Uncultivable microorganisms likely play significant roles in the ecology within the human body, with subtle but important implications for human health. Focusing on the oral microbiome, we are developing a processor for targeted isolation of individual microbial cells, facilitating whole-genome analysis without the need for isolation of pure cultures. The processor consists of three microfluidic modules: identification based on 16S rRNA fluorescence in situ hybridization (FISH), fluorescence-based sorting, and encapsulation of individual selected cells into small droplets for whole genome amplification. We present here a technique for performing microscale FISH and flow cytometry, as a prelude to single cell sorting.
We present concepts for self-assembly of diffractive optics with potential uses in biosensors and biocomputers. The simplest such optics, diffraction gratings, can potentially be made from chemically-stabilized microtubules migrating on nanopatterned tracks of the motor protein kinesin. We discuss the fabrication challenges involved in patterning sub-micron-scale structures with proteins that must be maintained in aqueous buffers to preserve their activity. A novel strategy is presented that employs dry contact printing onto glass-supported amino-silane monolayers of heterobifunctional crosslinkers, followed by solid-state reactions of these cross-linkers, to graft patterns of reactive groups onto the surface. Successive solution-phase addition of cysteine-mutant proteins and amine-reactive polyethylene glycol allows assembly of features onto the printed patterns. We present data from initial experiments showing successful micro- and nanopatterning of lines of single-cysteine mutants of kinesin interleaved with lines of polyethylene, indicating that this strategy can be employed to arrays of features with resolutions suitable for gratings.