Summary: Our research utilizes state of the art fluorescence microscopy to investigate molecular mechanisms of gene regulation, transcription and splicing from bacteria and humans. By combining methods for the visualization of protein and RNA we will elucidate how genetic information is stored, how individual genes are expressed and how gene expression programs are executed by direct visualization of single molecule dynamics in living cells. Interpretation of fluorescence fluctuation imaging requires an understanding of both molecular dynamics and experimental factors such as laser scanning, fluorescence excitation, and photon detection. This research applies physics-based fluctuation imaging and analysis to in vivo biochemistry (i.e., quantitatively measuring intercellular molecular concentrations and interactions in living cells). We will combine stochastic and dynamic computer simulations with in vivo fluorescence fluctuation imaging to address how specific factors such as finite cell thickness, endogenous non-fluorescent species, and mixed diffusion-binding dynamics can be taken into account in particular applications of fluorescence fluctuation imaging to biochemical measurements in the crowded environment of the cell.

Minimum Classes: NA

Projects: By editing the genome of bacteria or human cells we can label individual protein and RNA molecules with fluorescent protein. Projects this summer include: 1. Implementation of two photon 3D orbital tracking microscopy to monitor RNA synthesis and splicing in human cells. 2. Development of computer software for visualization, simulation and data analysis of 3D orbital tracking data. 3. Preliminary studies of gene regulation and biofilm formation in bacteria. 4. Preliminary studies of Estrogen Receptor dynamics in human cells. Techniques used will include bacterial and mammalian cell culture, RNA Fluorescence in Situ Hybridization (FISH), DNA transfection, live cell Fluorescence Microscopy, Fluorescence Correlation Spectroscopy (FCS and related techniques). Preferred (but not required) computer experience includes Mathematica, Matlab, IDL, Ansi C, Python and Java.

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