Capillary-based microfluidic sample confinement for studying dynamic cell behaviour

Cells in the body are in constant interaction with their surrounding environment. These interactions lead to creation of a variety of biophysical and biochemical events such as cell migration, neurite outgrowth and single cell protein secretion. In order to study these complex events, cells should be positioned in accurate spatial locations. This thesis is focused on application of microfluidics in studying cell dynamics based on a new capillary sample confinement approach. The main contributions of this thesis are the fundamentals of capillary-based trapping of biological samples (Chapter 3), microfluidic stamping method for studying cellular migration in patterned co-culture (Chapter 4), microfluidic cell and protein patterning for studying preferential neurite outgrowth dynamics (Chapter 5), and static droplet array for single cell trapping and long-term monitoring (Chapter 6). Using numerical simulation, liquid-air interface movement in a microchannel with different geometries is investigated. For hydrophobic channels, it is found that the slope of the channel geometry can be used to manipulate interface velocity and acceleration. Based on this understanding, microchannel junction geometry for liquid compartmentalization was proposed. The results revealed that the filling pressure and the relative dimensions of the channels at the junction are determinant factors in trapping liquid sample. Understanding of the mechanism of liquid-air interface stoppage in microchannels is used to develop a temporarily sealed microfluidic stamping device for patterning two adherent cell lines and biomolecules with well-defined interlacing configuration. Using this device, cell migratory patterns of endothelial cells co-cultured with cardiac stem cells are investigated. In addition, hippocampal neurons and inhibitory cue Nogo-66 are co-patterned revealing the axon outgrowth dynamics during CNS injury. The stamping device is operated using only a lab pipet and uses very low reagent volumes of 20 μl with cell injection efficiency of >70%. Based on the flow behaviour in junction geometry, a new sample trapping method is presented to easily and reliably generate an array of hundreds of dispersed nanoliter-volume semi-droplets for single-cells culture and analysis. The device isolates cells in droplet compartments and quantifies secretion profile of single or multiple cells over time period of hours up to days. The overall setup and injection procedure take less than 10 minutes, is insensitive to fabrication defects and supports cell recovery for downstream analysis