Thielen, P. | Search bioRxiv

bioRxiv2016

Tuning the course of evolution on the biophysical fitness landscape of an RNA virus

Predicting viral evolution remains a major challenge with profound implications for public health. Viral evolutionary pathways are determined by the fitness landscape, which maps viral genotype to fitness. However, a quantitative description of the landscape and the evolutionary forces on it remain elusive. Here, we apply a biophysical fitness model based on capsid folding stability and antibody binding affinity to predict the evolutionary pathway of norovirus escaping a neutralizing antibody. The model is validated by experimental evolution in bulk culture and in a drop-based microfluidics device, the \"Evolution Chip\", which propagates millions of independent viral sub-populations. We demonstrate that along the axis of binding affinity, selection for escape variants and drift due to random mutations have the same direction. However, along folding stability, selection and drift are opposing forces whose balance is tuned by viral population size. Our results demonstrate that predictable epistatic tradeoffs shape viral evolution.

evolutionary biology↗

bioRxiv2016

Heat-stable preservation of protein expression systems for portable therapeutics production

Many biotechnology capabilities are limited by stringent storage needs of reagents, largely prohibiting use outside of specialized laboratories. Focusing on a large class of protein-based biotechnology applications, we address this issue by developing a method for preserving cell-free protein expression systems under months of heat stress. Our approach realizes an unprecedented degree of long term heat stability by leveraging the sugar alcohol trehalose, a simple, low-cost, open-air drying step, and strategic separation of sets of reaction components during drying. The resulting preservation capacity opens the door for efficient production of a wide range of on-demand proteins under adverse conditions, for instance during emergency outbreaks or in remote or otherwise inaccessible locations. As such, our preservation method stands to advance a great number of different cell-free technologies, including remediation efforts, point of care therapeutics, and large-scale biosensing. To demonstrate this application potential, we use cell-free reagents subjected to months of heat stress and atmospheric conditions to produce sufficient concentrations of a pyocin protein to kill Pseudomonas aeruginosa, one of the most troublesome pathogens for traumatic and burn wound injuries. Our work makes possible new biotechnology applications that demand both ruggedness and scalability.

synthetic biology↗