Four short links: 10 November 2009

DIY Diagnostic Chips, Genetics on $5k a Genome, Cellphones as Diagnostic Microscopes, AR-Equipped Mechanics Do It Heads-Up

by Nat Torkington | @gnat | comments: 0

1. A children’s toy inspires a cheap, easy production method for high-tech diagnostic chips -- microfluidic chips (with tiny liquid-filled channels) can cost $100k and more. Michelle Khine used the Shrinky Dinks childrens' toy to make her own. "I thought if I could print out the [designs] at a certain resolution and then make them shrink, I could make channels the right size for micro­fluidics," she says. (via BoingBoing)
2. Complete Genomics publishes in Science on low-cost sequencing of 3 human genomes (press release) -- The consumables cost for these three genomes sequenced on the proof-of-principle genomic DNA nanoarrays ranged from $8,005 for 87x coverage to $1,726 for 45x coverage for the samples described in this report. Drive that cost down! There's a gold rush in biological discovery at the moment as we pick the low-hanging fruit of gross correlations between genome and physiome, but the science to reveal the workings of cause and effect is still in its infancy. We're in the position of the 18th century natural philosophers who were playing with static electricity, oxygen, anaesthetics, and so on but who lacked today's deeper insights into physical and chemical structure that explain the effects they were able to obtain. More data at this stage means more low-hanging fruit can be plucked, but the real power comes when we understand "how" and not just "what". (via BoingBoing)
3. Far From a Lab? Turn a Cellphone into a Microscope (NY Times) -- for some tests, you can use a camphone instead of a microscope. In one prototype, a slide holding a finger prick of blood can be inserted over the phone’s camera sensor. The sensor detects the slide’s contents and sends the information wirelessly to a hospital or regional health center. For instance, the phones can detect the asymmetric shape of diseased blood cells or other abnormal cells, or note an increase of white blood cells, a sign of infection, he said.
4. Augmented reality helps Marine mechanics carry out repair work (MIT TR) -- A user wears a head-worn display, and the AR system provides assistance by showing 3-D arrows that point to a relevant component, text instructions, floating labels and warnings, and animated, 3-D models of the appropriate tools. An Android-powered G1 smart phone attached to the mechanic's wrist provides touchscreen controls for cueing up the next sequence of instructions. [...] The mechanics using the AR system located and started repair tasks 56 percent faster, on average, than when wearing the untracked headset, and 47 percent faster than when using just a stationary computer screen.

Etech Session Liveblogging: Real Hackers Program DNA (Ginkgo Bioworks)

by Quinn Norton | comments: 6

GB is "Making the process of engineering biology easier."

Synth bio is the idea that biology is a technology to engineer novel systems- say drugs, biofuels, other sexy sexy projects.

This is to be a flavor of what engineering biology is all about.

We will be installing a program into E coli to make it turn red, glow in the dark, or smell like bananas... We get to pick!

The DNA is stapled to the pages that describe them in the notebook.

Some of the tools of synth bio: biobricks, interchangeable components that can be strung together into programs. The parts registry lets you snap programs together.

iGem participants get a kit in the mail and pick out parts and mix and match them into new programs they want- much like the one we're holding. The Scottish team made and E coli that turned red in response to arsenic contamination.

Standardized interchangeable components are limited, but let a lot more people get involved and democratizes access to the tools. This is still biology- it can seem kind of scary- do you trust your neighbor to engineer biology?

Question from the audience: how do you prevent the terrorists from building smallpox?
Answer: You can't perfectly. "How do you prevent a car bomb from blowing up outside?" You don't, but you can limit it, and create a community that self polices.

Question from the audience: What about release? Would the arsenic detector be scattered on the ground?
Answer: We don't understand how manufactured organisms will interact with the environment. We work with safe organisms, and we don't release our stuff. These E coli are pretty innocuous, so we're going to wash our hands before lunch.

It's pretty unlikely that anyone is going to make anything in a lab that's dangerous right now, but we should think about that.

It's a bit legally gray, the guidelines everyone follows are only required for people receiving NIH funding, and there's some places with local laws (like Cambridge) ... There's no clear answer.

We're punching out our DNA and dropping it in cells. (Ben has returned our vial, #19 and #10 to ice, while the receptive cells take up our dna)

We're installing on a plasmid. "You're literally just mixing the plasmid DNA with the cells." These cells are competent, which means they can take up DNA easily. We cool the DNA, then do a heat shot- then shock it in a 42 degree water bath for 30 seconds, time it, put it back on ice for two minutes. We're disrupting the membrane of the cells and letting them recover. Then we're adding media, food for the cells. Then we're incubating them with our bodies. I'm going to keep mine in my armpit, I think.

Can't mix the three bit of dna, because they're the same plasmid - they are ampecillin resistance plasmid, so there's a space collision, things aren't likely to play well together.

DIYbio.org is a good place to learn about good lab practices.

I am now heading to lunch, incubating a tube of e coli in each armpit. (Will update with pictures after lunch)

Update: I've now transferred my E. coli to a petri dish and a vial, freeing my arms.

...and no, I was in a hurry, and I didn't wash my hands before lunch. Phear my bad lab skillz. (& Know your organisms.)