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While launched Monday morning to the ISS, work on the project began over four years ago when Aaron was in a Postdoc program at the Goddard Space Flight Center. <\/p>\n<\/b>With the arrival of the SpaceX CRS-9 mission to the Space Station Wednesday morning, the first-ever in-space DNA sequencer experiment has arrived at the international orbiting lab. The experiment is designed to test the feasibility of DNA sequencing in a non-Earth environment as well as serve as a pathfinder for sequencing initiatives on long-duration human missions in the inner solar system and on Mars.<\/p>\n
DNA sequencing in space \u2014 the process to get to Station:<\/b><\/p>\n
NASASpaceflight.com\u2019s Chris Gebhardt recently sat down with two members of the Biomolecule Sequencer Project \u2013 Aaron Burton, the Principal Investigator and astrobiologist, and Kristen John, Deputy Project Manager and engineer \u2013 for an interview about the potentially revolutionary project.<\/p>\n
While launched Monday morning to the ISS, work on the project began over four years ago when Aaron was in a Postdoc program at the Goddard Space Flight Center. <\/p>\n
\u201cOur research was on astrobiology and trying to understand the origins of life. One of the people there talked to one of the inventors of nanopore sequencing, and they were interested in sending one of their sequencers up as a planetary science instrument to Mars in order to search for DNA-based life,\u201d related Aaron.<\/p>\n
When Aaron accepted a job at the Johnson Space Center in 2013, he thought that an initial step for nanopore sequencing in space could be sending a sequencer to the ISS to demonstrate that DNA sequencing was possible in a non-Earth environment.<\/p>\n
\u201cAt that point, the technology was still in the development phase. So we ended up getting turned down for the technology demonstration because we didn\u2019t have the sequencer in hand,\u201d said Aaron.<\/p>\n
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As the project continued, NASA astronaut Dr. Kate Rubins became involved, helping the team work through concepts and pre-mission planning activities involving the sample prep process (the samples that would be used to sequence DNA on orbit) and the experiment runs themselves.<\/p>\n
Space Shuttle models (adsbygoogle = window.adsbygoogle || []).push({});<\/p>\n Then, in late-December 2014, Oxford University \u201cput out a call to get beta testers for their MinION nanopore DNA sequencer,\u201d noted Aaron.<\/p>\n The team submitted a proposal and were delighted to learn in early 2015 that they were accepted as beta testers and that their desire to send a sequencer to space resonated with the research team in Oxford.<\/p>\n Coincidentally and beneficially, at the same time, engineers at the Johnson Space Center initiated a new certification process for hardware flying to the ISS. <\/p>\n According to Aaron, \u201cNormally flight Hardware is Class 1, and they came up with a new designation called Class 1E \u2013 meaning experimental hardware, technology that is not on the critical path for crew or life support. <\/p>\n This new Class 1E designation, while still adhering to safety requirements for humans and the vehicle itself, allows researchers to assume slightly more risk about whether or not their hardware will work. <\/p>\n That \u201cslightly more risk\u201d accommodation means that teams are not required to do parabolic flight testing or vibration testing on their equipment if they think their technology won\u2019t need that prior to flight.<\/p>\n Moreover, since the hardware itself, the MinION from Oxford, was an off-the-shelf product with nothing that needed to be designed in house, the experiment was officially selected for flight in February 2015, with final hardware delivery in December 2015 after just 10 months of development.<\/p>\n Both Aaron and Kristen noted that the 10 month timeframe would normally have taken three to four years under the Class 1 designation.<\/p>\n Moreover, the team was expressly trying to overlap the experiment with Dr. Rubins\u2019 flight.<\/p>\n \u201cIn principle, we would like for anyone to be able to do this,\u201d stated Aaron. <\/b>\u201cIf you had a crew member who didn\u2019t have a biology background [like Dr. Rubins does], it might require more hands-on training time with them. <\/p>\n \u201cSo it\u2019s not a requirement that Dr. Rubins do the experiment, and we want to make it \u2013 especially as we develop procedures to use in-flight down the road \u2013 so that anyone can do it. But having Kate for our first try when we\u2019re trying to show that it works at all is incredibly fortunate.\u201d<\/p>\n \u201cThe MinION is a handheld device that weighs 120 grams (0.264 lbs) and fits in your hand,\u201d noted Aaron. \u201cThe next closest sequencer is about the size of a large microwave, and it weighs about 110 pounds. <\/p>\n \u201cIf you\u2019re going to do a technology demonstration and you\u2019ve got something like we have, which is two MinIONs, 9 flow cells, 9 samples, some positive displacement pipettes, and a Surface Pro 3, all of that is under 5 pounds \u2013 which means it costs significantly less to launch all of that to the Station then it would that microwave sized sequencer.