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 Squeeze it like toothpaste: The flexible brain of marsupial mammals thumbnail

Hexbyte Glen Cove Squeeze it like toothpaste: The flexible brain of marsupial mammals

Hexbyte Glen Cove

Credit: Pixabay/CC0 Public Domain

Being stretchy and squeezable may be the key to finding space for the brain in mammals, including humans.

An international study, co-led by Flinders University’s Vera Weisbecker, has revealed that marsupial mammals like possums, kangaroos, and wombats appear to have a lot of flexibility when it comes to accommodating their brains into their skulls.

“The brain is one of the heaviest parts of the head, particularly in smaller mammals. But it needs to be placed in a way that doesn’t interfere with the many vital functions of the head, such as seeing, hearing, smelling and of course feeding,” says Dr. Weisbecker.

“Stowing” a large brain into the head is a general challenge for mammals, which have much larger brains relative to their body size compared to their reptile-like ancestors. It is also a particularly intriguing issue in humans and their primate relatives, which tend to have extremely large relative brain sizes compared to other mammals.”

“We wanted to use a diverse group of mammals to assess if there is general pattern of brain shape variation to explain the ability of mammals to fit their brains into the great diversity of head shapes without interfering with head function. Marsupial mammals fit the bill perfectly because they are a well-understood group of mammals with diverse head sizes and functions.”

The team used CT scanning and 3-D visualization to extract the shape of the brain cavity in the diverse group of Australian marsupial mammals.

“These so-called “endocasts” give us a good idea of what the brain itself looks like,” says Dr. Weisbecker.

“I then placed landmarks—which work a bit like a coordinate system for shape—all over the endocasts of just under 60 marsupial species, including some really cool fossils like the marsupial lion.”

When co-author Dr. Emma Sherratt from The University of Adelaide analyzed the data, the team were in for a surprise:

“The biggest difference between the brains is basically whether they are more cylindrical or more globular. We were struck by how extreme this stretch-compress pattern was—we saw brains that look like marbles, and others that nearly look like tubes!” says Dr. Sherratt.

“Intriguingly, this matches the characteristically rounded shape of the human brain, which is sometimes thought to arise from the need to “stack” all the brain tissue into the skull efficiently,” says Dr. Weisbecker.

“It is therefore possible that human brain shape arises from an ancient general tendency of the brain to assume a range of shapes from rounded to elongate.”

Another interesting find was the many unusual brain shapes the team saw.

“Within the general pattern of spherical versus stretched-out, we saw some outlandish endocast shapes. For example, some species had totally flat brains, while others seemed to have parts of the brain “squished aside” by the bone around the middle ear.”

The researchers say that the Tasmanian tiger has enormous olfactory bulbs, which are responsible for smell, and some unusually compact and rounded cerebral hemispheres.

“We believe that a round-to-cylindrical brain shapes are probably the most easily achieved evolutionary pathway of fitting the brain into the skull. However, within this overall pattern, the brain seems incredibly flexible, nearly as if it was toothpaste than can be squeezed into any mold,” says Dr. Weisbecker.

“This might also explain why we saw substantially different brain shapes in individuals of the same species.”

The teams find matches well with evidence that the brain of some mammals can change size and shape during an animals’ lifetime.

“We suspect that a flexible brain is the key to success in other animals as well. For example, some crocodiles and ancient coelacanth fishes have extremely long brains; and birds have their eyes imprinted on their brain shape. It appears that the brain is capable of functioning regardless of where it goes in the skull.”

The research shows brain function might not be easy to determine from brain shape.

“We found no correspondence of brain shape with movement patterns, for example if animals a species climbs trees, glides, hops, or walks on all fours.”

“We suspect that the overall shape of the mammalian brain is strongly determined by the requirements of the skull. Understanding specific adaptations of the brain probably require investigation of finer detail than overall .”



More information:
Vera Weisbecker et al. Global elongation and high shape flexibility as an evolutionary hypothesis of accommodating mammalian brains into skulls, Evolution (2021). DOI: 10.1111/evo.14163

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