Discoveries

Massive star's dying blast caught by rapid-response telescopes

Tempe campus

July 26, 2017

Blast of gamma rays is helping astronomers resolve long-standing questions about universe's most powerful explosions

In June 2016, an international team of 31 astronomers, led by the University of Maryland's Eleanora Troja and including Arizona State University's Nathaniel Butler, caught a massive star as it died in a titanic explosion deep in space.

The blast of the dying star released in about 40 seconds as much energy as the sun releases over its entire lifetime, all focused into a tight beam of gamma rays aimed by chance toward Earth.

The team's findings, reported in the scientific journal Nature, provide strong evidence for one of two competing models for how gamma-ray bursters (GRBs) produce their energy.

"These are the brightest explosions in the universe," said Butler, an associate professor in ASU's School of Earth and Space Exploration. "And we were able to measure this one's development and decay almost from the initial blast."

Quick reflexes

The gamma-ray blast on June 25, 2016, was detected by two NASA satellites that monitor the sky for such events, the Fermi Gamma-ray Space Telescope and the Swift Gamma-Ray Burst Mission.

The satellite observatories detected the burst of gamma rays, identified where in the sky it came from, and sent its celestial position within seconds to automated telescopes on the ground.

The MASTER-IRC telescope at the Teide Observatory in the Canary Islands observed it first, within a minute of the satellite notification. The telescope is part of Russia's MASTER network of robotic telescopes at the Teide Observatory. It made optical light observations while the initial phase was still active, gathering data on the amount of polarized optical light relative to the total light produced.

After the sun set over this facility eight and a half hours later, the RATIR camera in which ASU is involved began observing. RATIR stands for Reionization And Transients InfraRed camera; it is mounted on a 1.5-meter (60-inch) robotically controlled telescope located on San Pedro Mártir Peak, at Mexico's National Astronomical Observatory in Baja California. Butler is the principal investigator for the fully automated camera.

The RATIR camera, directed from ASU, is mounted on on an automatically controlled telescope at Mexico's National Astronomical Observatory. RATIR allows astronomers to follow up (within a minute or two) on rapidly changing celestial events, such as gamma-ray bursters. Photo by Nathaniel Butler/ASU

"At best, it takes a minute or two for our telescope to slew to the burst's position," Butler said. "In this case, we had to wait for it to rise over the horizon. This means the gamma-ray burst itself had ended, and we were observing what's called the afterglow. This is the fading explosion as the radiation shocks up the interstellar medium around the star that exploded.

"The RATIR camera lets us take simultaneous images in six colors, two optical and four near-infrared. Over the past five years, RATIR has imaged 155 gamma-ray bursts."

Mystery beams of energy

While gamma-ray bursters have been known for about 50 years, astronomers are still mostly in the dark about how they erupt.

"Despite a long history of observations," Butler said, "the emission mechanism driving gamma-ray bursters remains largely mysterious."

Gamma-ray bursts are detected approximately once per day and are brief, but intense, flashes of gamma radiation. They come from all different directions in the sky, and they last from tens of milliseconds to about a minute, making it hard to observe them in detail.

Astronomers believe most of these explosions are associated with supernovas. These occur when a massive star reaches the end of its normal existence and blows up in a colossal explosion. A supernova throws off some of the star's outer layers, while its core and remaining layers collapse in a few seconds into a neutron star or, in the case of highly massive stars, a black hole.

Above: The RATIR camera captured the fading afterglow (arrow) of the June 2016 gamma-ray burster in this sequence running from June 26 through Aug. 20, 2016. Images by Nathaniel Butler/ASU

Continued RATIR observations over weeks following the June 2016 outburst showed that the gamma rays were shot out in a beam about two degrees wide, or roughly four times the apparent size of the moon. It was sheer chance that Earth happened to lie within the beam.

Beaming effects, Butler said, may result from the spin of the black hole produced after the supernova explosion, as it releases material along its poles.

Magnetic focus

"We think the gamma-ray emission is due to highly energetic electrons, propelled outward like a fireball,” Butler said. Magnetic fields must also be present, he added, and theories differ as to how the fields are produced and to what extent the flow of magnetic energy outward is important.

