We construct experiments to examine a variety of biophysical topics, exploring systems in which the complex interactions between individual components, such as biomolecules or cells, can give rise to, or be described by, simple and robust physical patterns. Our projects fall under two main umbrellas: biophysics of the gut microbiome and membrane biophysics. To explore these themes, we develop new optical and computational tools.
Some glimpses of our research projects are given below.
How do cells organize themselves into complex tissues and organs in a developing animal? How are geometry, mechanics, and signaling connected to give rise to robust, functional forms? Most of of our work on this theme focuses on the gut microbiome. You, like all animals, are not really a single species -- each of us is host to hundreds of trillions of microbes, mostly resident in the intestines, that whose profound importance to health, disease, and development are just beginning to be realized. (See here for a popular article on this.) Conventional methods, based mainly on DNA sequencing, yield important information about the compositions of these commensal microbial communities (i.e. what species are present), but provide little or no insights into their structure and dynamics. How do bacterial colonies nucleate and grow? (Can we apply to them our understanding of growth modes of snowflakes, soot particles, and other non-living systems?) How do microbial groups compete? What does "equilibrium" look like in a complex system of interacting agents?
Our approach to these questions involves directly visualizing gut microbial communities in living organisms. For this we need new sorts of microscopes for three-dimensional imaging, and a good model system to look at.
For the former, we make use of light sheet fluorescence microscopy, a remarkable and recently developed imaging technique in which shaping fluorescence excitation light into a thin sheet allows rapid three-dimensional imaging with low phototoxicity. We built our own light sheet microscope, pictured below, and are presently working on "next generation" instruments. For the latter we make use of zebrafish, a popular model organism that can be raised initially "germ-free" (i.e. devoid of microbes), and then introduced to particular, controlled, sets of microbial species. To read more...
Video: Light sheet fluorescence microscopy of Vibrio bacteria expressing green fluorescent protein, swimming in the intestine of a larval zebrafish. Our lab uses imaging-based approaches to study the gut microbiome, examining bacterial colonization, growth, and interactions.
Scale bar: 50 microns (0.05 mm); Time: real time
Cellular membranes are remarkable materials -- flexible, two-dimensional fluids at which mobile, nanometer-scale proteins play reactive and structural roles (see illustration). How do the material properties of membranes -- their rigidity, the mobility of lipids and proteins, their various phase transitions -- contribute to their function and their ability to spatially organize? How do the unusual structures and compositions of the membranes of various organisms contribute to their survival?
Two-dimensional fluidity is one of the most important properties of biological membranes, as it allows lipids and proteins to interact with one another in spatially and temporally dynamic ways. Despite the importance of 2D mobility, its physical underpinnings are poorly understood, and 2D viscosity is not well quantified. We are exploring these topics using microrheological methods -- analyzing the Brownian motion of membrane-anchored particles and lipid domains.
We've developed two new approaches to measuring membrane viscosity. One involves simultaneously examining the rotational and the translational diffusion of membrane-anchored colloidal particles (illustrated below). For a description of our recent paper in Physical Review Letters on this topic,see: here. The other involves a method known as "two-point microrheology," in which correlations between the Brownian trajectories of objects in a membrane reveal the viscosity of the embedding membrane.
The trafficking of cargo in cells involves dramatic transformations of membrane shape and topology by particular trafficking proteins. How do these proteins harness forces, energies, and local material properties to sculpt transport vesicles? How do proteins create curvature? Experiments in our lab seek to illuminate the mysterious mechanics of trafficking with experiments that directly construct, deform, and observe membranes interacting with trafficking proteins.
We have found that Sar1, a protein that regulates vesicle trafficking from the endoplasmic reticulum, lowers the rigidity of the lipid bilayer membrane to which it binds -- by up to as much as 100% as a function of its concentration. This is the first demonstration that a vesicle trafficking protein lowers the rigidity of its target membrane. Our experiments, illustrated below, involve using optically trapped microspheres to create membrane tethers whose properties reveal membrane mechanical properties.
Here's a movie that illustrates a different approach we've taken to studying membrane mechanics (see here for a discussion):
Thermally driven shape fluctuations of a giant lipid vesicle, incubated with the vesicle trafficking protein Sar1. Analysis of the fluctuation spectrum reveals the rigidity of the membrane, which is dramatically lowered by Sar1. From Andrew F. Loftus, Sigrid Noreng, Vivian L. Hsieh, and Raghuveer Parthasarathy, "Robust Measurement of Membrane Bending Moduli Using Light Sheet Fluorescence Imaging of Vesicle Fluctuations," Langmuir 29: 14588--14594 (2013).
To explore the above-mentioned topics, we use and also develop a variety of advanced optical microscopy techniques. These include light sheet microscopy, interferometry, optical trapping, particle tracking, and other methods.
For a description of some of the computational challenges associated with our bacterial imaging projects, see here. Since writing that, we've devoted even more efforts to machine learning for analyzing complex image data, especially using convolutional neural nets, which is turning out to be very interesting!
A few years ago, weq invented a new, fast, accurate, particle tracking method based on analytic determination of the radial-symmetry-center of a particle image. Please see our Particle Tracking page for the citation, software, and more.
Illustration of particle tracking based on radial symmetry. (a) A simulated CCD image of a point source with shot noise, generated from the noise-free high-resolution simulated image shown in (b). The red X indicates the true center. (c) The gradient of the intensity (orange arrows) is calculated from the image in (a) at the midpoints between pixel centers. Circles indicate the pixel centers. Yellow lines are drawn through each midpoint, parallel to the gradient. (d) The point of minimal distance to the yellow lines in (c), indicated by the orange circle, provides an accurate, analytically calculable estimate of the particle center location.
We gratefully acknowledge support from the National Science Foundation, the National Institutes of Health, the Research Corporation for Science Advancement, the Gordon and Betty Moore Foundation, and Simons Foundation, the M. J. Murdock Trust, and the Kavli Foundation.