Physical tools to study molecules, cells, and organisms.

We invent new physical tools to probe biological structures. We use our tools to make new measurements. We choose problems by looking in unexplored regimes of time and space. We combine protein engineering, lasers, nanofabrication, microfluidics, electronics, biochemistry, and computers to generate data; and we apply statistics and physical modeling to understand the data.

Microbial rhodopsins as fluorescent voltage-indicating proteins: Microbial rhodopsin proteins are found in aquatic organisms throughout the world and in all kingdoms of life. In the wild, these proteins transduce sunlight into changes in membrane potential, which their host organisms use for phototaxis and solar energy capture. Recently, several labs have expressed microbial rhodopsins in other cell types, enabling optical control of membrane potential. We engineered several microbial rhodopsins to run in reverse: to transduce changes in membrane potential into an optical signal. These voltage-indicating proteins provide a fast and sensitive tool for monitoring electrical dynamics in cells.

Optical selection and profiling of single cells: The ability to select a small number of cells from a heterogeneous population is fundamental to many aspects of biological research. Selections form the basis of genetic screens, of protein engineering and directed evolution, and of protocols to produce stably transformed or genome-edited cell lines. In many instances, one would like to select cells on the basis of complex dynamic or morphological features. For example, in a culture of olfactory neurons, one might screen for calcium flux in response to a specific odorant; and then wish to select responsive cells for subsequent transcriptional profiling. Or in a culture with single genes knocked down by an siRNA library, one might find cells with unusual shapes, organelle sizes, or metabolic responses; and then wish to select these cells to determine which gene had been knocked down. These types of selections are difficult to perform with existing tools.

Spectroscopy and voltage-dependent nonlinear control with microbial rhodopsins:  Microbial rhodopsin proteins have wondrously complex and fascinating optical responses. These proteins have a multitude of conformational states, each with unique spectral and electrical properties. Optical or thermal excitations drive transitions between these states. By mapping the conformational landscapes of microbial rhodopsin proteins, we have learned about basic mechanisms which then allow us to engineer new kinds of molecular logic into these versatile tools.

Synthetic bioelectrical systems: electrophysiology of minimal spiking cells: Neurons and cardiomyocytes use a complex panoply of ion channels to achieve precisely regulated firing patterns and responses to external stimuli. We asked, what is the simplest cellular system that can generate electrical spikes? Electrically inert HEK cells can be rendered electrically active through expression of just two ion channels: an inward-rectifier potassium channel and a voltage-gated sodium channel. We have been using spiking HEK cells to study fundamental aspects of cellular computation, and as a tool for discovering and probing electrically responsive transmembrane proteins.

Selected Publications: