Microscale tools for the development of bacterial microarrays

Abstract

Heterogeneity within bacterial populations is a phenomenon that has gained much interest over the last decades. It has been shown that even isogeneous colonies under homogeneous conditions can display different phenotypes. This heterogenous gene expression in bacteria is considered to be an evolutionary developed trait that increases the chance of survival under changing environmental conditions. This also impacts human health as some phenotypic traits can enable bacteria to survive antibiotic treatment, resulting in reoccurring bacterial infections. There is understandably much interest in uncovering the underlying mechanisms of such phenotypic differences, both for optimized medical treatments and to improve our understanding of the behavior of bacterial populations.

Standard methods utilized in microbiology are however based on average measurements, and hereby inherently masking the existence of small subpopulations and other rare events. With the emergence of techniques capable of large scale single cell measurements, e.g. flow cytometry, much focus has been put on the understanding of heterogeneity of bacterial populations. There is however a need for single cell measurements that provide time resolution in order to study the dynamics of such phenomena. Such time resolution can be obtained through time laps imaging of bacteria. Large scale single cell measurements could however benefit from an ordered attachment of bacteria onto a substrate. In this thesis I present methods for fabrication of bacterial microarrays, focusing on utilizing methods and chemicals that are applicable in standard biological laboratories. The presented method is based on micro contact printed patterns of chemicals on glass substrates for the selective adhesion of bacteria. Such arrays were utilized to inspect the heterogeneity in expression of green fluorescent protein from two different plasmids carried by the bacteria. The results were comparable to results obtained based on measurements of the same system preformed on a flow cytometer.

The surface patterning technique presented was also adapted for the selective adhesion of alginate microgels onto glass substrates. Encapsulation of cells in such alginate microgels allowed for inspection of three dimensional culture growth and the possibility of selective removal of single microgels utilizing a micropipette controlled by a micromanipulator.