Gene expression analysis of Escherichia coli grown in miniaturized bioreactor platforms for high-throughput analysis of growth and genomic data

Combining high-throughput growth physiology and global gene expression data analysis is of significant value for integrating metabolism and genomics. We compared global gene expression using 500 ng of total RNA from Escherichia coli cultures grown in rich or defined minimal media in a miniaturized 50-μl bioreactor. The microbioreactor was fabricated out of poly(dimethylsiloxane) (PDMS) and glass and equipped to provide on-line, optical measurements. cDNA labeling for microarray hybridizations was performed with the GeniconRLS system. From these experiments, we found that the expression of 232 genes increased significantly in cells grown in minimum medium, including genes involved in amino acid biosynthesis and central metabolism. The expression of 275 genes was significantly elevated in cells grown in rich medium, including genes involved in the translational and motility apparatuses. In general, these changes in gene expression levels were similar to those observed in 1,000-fold larger cultures. The increasing rate at which complete genomic sequences of microorganisms are becoming available offers an unprecedented opportunity for investigating these organisms. Our results from microscale cultures using just 500 ng of total RNA indicate that high-throughput integration of growth physiology and genomics will be possible with novel biochemical platforms and improved detection technologies.     

A well-mixed, polymer-based microbioreactor with integrated optical measurements

We describe a 150 microL microbioreactor fabricated in poly(methylmethacrylate) (PMMA) and poly(dimethylsiloxane) (PDMS) to cultivate microbial cell cultures. Mixing is achieved by a small magnetic stir bar and fluorescent sensors are integrated for on-line measurement of pH and dissolved oxygen. Optical transmission measurements are used for cell density. The body of the reactor is poly(methylmethacrylate) with a thin layer of poly (dimethylsiloxane) for aeration, oxygen diffuses through this gas-permeable membrane into the microbioreactor to support metabolism of bacterial cells. Mixing in the reactor is characterized by observation of mixing of dyes and computational fluid dynamics simulations. The oxygenation is described in terms of measured K(L)a values for microbioreactor, 20-75/h corresponding to increasing stirring speed 200-800 rpm. Escherichia coli cell growth in the microbioreactor is demonstrated and the growth behavior is benchmarked with conventional bench-scale bioreactors, flasks and tubes. Batch culture experiments with Saccharomyces cerevisiae further demonstrate the reproducibility and flexibility of the microbioreactor system.     

Application of a multiphase microreactor chemostat for the determination of reaction kinetics of Staphylococcus carnosus

Bioprocess and Biosystems Engineering - Bioreactors at the microliter scale offer a promising approach to accelerate bioprocess development. Advantages of such microbioreactors include a reduction...     

Detection of Pseudomonas aeruginosa in water samples using a novel synthetic medium and impedimetric technology

AIMS: To investigate whether the use of a novel synthetic medium in conjunction with impedimetric technology could provide a rapid and automated detection of Pseudomonas aeruginosa in water samples. METHODS AND RESULTS: A selective synthetic medium (Z-broth) in which the only carbon and nitrogen source is acetamide was applied in direct impedimetric examination for the selective isolation of P. aeruginosa. A total of 1036 tap-water, well-water, swimming-pool water and dialysis water samples were investigated, and any P. aeruginosa contamination was detected in 7-24 h. Neither false-negative nor false-positive results were observed. CONCLUSIONS: The results of the present evaluation demonstrate that impedance measurement with the use of Z-broth is suitable for the rapid and automatic detection of P. aeruginosa in water. SIGNIFICANCE AND IMPACT OF THE STUDY: The main advantages of the method: 240 samples can be examined in one step, the procedure is fully automated, the results are obtained quickly and the labour and media requirements are low.     

Differential gene expression profiles and real-time measurements of growth parameters in Saccharomyces cerevisiae grown in microliter-scale bioreactors equipped with internal stirring

Combining real-time growth kinetics measurements with global gene expression analysis of microbial cultures is of significant value for high-throughput biological research. We have performed differential gene expression analysis in the eukaryotic model Saccharomyces cerevisiae grown in galactose and glucose media in 150 muL bioreactors equipped with sensors for in situ and real-time measurements of optical density (OD), pH, and dissolved oxygen (DO). The microbioreactors were fabricated from poly(dimethylsiloxane) (PDMS) and poly(methyl methacrylate) (PMMA) and equipped with internal magnetic ministirrers and evaporation compensation by water replacement. In galactose-grown cells, the core genes of the GAL operon GAL2, GAL1, GAL7, and GAL10 were upregulated at least 100-fold relative to glucose-grown cells. These differential gene expression levels were similar to those observed in large-scale culture vessels. The increasing rate at which complete genomic sequences of microorganisms are becoming available offers an unprecedented opportunity for comparative investigations of these organisms. Our results from S. cerevisiae cultures grown in instrumented microbioreactors show that it is possible to integrate high-throughput studies of growth physiology with global gene expression analysis of microorganisms.