Enzymes From The Deep – The Polymerase

March 22, 2016 by Nava Whiteford 46 Comments

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-replication — 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.

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Guerrilla Grafters Grow Great Gifts For Greater Good

December 19, 2015 by Bryan Cockfield 59 Comments

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!

Basic Toolkit For The Basement Biohacker

November 27, 2015 by Dan Maloney 5 Comments

Laying hands on the supplies for most hacks we cover is getting easier by the day. A few pecks at the keyboard and half a dozen boards or chips are on an ePacket from China to your doorstep for next to nothing. But if hacking life is what you’re into, you’ll spend a lot of time and money gathering the necessary instrumentation. Unless you roll your own mini genetic engineering lab from scratch, that is.

Taking the form of an Arduino mega-shield that supports a pH meter, a spectrophotometer, and a PID-controlled hot plate, [M. Bindhammer]’s design has a nice cross-section of the instruments needed to start biohacking in your basement. Since the shield piggybacks on an Arduino, all the data can be logged, and decisions can be made based on the data as it is collected. One example is changing the temperature of the hot plate when a certain pH is reached. Not having to babysit your experiments could be a huge boon to the basement biohacker.

Biohacking is poised to be the next big thing in the hacking movement, and [M. Bindhammer]’s design is far from the only player in the space. From incubators to peristaltic pumps to complete labs in a box, the tools to tweak life are starting to reach critical mass. We can’t wait to see where these tools lead.

Conductive Circuit Board Tattoos: Tech Tats

November 25, 2015 by James Hobson 18 Comments

While hardcore body-hackers are starting to freak us out with embedded circuit boards under their skin, a new more realistic option is becoming available — temporary tech tattoos. They’re basically wearable circuit boards.

Produced by [Chaotic Moon], the team is excited to explore the future of skin-mounted components — connected with conductive ink in the form of a temporary tattoo. And if you’re still thinking why, consider this. If these tattoos can be used as temporary health sensors, packed with different biometric readings, the “tech tat” can be applied when it is needed, in order to monitor specific things.

In one of their test cases, they mount an ATiny85 connected to temperature sensors and an ambient light sensor on the skin. A simple device like this could be used to monitor someone’s vitals after surgery, or could even be used as a fitness tracker. Add a BLE chip, and you’ve got wireless data transfer to your phone or tablet for further data processing.

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Bioluminescent Challenge Has Students Feeding Their Lamps

October 20, 2015 by Al Williams 11 Comments

[Tom Lombardo] is an engineer and an educator. When a company sent him a Dino Pet–a bioluminescent sculpture–he found it wasn’t really usable as a practical light source. He did, however, realize it would be an interesting STEAM (science, technology, engineering, art, and math) project for students to produce bioluminescent sculptures.

The lamps (or sculptures, if you prefer) contain dinoflagellates which is a type of plankton that glows when agitated. Of course, they don’t put out a strong light and–the main problem–you have to agitate the little suckers to get them to emit light. [Tom] found that there was a mild afterglow when you stop shaking, but not much. You can get an idea of how much light they make in the video below. The idea for a school project would be to make practical ambient lighting that didn’t require much input power to agitate the plankton.

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CyberPunk Yourself – Body Modification, Augmentation, And Grinders

October 12, 2015 by Cameron Coward 116 Comments

“We accept pain as a price of doing business, even if it is just for aesthetic purposes. You want to put a magnet in your finger, a doctor will ask you why; a mod artist will ask when you can start.” As with many other people who are part of the growing grinder movement, [Adam] has taken a step that many would consider extreme – he’s begun to augment his body.

Grinders – men and women who hack their own bodies – are pushing the boundaries of what is currently possible when it comes to human augmentation. They’re hackers at heart, pursuing on an amateur level what they can’t get from the consumer market. Human augmentation is a concept that is featured heavily in science fiction and futurism, but the assumption most people have is that those kinds of advancements will come from medical or technology companies.

Instead, we’re seeing augmentation begin in the basements of hackers and in the back rooms of piercing studios. The domain of grinders is the space where body modification and hacking meet. It mixes the same willingness to modify one’s body that is common among the tattooed and pierced, and adds an interest in hacking technology that you find in hackerspaces around the world. When those two qualities intersect, you have a potential grinder.

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Ctrl-X, Ctrl-V For DNA

September 20, 2015 by Dan Maloney 23 Comments

Once upon a time, the aspiring nerdling’s gift of choice was the Gilbert chemistry set. Its tiny vials of reagents, rack of test tubes, and instruction book promised endless intellectual stimulation and the possibility of stink bombs on demand. Now a new genetic engineering lab-in-a-box Kickstarter, with all the tools and materials needed to create your own transgenic organisms, may help the young biohacker’s dreams come true.

The Kickstarter has been wildly successful. The initial goal was $1200AUD was met in a day, and currently stands at almost $6200AUD. Despite that success, color me skeptical on this one. Having done way more than my fair share of gene splicing, there seem to be a few critical gaps in this kit. For example, the list of materials for the full kit includes BL21 competent E. coli as the host strain. Those cells are designed to become porous to extracellular DNA when treated with calcium chloride and provided with a heat shock of 42°C. At a minimum I’d think they’d include a thermometer so you can control the heat shock process. Plenty of other steps also need fairly precise incubations, like the digestion and ligation steps needed to get your gene into the host. And exactly what technique you’d be using to harvest DNA from the animal, plant or fungal cells is unclear; the fact that most of the techniques for doing so require special techniques leads me to believe there’s a lot less here than meets the eye.

To be fair, I’ve been off the lab bench for the better part of two decades, and the state of the art has no doubt advanced in that time. There could very well be techniques I’m not familiar with that make the various steps needed to transform a bacterial culture with foreign DNA trivial. It could also be the case that the techniques I used in the lab were optimized for yield and for precise data, while the GlowGene kit provides the materials to get a “good enough” result. I hope so, because a kit like this could really expand the horizons of hackerdom and start getting the biohacking movement going.

[Thanks, Michael!]