A key diagnostic is measuring the radiation's polarization, he explained. This, astronomers think, is largely controlled by the strength of the magnetic fields that focus the radiation.

"Measuring the strength of magnetic fields by their polarization effects can tell us about the mechanisms that accelerate particles such as electrons up to very high energies and cause them to radiate at gamma-ray energies," Butler said.

In the case of the June 2016 blast, the scientists were able to measure polarization using MASTER within minutes, an unprecedented early discovery. The large amount of polarization the team observed indicates that powerful magnetic fields were confining and directing it. This lends support for the magnetic origin model for gamma-ray bursters.

Although gamma-ray bursters have many more mysteries to be unfolded, Butler said, "this is the first strong evidence that the early shocks generated by these bursts are magnetically driven."

The RATIR camera, seen here mounted on the back end of the telescope, is stabilized with struts to assure correct alignment with the telescope when the whole assembly rapidly slews to lock onto a new target. Pictured is Alex Farah, mechanical engineer at the observatory. Photo by Alan Watson/UNAM

Top photo: This image shows the most common type of gamma-ray burst, thought to occur when a massive star collapses, forms a black hole and blasts particle jets outward at nearly the speed of light. Image by NASA Goddard Space Flight Center

Robert Burnham

Science writer , School of Earth and Space Exploration

480-458-8207 Robert.Burnham@asu.edu

Living computers: RNA circuits transform cells into nanodevices

The interdisciplinary nexus of biology and engineering, known as synthetic biology, is growing at a rapid pace, opening new vistas that could scarcely be imagined a short time ago.In new research, Alex Green, an assistant professor at ASU’s Biodesign Institute, demonstrates how living cells can be induced to carry out computations in the manner of tiny robots or computers.The results of the ne...

Read the article

More from Discoveries

Discoveries

Living computers: RNA circuits transform cells into nanodevices

Tempe campus

July 26, 2017

ASU Biodesign researcher shows how cells can be induced to carry out computations — with implications in health and energy

The interdisciplinary nexus of biology and engineering, known as synthetic biology, is growing at a rapid pace, opening new vistas that could scarcely be imagined a short time ago.

In new research, Alex Green, an assistant professor at ASU’s Biodesign Institute, demonstrates how living cells can be induced to carry out computations in the manner of tiny robots or computers.

The results of the new study have significant implications for intelligent drug design and smart drug delivery, green energy production, low-cost diagnostic technologies and even the development of futuristic nanomachines capable of hunting down cancer cells or switching off aberrant genes.

“We’re using very predictable and programmable RNA-RNA interactions to define what these circuits can do,” Green said. “That means we can use computer software to design RNA sequences that behave the way we want them to in a cell. It makes the design process a lot faster.”

The study appears in the advance online edition of the journal Nature.

In new research, Alex Green, an assistant professor at ASU’s Biodesign Institute and School of Molecular Sciences, demonstrates how living cells can be induced to carry out computations in the manner of tiny robots or computers.

Designer RNA

The approach described uses circuits composed of ribonucleic acid or RNA. These circuit designs, which resemble conventional electronic circuits, self-assemble in bacterial cells, allowing them to sense incoming messages and respond to them by producing a particular computational output (in this case, a protein).

In the new study, specialized circuits known as logic gates were designed in the lab, then incorporated into living cells. The tiny circuit switches are tripped when messages (in the form of RNA fragments) attach themselves to their complementary RNA sequences in the cellular circuit, activating the logic gate and producing the desired output.

The RNA switches can be combined in various ways to produce more complex logic gates capable of evaluating and responding to multiple inputs, just as a simple computer may take several variables and perform sequential operations like addition and subtraction in order to reach a final result.

The new study dramatically improves the ease with which cellular computing may be carried out. The RNA-only approach to producing cellular nanodevices is a significant advance, as earlier efforts required the use of complex intermediaries, like proteins. Now, the necessary ribocomputing parts can be readily designed on a computer. The simple base-pairing properties of RNA’s four nucleotide letters (A, C, G and U) ensure the predictable self-assembly and functioning of these parts within a living cell.

