DNA Now Stands For Data And Knowledge Accumulation

February 18, 2020 by Bob Baddeley 33 Comments

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?

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Using Glow-in-the-Dark Fish Gut Bacteria To Make Art

December 7, 2019 by Sharon Lin 3 Comments

In New Orleans, a Loyola University professor has been creating original art out of glow-in-the-dark fish gut bacteria, enough to fill 1000 Petri dishes. Her first major foray into art was biomorphic abstractions, inspired by Impressionist painters, with her current work reflecting much of the abstraction of the earlier style.

The bacteria comes from the Pacific Rock Fish and glows a vibrant electric-blue. It is typically kept in a freezer and has a texture and color similar to water when it’s being used. The luminescence only lasts for 24 hours, presenting timing challenges when preparing artwork for a photoshoot, as artist [Hunter Cole] often does. With a Q-tip, [Cole] paints roses, lilies, and insects onto the Petri dishes and arranges them for surreal photography shoots. In addition to painting shapes in agar, she uses a light painting technique by filling clear water bottles with the bacteria for long-exposure shots.

[Cole] is planning on presenting her work at an art exhibit in New Orleans, along with showcasing a performance piece featuring models clad in chandelier-like costumes glowing with bioluminescent bacteria in petri dishes.

Fitness Tracker Hacked Into Optical Density Meter

September 20, 2019 by Dan Maloney 5 Comments

What do fitness trackers have to do with bacterial cultures in the lab? Absolutely nothing, unless and until someone turns a fitness band into a general-purpose optical densitometer for the lab.

This is one of those stories that shows that you never know from where inspiration is going to come. [Chinna Devarapu] learned that as a result of playing around with cheap fitness bands, specifically an ID107HR. A community has built up around hacking these bands; we featured a similar band that was turned into an EEG. With some help, [Chinna] was able to reflash the microcontroller and program it in the Arduino IDE, and began looking for a mission for the sensor-laden platform.

He settled on building a continuous optical densitometer for his biology colleagues. Bacterial cultures become increasingly turbid as the grow, and measuring the optical density (OD) of a culture is a common way to monitor its growth phase. This is usually done by sucking up a bit of the culture to measure, but [Chinna] and his team were able to use the hacked fitness band’s heartrate sensor to measure the OD on the fly. The tracker fits in a 3D-printed holder where an LED can shine through the growing culture; the sensor’s photodiode measures the amount of light getting through and the raw data is available via the tracker’s Bluetooth. The whole thing can be built for less than $20, and the plans have been completely open-sourced.

We really like the idea of turning these fitness bands into something completely different. With the capabilities these things pack into such a cheap and compact package, they should start turning up in more and more projects.

Hacked Heating Instruments For The DIY Biology Lab

November 12, 2018 by Dan Maloney 4 Comments

[Justin] from The Thought Emporium takes on a common molecular biology problem with these homebrew heating instruments for the DIY biology lab.

The action at the molecular biology bench boils down to a few simple tasks: suck stuff, spit stuff, cool stuff, and heat stuff. Pipettes take care of the sucking and spitting, while ice buckets and refrigerators do the cooling. The heating, however, can be problematic; vessels of various sizes need to be accommodated at different, carefully controlled temperatures. It’s not uncommon to see dozens of different incubators, heat blocks, heat plates, and even walk-in environmental chambers in the typical lab, all acquired and maintained at great cost. It’s enough to discourage any would-be biohacker from starting a lab.

[Justin] knew It doesn’t need to be that way, though. So he tackled two common devices: the incubator and the heating block. The build used as many off-the-shelf components as possible, keeping costs down. The incubator is dead simple: an insulated plastic picnic cooler with a thermostatically controlled reptile heating pad. That proves to be more than serviceable up to 40°, at the high end of what most yeast and bacterial cultures require.

The heat block, used to heat small plastic reaction vessels called Eppendorf tubes, was a little more complicated to construct. Scrap heat sinks yielded aluminum stock, which despite going through a bit of a machinist’s nightmare on the drill press came out surprisingly nice. Heat for the block is provided by a commercial Peltier module and controller; it looks good up to 42°, a common temperature for heat-shocking yeast and tricking them into taking up foreign DNA.

We’re impressed with how cheaply [Justin] was able to throw together these instruments, and we’re looking forward to seeing how he utilizes them. He’s already biohacked himself, so seeing what happens to yeast and bacteria in his DIY lab should be interesting.

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Infection? Your Smartphone Will See You Now

September 24, 2018 by Al Williams 8 Comments

When Mr. Spock beams down to a planet, he’s carrying a tricorder, a communicator, and a phaser. We just have our cell phones. The University of California Santa Barbara published a paper showing how an inexpensive kit can allow your cell phone to identify pathogens in about an hour. That’s quite a feat compared to the 18-28 hours required by traditional methods. The kit can be produced for under $100, according to the University.

Identifying bacteria type is crucial to prescribing the right antibiotic, although your family doctor probably just guesses because of the amount of time it takes to get an identification through a culture. The system works by taking some — ahem — body fluid and breaking it down using some simple chemicals. Another batch of chemicals known as a LAMP reaction mixture multiplies DNA and will cause fluorescence in the case of a positive result.

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Publish Or Perish: The Sad Genius Of Ignaz Semmelweis

August 28, 2018 by Dan Maloney 31 Comments

Of all the lessons that life hands us, one of the toughest is that you can be right about something but still come up holding the smelly end of the stick. Typically this is learned early in life, but far too many of us avoid this harsh truth well into adulthood. And in those cases where being right is literally a matter of life or death, it’s even more difficult to learn that lesson.

For Ignaz Semmelweis, a Hungarian physician-scientist in the mid-19th century, failure to learn that being right is attended by certain responsibilities had a very high cost. Ironically it would also save the lives of countless women with a revolutionary discovery that seems so simple today as to be self-obvious: that a doctor should wash his hands before seeing patients.

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Living 3D Printer Filament

December 22, 2017 by James Hobson 15 Comments

This is more than a printing filament hack — closer to bleeding edge bio-engineering — but we can’t help but be fascinated by the prospect of 3D printing with filament that’s alive on a cellular level.

The team from MIT led by [Xuanhe Zhao] and [Timothy Lu] have programmed bacteria cells to respond to specific compounds. To demonstrate, they printed a temporary tattoo of a tree formed of the sturdy bacteria and a hydrogel ‘ink’ loaded with nutrients, that lights up over a few hours when adhered to skin swabbed with these specific stimuli.

So far, the team has been able to produce objects as large as several centimetres, capable of being adapted into active materials when printed and integrated as wearables, displays, sensors and more.

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