NASA to sequence DNA in space for first time

July 16, a Falcon 9 rocket is scheduled to blast off from Cape Canaveral to the International Space Station carrying a DNA sequencer into space for the first time.

While this isn’t big-deal science, no one has ever tried to decode DNA in outer space before. Being able to is something that might come in handy on a Mars mission if a crewmember gets sick or alien mold appears in a spaceship.

“Right now we culture stuff and return it to Earth, but if you send people to Mars you aren’t going to send samples back,” says Aaron Burton, a NASA chemist in charge of the experiment. He said NASA is also interested in determining if the microbes in people’s guts change while they’re in space.

Also notable is that the instrument to be shot into space, called the MinION, is small enough to fit in a coat pocket and works by reading DNA as it’s sucked through a teensy nanopore.

The sequencer is made by the British company Oxford Nanopore, which claims that the device will lead to an era of ubiquitous sequencing—scanning for germs in every sewer, subway station, or jungle outpost.

It’s obviously a public relations coup to be the first sequencer in space. You even get a nifty patch for your jumpsuit. But scientists say they didn’t have much choice, since every pound flown to the ISS incurs a payload charge of about $10,000.

Research Overview

The International Space Station (ISS) lacks molecular biology capabilities. The capacity to perform DNA sequencing, a complex molecular biology technique, would enable:
  • Operational environmental monitoring of microorganisms
    • Allow for in-flight identification of microbes, which is currently not possible but is essential for travel beyond our moon.
    • Inform real-time decisions and remediation strategies.
  • Medical operations – Real-time analysis can impact medical intervention and define countermeasure efficacy.
  • Research – DNA from any organism can be sequenced to assist any scientific investigation on the ISS.
  • Astrobiology
    • ISS demonstration serves as functional testing for integration into robotics for Mars exploration missions.
    • This technology is superiorly suited for the detection of life based on DNA and DNA-like molecules.

Description

The objectives of Biomolecule Sequencer are to (1) provide proof-of-concept for the functionality and (2) evaluate crew operability of a DNA sequencer in the space environment. The immediate capabilities from the sequencer are, but are not limited to, in-flight microbial identification for crew and vehicle health assessments; monitoring changes at the DNA level in astronauts and microbes; and analyzing DNA-based life on other worlds if present. Molecular biology is a branch of biology aimed at understanding the molecular basis of biological activity at the level of DNA, RNA, and proteins. One of the most powerful applications of molecular biology techniques is in the identification of organisms; identification can be achieved using a variety of methods, each with their own advantages and disadvantages.
Despite the importance of microbial identification, there is currently no way to perform this task aboard the ISS, thus requiring samples to be returned to Earth for analysis. However, this is an area of priority and there are several molecular biology-capable devices being currently developed and/or certified for spaceflight. Two of these platforms (WetLab-2 and the RAZOR: part of the 2 x 2015 Water Monitoring Suite project) are based on real-time polymerase chain reaction. This technology functions by detecting the presence of specifically targeted DNA sequences by giving off a fluorescent signal. In order to identify a given microorganism, a primer (short strand of DNA that serves as a starting point for DNA synthesis) that is specific to your target microbe or DNA section of interest is absolutely required, meaning that you can only detect the organisms you are specifically targeting (i.e., have primers for). In contrast, the Biomolecule Sequencer functions by determining the nucleotide sequence of individual molecules of input DNA without the requirement for target-specific primers. Thus, rather than detecting specific targets, the Biomolecule Sequencer will provide data on the entirety of a sample (e.g., all microorganisms present or an entire genome). This means that DNA from a range of organisms can be identified in the context of a single analysis.
Biomolecule Sequencer, is an effort out of NASA Johnson Space Center (JSC) to test a COTS DNA sequencer aboard the ISS. The DNA is sequencer is the MinION, which is a thumb-drive sized sequencer. Because the technology is built on ion pores that are on the nanometer scale, the hardware itself is exceptionally small (9.5 x 3.2 x 1.6 centimeters), lightweight (less than 120 grams with USB cable), and powered only though connection to a laptop or tablet. The sequencing device is permanent, while the flow cells, to which the samples are added, are periodically replaced. The flow cells that perform the sequencing are best used within 60 days. The sequencer works by passing DNA strands through nanopores, and as the DNA passes through the pore, the device measures changes in current that are diagnostic of the sequence of the DNA passing through it. DNA from viruses, bacteria, and a mouse are used to demonstrate that you could sequence DNA from any organism. If successful, the sequencer could be used in-flight for microbial identification as well as research into how organisms are responding to spaceflight at the molecular level, through permanent changes in DNA or transient changes in RNA production. The sequencer could also be potentially used as a life detection instrument, though it would likely require some additional development effort.

