Biomolecule Extraction and Sequencing Technology (BEST) - 03.13.19

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

ISS Science for Everyone

Science Objectives for Everyone
The Biomolecule Extraction and Sequencing Technology (BEST) investigation studies the use of sequencing for the identification of unknown microbial organisms living on the International Space Station (ISS), and for understanding how humans, plants and microbes adapt to living on the ISS. Microbial Organisms are isolated and identified from various locations on the ISS using a swab-to-sequencer process that does not require cultivation of organisms prior to processing. Additional objectives of the BEST investigation include the comparison of mutation rates of bacteria grown on Earth to those of bacteria grown on the ISS using periodic whole-genome sequencing; and a demonstration that it is possible to sequence ribonucleic acid (RNA) isolated from any organism directly, utilizing the Biomolecule Sequencer and Genes in Space hardware already onboard the ISS.
Science Results for Everyone
Information Pending

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

OpNom: BEST

Principal Investigator(s)

Information Pending

Co-Investigator(s)/Collaborator(s)
Sarah Stahl, M.S., NASA Johnson Space Center, Houston, TX, United States
Mark Akeson, Ph.D., University of California-Santa Cruz, Santa Cruz, CA, United States
Aaron Steven Burton, NASA Johnson Space Center, Houston, TX, United States
KRISTEN KATHLEEN JOHN, NASA Johnson Space Center, Houston, TX, United States

Developer(s)
NASA Johnson Space Center, Houston, TX, United States
University of California-Santa Cruz, Santa Cruz, CA, United States
Oxford Nanopore Technologies, Oxford, United Kingdom

Sponsoring Space Agency
National Aeronautics and Space Administration (NASA)

Sponsoring Organization
NASA – International Space Station (NASA-ISS)

Research Benefits
Information Pending

ISS Expedition Duration
February 2018 - April 2020

Expeditions Assigned
55/56,57/58,59/60,61/62

Previous Missions
Information Pending

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Experiment Description

Research Overview

The Biomolecule Extraction and Sequencing Technology (BEST) investigation tests and evaluates the following objectives:
  1. There are microbes living aboard the International Space Station (ISS) that cannot be detected using current culture-based sampling methods. The BEST investigation compares swab-to-sequencing based microbe analyses against traditional culture-based methods to determine which microbes are currently going undetected, and provide insight into the development of strategies to ensure their future detection,
  2. Microbes respond to spaceflight by making changes at the genetic, epigenetic, and transcriptomic levels, and these responses can be observed with sequencing. To understand these responses, the changes are studied on a model organism grown over multiple generations on the ISS, and compared against populations of the same organism grown in parallel on the Earth.
  3. Additionally, BEST demonstrates the process of direct RNA sequencing, using the MinION miniature deoxyribonucleic acid (DNA) sequencer. Previously, the steps necessary for DNA sequencing on the ISS were successfully demonstrated using manual pipetting techniques. This objective extends the established process to enable the direct sequencing of RNA, enabling new avenues for inflight ISS research.

Description

The Biomolecule Extraction and Sequencing Technology (BEST) investigation tests three objectives:
  • Objective 1: Identify the microbes aboard the International Space Station (ISS) that are not detected with our current culture-based sampling methods.
  • Objective 2: Demonstrate that microbial responses to spaceflight, including changes at the genetic, epigenetic and transcriptomic levels, can be observed with sequencing.
  • Objective 3: Demonstrate direct RNA sequencing with the MinION miniature DNA sequencer.
The objectives range in terms of complexity, and can be assessed individually. All objectives are carefully designed to be flexible in the amount of crew time required, and timing of when associated activities would take place. Additionally, objectives 1 and 2 take advantage of existing procedures from the Biomolecule Sequencer (BSeq), Genes in Space-3 (GiS3), and the NASA Extreme Environment Mission Operations (NEEMO)-21 and/or NEEMO-22 projects. All objectives utilize previous experience in the rapid turnaround of science on station.
 
Objective 1: Find the missing microbes. Culture-based methods for microbial identification have been used for decades for microbial monitoring for crew health. However, recent advances in high-throughput DNA sequencing have enabled new approaches for microbial characterization, which have revealed that ~99% of all microbes cannot be cultured using commonly applied methods. This means that there is almost certainly a population of organisms present aboard the ISS that cannot be detected with current methods. Swab-to-Sequencing based microbe analyses are compared against traditional culture-based methods to determine what microbes are currently going undetected, and develop strategies to ensure their future detection. The overall goal is to reduce or eliminate the need for culturing, as well as return of samples to Earth for analysis.
 
To execute Objective 1, the Research Team worked with ISS Astronaut and microbiologist Dr. Kate Rubins, to identify key sites and objects within the ISS for both longitudinal and one time exploratory microbial studies. Swab samples are collected in key areas and either returned to Earth for ground processing, or sequenced onboard the ISS as crew time allows. With extremely minimal up and down mass (swabs and previously certified reagents), this objective can provide a tremendous amount of scientific insight, and can be adjusted as crew time dictates. Crew procedures already exist for swabbing and sample preparation, and sequencing would require only negligible modifications to ISS procedures by incorporating NEEMO procedures.
 
Objective 2: Understand microbial responses to spaceflight. Organisms respond to their environment by regulating gene expression. This can be done at varying levels of permanence, with transcription (RNA level) changes being temporary and reversible, epigenetic changes (methylation of DNA to turn genes on or off) being semi- to permanent, and genetic changes (mutations) being permanent. To understand how microbes respond to spaceflight, the genome, epigenome and transcriptome are characterized of a model organism grown over multiple generations on the ISS against populations of the same organism grown in parallel on the ground, enabling for a rigorous and robust analysis of the molecular basis behind microbial response to spaceflight.
 
