Kennedy, F. | Search bioRxiv

bioRxiv2024

Modeling the effects of vaccination against multiple strains of porcine reproductive and respiratory syndrome at the barn level

Porcine reproductive and respiratory syndrome (PRRSV) remains costly for the swine industry. Measures intended to irradicate or reduce the prevalence of PRRSV have limited effectiveness. Vaccination, the primary control strategy for PRRSV, has yet to be thoroughly investigated to ensure an optimal strategy is being implemented. Due to insufficient cross-immunity between strains, it is prudent to administer the most influential vaccine for the most dominant or threatening PRRSV strain in circulation at a given time. With this in mind, we demonstrated the benefits of targeted vaccination using metapopulation-based modeling. By using up-to-date data describing real farms to simulate the effects of variable vaccine efficacy in both a single and a double strain system, we showed that tailoring vaccines to prevalent PRRSV strains reduces infections, but using multiple vaccines may be more effective if strains vary in vaccine response. Therefore, the impact of the strain-specific effectiveness of market vaccines, paired with computational methods that allow tracking the effects on PRRVS dissemination at individual barns.

ecology↗

bioRxiv2023

Efficient Natural Plasmid Transformation of Vibrio natriegens Enables Zero-capital Molecular Biology

The fast-growing microbe Vibrio natriegens is capable of natural transformation where it draws DNA in from media via an active process under physiological conditions. Using an engineered strain with a genomic copy of the master competence regulator tfoX from Vibrio cholera in combination with a new minimal competence media (MCM) that uses acetate as an energy source, we demonstrate naturally competent cells which are created, transformed, and recovered entirely in the same media, without exchange or addition of new media. Cells are naturally competent to plasmids, recombination with linear DNA, and co-transformation of both to select for scarless and markerless genomic edits. The entire process is simple and inexpensive, requiring no capital equipment for an entirely room temperature process (Zero Capital protocol, 104 cfu/{micro}g), or just an incubator (High Efficiency protocol, 105-6 cfu/{micro}g). These cells retain their naturally competent state when frozen and are transformable immediately upon thawing like a typical chemical or electrochemical competent cell. Since the optimized transformation protocol requires only 50 minutes of hands-on time, and V. natriegens grows quickly even on plates, a transformation started at 9 AM yields abundant culturable single colonies by 5 PM. Further, because all stages of transformation occur in the same media, and the process can be arbitrarily scaled in volume, this natural competence strain and media could be ideal for automated directed evolution applications. As a result, naturally competent V. natriegens could compete with E. coli as an excellent chassis for low-cost and highly scalable synthetic biology.

synthetic biology↗