently, we developed an aerosol based vaccine strategy using the Spike protein as the main antigen. However, the nucleocapsid protein (N-protein) of this virus is also highly immunogenic and has potential for use as part of a vaccine strategy. Here, we use a combination of Structure-Based Epitope Predictions and Molecular Dynamics Simulations to find and investigate the stability of N-protein epitopes. We observed that the N-protein contains structures that are stable, and thus have potential for use in our new vaccine strategy. ***This project was completed with contributions from Esteban Dodero-Rojas and José N. Onuchic from Rice University.Item Assessing changes of a Third Ward food pantry exiting the COVID-19 pandemic: A retrospective study(2023-04-13) Armbruster, Bryan; Bhattacharya, Zahra; Bhat, SuryaThe University of Houston Food Insecurity Team (FIT) has been a dedicated force in addressing the issue of food insecurity in the Third Ward. We have partnered with the Houston Food Bank to establish student-led pantries in the Third Ward and have been committed to addressing the ever-changing demands of those who face food insecurity. As we strive to be aware of the evolving burden of food insecurity, we began to question how food insecurity has changed since the Covid-19 pandemic. The FIT research team sought to address this question by investigating how our clientele demographics have changed at Riverside Methodist Church food pantry located in the Third Ward. We have conducted a retrospective analysis of demographic data that was collected from the early months of the pandemic and compared it to the demographic data collected earlier this year. Our research and findings have helped the program gain a deeper understanding of how the pandemic has impacted food insecurity in our community, and how our community compares to other regions of the country. By examining changes in our clientele demographics, we have identified new challenges and opportunities for our program. We recognized that the Third Ward has stagnated in the battle against food insecurity as a result of the pandemic, and we believe that this finding will help us adapt our program to develop new innovative approaches to combat food insecurity in the near future.Item Azide addition in Iridium isocyanide complexes(2023-04-13) Nguyen, NgocDespite being preventable, suicide has consistently been one of the major leading causes of death for people ages 10-14 and 25-34 (Centers for Disease Control and Prevention [CDC], 2022). Research has identified depression and perceived stress as risk factors among others for suicide. Additionally, previous studies found that depression mediated the relationship between stress and suicidality in which greater stress was associated with more depressive symptoms, and hence, greater involvement in suicidal behaviors (Hirsch et al., 2019; Smith et al., 2015). The current study examined the interrelationship between depression, stress, and suicidal thoughts. We hypothesize that stress will strengthen associations between depression and stress. Logistic regression was used to analyze data from 958 participants taken from the UC Berkeley Social Networks Study. Results suggest that both depression and stress were positively associated with suicidal thoughts. However, contrary to our hypothesis, as depression increases, people with high stress are less likely to endorse suicidal thoughts in the past year. This finding contradicts prior research on stress and suicide, and proposes the possibility that stress could be a protective factor against suicidal thoughts for people with depression. However, more studies should be conducted to investigate the kind of stress underlying this relationship.Item Finding Molecular Inhibitors to Neutralize SARS-CoV-2 Infection and its Variants(2023-04-13) Islam, TasneemThe COVID-19 outbreak has affected global public health and resulted in 487 million confirmed cases. The SARS-CoV-2 spike protein binds to the human ACE2 receptor through its receptor binding domain which mediates viral entry and membrane fusion. The virus invades the body through the respiratory and circulatory systems of people of all ages. The pandemic has underscored a need to identify effective molecular inhibitors of the viral spike protein. We found a small molecule, CD04872SC, through Maybridge and ZINC library analysis and were able to show that it can neutralize SARS-CoV-2 infection, along with its Delta and Omicron variants. This inhibitor forms close associations with the hydrophobic residues of the spike protein's receptor binding domain in order to block binding with the ACE2 receptor. We also conducted a thermal shift assay in order to demonstrate the binding affinity between the known inhibitor and each viral protein. The data from our fluorescence and computational analyses indicates that the molecular inhibitor stabilizes each variant and has the potential to be broad-spectrum viral treatment.Item Fluorescence assay to monitor dormancy in M. luteus.