Research

We develop novel technologies integrating diverse chemical and physical principles to study intact, fully assembled biological systems with single cell/molecule resolution, at high throughput while retaining the spatial or environmental information of each cells in vivo. Intact organs are complex systems comprising highly heterogeneous cell populations that interact intensively with each other and with neighboring environments. Recent development of single cell sequencing technologies enables researchers to characterize the genomic/transcriptomic profile of individual cells, and to identify rare cell populations that may play a key role in determining the fate of an organ. However, most current single cell sequencing techniques involve disaggregation of tissues; therefore, it is still very challenging to correlate the spatial and environmental information of cells to their transcriptomic profiles. Interplay of cells among themselves or with neighboring environments often govern the overall function; therefore, the cellular heterogeneity data alone does not provide enough information to decipher the molecular and cellular mechanisms underlying the function or dysfunction of an organ. We leverage advances in nanotechnology, materials chemistry, bio-imaging, and drop-based microfluidics to pioneer technologies for correlating single cell sequencing data with the structural, molecular and environmental characteristics of each cell in intact organs. This approach allows us to 1) assess how the molecular profile of individual cells are organized throughput a tissue and 2) analyze how the extra-cellular environments of cells influence their molecular profiles and, ultimately, the function of the complete organ.

Microfluidic platforms developed for high throughput single cell can also be used for single virus genomics studies. Viruses have enormous impact on human lives, not only by causing diseases, but also by shaping our immune systems. Despite their ubiquity and influence, less than 0.01% of viral species have been identified and studied. The main challenge for sequencing novel viruses is the requirement for establishing cultivable virus-host systems. Ability to sequence viral genomes from a single virion eliminates the needs for cell culture and opens a wide door to novel virus discovery. In our lab, we invent microfluidic platforms for high throughput genome sequencing of single virus particles. Whole genome sequence data produced from uncultivable viruses will lead to new investigations into viral ecology, evolutionary biology, epidemiology and other clinical sciences, and identification of single virus mutations will facilitate our understanding on virus evolution and adaptation.

Following are the main technologies we use in the lab:

Intravital (in vivo) imaging
Imaging live animals at microscopic resolution, intravital imaging, allows researchers to directly study how cells are spatially organized, move, interact with each other and respond to pathological stimuli in their native states. We develop intravital imaging methods to probe the extra cellular environments of cells in vivo and record that information so that we can correlate the in vivo characteristics of cells with their molecular profiling.

bioimaging (1)

Quantum dot probes for bioimaging
Semiconductor nanocrystals, known as quantum dots (QDs), exhibit optimal properties for bioimaging applications: tunable bandgap, high molar extinction coefficients, broad absorption, excellent photostability, narrow (25-35 nm) and Gaussian-shaped emission profiles, etc. We synthesize high quality core-shell QDs and new surface coatings to prepare bright, compact, stable, and biocompatible QD probes so that we can improve the limitations of the current in vitro and in vivo imaging technologies.

Quantum dots

Drop-based Microfluidics for single cell/virus studies
Drop-based microfluidic offers the perfect platform for high-throughput molecular profiling of single-cells or viruses, owing to its scalability and high-throughput ability. In this technology, individual cells or viruses are compartmentalized into monodisperse, micron-sized droplets, which function as independent reaction vessels. The low volume of drops enables production of ten million drops from 100 µL-1 mL samples, yields high reaction efficiency, and ensures fast reaction time and low cost. Drops can be manipulated at the rate of 1000-30,000 Hz to add and subtract reagents allowing multi-step reactions. In addition, capture efficiency of cells into drops is high since all cells or viruses in a sample volume can, in principle, be captured in drops using a microfluidic drop maker. We combine drop-based microfluidics, materials chemistry, and various sorting technologies to develop new single cell/virus sequencing platforms.

microfluidics

Students in our lab will have the opportunity to learn: Nanocrystal synthesis, ligand synthesis, drop-based microfluidics, spectroscopic and analytical characterization, cellular imaging, single cell/virus genomics and transcriptomics, cell culture techniques, and molecular biology