Hexbyte Glen Cove Our DNA is becoming the world's tiniest hard drive thumbnail

Hexbyte Glen Cove Our DNA is becoming the world’s tiniest hard drive

Hexbyte Glen Cove

3D-model of DNA. Credit: Michael Ströck/Wikimedia/ GNU Free Documentation License

Our genetic code is millions of times more efficient at storing data than existing solutions, which are costly and use immense amounts of energy and space. In fact, we could get rid of hard drives and store all the digital data on the planet within a couple hundred pounds of DNA.

Using DNA as a high-density data storage medium holds the potential to forge breakthroughs in biosensing and biorecording technology and next-generation digital storage, but researchers haven’t been able to overcome inefficiencies that would allow the technology to scale.

Now, researchers at Northwestern University propose a new method for recording information to DNA that takes minutes, rather than hours or days, to complete. The team used a novel enzymatic system to synthesize DNA that records rapidly changing environmental signals directly into DNA sequences, a method the paper’s senior author said could change the way scientists study and record neurons inside the brain.

The research, “Recording Temporal Signals with Minutes Resolution Using Enzymatic DNA Synthesis,” was published Thursday (Sept. 30) in the Journal of the American Chemical Society.

The paper’s senior author, Northwestern engineering professor Keith E.J. Tyo, said his lab was interested in leveraging DNA’s natural abilities to create a new solution for storing data.

“Nature is good at copying DNA, but we really wanted to be able to write DNA from scratch,” Tyo said. “The ex vivo (outside the body) way to do this involves a slow, chemical synthesis. Our method is much cheaper to write information because the enzyme that synthesizes the DNA can be directly manipulated. State-of-the-art intracellular recordings are even slower because they require the mechanical steps of protein expression in response to signals, as opposed to our enzymes which are all expressed ahead of time and can continuously store information.”

Tyo, a professor in chemical and biological engineering in the McCormick School of Engineering, is a member of the Center for Synthetic Biology, and studies microbes and their mechanisms for sensing environmental changes and responding to them quickly.

Bypassing protein expression

Existing methods to record intracellular molecular and digital data to DNA rely on multipart processes that add new data to existing sequences of DNA. To produce an accurate recording, researchers must stimulate and repress expression of specific proteins, which can take over 10 hours to complete.

The Tyo lab hypothesized they could use a new method that they called Time-sensitive Untemplated Recording using Tdt for Local Environmental Signals, or TURTLES, to synthesize completely new DNA instead of copying a template of it, making a faster and higher resolution recording.

As the DNA polymerase continues to add bases, data is recorded into the on a scale of minutes as changes in the environment impact the composition of the DNA it synthesizes. The environmental changes, such as changes in the concentration of metals, are recorded by the polymerase, acting as a “molecular ticker tape” and indicating to scientists the time of an environmental change. Using biosensors to record changes into DNA represents a major step in proving TURTLES’ viability for use inside cells, and could give researchers the ability to use recorded DNA to learn about how neurons communicate with each other.

“This is a really exciting proof of concept for methods that could one day lets us study the interactions between millions of cells simultaneously,” said Namita Bhan, co-first author and a postdoctoral researcher in the Tyo lab. “I don’t think there’s any previously reported direct enzyme modulation recording system.”

From brain cells to polluted water

With more potential for scalability and accuracy, TURTLES could offer the basis for tools that catapult brain research forward. According to Alec Callisto, also a co-first author and graduate student in the Tyo lab, researchers can only study a tiny fraction of a brain’s neurons with today’s technology, and even then, there are limits on what they know they do. By placing recorders inside all the in the brain, scientists could map responses to stimuli with single-cell resolution across many (million) neurons.

“If you look at how current technology scales over time, it could be decades before we can even record an entire cockroach brain simultaneously with existing technologies—let alone the tens of billions of neurons in human brains,” Callisto said. “So that’s something we’d really like to accelerate.”

Outside the body, the TURTLES system also could be used for a variety of solutions to address the explosive growth in data storage needs (up to 175 zettabytes by 2025).

It’s particularly good for long term archival data applications such as storing closed-circuit security footage, which the team refers to as data that you “write once and read never,” but need to have accessible in the event an incident occurs. With technology developed by engineers, hard drives and disk drives that hold years of beloved camera memories also could be replaced by bits of DNA.

Outside of , the “ticker tape” function could be used as a biosensor to monitor environmental contaminants, like the heavy metal concentration in drinking water.

While the lab focuses on moving beyond a proof of concept in both digital and cellular recording, the team expressed hope that more engineers would take interest in the concept and be able to use it to record signals important to their research.

“We’re still building out the genomic infrastructure and cellular techniques we need for robust intracellular recording,” Tyo said. “This is a step along the way to getting to our long-term goal.”

More information:
Namita Bhan et al, Recording Temporal Signals with Minutes Resolution Using Enzymatic DNA Synthesis, Journal of the American Chemical Society (2021)

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Hexbyte Glen Cove Sea-level rise becoming a hazard for South Florida neighborhoods miles from ocean thumbnail

Hexbyte Glen Cove Sea-level rise becoming a hazard for South Florida neighborhoods miles from ocean

Hexbyte Glen Cove

Credit: CC0 Public Domain

Sea-level rise may appear to be a problem only for coastal residents, a hazard that comes with the awesome views and easy access to the beach.

