Microfluidic Extraction of DNA for Identification of Unknown Organisms in Microgravity

The goal of the Microfluidic Extraction of DNA for Identification of Unknown Organisms in Microgravity (MEDIUM) project is to develop a flight instrument capable of identifying organisms in situ with minimal requirements for crew time. In-flight environmental monitoring is an important technology for missions away from low-Earth orbit. An important aspect of environmental monitoring is the ability to identify and respond to microbiological threats. Automatable in situ monitoring technologies are essential when sample return is not practical. Microbial identification is readily achieved by identifying differences in Deoxyribonucleic Acid (DNA) sequences, such as direct sequencing or hybridization of the DNA strands. These analyses require the extraction and separation of DNA from cells. However, current methods for DNA isolation typically require technologies incompatible with spaceflight. In this project, we seek to develop a miniaturized MEDIUM device for the extraction of DNA from operationally relevant samples (i.e., potable water sources). We will compare the sequence data obtained from DNA extracted by MEDIUM with sequence data obtained from standard kit-based extraction methods. Future work will focus on developing a prototype device that integrates extraction and analysis, providing sample-to-answer capability ultimately reducing or eliminating the need for crew time. This device will enable rapid and automatable microbial identification aboard the International Space Station (ISS) and other manned spaceflight missions. Expanding human spaceflight beyond low-Earth orbit poses significant technological challenges. One of these challenges is environmental monitoring, specifically the ability to identify and respond to microbiological threats in real-time. Because returning samples to Earth for analysis is not practical from deep-space, in-flight environmental monitoring is an essential capability for missions away from low-Earth orbit. Microbial identification by direct sequencing is readily achieved by identifying species-specific differences in Deoxyribonucleic Acid (DNA) sequences. These analyses require the extraction and separation of DNA from cells, but current methods for DNA isolation typically require technologies incompatible with spaceflight. In-flight environmental monitoring is an important technology for missions away from low-Earth orbit. An important aspect of environmental monitoring is the ability to identify and respond to microbiological threats. Automatable in situ monitoring technologies are essential when sample return is not practical. Microbial identification is readily achieved by identifying differences in DNA sequences, such as direct sequencing or hybridization of the DNA strands. These analyses require the extraction and separation of DNA from cells. However, current methods for DNA isolation typically require technologies incompatible with spaceflight. We seek to develop a miniaturized MEDIUM device for the extraction of DNA from operationally relevant samples (i.e., potable water sources); the extracted DNA can then be used for microbial identification using one or more DNA-dependent molecular techniques, such as sequencing. Isolation of DNA for sequencing or other analyses typically requires technologies incompatible with spaceflight. For this reason we have carefully chosen digital microfluidics-based extraction cartridges due to their likely compatibility with microgravity. Unlike other DNA extraction methods that rely on gravitational forces, the microfluidics devices use electro-wetting to move liquids. This eliminates the requirement for pumps, centrifuges and other moving parts. The quality of the DNA extracted by the microfluidics-based platform and by conventional kit-based methods will be characterized for its suitability in next-generation sequencing applications.

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