Movie Encoded in DNA is the First Step Toward Datalogging with Living Cells

While DNA is a reasonably good storage medium, it’s not particularly fast, cheap, or convenient to read and write to.

What if living cells could simplify that by recording useful data into their own DNA for later analysis? At Harvard Medical School, scientists are working towards this goal by using CRISPR to encode and retrieve a short video in bacterial cells.

CRISPR is part of the immune system of many bacteria, and works by storing sequences of viral DNA in a specific location to identify and eliminate viral infections. As a tool for genetic engineering, it’s cheaper and has fewer drawbacks than previous techniques.

Besides generating living rickrolls and DMCA violations, what is this good for? Cheap, self-replicating sensors. [Seth Shipman], part of the team of scientists at Harvard, explains in an interview below a number of possible applications. His focus is engineering cells to act as a noninvasive data acquisition tool to study neurobiology, for example by using engineered neurons to record their developmental history.

It’s possible to see how this technique can be used more broadly and outside an academic context. Presently, biosensors generally use electric or fluorescent transducers to relay a detection event. By recording data over time in the DNA of living cells, biosensors could become much cheaper and contain intrinsic datalogging. Possible applications could include long-term metabolite (e.g. glucose) monitors, chemical detectors, and quality control.

It’s worth noting that this technique is only at the proof of concept stage. Data was recorded and retrieved manually by the scientists into the bacterial genome with 90% accuracy, demonstrating that if cells can be engineered to record data themselves, accuracy and capacity are high enough for practical applications.

That being said, if anyone is working on a MEncoder or ffmpeg command line option for this, let us know in the comments.

Continue reading “Movie Encoded in DNA is the First Step Toward Datalogging with Living Cells”

Get into Biohacking on the Cheap with this Electrophoresis Rig

If you want to get into electronics, it’s pretty straightforward: read up a little, buy a breadboard and some parts, and go to town. Getting into molecular biology as a hobby, however, presents some challenges. The knowledge is all out there, true, but finding the equipment can be a problem, and what’s out there tends to be fiendishly expensive.

So many would-be biohackers end up making their own equipment, like this DIY gel electrophoresis rig. Electrophoresis sorts macromolecules like DNA or proteins by size using an electric field. For DNA, a slab of agarose gel is immersed in a buffer solution and a current through the tank moves the DNA through the gel. The shorter the DNA fragment, the easier it can wiggle through the pores in the gel, and the faster it migrates down the gel. [abizar]’s first attempt at a DIY gel rig involved a lot of plastic cutting and solvent welding, so he simplified the process by using the little plastic drawers from an old parts cabinet. With nichrome and platinum wires for electrodes for the modified ATX power supply, it’s just the right size and shape for the gel, which is cast in a separate mold. The video below shows the whole build, and while [abizar] doesn’t offer much detail on recipes or techniques, there are plenty of videos online to guide you.

Need more apparatus to deck out your lab? We’ve got you covered there too.

Continue reading “Get into Biohacking on the Cheap with this Electrophoresis Rig”

Remote Controlling A Dog

Until the industrial revolution, humans made use of animals to make our labor easier. This is still seen in some niche areas, like how no machine yet has been invented that’s as good at sniffing out truffles as pigs are. [William] has hearkened back to humanity’s earlier roots, but in a more modern twist has made something of a general purpose dog that could feasibly do any work imaginable. Now his dog is remote-controlled.

[William] accomplished the monumental task in a literally cartoonish fashion using the old trope of hanging a hot dog in front of something’s face to get them to chase it. The attachment point was fitted with a remote control receiver and an actuator to get the hanging hot dog to dangle a little bit more to the dog’s right or left, depending on where the “operator” wants the dog to go. [William]’s bulldog seems to be a pretty good sport about everything and isn’t any worse for wear either.

Believe it or not, there has been some actual research done into remote controlling animals, although so far it’s limited to remote-controlled cockroaches. We like the simplicity of the remote-controlled dog, though, but don’t expect to see these rigs replacing leashes anytime soon!

Continue reading “Remote Controlling A Dog”

Soft Robot With Microfluidic Logic Circuit

Perhaps our future overlords won’t be made up of electrical circuits after all but will instead be soft-bodied like ourselves. However, their design will have its origins in electrical analogues, as with the Octobot.

