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Tips and Pointers: Capture and Keep Attention
No full textPoster Session Tips and Pointers 2025
Capture and keep attention!
Do you want to create an engaging poster for your next poster session? Come learn some tips and pointers that will capture and keep attention on your research! We will review content, design, and tools that will focus on your work
Synthesis of Alanine-Containing Peptides
No full textIntroduction:
Peptides are molecules composed of two or more amino acids linked by peptide bonds. Unique combinations of just twenty canonical amino acids can result in the production of hundreds of thousands of different peptides and proteins, each of which have different structures and thus different functions in the human body. Alanine (A) is one such fundamental amino acid, with important roles such as the facilitation of gluconeogenesis, which is linked to muscle metabolism and energy production. This research focuses on synthesizing short peptides containing alanine, i.e., the peptides VGTA, CAG and ACG.
Method:
Peptides were synthesized through solid phase peptide synthesis (SPPS), starting with the addition of rink amide resin to an SPPS vessel. The resin acts as the foundation for building the peptide chain. The procedure starts with a deprotection step using 20% piperidine in dimethylformamide (DMF) to remove the Fmoc protecting group from the resin. This allows for the first amino acid to be coupled to the deprotected resin. Prior to the amino acid coupling, the peptide goes through a series of wash steps involving methanol (MeOH) for removing unwanted polar byproducts, dichloromethane (DCM) for removing nonpolar impurities, and DMF for washing out any residual soluble reagents from prior deprotection steps. The coupling reaction utilizes Hexafluorophosphate Benzotriazole Tetramethyl Uronium (HBTU) as the activating agent, N,N’- Diisopropylethylamine (DIPEA) as the base, and DMF as the solvent. The process of deprotection and coupling is repeated until the desired peptide chain is successfully built. The resin is removed through cleavage using trifluoroacetic acid (TFA) for cleaving the peptide from the resin and for removing side chain protecting groups, phenol for stabilizing and protecting amino acid side chains during the process, triisopropylsilane (TIPS) for preventing any undesirable side reactions, and MilliQ water as the solvent. The cleaved peptide is then purified and shell frozen before being placed on the lyophilizer where the peptide undergoes sublimation to remove excess solvents and unbound reagents.
Results/Conclusion:
Multiple alanine-containing peptides were successfully synthesized and confirmed through mass spectrometry analysis. These peptides will be utilized in future research projects to thermochemical properties and reactivity
Enhancing Splice Site Detection Through Deep Learning and Retrieval-Augmented Generation
No full textSplice site recognition plays a critical role in understanding transcriptomic regulation, yet detecting these sites in single-cell RNA-seq data remains a major challenge due to sparsity and biological variability. This project focuses on building a deep learning framework that combines Convolutional Neural Networks (CNNs) for learning sequence patterns and Retrieval-Augmented Generation (RAG) for enhancing interpretability. CNNs are trained to distinguish donor and acceptor splice sites using k-mer encoded DNA sequences, capturing both local motifs and broader sequence context. In parallel, RAG is used to retrieve relevant biological knowledge and annotations that contextualize model predictions, offering a more interpretable explanation of splicing signals
Inhibitory Activities of Surface-Associated Bacteria from California and Florida Algae
No full textMarine algal surface-associated bacteria (SAB) inhabit highly competitive and diverse marine environments, where they face challenges such as high salinity, osmotic stress, and UV radiation. In response, these bacteria produce secondary metabolites that may serve as chemical defenses, including potential antibiotics active against human pathogens. To discover novel antibiotic drug leads, algae samples were collected from three California beaches (Stinson Beach, La Jolla, and Santa Cruz) and the Florida Keys. SABs were isolated from plates where algal surface swabs were plated on A1 medium, then cultured in liquid A1 medium (10 g/L starch, 4 g/L yeast, 2 g/L peptone), and cryopreserved. We utilized 3 antimicrobial screening methods—pour-over assay, disk diffusion, and single-dose broth assay— to test the 532 isolates against four human pathogens: Escherichia coli, Bacillus subtilis, Staphylococcus aureus, and Salmonella sp. In the pour-over assay, 11 isolates from an initial pool of 332 California SABs and 17 isolates from approximately 200 Florida SABs, produced zones of inhibition indicative of antibiotic production. The disk diffusion assay also confirmed antibiotic production in 14 samples. These antibiotic-producing isolates were then cultured large scale in 500 mL A1 media for 48 hours, extracted using XAD-16 resin, and then the broth was further extracted using ethyl acetate. Single-dose broth assay was conducted on the fractions from the large-scale extracts. The next steps will be isolation and characterization of the antibiotic secondary metabolites