Green’s work in this area began at the Wyss Institute at Harvard, where he helped develop the central component used in the cellular circuits, known as an RNA toehold switch. The work was carried out while Green was a post-doc working with nanotechnology expert Peng Yin, along with the synthetic biologists James Collins and Pamela Silver, who are all co-authors on the new paper.

“The first experiments were in 2012,” Green said. “Basically, the toehold switches performed so well that we wanted to find a way to best exploit them for cellular applications.”

Video courtesy of the Wyss Institute

After arriving at ASU, Green’s first grad student Duo Ma worked on experiments at the Biodesign Institute, while postdoctoral scholar Jongmin Kim continued similar work at the Wyss Institute. Both are also co-authors of the new study.

Nature’s Pentium chip

The possibility of using DNA and RNA, the molecules of life, to perform computer-like computations was ﬁrst demonstrated in 1994 by Leonard Adleman of the University of Southern California. Since then, rapid progress has advanced the field considerably, and recently, such molecular computing has been accomplished within living cells. (Bacterial cells are usually employed for this purpose as they are simpler and easier to manipulate.)

The technique described in the new paper takes advantage of the fact that RNA, unlike DNA, is single-stranded when it is produced in cells. This allows researchers to design RNA circuits that can be activated when a complementary RNA strand binds with an exposed RNA sequence in the designed circuit. This binding of complementary strands is regular and predictable, with A nucleotides always pairing with U and C always pairing with G.

With all the processing elements of the circuit made using RNA, which can take on an astronomical number of potential sequences, the real power of the newly described method lies in its ability to perform many operations at the same time. This capacity for parallel processing permits faster and more sophisticated computation while making efficient use of the limited resources of the cell.

Logical results

In the new study, logic gates known as AND, OR and NOT were designed. An AND gate produces an output in the cell only when two RNA messages A AND B are present. An OR gate responds to either A OR B, while a NOT gate will block output if a given RNA input is present. Combining these gates can produce complex logic capable of responding to multiple inputs.

Using RNA toehold switches, the researchers produced the first ribocomputing devices capable of four-input AND, six-input OR and a 12-input device able to carry out a complex combination of AND, OR and NOT logic known as disjunctive normal form expression. When the logic gate encounters the correct RNA binding sequences leading to activation, a toehold switch opens and the process of translation to protein takes place. All of these circuit-sensing and output functions can be integrated into the same molecule, making the systems compact and easier to implement in a cell.

The research represents the next phase of ongoing work using the highly versatile RNA toehold switches. In earlier work, Green and his colleagues demonstrated that an inexpensive, paper-based array of RNA toehold switches could act as a highly accurate platform for diagnosing the Zika virus. Detection of viral RNA by the array activated the toehold switches, triggering production of a protein, which registered as a color change on the array.

The basic principle of using RNA-based devices to regulate protein production can be applied to virtually any RNA input, ushering in a new generation of accurate, low-cost diagnostics for a broad range of diseases. The cell-free approach is particularly well suited for emerging threats and during disease outbreaks in the developing world, where medical resources and personnel may be limited.

The computer within

According to Green, the next stage of research will focus on the use of the RNA toehold technology to produce so-called neural networks within living cells — circuits capable of analyzing a range of excitatory and inhibitory inputs, averaging them and producing an output once a particular threshold of activity is reached, much the way a neuron averages incoming signals from other neurons. Ultimately, researchers hope to induce cells to communicate with one another via programmable molecular signals, forming a truly interactive, brain-like network.

“Because we’re using RNA, a universal molecule of life, we know these interactions can also work in other cells, so our method provides a general strategy that could be ported to other organisms,” Green said, alluding to a future in which human cells become fully programmable entities with extensive biological capabilities.

Media contact: Joe Caspermeyer, Biodesign Institute, 480-258-8972, joseph.caspermeyer@asu.edu.

Top image: Ribonucleic acid (RNA) is used to create logic circuits capable of performing various computations. In new experiments, ASU Assistant Professor Alex Green and his colleagues have incorporated RNA logic gates into living bacterial cells, which act like tiny computers.