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.

The (not as) unexpected absence of amino acids in heated CI chondrites

Ivuna meteorite

Amino acids are used in biology to make proteins. As such, they are essential for life as we know it. Amino acids of abiotic origin have also been found in meteorites, including seven of the eight different groups of carbonaceous chondrites, a subset of meteorites that contain up to 5 weight-percent carbon. Thus, the general assumption when carbonaceous chondrites are analyzed, then, is that indigenous amino acids will be found. Through the analysis of amino acid abundances and distribution in meteorites, our understanding of how these compounds could have been formed and how likely they are to be found throughout the solar system has been greatly improved.

Because amino acids are so widespread among carbonaceous chondrites, it is important to understand the range of conditions that allow amino acid synthesis to occur, and what conditions are inhospitable to these molecules, either by preventing their formation to begin with or leading to their rapid destruction. One way of identifying conditions that are favorable or disfavorable for amino acid formation and survival is to compare the amino acid distributions of meteorites that are chemically similar but experienced different parent body conditions (e.g., more or less heating, water activity, etc.).

A previous blog post on this subject discussed samples of the Sutter’s Mill meteorite, a CM2 chondrite that fell in Caloma, California in 2012. Because most CM2 chondrites contain indigenous amino acids, the Sutter’s Mill stones were expected to contain amino acids as well. This expectation was not borne out, however. Unlike most CM2 chondrites that experienced relatively low temperature aqueous alteration, the Sutter’s Mill meteorites had been heated to temperatures of 400 °C and above, in some cases. These observations, coupled with laboratory experiments by others that showed rapid degradation of amino acids in water at temperatures above 150 °C, led to the hypothesis that elevated parent body temperatures are not hospitable for amino acids.

We (Aaron Burton, NASA JSC, along with researchers from the NASA Goddard Space Flight Center and River Hill High School) observed a similar absence of amino acids in CI chondrites that had experienced parent body heating. More typical CI chondrites such as Orgueil and Ivuna experienced parent body temperatures 150 °C, and contain appreciable levels of amino acids. The meteorites analyzed in this study, Yamato 86029 and Yamato 980115 experienced temperatures of up to 600 °C in addition to the aqueous alteration that is ubiquitous in CI chondrites. Again, there is a correlation between heating and an absence of amino acids as we observed with the Sutter’s Mill meteorites, supporting the hypothesis that the combination of parent body heating and water activity either prevents the formation or leads to the destruction of amino acids in meteorite parent bodies.

These findings help us to place limits on the stability of amino acids, and inform us about whether or not we should expect to find amino acids and potentially other molecules of biological importance, on various planetary bodies in space.

A route to amino acids and peptides on the early Earth

By analyzing a suite of forgotten samples, university and NASA scientists found a new answer to a longstanding question in prebiotic chemistry. The samples were from reactions performed in 1958 by Dr. Stanley Miller; these reactions were variations on his well-known spark discharge experiments, which demonstrated that amino acids and other important prebiotic molecules could be formed by adding electrical energy to a variety of atmospheric conditions that could have existed  on the prebiotic Earth. A challenging question for prebiotic chemists to answer is how amino acids (or other monomers such as DNA or RNA nucleotides) can be combined into polymers called peptides. The condensation of amino acids into peptides produces water and water is the solvent for these reactions, and, in fact, all life as we know it. This poses a challenge, because net reaction rates slow down when there is a high abundance of product molecules in the system (Le Chatelier’s principle). Thus, the condensation of amino acids in water proceeds only very slowly.

Cyanamide is a condensing agent, a molecule that accelerates the rate of condensation reactions even in water. In the samples analyzed in the current study, Miller added additional cyanamide to his normal mix of gases for a round of spark discharge experiments, but the samples were not analyzed at the time. They surfaced some 50 years later and were now available for study. Eric Parker and co-workers (including myself) analyzed the archived samples and discovered that, in addition to the amino acids commonly produced by the spark discharge experiments, a number of small peptides were also produced. Importantly, cyanamide is also product of the spark discharge reactions, meaning that it is produced concurrently with the amino acids in the spark discharge experiments. Therefore, the spark discharge experiments simulate a plausible way to make peptides from simple gases such as nitrogen, hydrogen and methane, improving our understanding of how molecules important for the origins of life could be generated on a variety of terrestrial bodies in our universe.

The unexpected absence of amino acids in the Sutter’s Mill meteorite

Some of the more than 70 fragments of the Sutter’s Mill meteorite that have been collected to date.

Amino acids are the building blocks of proteins, the molecular machines that are necessary to speed up chemical reactions enough to make  life possible. The discovery of amino acids of extraterrestrial origin in the Murchison meteorite in the 1970s, coupled with the  abiotic formation of amino acids in the Miller-Urey spark discharge experiments, provided compelling evidence that the building blocks of life were likely readily available throughout the Solar System when life was starting.

Recently, Aaron Burton (now at the NASA Johnson Space Center) and researchers at the NASA Goddard Space Flight Center, SETI, and UC-Davis performed amino acid analyses of several fragments of the Sutter’s Mill (SM) meteorite, which fell in Caloma, California in April 2012. The findings of these analyses were published in the journal Meteoritics & Planetary Science.  Like the Murchison meteorite, the SM meteorite is classified as a CM2. It was thus expected that it would have similar amino acid abundances and distributions  as the  Murchison. Instead, the SM meteorite samples were nearly devoid of indigenous amino acids. While both meteorites experienced aqueous alteration (the ‘2’ of CM2 indicates mild to moderate aqueous alteration), the SM meteorite parent body also experienced heating at temperatures of 150 °C to 400 °C or higher. Because laboratory experiments have shown that amino acids degrade at temperatures above 160 °C in aqueous environments in the presence of minerals, the most likely explanation for the missing amino acids is that they were destroyed during this heating process. This finding helps place an upper limit on the temperatures that life’s building blocks can withstand, both in meteorite parent bodies as well as hydrothermal environments on the early Earth.