Developing a Raman-Assisted Microfluidic Cell Sorting Unit

UNLOCK is a unique facility for research on mixed microbial communities at an unprecedented scale and efficiency. One of the four platforms of UNLOCK is the Biodiscovery Platform, which is linked to the Laboratory of Microbiology, and which aims to provide infrastructure for the investigation and isolation of yet-unknown microorganisms. At the Biodiscovery Platform we are currently building a Raman-Assisted Microfluidic Cell Sorting Unit.

The Unit is composed of four major parts: (1) A Raman microscope, (2) an optical tweezer, (3) a microfluidics cell sorter, and (4) a single cell cultivation platform. Single cells are flowing through a microfluidic device and can be trapped using an integrated optical tweezer. When trapped, Raman spectroscopic detection can determine whether the cell has a characteristic of interest (e.g., isotopic labelling) allowing then to discard or isolate the cell for further downstream analysis.

By utilizing substrates that are labelled with stable isotopes, such as deuterium, carbon-13 (13C), or nitrogen-15 (15N), Stable Isotope Probing (SIP) techniques can differentiate cells that are metabolically active and labelled under specific conditions of interest. Through providing precise functional information at a single-cell level, SIP techniques provide a powerful tool to explore new ecological pathways and metabolisms. With Raman microspectroscopy, we can investigate the chemistry of cells in situ using inelastic scattering generated by lasers interacting with chemical bonds. Using SIP and Raman spectra to detect labelled cells within microbial communities, we can sort metabolically active cells of interest for downstream analysis from within microbial communities.

The aim of the thesis is to assist in the cultivation of microorganisms with labelled substrates and to characterize them under the Raman microscope.

In this project you will:

• use cultivation techniques
• spectroscopy and imaging