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  [ISS] DNA sequencing in space (MinION)

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Author Topic:   [ISS] DNA sequencing in space (MinION)
Robert Pearlman
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Posts: 38477
From: Houston, TX
Registered: Nov 1999

posted 08-29-2016 02:17 PM     Click Here to See the Profile for Robert Pearlman   Click Here to Email Robert Pearlman     Edit/Delete Message   Reply w/Quote
NASA release
First DNA Sequencing in Space a Game Changer

For the first time ever, DNA was successfully sequenced in microgravity as part of the Biomolecule Sequencer experiment performed by NASA astronaut Kate Rubins this weekend aboard the International Space Station. The ability to sequence the DNA of living organisms in space opens a whole new world of scientific and medical possibilities. Scientists consider it a game changer.

DNA, or deoxyribonucleic acid, contains the instructions each cell in an organism on Earth needs to live. These instructions are represented by the letters A, G, C and T, which stand for the four chemical bases of DNA, adenine, guanine, cytosine, and thymine. Both the number and arrangement of these bases differ among organisms, so their order, or sequence, can be used to identify a specific organism.

The Biomolecule Sequencer investigation moved us closer to this ability to sequence DNA in space by demonstrating, for the first time, that DNA sequencing is possible in an orbiting spacecraft.

With a way to sequence DNA in space, astronauts could diagnose an illness, or identify microbes growing in the International Space Station and determine whether or not they represent a health threat. A space-based DNA sequencer would be an important tool to help protect astronaut health during long duration missions on the journey to Mars, and future explorers could also potentially use the technology to identify DNA-based life forms beyond Earth.

Above: NASA Astronaut Kate Rubins sequenced DNA in space for the first time ever for the Biomolecule Sequencer investigation, using the MinION sequencing device.

The Biomolecule Sequencer investigation sent samples of mouse, virus and bacteria DNA to the space station to test a commercially available DNA sequencing device called MinION, developed by Oxford Nanopore Technologies. The MinION works by sending a positive current through pores embedded in membranes inside the device, called nanopores. At the same time, fluid containing a DNA sample passes through the device. Individual DNA molecules partially block the nanopores and change the current in a way that is unique to that particular DNA sequence. By looking at these changes, researchers can identify the specific DNA sequence.

Rubins, who has a background in molecular biology, conducted the test aboard the station while researchers simultaneously sequenced identical samples on the ground. The tests were set up to attempt to make spaceflight conditions, primarily microgravity, the only variables that could account for differences in results. For example, the samples were prepared on the ground for sequencing and researchers selected organisms whose DNA has already been completely sequenced so that they knew what results to expect.

Using the device in the microgravity environment introduces several potential challenges, according to Aaron Burton, NASA planetary scientist and principal investigator, including the formation of air bubbles in the fluid. On Earth, bubbles rise to the top of a liquid solution and can be removed by centrifuge, but in space, bubbles are less predictable.

"In space, if an air bubble is introduced, we don't know how it will behave," said Burton. "Our biggest concern is that it could block the nanopores."

The technology demonstration also seeks to validate that the device is durable enough to withstand vibration during launch and can operate reliably in a microgravity environment when it comes to the measurement of changes in current or the conversion of those changes into DNA sequences. In addition, researchers will be looking for any other factors that could produce errors or impact performance on orbit.

"Those are just the potential problems we've identified," said project manager and NASA microbiologist Sarah Castro-Wallace. "A lot of the things that might introduce errors are simply unknown at this point."

To minimize those unknowns, researchers recently tested the entire sequencing process on a NASA Extreme Environment Mission Operation, or NEEMO, in the Aquarius Base research facility 60 feet underwater off the coast of Florida.

"The NEEMO tests went smoothly," Castro-Wallace said. "In terms of a harsh environment, with different humidity, temperature and pressure, we looked at a lot of variables and the sequencer performed as expected."

NEEMO aquanauts collected environmental samples from the habitat, extracted and prepared the DNA for sequencing, and finally sequenced the DNA as part of a continuation of the Biomolecule Sequencer investigation. Testing this sample-to-sequencer process in an extreme environment is an important step towards its use on the ISS.

The investigation team includes others at NASA's Johnson Space Center, Goddard Space Flight Center and Ames Research Center, as well as partners at Weill Cornell Medical College and University of California at San Francisco.

As the researchers compare results from the sequences collected in microgravity and on Earth, so far everything seems to match up.

"A next step is to test the entire process in space, including sample preparation as well as performing the sequencing," said Castro-Wallace. Then astronauts can move beyond creating a known DNA sequence and actually extract, prepare and sequence DNA to identify unknown microbes on orbit.

"Onboard sequencing makes it possible for the crew to know what is in their environment at any time," Castro-Wallace said. "That allows us on the ground to take appropriate action – do we need to clean this up right away, or will taking antibiotics help or not? We can resupply the station with disinfectants and antibiotics now, but once crews move beyond the station's low Earth orbit, we need to know when to save those precious resources and when to use them."

