NASA and university scientists release space sequencing data to the public

 

As part of the Biomolecule Sequencer project, our team just wrapped up the first of what we hope are many rounds of sequencing in space. For this first set of experiments, our goal was to determine whether the MinION and associated flow cells could survive launch to the International Space Station (ISS) and be loaded in microgravity conditions. We analyzed four samples in flight and performed four synchronous ground controls, and benchmarked the flight sequence data against the Illumina and PacBio platforms on the ground; all samples were prepared on the ground and stored on Earth or sent to the ISS frozen, where they were thawed just prior to loading. The big take home message is that there was no decrease in MinION performance between the flight and ground samples.

The data from our flight and ground sequencing runs, along with orthogonal data from other sequencing platforms, are now available in NASA’s GeneLab Database. We’ve also released a pre-print of our analysis of the data, and before we sent the sequencer to the ISS, we tested it aboard a parabolic flight.

 

sequencing-overview-for-blog

Schematic of sequencing experiments performed on the International Space Station and on the ground. The image is from our bioRxiv preprint.

 Why on Earth would anyone want to sequence DNA in space?

Currently, we’re working on demonstrating that all of the steps necessary for sequencing can be performed on the ISS. The culmination of this would be and end-to-end, sample-to-sequence analysis of a sample collected aboard the ISS. Our ultimate goal is to have a functioning sequencing platform aboard the ISS. Some people we’ve talked to have been skeptical about the need for sequencing in space, and wonder whether this is just a gimmick. However, there are a number of applications for sequencing for space exploration:

  • Microbial monitoring. Microbes in the air, water and surfaces of the ISS are currently cultured to get microbial counts and samples are returned to Earth for identification (see here and here). Having in-flight identification capability would enable targeted remediation, and, as exploration moves beyond low-Earth orbit (i.e., towards Mars), it will not be feasible to return samples to Earth for identification.
  • Crew health. It has been observed that the human immune system becomes dysregulated in response to spaceflight, and that microbes can become more virulent. This means that even without new pathogens being introduced to the environment, it is possible that crew members could develop infections. One example of this is viral reactivation, which happens on Earth (i.e., getting shingles virus after you’ve had chicken pox). Sequencing in-flight would allow you diagnose the infectious agent and choose the appropriate antimicrobial treatment.
  • Microbiome studies. The ISS is a unique environment for microbes. It has been continuously inhabited by humans and microbes in constant microgravity with increased space radiation for over 15 years. These conditions place a different set of evolutionary pressures on microbial populations in the ISS, and within the humans that occupy it (see also here). Having a sequencer facility aboard the ISS would enable you to sample regions of interest on demand, and you could even track the accumulation of genetic mutations over time, without having to return samples to Earth coincident with the return of cargo re-supply ships.
  • Gene expression changes. Analysis of mutations at the DNA level allows you to see the permanent effects of spaceflight on organisms. Equally important is understanding how organisms themselves are responding to life on the ISS, and one powerful way of understanding how organisms are responding is by looking for changes in their gene expression (i.e., determining which genes are being upregulated and which are being downregulated). A particular challenge for measuring changes in gene expression is that they can occur on the timescale of minutes to hours, so bringing organisms back to Earth means that they may have re-acclimated. It is possible to extract the RNA and then return the samples to Earth, but there are risks with this method as well, because RNA is susceptible to degradation even when it is stored in a freezer. Having a sequencer aboard the ISS would allow you to perform these analyses in situ, without risk of re-acclimation or sample degradation during storage.
  • Search for extraterrestrial life elsewhere in the solar system. We know that the DNA/RNA/protein paradigm for life on Earth is capable of supporting life in environments ranging from below-freezing polar oceans to above-boiling hot springs, in the presence or absence of oxygen, using an incredible range of energy sources. This includes single-celled bacteria and archaea, to plants, and animals ranging from tardigrades to dinosaurs. At least in principle, then, the molecular basis for life as we know it is a reasonable starting point in the search for life elsewhere. Nanopore-based sensors that perform direct molecular analysis have been used to analyze RNA and even proteins, highlighting their potential to analyze a range of DNA-like molecules that could potentially support life.

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