Bottom-up systems biology using multidimensional optical proteomics

The group specializes in developing and applying novel forms of optical microscopy to investigate complex biological processes at the level of single molecules.

Our research specializes on the theme of “Single molecule cellular biophysics”. This is becoming a highly topical area of life sciences research which strives to move towards a greater physiological relevance to single molecule biophysics experimentation, either by combining in vivo cellular biology techniques with those of cutting-edge single molecule biophysics or by creating a greater level of molecular complexity to single biomolecule experiments in vitro, and is in effect emerging as a novel disciple in its own right which is likely to increase in application significantly over the next few years as these techniques become more widely used. We use a range of cutting-edge biophotonics and photophysical methods in combination with state-of-the-art genetics. Our group has a depth of expertise in physics applied to biology at the single molecule level, and has worked on bio-molecule mechanical manipulation and force spectroscopy using both AFM and laser-tweezers, low-light fluorescence imaging in vivo and customized advanced microscope design involving development of nanometer length scale imaging with millisecond time resolution. We have a reputation in single molecule investigations on living cells involving several multi-institutional collaborations.

General biological questions of interest to us involve addressing the molecular basis of the cell, seeing how single molecule properties in a living organism scale up to bring about whole-organism functionality, striving to bridge our gap in understanding between molecular biology and cell science in a rational, predictive context. These pose some of the hardest and most fundamental challenges to the future of biophysics research. Full understanding of processes in living organisms is only achievable if all molecular interactions are considered. Cell biology strives to cultivate a full insight into the mechanisms of living cells by investigating interactions that elicit and direct cellular events, though to date the shear complexity of biological systems has caused precise single-molecule experimentation to be far too demanding, instead focusing on studies of single systems using relatively crude bulk ensemble-average measurements. One way forward which we're currently pushing is to monitor several biological systems simultaneously in living, functioning cells using more powerful and precise single molecule techniques, in effect investigating systems level biology from a bottom-up molecular level, eradicating noise rife in systems biology data associated with cell population stochasticity.

Using novel microscopy techniques and state-of-the-art genetics (Nature 2006, 443, 355; PNAS 2008, 105, 15376; Science 2010, 328, 498), we have developed means to monitor single proteins within a living, functioning cell and to observe exchange with other molecules in a complex, functioning biological system. Our objectives are to drive these optical techniques to a much higher level to permit fast, real-time, molecular in vivo imaging of several different proteins in multiple, complex biological systems, to establish and validate mathematical models of complex systems down to the molecular level, and to push forward the genetic development of cell strains for use in these “optical proteomics” studies. Currently we are targeting several biological systems including motility, protein transport, cell signalling, bioenergetics and the "lifecycle" of the DNA molecule.

Our primary experimental technique utilizes advanced approaches of fluorescence microscopy such as total-internal-reflection fluorescence (TIRF) and Slimfield imaging, generally necessitating customized construction, combined with cutting-edge Fluorescent protein fusion molecular genetics technology.