Biology subjects

Wilbourn, E. K.

Publications and source records attributed to Wilbourn, E. K..

3 recordsLinked to original sources

bioRxiv2026

Temperature-Switchable Genome Editors from Extremophile-Derived Integrases

Integrases are site-specific recombinases encoded by phages and other mobile genetic elements. They mediate DNA integration, excision, and inversion between cognate attachment (att) sites. Although integrases are powerful tools for genetic engineering and synthetic biology, most systems lack intrinsic mechanisms that limit activity after expression, creating potential for unintended recombination. We hypothesized that extremophiles could provide temperature-responsive integrases because their enzymes evolved under selective pressure to operate within the thermal ranges experienced by their hosts. To test this concept, we linked integrase-att pairs from 458,683 prokaryotic genome assemblies to curated host growth-temperature metadata. This analysis revealed temperature-associated structure among integrase clusters and established a candidate pool for testing temperature-responsive recombinases. GC content in tyrosine integrase-associated attB sites showed a modest increase in higher-temperature hosts. We developed an inversion assay using a single-copy reporter plasmid and sacB counterselection to quantify integrase activity across temperatures. Thermophile derived integrases from Thermus thermophilus and Geobacillus stearothermophilus displayed hot-ON/cold-OFF activity profiles, whereas an integrase derived from the psychrotroph Pseudomonas cerasi showed cold-ON/hot-OFF activity. Together, these results establish host thermal niche as a guide for discovering intrinsically temperature switchable integrases and provide a foundation for engineering thermally controlled genome editing systems.

molecular biology↗

bioRxiv2026

Characterizing Industrial Pond Ecology Timeline in DISCOVR Cultivation Trials for Early Detection of Pond Crashes

For sustainable algal biomass cultivation, we need substantial improvement in annualized productivity by reducing the frequency of crop failure and improved growth in open raceway pond systems. In this study, high-performing strains were identified and optimized for biomass productivity. We utilized next-generation sequencing methods to quantify the ecological features of open raceway systems cultivated at in Arizona. We utilized data from several months of cultivation runs to construct a rich time-series of the ecology dynamics using amplicon sequencing and used custom anomaly detection, "PondSentry", for the early prediction of pond crashes. PondSentry uses tensor decomposition of higher-order joint moments to detect incipient anomalies in multivariate data and displays significant improvements from standard knowledge-based anomaly detection methods. The PondSentry strategy identifies signs of deteriorating pond health at an average of three days before an actual crash event, with rank order of the ecological features plausible for crop failures driven by organisms such as Amoeboaphelidium occidentale FD01. These findings are independently confirmed with PCR and microscopy studies at an Arizona cultivation site. PondSentrys time-series-based anomaly detection of crashes provides a suitable monitoring strategy for eukaryotic crash agents in unialgal culture. The early warnings can be used to time interventions or harvests to prevent biomass loss. The PondSentry strategy strengthens the role of data science and data-driven methods in algal cultivation and can increase the feasibility of algal-biomass based products.

ecology↗

bioRxiv2026

Protection of algae grown for biofuel using a consortium of environmentally harvested bacteria

Crop loss due to infection by pests and pathogens is a major barrier to the large-scale production of algal biofuels. Test systems have seen loss of green algae crops due to infection by the fungus-like Amoeboaphelidium occidentale FD01. While current antifungal compounds are effective in inhibiting the infection, their application raises the overall cost of the crop and lowers its economic viability as a biofuel source. Here we show that co-culturing environmentally harvested bacteria alongside algae crops can drastically lower the rate of infection in two different green algae species of interest for biofuel production. These bacteria-algae consortia increase the mean time to crop failure (MTTF) by up to 350% when tested under environmentally relevant conditions. While there was an increase in diversity over time, there was no statistically significant correlation between an increase in diversity and a longer MTTF. Community composition analysis reveals similarities between the bacterial genera growing alongside both green algae species even as bacterial harvest locations differed, although there was not a single dominant genus responsible for the increase in crop protection. These results show a promising new method of anti-fungal crop protection that can be applied to algal biofuels with no increase in fuel cost. HighlightsO_LIBacteria-algal cocultures protect against fungal pests without impact to productivity C_LIO_LIBacterial community composition is variable over time even as protection persists C_LIO_LIBacterial consortia can increase mean time to failure by 350% C_LI

microbiology↗