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ERC

Micro-RIP Report Summary

Project ID: 615146
Funded under: FP7-IDEAS-ERC
Country: Finland

Mid-Term Report Summary - MICRO-RIP (Functional analysis of uncultivated microbes using radioisotope probing)

The “Micro-RIP - Functional analysis of uncultivated microbes using radioisotope probing” project develops novel high throughput techniques and assays that help environmental microbiologists solve the main questions in the field: who is doing what, when, and under what control. Better understanding of the microbes responsible for cycling of nutrients, degradation of terrestrial carbon stocks, or bioremediation of recalcitrant organic pollutants, is essential for better management of such processes and improved forecasting of future trends.
The main task is to set up the Micro-RIP method, which enables two-dimensional analysis microbial communities in complex environmental samples: who are there, and which of the community members are responsible for a specific observed function. The method builds on a commercially available semiconductor sequencing platform and our patented invention of radioactivity measurement via pH analysis. Reverse engineering, including programming, measurement configuration and making the necessary minor modifications to the measurement hardware, have been completed. The biggest challenges have proved be in the optimization of the detection chemistry in the dimensions (physical, chemical, electronical) determined by the sequencing chip chamber. Novel autoradiographic emulsion and its application protocol, developer and reference buffer have been developed and optimized that now enable sensitive detection of C-14 exposure as pH decrease in the exposed areas of the sequencing chip chamber. Areal detection is necessary for the development of signal processing protocols, before proceeding to single-well micro-scale detection and DNA/RNA-based assays. For the latter, protocols are already developed that enable specificity and minimize false positives, and positive references that control for false negatives.

Besides the Micro-RIP application, the know-how gained in the project has already created the basis for several spin-off applications and a new project to commercialize medical applications (MUTTE 1.1.2017-31.6.2018, funded by Tekes – the Finnish Funding Agency for Innovation). All these efforts serve the same purpose: functional analysis of uncultivated microbes or detection of important biomolecules. Also new approaches have been developed for e.g. improving newly described epicPCR, and for separation of radiolabeled single cells, enabling further identification of genomes, proteomes and metabolomes of uncultivated microbes in a high throughput manner.

Reported by

JYVASKYLAN YLIOPISTO
Finland
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