Undergraduate Advocacy on Capitol Hill: Student Experiences in the Scholars Transforming Though Undergraduate Research (STR) Program
No full textThree students, Jessica Lacap, Karen Nateras Perez, Elizabeth Monterroso, and Communication Professor Dr. Qingwen Dong, participated in the national STR program this March 2025. The program is an opportunity for students to develop advocacy and communication skills to convey the importance of their undergraduate research to stakeholders (i.e., congressmen) through four online webinars and a final session in Washington, DC. 54 institutions from 22 states with a total of 61 campus representatives and 142 undergraduate research participated in this competitive program during 2024-2025. The webinar covered four topics: how research is used in policy, policy actors and actions, how to write an Op-ed, and how to write a policy brief. The D.C. trip was two days, the first being a seminar on connecting with policymakers and public interview skills. The second day was for students to meet their state senators and local representative(s). Meeting with aides of California Senators Adam Schiff and Alex Padilla, each undergraduate student introduced themselves and their research study to advocate for the importance of their topics and increased funding for research. After that, Elizabeth, Karen, and Jessica met with the aide of California Representative Josh Harder. Elizabeth emphasized her research on improving the ESL learning experience, Karen highlighted the need for publicizing homelessness resources, and Jessica stressed the importance of keeping Diversity, Equity, and Inclusion within higher education. Together, the aide used their knowledge of local resources and Josh Harder’s priorities to develop solutions to solving these critical issues, which were then relayed to the Senator. The three students reflected on their experience with four themes emerging: The connection of research to real-world change, the Importance of learning advocacy in a shifting political landscape, preparation for the future, and the lasting impact of STR on professional development
Wood Delights: Therapy and Hobby
No full textThis presentation explores my journey as a self-taught woodworker transforming unwanted wood - trimmed tree branches and scrap wood - into decorative and occasionally utilitarian objects. Emphasizing the therapeutic potential of woodworking, the presentation highlights how this hobby serves as both a creative outlet and, more importantly, a form of therapy. I am eager to share this process, showing how working with discarded materials can provide both artistic fulfillment and mental well-being. The presentation showcases examples of completed pieces, allowing the audience to see the tangible outcomes of this therapeutic craft. Attendees will see and learn about the various sources of wood, the inspiration behind the creations, and the tools and methods used in the crafting process. Through samples on display, participants gain insight into the rewarding practice of turning scrap materials into meaningful art
Analyzing Medicare Cost Distribution and Coverage Disparities: Insights from Data-Driven Analysis
No full textThis study investigates 2022 Medicare Part B claims data to evaluate systemic disparities in healthcare costs and service utilization across U.S. regions. Using descriptive statistics and visual analytics on 270,673 service records, we identify a 5.6-fold gap between provider-submitted charges and Medicare standardized payments, with significant disparity variations in payment structures. Key visualizations reveal weak correlations between charges and reimbursements and outlier-driven cost distributions in high-service regions. The findings advocate for granular reporting standards and transparent pricing models to reduce beneficiary financial burdens
Induction of lysogenic bacteriophages from MF160 using UV light from various sources
No full textMany bacterial species harbor temperate bacteriophages in their genomes. These viruses that infect bacteria are replicated along with their hosts, but can often be induced to enter the lytic cycle. The induction of lysogenic bacteriophages via ultraviolet (UV) light is a standard approach to explore bacteriophage-bacteria interactions and optimize phage production. In this study, we investigate the impact of different UV exposure sources and durations on phage induction efficiency and bacterial survival in strain MF160. Cultures inoculated with strain MF160 are diluted to an optical density of approximately 0.2 and exposed to UV light from three sources: a handheld UV flashlight, a UV chamber located in the biology building, and a dedicated UV chamber in the microbiology laboratory. Exposure times range from 10 to 60 seconds, with intervals of 10 seconds, to identify optimal induction conditions.
