(1:00-1:15)
[34 - 180-237]: A Pan-Genome Based Machine Learning Framework for Antibiotic Resistance Prediction
Olga Carvallo1†★, Trotter McLamore2★, Ella Yam2★, Paul Anderson2, Jean Davidson11 Department of Biological Sciences, 2 Computer Science and Software Engineering, †Frost Support, ★Speaker
Antimicrobial resistance (AMR) represents one of the most significant threats to modern medicine. As pathogens evolve to evade existing treatments, conventional diagnostics for bacterial infections such as urinary tract infections (UTIs) remain costly and time?consuming, often delaying effective treatment. As genome sequencing rapidly becomes more accessible in clinical settings, we aim to develop a precision medicine tool that improves and individualizes patient diagnostics. We implemented a machine learning framework for antibiotic resistance (ABR) prediction using pan-genome data, a large-scale genomic analysis approach. This pipeline, previously validated in E. coli, was benchmarked for reproducibility and then extended to a more diverse dataset to improve generalizability. In line with our goal of creating easy-to-access tools, we expanded
upon previous work in this space and developed a fully pre-trained model capable of predicting on completely new E. coli data. We are currently working towards expanding this pipeline to predict on other commonly resistant pathogens, such as P. mirabilis and K. pneumoniae. By analyzing pan-genome patterns from clinical bacterial isolates, we aim to create an easy to use diagnostic tool capable of identifying resistance emergence across diverse pathogens. The successful utilization of the E. coli pan-genome based ML model validates the development of a comprehensive effort to train new ML models on available genomic datasets of other multi-drug resistant pathogen species. |
(1:15-1:30)
[35 - 180-237]: Macroalgal pH Buffering Enhances Juvenile Pacific Oyster Growth in an IMTA System
Lara Carrion★§, Sophia Duck§, Liam Hill§, Johnny Paneno, Kevin Johnson§Department of Biological Sciences, §Santa Rosa Creek Foundation Support, ★Speaker
Ocean acidification, driven by increasing atmospheric CO2 levels, reduces seawater pH and carbonate availability, thereby inhibiting the calcification process of shell-forming species, such as oysters. Macroalgae, including Ulva lactucae, can elevate the pH of seawater through photosynthetic CO2 uptake, offering a potential mitigation strategy. Integrated multi-trophic aquaculture (IMTA) can leverage these interactions by co-culturing different species like seaweed and shellfish in a tumble tank system to improve water quality and improve calcification. This project evaluated the effectiveness of a land-based IMTA system integrating juvenile Pacific oysters (Crassostrea gigas) and macroalgae (U. lactucae) at the Cal Poly Pier. The effect of macroalgae on the growth of Pacific oysters, and the oyster’s influence on the macroalgae biomass was monitored over an 8-week trial. The experimental system included three treatment groups: oysters co-cultured with U. lactucae, oysters without U. lactucae, and U. lactucae without oysters. Oyster growth (shell size and mass), macroalgal biomass, and seawater chemistry, including pH, were monitored throughout the experiment. Oysters co-cultured with the U. lactucae exhibited greater growth rates and were maintained under higher pH conditions compared to the oysters grown alone. Additionally, U. lactucae biomass increased more rapidly when co-cultured with oysters than in a monoculture. These results suggest a mutually beneficial interaction in which macroalgae buffers seawater pH, enhancing oyster calcification, while oysters contribute nutrients that promote macroalgal growth. |
(1:30-1:45)
[36 - 180-237]: Impact of Iron Availability on the Motility of Uropathogenic Escherichia coli
Jin Ko†★, Kelsey Cliburn†, Alejandra Yep†Department of Biological Sciences, †Frost Support, ★Speaker
Urinary tract infections (UTIs) are the second most common bacterial infection, affecting primarily women. Our lab explores inhibition of iron acquisition as an antimicrobial strategy against UTIs. Motility and attachment are important virulence factors in uncomplicated UTIs caused by uropathogenic strains of Escherichia coli. In this work, we explore how iron availability impacts swimming and swarming motility.
