Biomolecule Sequencer (Biomolecule Sequencer) - 07.20.16

Overview | Description | Applications | Operations | Results | Publications | Imagery

ISS Science for Everyone

Science Objectives for Everyone
Living organisms contain DNA, or deoxyribonucleic acid, and sequencing DNA is a powerful way to understand how they respond to changing environments. The Biomolecule Sequencer investigation seeks to demonstrate, for the first time, that DNA sequencing is feasible in an orbiting spacecraft. A space-based DNA sequencer could identify microbes, diagnose diseases and understand crew member health, and potentially help detect DNA-based life elsewhere in the solar system.
Science Results for Everyone
Information Pending

The following content was provided by Aaron Burton, Ph.D., and is maintained in a database by the ISS Program Science Office.
Experiment Details

OpNom: Biomolecule Sequencer

Principal Investigator(s)
Aaron Burton, Ph.D., NASA JSC, Houston, TX, United States

Co-Investigator(s)/Collaborator(s)
Sarah Castro-Wallace, Ph.D., NASA JSC, Houston, TX, United States
Kristen John, Ph.D., NASA JSC, Houston, TX, United States
Sarah Stahl, M.S., NASA Johnson Space Center, Houston, TX, United States
Douglas Botkin, Ph.D., Johnson Space Center, Houston, TX, United States
Jason Dworkin, Ph.D., NASA GSFC, Greenbelt, MD, United States
Mark Lupisella, Ph.D., NASA GSFC, Greenbelt, MD, United States
David Smith, Ph.D., NASA Ames, Moffett Field, CA, United States
Christopher Mason, Ph.D., Weill Cornell Medical College, New York, NY, United States
James Brayer, Oxford Nanopore Technologies Inc., Cambridge, MA, United States

Developer(s)
NASA Johnson Space Center, Houston, TX, United States

Sponsoring Space Agency
National Aeronautics and Space Administration (NASA)

Sponsoring Organization
Technology Demonstration Office (TDO)

Research Benefits
Earth Benefits, Scientific Discovery, Space Exploration

ISS Expedition Duration
March 2016 - September 2016

Expeditions Assigned
47/48

Previous Missions
Information Pending

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Experiment Description

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.

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Decadal Survey Recommendations

Information Pending

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Results/More Information

Information Pending

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Results Publications

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Ground Based Results Publications

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ISS Patents

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Related Publications

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Related Websites

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Imagery

image The MinION (aka Biomolecule Sequencer), a miniaturized DNA sequencer, by Oxford Nanopore Technologies is 3 ¼ x 1 ¼ x 5/8 inches and has a mass of 120 grams. The sequencer is powered via USB connection to a laptop or tablet and does not require a battery. Credit: Oxford Nanopore Technologies
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image The MinION and accompanying flow cell. Credit: Oxford Nanopore Technologies
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image A sample being loaded into a flow cell attached to the MinION. The MinION is powered through a USB cable connected to a laptop or tablet. Credit: Oxford Nanopore Technologies
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The Biomolecule Sequencer (circled) is sitting on top of Illumina’s MiSeq Benchtop Next-Generation Sequencer, the current state of the art.
 
Credit: Douglas Botkin
 

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