(2023-04-13) Tran, TungTuberculosis is one of the most prevalent infectious diseases, afflicting nearly 10 million and killing ~ 1.5 million people in 2021 (2). Mycobacterium tuberculosis cannot be eradicated entirely because it undergoes clinical dormancy during antibiotic challenge. In this state, the bacteria are not susceptible to antibiotics. How Mycobacterium tuberculosis enters dormancy is key to develop drugs that can prevent dormancy and lead to eradication. Micrococcus luteus (M. luteus) is used as a model organism for studying M. tuberculosis because it is a nonpathogenic Actinobacteria with a short doubling time, smaller genome that has a reproducible dormant state like M. tuberculosis (1). Dormancy is described as a Viable But Non Culturable (VBNC) state of bacteria where dormant cells fail to grow on solid media (1). A more sensitive and convenient measure of dormancy is required for rapid determination of when cells enter or exit dormancy. This assay will allow us to monitor the change in fluorescent signals of individual cells as they switch from active state to dormancy. In this subproject, we aim to create a plasmid that allows the transfer and insertion of any gene, specifically the Green Fluorescent Protein (GFP) gene, into the M. luteus genome via homologous recombination. The plasmid consists of the open reading frame of a growth-neutral gene in M. luteus called ctrE, the chloramphenicol resistance gene (CMr), and the flanking sequences that are complementary to the regions surrounding crtE gene in M. luteus genome.Item High-throughput tuning of methacrylic-acid-based hydrogels with calcium and chitosan as secondary ionic cross-linkers(2023-04-13) Allen, Natalie; Rabago, Leonardo; Valdez, Lizbet; Wallaert, SamuelCovalent hydrogel networks predominantly derived from methacrylic acid were developed as a platform for the exploration of atomic (in the form of calcium) and biopolymer polyelectrolyte (in the form of chitosan) secondary ionic cross-linkers. Well-defined chitosan was prepared from chitin and incorporated at various loadings in hydrogel precursor solutions, resulting in template polymerizations. Resultant hydrogels were soaked in various concentrations of aqueous calcium chloride and characterized by compression testing.Item Invesitgation of fecal pH in Healthy Volunteers Receiving Oral Omadacycline or Vancomycin(2023-04-13) Agyapong, Samantha; Jo, Jinhee; Lancaster, Chris; Gonzales-Luna, Anne J.Antibiotics have profound disrupting effects on the gut microbiome including pH. An easy method to measure gut dysbiosis is not currently available. This study aims to investigate the fecal pH in healthy volunteers receiving antibiotics and to assess the utility of fecal pH as a potential gut dysbiosis marker. Antibiotics have profound disrupting effects on the gut microbiome including pH. An easy method to measure gut dysbiosis is not currently available. The aim of this study was to investigate the fecal pH in healthy volunteers receiving antibiotics and to assess the utility of fecal pH as a potential gut dysbiosis marker. Healthy subjects aged 18 and 40 years were recruited and randomized to receive either oral omadacycline or vancomycin for 10 days. Fecal samples were collected at baseline, during therapy, and follow-ups. Approximately 100 mg of solid fecal sample was treated with 50 uL of NaCl for the pH measurement. A major shift from the baseline pH was observed on day 9 in the vancomycin group (7.12 ± 0.74; mean ± SD) while on day 5 in the omadacycline group (6.86 ± 0.8; mean ± SD). Both antibiotic groups had an increasing trend during therapy and a decreasing trend by the follow up days. The findings of our study suggest that both omadacycline and vancomycin modify the pH of the gastrointestinal tract of otherwise healthy adults to be more alkaline. Future studies are needed to better understand the implications of this phenomenon.Item Real-Time Monitoring of T-Cell Function to Identify Tumor Evasion Mechanisms(2023-04-13) Adeleye, Adeola; Elldakli, HadilImproving immunotherapy depends on a better understanding of the tumor microenvironment (TME). Recent research has shed light on tumor intrinsic factors that lead to exhaustion of immune cells, particularly T-cells. Identifying tumor intrinsic factors will help us develop effective immunotherapies. However, lack of real time T-cell monitoring has hindered identification of tumor intrinsic factors with immune suppressive roles. Calcium ions are used by T-cells to communicate and coordinate their activities. Thus, the intracellular levels of Ca2+ could be used to monitor T-cell function. We aim to develop a real-time T-cell monitoring platform based on calcium influx to evaluate the function