But neighborhoods 20 miles inland are starting to feel the impact, as the Atlantic Ocean’s higher elevation makes it harder for drainage canals to keep them dry. The problem showed up last year in Tropical Storm Eta, when floodwater remained in southwest Broward neighborhoods for days, partly because the elevated ocean blocked canals from draining the region.

“It was pretty scary,” said Barb Besteni, who lives in far west Miramar. “I stepped out of house into ankle-deep . It came three-fourths up the driveway. I’d never seen the water that high. It was scary because I didn’t know if it was going to continue to rise.”

Although her house in the Sunset Lakes community stands at the edge of the Everglades, the Atlantic’s higher elevation prevented it from draining as efficiently as in the past.

“It took a very, very long time to recede,” she said. “Two or three weeks to recede to .”

The South Florida Water Management District, which operates the big canals that sweep water into the ocean, submitted a funding request to the state this week for fixing the system, with the preliminary list of projects carrying a price tag of more than $1.5 billion. Although expensive, the pumps and other improvements would help restore the efficiency of a system built after World War II that has become more difficult to operate at a time of rising sea levels.

“When is higher, we cannot discharge, so we close the gates to avoid ocean water coming inside,” said Carolina Maran, district resiliency officer for the South Florida Water Management District. “During Eta, it was much higher than normal. And that means again that we cannot discharge to the ocean and that diminished our capacity to prevent and address flooding.”

Storms overwhelm flood-control systems

Although there’s never a great time to endure 15-plus inches of rain, Tropical Storm Eta struck South Florida at a particularly challenging period.

The ground already had been saturated by previous storms. And coastal waters were undergoing a king tide, a phenomenon that occurs when the positions of sun and moon combine to produce the highest tides of the year. As sea levels rise, king tides get higher.

The wide canals that run through Broward and Miami-Dade counties, carrying rainwater to the ocean, depend partly on gravity. When rainwater raises the level of the on the inland side, water managers lift the gate dividing it from the ocean side of the canal and the water flows away, eventually reaching the Atlantic.

But when the Atlantic side is high, there may be no difference in elevations between each side of the gate, so when it’s lifted, the water doesn’t move. Or worse, the Atlantic side could be higher, so lifting the gate would allow ocean water to pour inland.

During Tropical Storm Eta, staffers at the South Broward Drainage District found themselves consulting tide charts to determine when they could open the gates and discharge water.

“We had to close our gate because the downstream gets equal to our upstream,” said Kevin Hart, district director of the South Broward Drainage District, which operates the canal system that feeds into the larger canals that drain into the ocean. “We don’t want to drain in, we want to drain out. We’ve got to close our gate.

“We were looking at tide charts—Low tides going to be at 2 o’clock and at 5 or 6 we can see the levels dropping and open our gate again.”

Aging system confronts sea-level rise

Constructed largely in the 1940s and 1950s, South Florida’s drainage system has been an efficient—some would say too efficient—system for keeping a once-swampy part of Florida dry.

The system contributed to the decline of the Everglades, at times flooding the area, at other times drying it out. But it accomplished what it was supposed to do, keeping the land dry for cities such as Pembroke Pines and Miramar by swiftly moving rainwater through a system of canals to the ocean.

But now that movement of water isn’t that swift and doesn’t always happen. As a result, people in cities without ocean views are finding that the water level of the Atlantic Ocean can affect their homes.

Although cities are installing pumps and other flood-control devices, they need capacity in the canals to get rid of the water.

“No matter what we do, if they don’t lower those canals so our water can escape, there’s nothing to be done,” said Angelo Castillo, a Pembroke Pines commissioner. “We can spend as much money as we want on drainage but if they can’t access the canals because the canals won’t take that capacity, nothing that we do in terms of conveying water faster to those canals will work.”

Sea levels have been rising at an accelerating rate, largely due to climate change caused by pollution from cars, power plants and other sources of heat-trapping gasses. A NOAA study says global sea levels have gone up 3.4 inches from 1993 to 2019.

In South Florida, estimates from the Southeast Florida Regional Climate Change Compact, which represents local governments, call for sea levels to rise another 10-17 inches by 2040.

Hoping to revamp the system for an age of rising sea levels, the water management district has proposed improvements at 23 drainage structures in Broward and Miami-Dade counties. They range from southern Miami-Dade County to the Hillsboro Canal, which separates Broward and Palm Beach counties.

The major projects would be the addition of powerful pumps to allow water to be moved to the ocean side of the canal when the is too high to move water by gravity. But these projects are expensive.

The improvements, assuming they go through, could help homeowners with their flood insurance bills. A better drainage system could hold down rates and reduce the number of properties required to get flood insurance.

The water management district is seeking federal and state money for the work. As soon as the first funding comes through, the district plans to start designing the new pumps and other improvement for water-control structures on the canal that drains southern Broward and the one that drains northeast Miami-Dade.

Jennifer Jurado, who oversees climate-change planning for Broward County, said the improvements will help prevent neighborhoods from flooding in future storms, but the region needs to come up with ways to keep as much water as possible rather than just pumping it away.

“It’s trying to ensure the system works at least as well as it was intended,” she said. “It’s a huge part of the fix. Our system can’t just pump it out. We have to be able to store as much of it as we can because the rain that falls is the rain we use for our water supply. We need to capture and store that water, in addition to providing flood relief.”

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