19304 research outputs found
Sort by
Multiplexed Force Spectroscopy to Study Ribosomal Frameshifting and Power Stroke
No full textRibosome translocation catalyzed by elongation factor G (EF-G) is a critical step in protein synthesis, where the ribosome typically moves along the mRNA by three nucleotides at each step. The large conformational changes of EF-G in this process generate significant mechanical force, referred to as power stroke. To investigate this process, we have developed a novel multiplexed force spectroscopy technique that, for the first time, offers single-nucleotide resolution for multiple samples and efficiently probes power stroke amplitudes. This technique combines multiple acoustic force generators with the smallest atomic magnetometer designed for biological research. Details on instrumental design and characterization are provided. Using this technique, we demonstrated two applications. In the first application, we showed that EF-G mutation at the GTP binding pocket, T48V, resulted in the ribosome moving only two nucleotides on both ends of the mRNA, thereby compromising ribosome translocation. This finding suggested a direct link between GTP hydrolysis and ribosome translocation. Our results not only provided mechanistic insights into the role of GTP binding pocket but also illuminated how allosteric mutations can manipulate translocation. In the second application, we quantified EF-G power stroke more precisely and efficiently than previous works, and revealed its correlation with translocation fidelity for the first time. Two EF-G mutants, H584K and Q508K, were expressed, with the mutated residues directly interacting with tRNA. H584K, which interacts on codon-anticodon minihelix, produced a much reduced power stroke of 60 ± 6 pN and induced -1 frameshifting, wherein the ribosome translocated only two nucleotides on both sides of the mRNA. In contrast, Q508K, which interacts with tRNA residue 37 immediately outside the codon-anticodon minihelix, exhibited a power stroke of 89 ± 11 pN and maintained canonical 3-nt translocation, similar to wild-type EF-G. These findings provided direct mechanistic evidence that the pivotal point and force projection exerted by EF-G are critical for maintaining translocation fidelity. We anticipate broader applications of our technique in the ribosome field, leveraging its high efficiency and single-nucleotide resolution
The Inability of AI Chatbots to Write Poetry
No full textMy research poster details the major information of my project, which analyzes the inability of AI chatbots, such as ChatGPT, to write poetry. The poster first introduces the project and its purpose. Then, it describes the methodology that was involved to reach the conclusion that AI cannot craft poetry. This was done by analyzing two prominent definitions of poetry, while also arguing for authorial intent. Finally, the poster features the drawbacks of the methodology in this project as well as the conclusion that was reached.Honors CollegeEnglish, Department o
Our Beloved Swarm: Confronting Black Women's Mental Health Stigma Through the Lens of Horror
No full textThe aim of my research is to explore how the Horror genre challenges the stigma surrounding Black women's mental health. By comparing Toni Morrison's Gothic Horror novel *Beloved* (1987) with Janine Naber's Psychological Horror miniseries *Swarm* (2023), I analyze how both works, despite a 40-year gap, address codependent relationships and portray mental health as a powerful, yet unnamed force. These Black Feminist Speculative Fiction stories shed light on issues like depression, anxiety, low self-esteem, and lack of boundaries, which are often overlooked within larger family crises. In "Beloved", Morrison explores trauma's lasting effects, particularly through Denver, whose emotional struggles reveal the deep wounds of slavery. The ghost of Beloved symbolizes unresolved generational trauma, emphasizing how these legacies shape Black women's mental health across generations. "Swarm" similarly focuses on Dre's character, whose untreated mental health issues-triggered by her sister's suicide-spiral into a dangerous parasocial obsession, underscoring how unaddressed trauma can drive extreme behaviors. Both narratives highlight the critical need for attention to Black women's mental health, illustrating the destructive outcomes of generational trauma and societal neglect. Through the characters of Denver and Dre, "Beloved" and "Swarm" emphasize the urgency of greater mental health awareness and care for Black women.English, Department ofHonors Colleg
Energy Feasibility Studies in the Democratic Republic of Congo
No full textThe research team worked with Nuru, a solar company based in the Democratic Republic of Congo (DRC) to conduct studies into the ability of hydrokinetic, run-of-river, hydropower, geothermal, green hydrogen, blue hydrogen, natural gas, and micro-nuclear power to provide 1-4 MW of electricity generation capacity to supplement the existing solar systems during the night. The technological feasibility of each resource was assessed using data from comparable existing projects, including the natural resources required and their availability in eastern DRC. The economic feasibility of each energy source was estimated using the cost of similar projects, the cost of individual mechanisms, and the cost of fuel. After the seven feasibility studies were conducted, it was determined that natural gas and geothermal were the most closely aligned with Nuru's capacity and goals. It was found that methane extracted from Lake Kivu, near Goma, DRC, could power a 1-4 MW natural gas plant. A 4 MW plant was estimated to cost 35-45 million USD, with majority of that cost relating to pipeline construction. For geothermal power, the Mayi-ya-Moto volcano was identified as having particular potential for a binary-cycle power plant. A 4 MW plant of this kind is estimated to cost $22 million USD.Honors CollegeMechanical and Aerospace Engineering, Department ofChemical and Biomolecular Engineering, William A. Brookshire Department o