We studied the uropathogenic strain E. coli CFT073 and two isogenic mutants with different expected intracellular iron concentrations. CFT073 ?tonB lacks the TonB complex that transduces the proton-motive force to drive iron import, yielding low intracellular iron. CFT073 ?fur lacks the ferric uptake regulator, derepressing iron import and increasing intracellular iron. Additionally, we varied extracellular iron by supplementing with FeSO4 or the iron chelator dipyridyl. Growth curves confirmed that changes in motility were not due to growth defects.
In swimming plates, WT motility decreased with added iron and under iron depletion. Additionally, ?fur showed lower swimming motility and ?tonB higher motility than WT in the absence of added iron or chelators, supporting that low iron may drive increased motility. However, no significant changes were observed for either mutant across the range of added or depleted iron concentrations.
In swarming motility, WT showed no significant differences with added iron. In control conditions, WT swarmed more than ?tonB and ?fur. Overall, although there is a trend toward iron depletion leading to increased swimming motility, there is not a significant impact that could lead to a hypervirulent strain when iron inhibition is used as a therapeutic tool.
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(1:45-2:00)
[37 - 180-237]: Development of Water-Soluble R3-Noria Macrocycles for Protein Coupling and Targeted HyperCEST MRI
Elle Fishwick1†★, Carson Hasselbrink2†1 Department of Biological Sciences, 2 Department of Chemistry and Biochemistry, †Frost Support, ★Speaker
Hyperpolarized xenon chemical exchange saturation transfer (HyperCEST) is an emerging molecular imaging strategy that enhances MRI sensitivity through the reversible binding of hyperpolarized ¹²?Xe to host macrocycles, offering strong potential for targeted clinical imaging applications. Macrocycles such as R3-noria derivatives are promising HyperCEST scaffolds because they can be adapted for selective delivery to biological targets through protein conjugation. In this work, water-soluble derivatives of the R3 macrocycle, including R3S and R3A, were considered as platforms for xenon-based HyperCEST protein coupling, with particular focus on development of maleimide-linkers to bind these derivatives to engineered antibodies. Functionalization with 3-maleimidopropanoic acid NHS ester (MalNHS) produced a reactive linker capable of selective thioether formation with protein thiols. Residual maleimide content was quantified using a DTNB back-calculation assay with cysteamine, giving substitution ratios that indicate efficient but controlled linker incorporation. Protein conjugation was further evaluated with egg white lysozyme under reducing conditions, where SDS-PAGE analysis showed progressive mobility shifts consistent with increasing degrees of macrocycle attachment. These results demonstrate that water-soluble R3-derived macrocycles can be successfully adapted for tunable protein coupling, supporting their broader use as targeted HyperCEST MRI contrast agents. |
(2:00-2:15)
[38 - 180-237]: Northern elephant seal (Mirounga angustirostris) weanling mass and morphometrics at Piedras Blancas
Marshall Rottier Johnson1†★§, Alie Hall2, Julia Schedler2, Heather Liwanag11 Department of Biological Sciences, 2 Department of Mathematics, †Frost Support, §Santa Rosa Creek Foundation Support, ★Speaker
For animals with parental care, the transition to independence is a critical life history juncture. As capital breeders that fast during the lactation period, northern elephant seal (Mirounga angustirostris) mothers abruptly wean their pup after a short, 4-week nursing period. Post-weaning survival rates to the next year are less than 50% for northern elephant seals, and mass at weaning is a critical predictor of weanling survival. The objective of this study was to examine the factors affecting weanling mass and morphometrics (standard length, curvilinear length, and axillary girth) at Piedras Blancas, the largest mainland northern elephant seal colony, from 2018-2025. A multiple regression model of weaning mass revealed no significant difference in average weaning mass among different beaches at Piedras Blancas, but did indicate a positive association between weanling mass and the girth/length ratio. We also assessed whether changes in SOI, a proxy for El Niño/La Niña conditions, would correspond to fluctuations in average mass over the season; however, because SOI data are annual we detected no significant association with just 8 years of data. These findings have implications for our ongoing monitoring efforts, as we work towards building a framework for potential early detection of deviations from a healthy population at carrying capacity. |