of T-cells and identify tumor evasion mechanisms. The plasmid encoding a Ca2+ indicator (GCaMP6f) fused with another fluorescent protein (dTomato) was constructed using Gibson Assembly. After sequencing, constructed plasmid was analyzed using BLAST and SnapGene. Retrovirus expressing the constructed plasmid was generated by Plat-E cells transfection. The retrovirus was transduced into murine pmel T-cells. Flow cytometry analysis was used to determine the transduction efficiency. The changes of Ca2+ levels in response to TCR-independent stimulation (Ionomycin) and TCR-dependent stimulation (tumor) were determined to evaluate the performance of the real-time T-cell monitoring platform. We found that there was a 71% transduction efficiency of double positive GFP and dTomato expression in pmel T-cells. Dynamic changes of EGFP intensity in dTomato-positive T-cells after stimulation were observed in both experimental settings. Our data suggests that we successfully generated a virus vector which was used to express EGFP to monitor T-cell function.Item Suppression of native plant by invasives' Verbena brasiliensis' increases with soil fertility.(2023-04-13) Romero, CarlaThe Stress Gradient Hypotheses suggests that plants in highly stressful environments compete less aggressively with one another and move more toward facilitation. Verbena Brasiliensis is an invasive perennial plant in Texas that often co-occurs with the native forb Lythrum alatum. Understanding how these plants respond to one another under different precipitation and soil nutrient conditions would be helpful in setting priorities for management of invasive plants, especially in the context of climate change. My research asks the question whether V. brasiliensis is less suppressive of the growth of the native L. alatum under increasing levels of nutrient and water stress. My expectation is that consistent with the Stress Gradient Hypothesis, the suppression of L. alatum growth by V. brasiliensis will be weaker at lower water and nutrient levels.Item Synthesis of an Asymmetric Imine/bis(pyrazolyl)alkane Ligand(2023-04-13) Seto, NathanThe field of coordination chemistry has a variety of applications, both biological and industrial. Some notable products include pharmaceutical compounds like L-DOPA (used as a treatment for Parkinsonï¾’s disease) and cisplatin (an anticancer drug), and consumer-grade products like fibers and plastics (through polymerization of ethylene and propylene). To that end, the use of metal coordination complexes is a crucial part of ensuring efficient reactions. In this experiment, we explore the synthesis of nonsymmetrical ligands using an imine/bis(pyrazolyl)alkane as a base for the production of new bimetallic coordination complexes. A successful synthesis was achieved using 2,6-diformyl-4-tert-butylphenol followed by a two-step di-substitution reaction of aniline and bis-(3,5-dimethylpyrazolyl)methanone. Product identity was confirmed by proton NMR. Additionally, it was found that by using an unsubstituted aniline, and in the absence of acid, synthesis of the asymmetric ligand could be achieved with close to 99% yield and in relatively high purity. Furthermore, under scaled-up conditions, the reaction had similar yield and purity when compared to the small-scale reaction. These results show promise, as large amounts of ligand can be made for future metal ion chelation. The next step in our research is to use our imine/bis(pyrazolyl) ligand for hetero- and homobimetallic substitutions using main group elements, like zinc and lithium.Item Ventral Spinal Cord Astrocyte Reactivity is Context Dependent on TF Nkx6.1(2023-04-13) Maleki, EhsonAstrocytes, glial cells essential for the maintenance and function of neuronal circuits in the central nervous system (CNS), are functionally diverse across CNS regions. To determine the maintenance of this diversity, we identified transcription factors (TF) with region-specific expression. Through immunohistochemical staining, we have been able to identify the expression of five neurodevelopmental TFs in mature spinal cord astrocytes: Nkx6.1, Nkx6.2, Nkx2.2, Msx1, and Olig2. Notably, Nkx6.1 expression is expressed specifically in mature ventral spinal cord astrocytes. The functional role of Nkx6.1 in homeostatic conditions remains unknown and in disease state also remains unknown. By leveraging immunohistochemistry, we identified the expression of Nkx6.1 in astrocytes of multiple sclerosis and ALS mouse models, suggesting that these astrocytes play a role in disease states. Indeed, we found that the Nkx6.1 cKO astrocytes become more reactive in multiple sclerosis and that Nkx6.1 expression is reduced in ventral spinal cord astrocytes of ALS mice compared to controls. ***This project was completed with contributions from Benjamin Deneen and Navish A. Bosquez Huerta from the Baylor College of Medicine.