Technology frequently looks at nature to make improvements in efficiency, and we may be nearing a new breakthrough in copying how nature stores data. Maybe some day your thumb drive will be your actual thumb. The entire works of Shakespeare could be stored in an infinite number of monkeys. DNA could become a data storage mechanism! With all the sensationalism surrounding this frontier, it seems like a dose of reality is in order.
The Potential for Greatness
The human genome, with 3 billion base pairs can store up to 750MB of data. In reality every cell has two sets of chromosomes, so nearly every human cell has 1.5GB of data shoved inside. You could pack 165 billion cells into the volume of a microSD card, which equates to 165 exobytes, and that’s if you keep all the overhead of the rest of the cell and not just the DNA. That’s without any kind of optimizing for data storage, too.
This kind of data density is far beyond our current digital storage capabilities. Storing nearly infinite data onto extremely small cells could change everything. Beyond the volume, there’s also the promise of longevity and replication, maintaining a permanent record that can’t get lost and is easily transferred (like medical records), and even an element of subterfuge or data transportation, as well as the ability to design self-replicating machines whose purpose is to disseminate information broadly.
So, where is the state of the art in DNA data storage? There’s plenty of promise, but does it actually work?
Continue reading “DNA Now Stands For Data And Knowledge Accumulation”
When the first thermal cyclers for the polymerase chain reaction came out in the 1980s, they were as expensive as a market driven by grant money could make them. Things haven’t got much better over the years, largely shutting STEM classes and biohackers out of the PCR market. That may be about to change, though, if the €99.00 PocketPCR thermal cycler takes hold.
PCR amplifies DNA in a three-step process: denaturation, which melts double-stranded DNA into single strands; annealing, which lets small pieces of primer DNA bind to either side of the region of interest; and elongation, where the enzyme DNA polymerase zips along the single strands starting at the primer to replicate the DNA. The cycle repeats and copies of the original DNA accumulate exponentially. Like any thermal cycler, [Urs Gaudenz]’s PocketPCR automates those temperature shifts, using a combination of PCB-mounted heating elements and a cooling fan. The coils rapidly heat a reaction block up to the 99°C denaturation temperature, the fan brings that down to the 68°C needed for annealing, and then the temperature ramps back up to 72°C for elongation with thermostable DNA polymerase. PID loops keep the reaction temperature precisely controlled. The whole thing is, as the name suggests, small enough to fit in a pocket, and can either be purchased in kit form or scratch-built from the build files on GitHub.
We applaud [Urs]’ efforts to get the power of PCR into the hands of citizen scientists. Quick and dirty thermal cyclers are one thing, but Pocket PCR has a great fit and finish that makes it more accessible.
Thanks to [Abe Tusk] for the tip.
Join us on Wednesday at noon Pacific time for the open-source biology and biohacking Hack Chat!
Justin Atkin‘s name might not ring a bell, but you’ve probably seen his popular YouTube channel The Thought Emporium, devoted to regular doses of open source science. Justin’s interests span a wide range, literally from the heavens above to the microscopic world.
His current interest is to genetically modify yeast to produce spider silk, and to perhaps even use the yeast for brewing beer. He and the Thought Emporium team have been busy building out a complete DIY biology lab to support the effort, and have been conducting a variety of test experiments along the way.
Please join us for this Hack Chat, in which we’ll cover:
- The how’s and why’s of yeast genetic engineering;
- What it takes to set up an effective biology lab from scratch;
- An update on the current status of the spider-silk yeast project; and
- Where the open-source biology field is, and where it’s going.
You are, of course, encouraged to add your own questions to the discussion. You can do that by leaving a comment on the Open-Source Biology and Biohacking Hack Chat event page and we’ll put that in the queue for the Hack Chat discussion.
Our Hack Chats are live community events on the Hackaday.io Hack Chat group messaging. This week we’ll be sitting down on Wednesday, February 13, at noon, Pacific time. If time zones have got you down, we have a handy time zone converter.
Click that speech bubble to the right, and you’ll be taken directly to the Hack Chat group on Hackaday.io. You don’t have to wait until Wednesday; join whenever you want and you can see what the community is talking about.