(2:15-2:30)
[39 - 180-237]: Spatial variation in growth and movement of Pismo clams (Tivela stultorum) along Pismo Beach
Jacob Hinshaw★§, Benjamin RuttenbergDepartment of Biological Sciences, §Santa Rosa Creek Foundation Support, ★Speaker
The Pismo clam (Tivela stultorum) is a historically important species to California’s coast, which once supported a local commercial fishery and continues to support a recreational fishery. In recent decades, the population declined substantially but has recently begun to recover, bringing the species back into public attention. However, many gaps in knowledge still exist regarding its current status and interactions with the public. For the last five years, a mark and recapture study has been implemented to monitor individual growth rates and movement at a single site on Pismo Beach. This project expands the existing mark and recapture project to multiple sites along Pismo Beach to assess spatial variation in individual growth and movement, as well as recapture rates between sites. |
(2:30-2:45)
[40 - 180-237]: Evaluation of the effect of the RRE signal and truncated HIV Rev co-expression on genomic RNA packaging efficiency in an S. cerevisiae lentivirus assembly system
Katie Drew1★, Lizzy Johnson2, Lily Nielson2, Michael Black21 Department of Chemistry and Biochemistry, 2 Department of Biological Sciences, ★Speaker
HIV-derived lentiviral vectors have been extensively used in the field of regenerative medicine for applications in research and clinical gene therapy. The current method for producing lentiviral vectors is costly and difficult to scale. We seek to produce a lentiviral assembly system using Saccharomyces cerevisiae as a helper strain as a cost-effective and scalable alternative to mammalian cell culture. Previous work has shown spontaneous formation of virus-like-particles (VLPs) in S. cerevisiae. In our effort to increase the packaging efficiency of recombinant genomic RNA into yeast-derived VLPs, we examine the effect of the RRE sequence and the co-expression of HIV Rev and a mutant version of Rev, truncated upstream of the nuclear export signal. We found that co-expression of Rev was not associated with increased packaging efficiency. However, co-expression of truncated Rev with RRE-containing gRNA resulted in decreased production of VLPs and increased packaging efficiency of gRNA. In strains expressed with non-RRE-containing gRNA, this effect was not observed. This suggests that lentiviral production in S. cerevisiae does not follow the Rev/RRE pathway, but truncated Rev may interact with the RRE region to elevate the level of gRNA incorporation into VLPs. |
(2:45-3:00)
[41 - 180-237]: Effects of tide and temperature on harbor seal (Phoca vitulina) haulout behavior in Morro Bay, California
Lucy Bentsen†★, Claire Savage†, Heather LiwanagDepartment of Biological Sciences, †Frost Support, ★Speaker
Harbor seals are coastal marine mammals that haul out close to areas of human activity, and they are notoriously reactive to human disturbance. Plans for a windfarm offshore of Morro Bay, CA, are likely to increase ship traffic and other human activity in the area. However, there is currently no formal monitoring program documenting the occurrence of harbor seals along the central coast of California. The goal of this project was to develop a baseline dataset documenting the location and timing of harbor seal haulout behavior in Morro Bay and surrounding areas, prior to construction of the offshore wind farm. To do this, we used binoculars and a spotting scope to conduct frequent ground surveys of harbor seals at three sites in and around Morro Bay. We examined the relationship between harbor seal haulout behavior and abiotic factors, including tide level, air temperature, and wind speed. These factors affected harbor seal abundance in different ways at the different sites. Harbor seal abundance was positively associated with tide height in the marshy estuary of Morro Bay; in contrast, seal abundance and tide were inversely related in Los Osos, an exposed sandbar habitat; seals were only present between the 3-ft and 6-ft tides on the offshore rocks of Estero Bluffs. Temperature inversely influenced haulout abundance at Estero Bluffs. Wind speed did not show a significant impact on haulout abundance at any of the sites. We are using these data to assess when scat collection would be possible – in the absence of the seals, and before the tide washes the scat away – to facilitate future scat sampling for diet composition and health markers. This will ultimately be used to understand the impacts of increased activity associated with the offshore windfarm on our local harbor seals’ abundance and health. |