To execute Objective 2, a Biosafety Level-1 organism is selected that is easily cultured on the ISS, and does not pose concerns for operations outside of the Microgravity Sciences Glovebox (MSG). The organism is launched in a frozen state, cultured by bringing it to ambient ISS temperature, and then prepared for sequencing using an already baselined Genes in Space-3 procedure.
 
Objective 3: Demonstrate direct RNA sequencing on the ISS to make this capability available for researchers. It was demonstrated with the Biomolecule Sequencer and Genes in Space-3 payloads, that all steps necessary for DNA sequencing on the ISS can be performed using manual pipetting techniques. In this objective, the established process is extended to enable the direct sequencing of RNA, making this capability available for members of the research community to use for other ISS investigations.
 
RNA sequencing uses the same sequencing hardware as DNA sequencing; thus, by modifying the enzymatic processes currently used for DNA sequencing on the ISS enable RNA sequencing, it should be possible to open new avenues for inflight ISS research, including transcriptomics and epitranscriptomics.

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Applications

Space Applications
The DNA and RNA sequencing components of the BEST payload provide important information on the microbial occupants of the ISS, including their ecology (i.e., which organisms are present) and how they respond to the spaceflight environment. This knowledge can provide better insight into the development of requirements and procedures necessary for human exploration, both on the ISS and in future exploration beyond low-Earth orbit. The validation of direct RNA sequencing has the potential to be a game-changer for research into crew health, and understanding how organisms respond to spaceflight.

Earth Applications
The ISS is a remote, constrained resource environment. These constraints require the development of simple, effective processes and procedures to monitor the presence of microbial life in these types of environments, some of which may be harmful. The knowledge gained from BEST can be implemented directly by scientists and health professionals in remote locations on the Earth, and provide new ways to monitor the presence of microbes in those locations.

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Operations

Operational Requirements and Protocols

Objective 1: Find the missing microbes. Samples are collected via swabbing at locations chosen by the crew. A subset of these samples are processed on orbit, and the remainder are frozen for return to Earth for later processing. For flight processed samples, DNA is: extracted, purified, and amplified using miniPCR, subjected to a second purification, prepared for sequencing, and then sequenced with the Biomolecule Sequencer hardware.
 
Objective 2: Remove frozen liquid cultures from MELFI and incubate at ambient ISS temperature (incubation times can be varied dependent on crew timeline). Cultures are allowed to grow, with aliquots collected for dilution and further growth, and genomic sequencing using procedures from Genes in Space 3; the remainder of the sample is stored frozen for Earth-return and further DNA and RNA sequencing. It is expected that three cycles of growth, sampling, and dilution are performed.
 
Objective 3: Demonstrate direct RNA sequencing on the ISS. Samples containing: RNA prepared for sequencing, cDNA prepared for sequencing, and purified RNA to be prepared for sequencing in flight (3 samples each) are flown to the ISS and sequenced onboard.

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Decadal Survey Recommendations

Information Pending

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Results/More Information

Information Pending

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Related Websites
Oxford Nanopore Technologies, maker of the MiniION DNA Sequencer

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Imagery

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NASA Image: JSC2018E040417 - Photographic support for ISS Research Project Biomolecule Extraction and Sequencing Technology (BEST) shows procedures to be used on orbit utilizing the miniPCR and MiniION hardware. 

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NASA Image: JSC2018E040453 - Photographic support for ISS Research Project Biomolecule Extraction and Sequencing Technology (BEST) shows procedures to be used on orbit utilizing the miniPCR and MiniION hardware.

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NASA Image: JSC2018E040456 - Photographic support for ISS Research Project, Biomolecule Extraction and Sequencing Technology (BEST), shows procedures to be used on orbit utilizing the miniPCR and MiniION hardware.
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NASA Image: JSC2018E059572 - Photographic support for Biomolecule Extraction and Sequencing Technology (BEST) investigation that shows the miniPCR and MiniION hardware used on orbit.

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NASA Image: ISS056E097517 - NASA astronaut Ricky Arnold during preparation of amplified DNA for sequencing using the Biomolecule Sequencer at the Maintenance Work Area (MWA), Part Number (P/N): BS-BS, Serial Number (S/N): 01, Barcode: 00237502J. Photo taken by Expedition 56 crew.

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NASA Image: ISS056E097438 - View of the preparation of amplified DNA for sequencing using the Biomolecule Sequencer at the Maintenance Work Area (MWA). Photo taken by Expedition 56 crew.

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NASA Image: ISS056E097421 - NASA astronaut Ricky Arnold swabs surfaces in the International Space Station to collect microbe samples. He then processes the microbial DNA using the Biomolecule Sequencer, a device that enables DNA sequencing in microgravity, to identify microbes able to survive in microgravity.

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NASA Image: ISS056E097419 - NASA astronaut Ricky Arnold swabs surfaces in the International Space Station to collect microbe samples. He then processes the microbial DNA using the Biomolecule Sequencer, a device that enables DNA sequencing in microgravity, to identify microbes able to survive in microgravity.

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NASA Image: ISS057E000185 - Biomolecule Sequencer for the BEST investigation floating in front of Window 7 in the Cupola module. Earth is in the background. The Biomolecule Sequencer 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.

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