Post-exposure survival and phage induction efficiency is assessed by counting surviving bacterial colonies and plaque-forming units (PFU). CFU are determined by standard serial dilution, while PFU are determined using a top agar plating technique. We hypothesize that there will be an increase in phage induction with increasing UV exposure, but over some threshold the viability of the cell population will reduce phage production. Our goal is to determine an optimal UV exposure strategy in terms of source and time that maximizes phage yield without excessive bacterial lethality. Preliminary experiments with strain MF160 have demonstrated successful phage induction using UV treatment, validating the potential of this strain for exploring phage production strategies
Protein Cousins: Characterizing Ubiquitin-Like Proteins within the Ubiquitin Code
No full textUbiquitin-like proteins (UBLs) are a group of small proteins that share sequence homology with ubiquitin. Although structurally like ubiquitin, UBLs are a protein group that play a distinct role in biological signaling ranging from DNA repair to cellular inflammatory response. The group achieves this by participating in enzymatic cascades that are intricately adjacent to that of the ubiquitin-proteasome machinery yet remain functionally distinct. Due to the unique duality of UBLs, researchers over the past three decades have sought to answer the fundamental question: Do the conjugation machinery of both protein classes overlap, and if so, which specific enzymes mediate such interaction?
E2 ubiquitin-conjugating enzymes are one place of overlap in which overlaps exist. Often referred to as the “middlemen,” E2s play a crucial role in the ubiquitin cascade by facilitating the transfer of activated ubiquitin to protein substrates, in collaboration with ubiquitin ligases (E3s). Through extensive research, these same enzymes have also been shown to conjugate specific UBLs, facilitating their attachment to protein substrates in a manner like ubiquitin. Despite such findings, there is still a gap in understanding how E2s mediate the interplay between both cascades. Consequently, the drive to deepen our understanding of how UBLs interact with E2s is compelling, as it offers a clearer insight into how these protein families converge within the broader context of cellular function and disease. This project aims to characterize nine UBLs and one Ub variant through a series of biochemical assays to elucidate their interactions with E2s
Screening for Antioxidant-Producing Actinomycetes
No full textAntioxidants are essential for combating free radicals and preventing oxidative damage, making them imperative for our health and wellness. Actinomycetes are gram-positive bacterial species known for their filamentous growth and secondary metabolite production. This study aimed to identify the antioxidant-producing actinomycetes in our collection using a free radical assay. Briefly, radical scavenging was quantified using the color-changing reagent 2,2-diphenyl-1-picrylhydrazyl (DPPH). Isolates were grown in 2 L of A1 or A1DI media for marine or freshwater strains respectively made with starch, yeast extract, and peptone. Cultures were extracted using the polymeric XAD16-resin for 24 h, the resin was then rinsed with acetone to release secondary metabolites. The extract was dried and partitioned between ethyl acetate and water. The ethyl acetate partition was fractionated using silica gel SPE. For the assay, a 0.2 mM DPPH solution in methanol was prepared, and 109 fractions were tested in a 96-well microplate and compared against a negative control. Samples were tested in 8 serial dilutions from 512 μg/mL to 8 μg/mL to determine the EC50 of the antioxidant activity. After 30 min incubation, absorbance was measured at 515 nm to assess radical scavenging activity based on absorbance. Future directions are to grow the most active cultures in large-scale (6 L) to isolate the small molecules exhibiting free radical scavenging. This could lead to the discovery of novel antioxidant applications in healthcare, nutraceuticals, or beauty products supporting enduring wellness