Get Out the Vote! An Analysis of Voter Turnout in Midterm Elections Across Harris County Census Tracts
No full textIn 2020, Harris County implemented new voting accessibility measures, such as 24-hour and drive-through voting locations, to accommodate the social distancing requirements during the COVID-19 pandemic. In response, the Texas Legislature passed Senate Bill 1 (the Election Integrity Protection Act of 2021) in a special session during the 87th legislative session. This study investigates the relationship between the passage of Senate Bill 1 and changes in voter turnout across census tracts in Harris County between 2018 and 2022. Initially, this research aimed to establish a causal relationship between the passage of Senate Bill 1 and voter turnout. However, upon further analysis, this research cannot prove a causal relationship; rather, it identifies correlations between voter turnout changes and census tracts' socioeconomic characteristics. This research provides a framework for future studies exploring the effects of Senate Bill 1 on voter turnout in Texas.Honors Colleg
Bowman's Capsule Rupture and Podocyte Loss As Revealed by Spatial Proteomics Is Correlated to Histological Activity and Chronicity in Lupus Nephritis
No full textBowman's capsule rupture (BCR) is a renal lesion caused by severe inflammation that damages the glomerular basement membrane of the Bowman's capsule. Patients with BCR present with more severe clinical and renal pathology and face a higher risk of progression to ESRD with a poorer prognosis. BCR is a key pathological event in lupus nephritis (LN) disease pathogenesis and can be used as a pathological marker in histological activity and chronicity indices (AI/CI) of LN. Spatial proteomic analysis was conducted to assess glomerular structural integrity in kidney biopsies from lupus nephritis (LN) and healthy transplant control kidneys. Spatial proteomic data was correlated with histopathological evaluation. Comparison between LN and healthy controls revealed a higher prevalence of BCR in LN, with BCR percentages correlating positively with renal pathology scores (AI: r = 0.93, CI: r = 0.67). Further analysis demonstrated that increased BCR was linked to cellular crescents, glomerular sclerosis, and fibrous crescents. Resident glomerular cell analysis showed a significant reduction in podocyte (Vimentin+ve) numbers in LN glomeruli, but not in mesangial (SMA+ve) or endothelial (CD31+ve) cell populations. Podocyte loss correlated negatively with renal pathology metrics and was more pronounced in glomeruli with extensive BCR. Immune cell infiltration analysis revealed a positive correlation between BCR and M1 macrophages, M2 macrophages, and T cells, with M1 macrophages showing the strongest association. These findings highlight the interplay between glomerular structural integrity, immune cell infiltration, and podocyte loss in LN progression. [This project was completed with the contributions from Luan Truong from Houston Methodist Hospital.]Biomedical Engineering, Department ofHonors Colleg
Plasma-Assisted Atomic Layer Etching of Si in Cl and Br-Containing Plasma
No full textAtomic-scale precision in silicon plasma etching is indispensable for the fabrication of next-generation three-dimensional (3D) semiconductor devices. Yet plasma-assisted atomic layer etching (PA-ALE) continues to be limited by low throughput, poor self-limiting behavior, and an incomplete understanding of surface kinetics. My research tries to address these challenges through a systematic study performed in a modified continuous-wave (CW) inductively coupled plasma (ICP) reactor. Time-resolved, in-situ optical emission spectroscopy (OES) is established as a quantitative tool of surface reactions during ALE cycles employing Cl₂, HBr, and Br₂ chemistries. The measurements show that SiCl₂ and SiCl constitute the primary products in Cl₂-based ALE. Two process sequences—gas dosing and plasma gas dosing—are explored and compared: pseudo-self-limiting behavior emerges in HBr plasma gas dosing cycles, whereas Br₂ have greater Br surface coverage and higher etch rates under gas-dosing conditions compared to HBr. Because both Br₂ and HBr have high sticking coefficients, gas residence time experiments reveal a two-stage purge consisting of a volume-limited decay followed by wall retention limited desorption; wall passivation via temperature control, Ar/SF₆/O₂ conditioning, and increased total flow substantially shortens the wall retention time. Moreover, fast-pulsed substrate bias with continuous gas flow effectively decouples the dose and etch steps, eliminating mechanical gas-pulsing hardware and markedly increasing throughput. Simultaneously tracking the ALE percentage and the bias-on integrated intensity of dominant OES lines enables evaluation of both self-limiting fidelity and etch rate. Collectively, this work (i) elucidates the primary reaction products and pathways in Si ALE for multiple halogen chemistries, (ii) delivers robust, high-throughput recipes that achieve sub-nm precision with cycle times below 2 s, and (iii) provides diagnostic and hardware guidelines transferable to other ICP tools. These advances expedite the transition of PA-ALE from lab to high-volume manufacturing, making a further step to achieve damage-free patterning of sub-10 nm features for future logic and memory devices
Engaging in a Collaborative Social Justice-Themed Choral Performance: From Conception to Reflection