\u201d<\/p>\n That microwave-sized sequencer also uses \u201cconventional sequencing with fluorescently labeled nucleotides (organic molecules \u2013 A, G, T, and C \u2013 that serve as the monomers, or subunits, of nucleic acids like DNA). And so you\u2019ll have a strand of DNA, and you copy it. When you incorporate a new nucleotide, you get a fluorescent signal that comes off. <\/p>\n \u201cThose fluorescent measurements are how you read conventional sequencing. But that means you also have to have lasers that are very carefully aligned.\u201d<\/p>\n The MinION, on the other hand, operates through electrochemical detection, a much more simple and effective way of sequencing for space-based operations. <\/p>\n \u201cThe way the MinION works is that we have these nanopores that are just big enough to allow a single strand of DNA to pass through. <\/p>\n \u201cHow we actually sequence DNA using the MinION is that normally there is nothing in the nanopore, and you have a certain amount of ions that are flowing through. That\u2019s our baseline current. <\/p>\n \u201cThen, as DNA passes through the pore, the current changes. And that change in current is diagnostic of the sequence of DNA passing through it.<\/p>\n \u201cThe pore is big enough so that five nucleotides fit in there at one time. So if you had five As sitting in there, you would get a characteristic current. And then the next nucleotide is fed through by a protein, pushing the first A out. And let\u2019s say that new nucleotide is a T, then the next current you\u2019re going to measure is the current of four As and one T. <\/p>\n \u201cThe MinION will then feed through another nucleotide, and you\u2019ll see a different current. So basically you\u2019re measuring how the DNA is blocking the pore, and the current changes depending on which nucleotides are in the pore.\u201d<\/p>\n This is simple, from the science standpoint, and importantly is not the part of the process that the team is worried about in terms of proving that DNA sequencing is possible in space.<\/p>\n According to Aaron and Kristen, one of the primary concerns with this experiment is air bubbles. To this end, there\u2019s an initial step before loading the sample into the machine where the air bubbles have to be extracted before the sample is loaded \u2013 all while trying not to introduce any new air bubbles.<\/p>\n \u201cIn space, though, there\u2019s no gravity environment that causes the air bubbles to rise or go anywhere,\u201d noted Aaron. They kind of want to glomb together and make bigger bubbles. <\/p>\n \u201cSo our biggest concern is that if you do get an air bubble introduced in the MinION, what\u2019s it going to do? Is it going to stick to a surface? Is it going to interact with the pores? Is it going to block part of the pore?\u201d<\/p>\n The other principal concern that could make the experiment unfeasible in space is the launch vibration environment. <\/p>\n As Aaron related, the samples are \u201cnaturally occurring proteins sitting in a membrane. So if you get enough vibration at the right frequency you can actually disrupt those membranes and they can start falling apart.\u201d<\/p>\n \u201cSo we actually don\u2019t have a huge question of whether or not the machine, the MinION, will be able to sequence DNA. We\u2019re quite confident on that,\u201d stated Aaron. \u201cIt\u2019s the other two things that could hold us up.\u201d<\/p>\n On Station \u2014 doing the experiment and getting the data back to Earth<\/b><\/p>\n Now that the experiment has arrived on Station, the next step is finalizing the precise time when Dr. Rubens will actually perform the experiment. <\/p>\n According to Kristen, \u201cCrew time is extremely limited on the Station, so getting five hours of dedicated time is actually a lot and should let us do three complete runs of the experiment.\u201d<\/p>\n In fact, limited crew time was a prime consideration for how this first experiment was designed, with the samples that will be sent through the MinION prepared on the ground before launch.<\/p>\n The current NEMO expedition off the coast of Florida as well as researchers at Oxford are working on ways to get this preparation time down to as little as 10mins with non-microbiologists, but for now, it\u2019s a multi-hour process.<\/p>\n \u201cHopefully, going forward, any astronaut will be able to do this in flight. But for this initial run, we wanted to make sure that the sequencer actually works,\u201d noted Aaron. \u201cSo in-flight sample preparation wasn\u2019t a priority.\u201d<\/p>\n Regardless of future sample preparation, the current experiment will specifically test the MinION\u2019s ability to successfully detect and sequence DNA from three different types of creatures: a virus, a bacterium, and a mammal.