Cell encapsulation is a promising concept in regenerative medicine and stem cell treatment of diseases. Cells encapsulated in hydrogels have shown to yield better therapeutic outcome over cells in suspension. Microfluidic platforms have facilitated the process of cell encapsulation through the controlled mixing of aqueous cell solution and hydrogel with an immiscible liquid to yield a monodispersed population of microcapsules at a high throughput. However, given that the microfluidic process of placing cells in microcapsules is completely random, yielded samples are often riddled with empty microcapsules, raising the need for a post-encapsulation purification step to sort empty microcapsules from cell-laden ones. Sorting of microcapsules can be achieved through several techniques, most desirable of which are electrokinetic such as dielectrophoresis (DEP) and electrophoresis (EP). The advantages of DEP and EP techniques are that they support label-free sorting and yield a high throughput. However to achieve true effective DEP or EP sorting, there is a need to understand how empty microcapsules react to these electrokinetic forces versus occupied microcapsules. This study developed microfluidic devices for characterising the electrokinetic effects on microcapsules using DEP and EP. Results of both characterization techniques showed notable differences in the response of empty microcapsules versus cell-laden ones, reinforcing their potentials for sorting. Furthermore, this study proposed designs for microcapsules sorting devices that leverage EP and DEP.

The main focus of this research was the development of microfluidic technology for ultrasensitive and fast molecular analysis of cells. Chromatin immunoprecipitation (ChIP) assay followed by next generation sequencing serves as the primary technique to characterize the genomic locations associated with histone modifications. However, conventional ChIP-seq assay requires large numbers of cells. We demonstrate a novel microfluidics-based ChIP-seq assay which dramatically reduced the required cell number. Coupled with next generation sequencing, the assay permitted the analysis of histone modifications at the whole genome from as few as ~100 cells. Using the same device, we demonstrated that MeDIP-seq with tiny amount of DNA (<5ng) generated high quality genome-wide profiles of DNA methylation. Off-chip sonication often leads to sample loss due to multiple tube transferring. In addition, conventional sonicators are not able to manipulate samples with small volume. We developed a novel microfluidic sonicator, which is able to achieve on-chip DNA/chromatin shearing into ideal fragment size (100~600bp) for both chromatin immunoprecipitation (ChIP) and methylated DNA immunoprecipitation (MeDIP). The integrated on-chip sonication followed by immunoprecipitation (IP) reaction can significantly reduce sample loss and contamination. Simple and accessible detection methods that can rapidly screen a large cell population with single cell resolution have been seriously lacking. We demonstrate a simple protocol for detecting translocation of native proteins using a common flow cytometer which detects fluorescence intensity without imaging. Using our approach, we successfully detected the translocation of native NF-kappa B (an important transcription factor) at its native expression level and examine the temporal dynamics in the process. Droplets with encapsulated beads and cells have been increasingly used for studying molecular and cellular biology. However, a mixed population of droplets with an uneven number or type of encapsulated particles is resulted and used for screening. We developed a fluorescence-activated microfluidic droplet sorter that integrated a simple deflection mechanism. By passing droplets through a narrow interrogation channel, the encapsulated particles were detected individually. The microcontroller conducted the computation to determine the number and type of encapsulated particles in each droplet and made the sorting decision. Our results showed high efficiency and accuracy for sorting and enrichment. / Ph. D.