The Octobot is the brainchild a team of Harvard University researchers who recently published an article about it in Nature. Its body is modeled on the octopus and is composed of all soft body parts that were made using a combination of 3D printing, molding and soft lithography. Two sets of arms on either side of the Octobot move, taking turns under the control of a soft oscillator circuit. You can see it in action in the video below.

Continue reading “Soft Robot With Microfluidic Logic Circuit”

Tissue-Engineered Soft Robot Swims Like a Stingray

We’re about to enter a new age in robotics. Forget the servos, the microcontrollers, the H-bridges and the steppers. Start thinking in terms of optogenetically engineered myocytes, microfabricated gold endoskeletons, and hydrodynamically optimized elastomeric skins, because all of these have now come together in a tissue-engineered swimming robotic stingray that pushes the boundary between machine and life.

In a paper in Science, [Kevin Kit Parker] and his team at the fantastically named Wyss Institute for Biologically Inspired Engineering describe the achievement. It turns out that the batoid fishes like skates and rays have a pretty good handle on how to propel themselves in water with minimal musculoskeletal and neurological requirements, and so they’re great model organisms for a tissue engineered robot.

The body is a laminate of silicone rubber and a collection of 200,000 rat heart muscle cells. The cardiomyocytes provide the contractile force, and the pattern in which they are applied to the 1/2″ (1.25cm) body allows for the familiar undulating motion of a stingray’s wings. A gold endoskeleton with enough stiffness to act as a spring is used to counter the contraction of the muscle fibers and reset the system for another wave. Very clever stuff, but perhaps the coolest bit is that the muscle cells are genetically engineered to be photosensitive, making the robofish controllable with pulses of light. Check out the video below to see the robot swimming through an obstacle course.

This is obviously far from a finished product, but the possibilities are limitless with this level of engineering, especially with a system that draws energy from its environment like this one does. Just think about what could be accomplished if a microcontroller could be included in that gold skeleton.

Continue reading “Tissue-Engineered Soft Robot Swims Like a Stingray”

Enzymes From The Deep – The Polymerase

Our bodies rely on DNA to function, it’s often described as “the secret of life”. A computer program that describes how to make a man. However inaccurate these analogies might be, DNA is fundamental to life. In order for organisms to grown and replicate they therefore need to copy their DNA.

DNA structure and replication

Since the discovery of its structure in 1953, the approximate method used to copy DNA has been obvious. The information in DNA is encoded in 4 nucleotides (which in their short form we call A,T,G, and C). These couple with each other in pairs, forming 2 complimentary strands that mirror each other. This structure naturally lends itself to replication. The two strands can dissociate (under heat we call this melting), and new strands form around each single stranded template.

However, this replication process can’t happen all by itself, it requires assistance. And it wasn’t until we discovered an enzyme called the DNA polymerase that we understood how this worked. In conjunction with other enzymes, double stranded DNA is unwound into 2 single strands which are replicated by the polymerase.

Continue reading “Enzymes From The Deep – The Polymerase”

Guerrilla Grafters Grow Great Gifts for Greater Good

If you’ve been to downtown San Francisco lately, you might have noticed something odd about the decorative trees in the city: they’re now growing fruit. This is thanks to a group of people called the Guerrilla Grafters who are covertly grafting fruit-bearing twigs to city tress which would otherwise be fruitless. Their goal is to create a delicious, free source of food for those living in urban environments.

Biology-related hacks aren’t something we see every day, but they’re out there. For those unfamiliar with grafting, it’s a process that involves taking the flowering, fruiting, or otherwise leafy section of one plant (a “scion”) and attaching them to the vascular structure of another plant that has an already-established root system (the “stock”). The Guerrilla Grafters are performing this process semi-covertly and haven’t had any run-ins with city officials yet, largely due to lack of funding on the city’s part to maintain the trees in the first place.

This hack doesn’t stop at the biological level, though. The Grafters have to keep detailed records of which trees the scions came from, when the grafts were done, and what characteristics the stock trees have. To keep track of everything they’ve started using RFID tags. This is an elegant solution that can be small and inconspicuous, and is a reliable way to keep track of all of one’s “inventory” of trees and grafts.

It’s great to see a grassroots movement like this take off, especially when it seems like city resources are stretched so thin that the trees may have been neglected anyway. Be sure to check out their site if you’re interested in trying a graft yourself. If you’re feeling really adventurous, you can take this process to the extreme.

Thanks to [gotno] for the tip!