Everyone starts their day with a routine, and like most people these days, mine starts by checking my phone. But where most people look for the weather update, local traffic, or even check Twitter or Facebook, I use my phone to peer an inch inside my daughter’s abdomen. There, a tiny electrochemical sensor continuously samples the fluid between her cells, measuring the concentration of glucose so that we can control the amount of insulin she’s receiving through her insulin pump.
Type 1 diabetes is a nasty disease, usually sprung on the victim early in life and making every day a series of medical procedures – calculating the correct amount of insulin to use for each morsel of food consumed, dealing with the inevitable high and low blood glucose readings, and pinprick after pinprick to test the blood. Continuous glucose monitoring (CGM) has been a godsend to us and millions of diabetic families, as it gives us the freedom to let our kids be kids and go on sleepovers and have one more slice of pizza without turning it into a major project. Plus, good control of blood glucose means less chance of the dire consequences of diabetes later in life, like blindness, heart disease, and amputations. And I have to say I think it’s pretty neat that I have telemetry on my child; we like to call her our “cyborg kid.”
But for all the benefits of CGM, it’s not without its downsides. It’s wickedly expensive in terms of consumables and electronics, it requires an invasive procedure to place sensors, and even in this age of tiny electronics, it’s still comparatively bulky. It seems like we should be a lot further along with the technology than we are, but as it turns out, CGM is actually pretty hard to do, and there are some pretty solid reasons why the technology seems stuck.
Continue reading “Why Is Continuous Glucose Monitoring So Hard?”
Would you pop a homemade pill containing genetically engineered virus particles just so that you can enjoy a pizza? Not many people would, but then again, if you’ve experienced the violent reaction to lactose that some people have, you just might consider it.
Such was the position that [The Thought Emporium] found himself in at age 16, suddenly violently lactose intolerant and in need of a complete diet overhaul. Tired of scanning food labels for telltale signs of milk products and paying the price for the inevitable mistakes, he embarked on a journey of DIY gene therapy to restore his ability to indulge in comfort foods. The longish video below details a lot of that journey; skip to 15:40 if you want to cut to the chase. But if you’re at all interested in the processes of modern molecular biology, make sure you watch the whole thing. The basic idea here is to create an innocuous virus that carries the lac gene, which encodes the enzyme β-galactosidase, or lactase, and use it to infect the cells of his small intestine. There the gene will hopefully be expressed, supplementing the supply of native enzyme, which in most adult humans is no longer expressed at the levels it was when breast milk was our primary food.
Did it work? We won’t ruin the surprise, but in any case, the video is a fascinating look at mammalian cell transfection and other techniques of genetic engineering that are accessible to the biohacker. Still, it takes some guts to modify your own guts, but bear in mind that this is someone who doesn’t mind inserting magnetic implants in his fingers.
Continue reading “Biohacking Lactose Intolerance”
Biochemistry texts are loaded with images of the proteins, nucleic acids, and other biopolymers that make up life. Depictions of the 3D structure of macromolecules based on crystallography and models of their most favorable thermodynamic conformations are important tools. And some are just plain beautiful, which is why artist [Mike Tyka] has taken to using lost-PLA casting to create sculptures of macromolecules from bronze, copper, and glass.
We normally don’t cover strictly artistic projects here at Hackaday, although we do make exceptions, such as when the art makes a commentary on technology’s place in society. In [Mike]’s case, not only is his art beautiful and dripping with nerd street cred, but his techniques can be translated to other less artsy projects.
For “Tears”, his sculpture of the enzyme lysozyme shown in the banner image, [Mike] started with crystallographic data that pinpoints every peptide residue in the protein. A model is created for the 3D printer, with careful attention paid to how the finished print can be split apart to allow casting. Clear PLA filament is used for the positive because it burns out of the mold better than colored plastic. The prints are solvent smoothed, sprues and air vents added, and the positive is coated with a plaster mix appropriate for the sculpture medium before the plastic is melted out and the mold is ready for casting.
[Mike]’s sculpture page is well worth a look even if you have no interest in macromolecules or casting techniques. And if you ever think you’ll want to start lost-PLA casting, be sure to look over his build logs for plenty of tips and tricks. “Tears” is executed in bronze and glass, and [Mike]’s description is full of advice on how to handle casting such vastly different media.
Thanks to [Dave Z.] for the tip.