No full textThis paper documents the conception, process, and reflection of a social justice-themed lecture recital performed at the collegiate level in Arkansas. It brings attention to composers Joel Thompson, Melissa Dunphy, Alexander Lloyd Blake, Saro Lynch-Thomason, Saunder Choi, and Ysaÿe M. Barnwell as well as their compositions’ contributions to the social justice choral landscape. This empirical account also describes the implementation of culturally responsive pedagogy and documents social justice praxis through audio transcriptions of classroom dialogue, student artifacts, and daily reflections. This account is deliberately descriptive; problems, successes, and growth are openly shared so readers can form their own conclusions about employing social justice pedagogy in their own practice moving forward
Directed Evolution of Protein-Based Sensors for Anaerobic Biological Activation of Methane and Short-chain Alkanes
No full textMetabolic and protein engineering are powerful approaches to design customized enzymes and microorganisms capable of novel and/or enhanced production of target compounds. In this context, the combination of gene library generation and high-throughput screening comprise a highly effective means to identify improved biocatalysts, or components thereof. Genetically-encoded biosensor/reporter systems developed from small molecule-responsive transcription factors (TFs) have proven to be useful tools for metabolite detection and metabolic monitoring, toward the design of new biocatalysts. In this study, interest lies in microbial alkane degradation pathways, which provide biological routes for converting these hydrocarbons into higher value products. The functional expression of a methyl-alkylsuccinate synthase (Mas) system in Escherichia coli, enabling heterologous anaerobic activation of short-chain alkanes (C3-C6), was recently reported. To date, no system for methane activation has been identified, and putative enzyme systems for activating ethane, propane, and butane are yet to be functionally expressed. Here, the objective was to design a TF-based sensor/reporter system for high-throughput screening of alkylsuccinate synthase activity on various short-chain alkanes. While there are no known regulatory proteins that control gene expression in response to an alkylsuccinate, ItcR from Yersinia pseudotuberculosis exhibits high sensitivity to methylenesuccinate (IA), showing ~100-fold lower response to the structurally similar methylsuccinate (MS). Thus, the focus was on employing protein engineering techniques to alter the inducer specificity of ItcR toward MS firstly, and subsequently other, longer chain alkylsuccinates. The resulting variants represent the first generation of sensors for endogenous molecular reporting of alkylsuccinate biosynthesis, by placing reporter and/or selection genes under control of the ItcR cognate promoter (Pccl). Random mutagenesis followed by fluorescence-activated cell sorting (FACS), combined with site-directed mutagenesis and further protein characterization yielded several MS-responsive ItcR variants. Structural modeling and analysis of the ItcR ligand binding pocket provided mechanistic insights into the altered molecular recognition. Subsequent rounds of directed evolution targeted responsiveness to ethylsuccinate (ES) and methylpentylsuccinate (MPS) and yielded multiple variants with improved response to these compounds. The most sensitive MPS biosensor developed was effectively utilized for detecting the biosynthesis of this compound in the previously established heterologous host capable of hexane activation. Structural analysis and biochemical characterization of WT-ItcR and its variants are presented, providing insights for further biosensor design and applications for engineering microbes capable of converting short alkanes into value-added products
The Role of the Sentence Constraint in New Word Acquisition While Reading in Adolescents: The ERP N400 and P600 and Reading-Related Skills
No full textBackground/Objectives. Vocabulary acquisition is a lifelong process, with the most rapid growth occurring from early childhood to school age. Different contextual factors influence how new vocabulary is acquired across various age groups during reading. Methods. We studied the process of new word acquisition in different constraining contexts in adolescents aged 11–17 years old and how individual differences in reading comprehension, vocabulary, and verbal working memory affect word acquisition. In the learning stage, the new words were presented in sentences with low and high contextual constraints, and word acquisition was assessed in a word recognition test where behavioral measures and the N400 and P600 components of the event-related potentials (ERPs) were examined. Results. Our study reveals that while the accuracy of word recognition was at a chance level, adolescents had faster responses to words learned in high-constraining contexts compared to words from low-constraining contexts. Neural responses were influenced by context, with explicit recollection processes reflected in the P600 being modulated by the type of sentence constraint, while implicit familiarity related to the N400 did not show this effect. Higher reading comprehension, vocabulary, and verbal working memory scores improved accuracy, while reaction times were improved by just vocabulary. Additionally, reading comprehension and vocabulary impacted the implicit N400 old/new effect, and reading comprehension correlated with explicit recognition processes (P600 old/new effect). Conclusions. Therefore, the present study showed that the type of constraint of new word learning and individual skills affected the word acquisition process in adolescents