Welcome to the Farny Lab @ WPI:

Synthetic Biology for Environmental Applications

We are broadly interested in the interface of cells and their environments, under many contexts and across many scales. Our lab builds tools, models, and engineered communities to monitor and remediate contaminants in water and soil. We use the tools of synthetic biology, cell biology, genetic engineering, and bioinformatics to build cells and systems that can sense and remediate contaminants including heavy metals, explosives, and plasiticizing agents. We also use high-throughput fixed cell and live cell microscopy to understand the role of physiologically relevant contaminant exposures on the integrated stress response in human cells.

Building Better Biosensors with Synthetic Biology

Contaminants are a persistent problem in our water and soil. We seek to build cell-based and cell-free biosensor systems that can detect and remediate contaminants in water and soil, particularly metals and metalloids like arsenic, lead, cadmium, and chromium. Many synthetic gene biosensors have been built in bacterial cells using synthetic biology approaches. However few of these systems function in organisms outside of laboratory E. coli strains. Fewer of these function when the cell is grown in a real-world environment such as a water supply or in soil. Our lab is using a combination of synthetic biology and transcriptomics in native soil organisms such as Pseudomonas putida to re-engineer synthetic gene circuits to function in real-world environments. Read our latest paper on bacterial engineering here!

Survival and Function of Engineered Organisms in Model Soil Environments

Many engineered organisms have been developed in recent years for soil-related applications including biosensing, bioremediation, and pathogen control. However, it is unclear how to deploy these solutions safely, as it is difficult to predict survival and persistence of a genetically engineered microbe (GEM) in a given soil environment. Further complicating the issue, many well characterized synthetic genetic circuits function well within the lab but fail when introduced to the natural soil environment. In order to enable deployment of synthetic biology solutions in soil, two developments are needed: 1) improved genetic circuit designs optimized for function in the soil environment; and 2) enhanced laboratory models of the soil environment that permit automated, high throughput assessment of GEM survival and function. We have developed an automatable and scalable liquid soil extract model for monitoring survival and genetic circuit function of an engineered soil organism Pseudomonas putida, and have successfully employed this model to examine the relationship of engineered P. putida to dominant soil microbes and the native microbiome. We have employed both targeted design and transcriptomics mining approaches to identify both constitutive and inducible promoters with enhanced performance in P. putida under a variety of environmental conditions. Our improved tools are expanding our understanding of the relationship of GEMs to the native soil microbiome and advancing knowledge that will enable future deployment of synthetic biology solutions to global soil challenges. Watch my SynBYSS Seminar on this topic here!

Cellular Stress Response and Regulation of Stress Granule Formation

Environmental exposures to chemicals including heavy metals, metalloids, and plasticizing agents at acute high doses trigger the formation of stress granules (SGs). SGs are cytoplasmic aggregates of mRNAs and proteins that form in response to translational arrest and polysome disassembly. SGs are thought to protect the cell from apoptosis and permit cells to redirect translational control toward survival mechanisms. SGs are conserved throughout eukaryotes. Most studies of SGs focus on brief, acute exposures that are highly unlikely to occur in humans. In the Farny lab, we are interested in how physiologically relevant, low-dose, and chronic exposures to metals like lead, cadmium, chromium and arsenic affect SGs and the integrated stress response, and how these exposures are related to the development of human disease. We are also interested in the relationship of UV stress to SG formation and the ISR. Read our latest SG paper here!

SUPPORT

The Farny Lab is supported by WPI School of Arts and Sciences, the NIH National Institue on Aging, the Defense Advanced Research Projects Agency, the National Science Foundation, the U.S. Environmental Protection Agency, and Robert Ferrari of Northeast Water Solutions, Inc.