In addition, the sequencer can become a tool for other science investigations aboard the station. For example, researchers could use it to examine changes in genetic material or gene expression on orbit rather than waiting for the samples to return to Earth for testing.

"Welcome to systems biology in space," said Rubins after the first few DNA molecules had been sequenced successfully. She went on to thank the ground team for their efforts. "It is very exciting to be with you guys together at the dawn of genomics biology and systems biology in space."

Robert Pearlman
Editor

Posts: 38477
From: Houston, TX
Registered: Nov 1999

posted 12-20-2017 08:56 AM     Click Here to See the Profile for Robert Pearlman   Click Here to Email Robert Pearlman     Edit/Delete Message   Reply w/Quote
NASA release
Genes in Space-3 Successfully Identifies Unknown Microbes in Space

Being able to identify microbes in real time aboard the International Space Station, without having to send them back to Earth for identification first, would be revolutionary for the world of microbiology and space exploration. The Genes in Space-3 team turned that possibility into a reality this year, when it completed the first-ever sample-to-sequence process entirely aboard the space station.

Above: NASA astronaut Peggy Whitson performed the Genes in Space-3 investigation aboard the space station using the miniPCR and MinION, developed for previously flown investigations.

The ability to identify microbes in space could aid in the ability to diagnose and treat astronaut ailments in real time, as well as assisting in the identification of DNA-based life on other planets. It could also benefit other experiments aboard the orbiting laboratory. Identifying microbes involves isolating the DNA of samples, and then amplifying – or making many copies - of that DNA that can then be sequenced, or identified.

The investigation was broken into two parts: the collection of the microbial samples and amplification by Polymerase Chain Reaction (PCR), then sequencing and identification of the microbes. NASA astronaut Peggy Whitson conducted the experiment aboard the orbiting laboratory, with NASA microbiologist and the project's Principal Investigator Sarah Wallace and her team watching and guiding her from Houston.

As part of regular microbial monitoring, petri plates were touched to various surfaces of the space station. Working within the Microgravity Science Glovebox (MSG) about a week later, Whitson transferred cells from growing bacterial colonies on those plates into miniature test tubes, something that had never been done before in space.

Once the cells were successfully collected, it was time to isolate the DNA and prepare it for sequencing, enabling the identification of the unknown organisms – another first for space microbiology. An historic weather event, though, threatened the ground team's ability to guide the progress of the experiment.

"We started hearing the reports of Hurricane Harvey the week in between Peggy performing the first part of collecting the sample and gearing up for the actual sequencing," said Wallace.

When JSC became inaccessible due to dangerous road conditions and rising flood waters, the team at Marshall Space Flight Center's Payload Operations Integration Center in Huntsville, Alabama, who serve as "Mission Control" for all station research, worked to connect Wallace to Whitson using Wallace's personal cell phone.

With a hurricane wreaking havoc outside, Wallace and Whitson set out to make history. Wallace offered support to Whitson, a biochemist, as she used the MinION device to sequence the amplified DNA. The data were downlinked to the team in Houston for analysis and identification.

"Once we actually got the data on the ground we were able to turn it around and start analyzing it," said Aaron Burton, NASA biochemist and the project's co-investigator. "You get all these squiggle plots and you have to turn that into As, Gs, Cs and Ts."

Those As, Gs, Cs and Ts are Adenine, Guanine, Cytosine and Thymine – the four bases that make up each strand of DNA and can tell you what organism the strand of DNA came from.

"Right away, we saw one microorganism pop up, and then a second one, and they were things that we find all the time on the space station," said Wallace. "The validation of these results would be when we got the sample back to test on Earth."

Soon after, the samples returned to Earth, along with Whitson, aboard the Soyuz spacecraft. Biochemical and sequencing tests were completed in ground labs to confirm the findings from the space station. They ran tests multiple times to confirm accuracy. Each time, the results were exactly the same on the ground as in orbit.

"We did it. Everything worked perfectly," said Sarah Stahl, microbiologist.

Above: Sarah Wallace (L), NASA microbiologist and Genes in Space-3 principal investigator, and Sarah Stahl (R), microbiologist, are seen in their Johnson Space Center lab with the in-flight sample from the Genes in Space-3 investigation.

Developed in partnership by NASA's Johnson Space Center and Boeing, this National Lab sponsored investigation is managed by the Center for the Advancement of Science in Space.

Genes in Space-1 marked the first time the PCR was used in space to amplify DNA with the miniPCR thermal cycler, followed shortly after by Biomolecule Sequencer, which used the MinION device to sequence DNA. Genes in Space-3 married these two investigations to create a full microbial identification process in microgravity.

"It was a natural collaboration to put these two pieces of technology together because individually, they're both great, but together they enable extremely powerful molecular biology applications," said Wallace.

denali414
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Posts: 111
From: Raleigh, NC USA
Registered: Aug 2017

posted 12-20-2017 10:00 AM     Click Here to See the Profile for denali414   Click Here to Email denali414     Edit/Delete Message   Reply w/Quote
Awesome news! The ability to identify biologic threats and diagnose illness a huge step in the process of long term outer space and moon/Mars habitation.

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