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Applications

Space Applications
Crew members on the ISS frequently participate in DNA testing, but these tests require collecting samples and sending them back to Earth to be analyzed. This investigation studies a miniature sequencer that may work in space. The sequencer could greatly improve scientific research on the ISS through advancements in microbe identification, disease diagnostics, and collection of real-time genomic data. Spaceflight-compatible DNA sequencing technology can also be integrated into astrobiology-based exploration missions.

Earth Applications
DNA sequencing is typically difficult and time-consuming and requires bulky and expensive equipment. This investigation tests a miniature sequencer that can be used to diagnose infectious diseases. Understanding how to sequence DNA with minimal resources benefits people on Earth, especially those in remote locations and in developing countries. In addition, using the miniature sequencer on the ISS benefits scientific investigations on human health, benefiting people on Earth.

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Operations

Operational Requirements and Protocols

Optimal testing of the DNA Sequencer involves sequencing three separate samples on three different flow cells. These sequencing sessions do not have to occur back-to-back, but as crew time permits. Cold stowage of the flow cell and sample syringes is required. Downlinking of the DNA sequence data is needed. Return of the used flow cells is requested to determine their functionality in the space environment. The used flow cells do not need to be maintained in cold stowage prior to their return.
Crew member retrieves Sample Syringe-1 and Flow Cell-1 from cold stowage. The Sequencer and Surface Pro3 Tablet are retrieved from stowage and setup. Crew member installs Flow Cell-1 in Sequencer, loads Sample Syringe-1 in Sequencer then discards syringe. Sequencer then runs for up to 48 hours unattended and shuts itself down. When run is finished, crew member starts data transfer (~10GB) from Surface Pro3 for ISS downlink, then removes Flow Cell-1 from Sequencer and bag for return. Sequencer, Flow Cell-1 bag, USB cable, and Surface Pro3 are stowed after completion of experiment. Total crew time estimate required to perform experiment is about 3.00 hours total.

Video captured during an attempt to sequence DNA in microgravity during a parabolic airplane flight.
Christopher Mason, a biophysicist at Weill Cornell Medical College in New York who is participating in the effort, says the 100-gram device is going to cost about $2,000 to fly. Most sequencing machines are the size of a mini-fridge and weigh 60 to 120 pounds. That would cost $1.2 million.

Mason previously sent the MinION for a ride on the “vomit comet,” a NASA airplane that mimics zero gravity by going into a nosedive. “It’s a technical demonstration to make sure it does work, which means when something is weirdly growing on the space station or on someone in the space station you could characterize it,” says Mason.

The space experiments are slated to be run by astronaut and virologist Kate Rubins, who will arrive on the ISS earlier in July, on her first trip off the planet. She’ll be sequencing the DNA of a virus, the bacterium E. coli, and of a mouse.

Although the MinION is tiny, it still requires a computer and an Internet connection to function. Also, further supplies are needed to prepare DNA samples. To skip that step, NASA plans to ready the DNA samples on Earth and send them up frozen, in syringes. Mason says no human DNA will be studied because of privacy concerns.

Once upon an alien world, or just the moon, says NASA’s Burton, a sequencer like Oxford’s could eventually be used to test for signs of life, or the molecules needed for life.

 

Credit :NASA & MIT

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