<\/p>\n As Aaron stated, the reason for such a diverse test is because \u201cwe want to show that you can sequence DNA from basically anything, whether it\u2019s a virus or an entire organism.\u201d<\/p>\n For the actual experiment, Aaron and Kristen noted that there\u2019s a total of about 100 nanograms of DNA in the samples, and they\u2019re hoping to get somewhere around 10,000 sequence reads from the MinION on the samples.<\/p>\n The sequences will be measured in a current vs. time plot because the MinION measures the change in current over a length of time that nucleotides are blocking the pore entrance.<\/p>\n Because of the fast-paced nature of the sequencing process, the sequencer will be hooked up to a USB 3.0 connection that will tie the sequencer to a solid state recorder in the Surface Pro 3, where all of the data will be recorded locally before it\u2019s transmitted in its raw form to the ground for analysis.<\/p>\n In-space DNA sequencing \u2013 a tool for astrobiology with Earth-based benefits:<\/b><\/p>\n As with many, if not all of the experiments performed on the ISS, this in-space DNA sequencing experiment holds potentially enormous benefits for future exploration of the inner solar system in terms of astrobiology as it also does for real-world applications on Earth. <\/p>\n For those real-world applications, Aaron noted that \u201cIn many ways, the ISS is analogous to how it is in third world countries. If you\u2019re out in Africa studying the recent Ebola outbreak, which people were actually doing with the MinION, you need to have portable diagnostic capability in the field, and you need the machine to not require a lot of resources. <\/p>\n In terms of astrobiology, Aaron stated, \u201cThere have been a lot of cases made for why both Mars and Earth might have DNA-based life. Some of the basic ones are that we have Martian meteorites here on Earth, so we know that material was exchanged between the planets. <\/p>\n \u201cAt some point in its past, Mars probably had more of an atmosphere and had liquid water. So it had a similar sort of environmental context. So if an organism had traveled from one planet to the other, common conditions might not have been so dissimilar that life would have necessarily died.<\/p>\n Moreover, if life \u2013 even fossilized life \u2013 were to be found on Mars, it\u2019s entirely possible that all other sequencers would not be able to sequence that life\u2019s DNA because of those sequencers\u2019 need to copy the DNA itself.<\/p>\n \u201cMost of the sequencing technologies require you to copy the DNA you have,\u201d states Aaron. \u201cWe have a lot of really good methods for copying DNA using biological enzymes. But these enzymes are highly evolved to only recognize the A, G, T, and C nucleotides of DNA.<\/p>\n \u201cSo if you had some alien organism that instead of A, G, C, and T had H, I, J, and K \u2013 whatever the letters of that alphabet are \u2013 our enzymes here on Earth would not recognize those. So you wouldn\u2019t be able to do any type of sequencing that was dependent on copying the DNA. <\/p>\n \u201cAnd that pattern should be something that is not repeating, but not random either. We call that semi-repeating, like our DNA is, and it\u2019s basically saying \u2018Hey, there\u2019s some information here.\u2019\u201d<\/p>\n Moreover, Aaron noted that nanopore sequencing could help with in situ investigation of biological components on Mars in terms of making sure that any life we might find there isn\u2019t life we brought with the spacecraft or humans from Earth. <\/p>\n \u201cWe do our best to sterilize spacecraft, but even the Curiosity Rover had somewhere around 500,000 spores that were considered viable,\u201d noted Aaron. \u201cWe know we\u2019ve brought Earth life to Mars. <\/p>\n In terms of more practical applications for astronauts, nanopore sequencing technology like the MinION would also be able to help better diagnose in-flight infections among crew members. <\/p>\n According to Aaron, \u201cRight now, if a crewmember gets an infection, they take a picture or just talk to their flight surgeon and do the best they can. <\/p>\n \u201cBut being able to know whether the infection is something that actually requires antibiotics, and if so what kind of antibiotic \u2013 if any \u2013 is needed for treatment, would really help with diagnostic capability.\u201d<\/p>\n (Images: NASA, Nanopore Tech, Sarah Castro)<\/p>\n","protected":false},"excerpt":{"rendered":" With the arrival of the SpaceX CRS-9 mission to the Space Station Wednesday morning, the first-ever in-space DNA sequencer experiment has arrived at the international orbiting lab. The experiment is designed to test the feasibility of DNA sequencing in a non-Earth environment as well as serve as a pathfinder for sequencing initiatives on long-duration human […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"","ping_status":"","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"inline_featured_image":false,"footnotes":"","_links_to":"","_links_to_target":""},"categories":[2],"tags":[4520,1395,233],"class_list":["post-39004","post","type-post","status-publish","format-standard","hentry","category-news","tag-dna","tag-dragon","tag-iss"],"acf":[],"_links":{"self":[{"href":"https:\/\/starpath.global\/blog\/wp-json\/wp\/v2\/posts\/39004"}],"collection":[{"href":"https:\/\/starpath.global\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/starpath.global\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/starpath.global\/blog\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/starpath.global\/blog\/wp-json\/wp\/v2\/comments?post=39004"}],"version-history":[{"count":0,"href":"https:\/\/starpath.global\/blog\/wp-json\/wp\/v2\/posts\/39004\/revisions"}],"wp:attachment":[{"href":"https:\/\/starpath.global\/blog\/wp-json\/wp\/v2\/media?parent=39004"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/starpath.global\/blog\/wp-json\/wp\/v2\/categories?post=39004"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/starpath.global\/blog\/wp-json\/wp\/v2\/tags?post=39004"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}![\"Screen](\"\/\/www.nasaspaceflight.com\/wp-content\/uploads\/2016\/07\/Screen-Shot-2016-07-21-at-15.48.49-350x259.png\")
\u201cIf it doesn\u2019t work, people\u2019s lives aren\u2019t in danger.\u201d<\/p>\n![\"Screen](\"\/\/www.nasaspaceflight.com\/wp-content\/uploads\/2016\/07\/Screen-Shot-2016-07-21-at-15.56.56-350x233.png\")
However, while the experiment was ready to fly in December 2015, more than enough time to make the April 2016 launch date of SpaceX\u2019s CRS-8 mission, the experiment itself required Cold Storage capability aboard SpaceX\u2019s Dragon capsule.<\/p>\n![\"Screen](\"\/\/www.nasaspaceflight.com\/wp-content\/uploads\/2016\/07\/Screen-Shot-2016-07-21-at-15.49.18-350x347.png\")
Also fortunate for the team was the size and weight of the MinION itself and the various frozen samples prepared before flight. <\/p>\nSee Also<\/h4>\n
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![\"Screen](\"\/\/www.nasaspaceflight.com\/wp-content\/uploads\/2016\/07\/Screen-Shot-2016-07-21-at-15.49.33-350x196.png\")
\u201cAnd that is a different current than the one with 5 As.<\/p>\n![\"2016-07-17-175859\"](\"\/\/www.nasaspaceflight.com\/wp-content\/uploads\/2016\/07\/2016-07-17-175859-350x260.jpg\")
On Earth, this is accomplished by putting the sample in a centrifuge, and all the air bubbles rise to the top.<\/p>\n![\"Screen](\"\/\/www.nasaspaceflight.com\/wp-content\/uploads\/2016\/07\/Screen-Shot-2016-07-21-at-16.16.47-350x234.png\")
While precise dates and times have not been determined (though the samples have to be used no later than 8 weeks after preparation \u2013 which occurred just prior to launch in mid-July), the team plans three full sequencing runs, which will require approximately five hours of crew time.<\/p>\n![\"2016-07-22-214423\"](\"\/\/www.nasaspaceflight.com\/wp-content\/uploads\/2016\/07\/2016-07-22-214423-350x239.jpg\")
As Aaron stated, \u201cThe process of preparing samples for sequencing takes between three and four hours, and that\u2019s by someone who\u2019s trained and who\u2019s done it many times. And it\u2019s on the ground where you know how things work.<\/p>\n![\"2016-07-22-215831\"](\"\/\/www.nasaspaceflight.com\/wp-content\/uploads\/2016\/07\/2016-07-22-215831-350x237.jpg\")
The three specific DNA samples are all from viruses, bacteria, and mammals that have well-known, understood, and characterized DNA \u2013 providing a clear baseline for each DNA sequence in the experiment.<\/p>\n![\"2016-07-22-215922\"](\"\/\/www.nasaspaceflight.com\/wp-content\/uploads\/2016\/07\/2016-07-22-215922-350x252.jpg\")
\u201cWe\u2019ve done our best to ensure that there\u2019s an equal number of virus, bacteria, and mammal in the samples. So hopefully we\u2019ll be able to get about 3,000 sequences from each organism,\u201d stated Aaron.<\/p>\n![\"2016-07-22-220510\"](\"\/\/www.nasaspaceflight.com\/wp-content\/uploads\/2016\/07\/2016-07-22-220510-350x257.jpg\")
\u201cAnything we can do to make this technology usable by anyone, not just trained microbiologists, means that a non-specialist doing field work on water monitoring in a resource limited place on Earth would be able to use it.\u201d<\/p>\n![\"2016-07-22-220551\"](\"\/\/www.nasaspaceflight.com\/wp-content\/uploads\/2016\/07\/2016-07-22-220551-350x262.jpg\")
\u201cAnd so if you did have DNA-based life on Mars, the MinION could help us detect that without having to replicate the DNA as other sequencers do.\u201d<\/p>\n![\"2016-07-22-220627\"](\"\/\/www.nasaspaceflight.com\/wp-content\/uploads\/2016\/07\/2016-07-22-220627-350x232.jpg\")
\u201cWhereas with nanopore sequencing, as long as you can feed it through that pore, you\u2019re going to get a current profile vs. time that should be able to see a pattern even if you don\u2019t know what the DNA sequence letters are.<\/p>\n![\"2016-07-22-220728\"](\"\/\/www.nasaspaceflight.com\/wp-content\/uploads\/2016\/07\/2016-07-22-220728-350x232.jpg\")
\u201cSo if we were to find life on Mars, we\u2019d like to be able to know that it\u2019s not something we brought with us on our spacecraft or something that came with the human that was there.\u201d<\/p>\n