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From the lab to the kitchen and back again

Our work on plant temperature responses requires accurate temperature control. We had been using non circulating water baths. The temperatures of these baths fluctuate by several degrees from their set point and, because the water in them is not actively mixed, the temperature also varies spatially across each bath. One solution to both of these problems is to buy circulating water baths. Circulating water baths start at a couple of thousand dollars so if you need a couple it gets expensive quickly.

Sous-vide cooking, a technique used in molecular gastronomy, involves cooking food in a vacuum sealed bag at controlled temperatures. The lore is that chefs started using laboratory recirculating water baths in their kitchens and, as the technique became more popular, cheaper circulation cookers were developed for the home market.

Instead of spending $10k for a set of four lab grade circulating water baths we decided to try out cheap sous vide cookers (Anova bluetooth precision sous vide cookers – $100 each at the time we bought them). This model can be calibrated using a cell phone app which connects to the cooker using Bluetooth (there is a WiFi version as well). Temperature settings can be changed in 0.5ºC increments using a dial on the front of the cooker and the app allows the calibration to be changed in  0.1ºC increments. This suggests that you should be able to get within 0.05ºC of your set temperature as long as your desired set temperature is either xx.0ºC or xx.5ºC.

How good are these cookers? We set up our baths, let them come up to temperature, and then measure the temperature of each bath using a Thermoworks reference thermometer. Two of the four cookers required calibration. In each case the temperature was off by approximately 0.1ºC. Once calibrated, temperatures fluctuated by a couple of hundredths of a degree, were very even throughout the bath, and were stable over long periods of time (20+ hours). These baths perform much better than the ones they replaced.

I’ll update this post if we find that the performance of the cookers degrades over time. For now we’re quite happy with bringing lab inspired kitchen equipment back into the lab.

As of February 2020 the official Anova app no longer includes the ability to calibrate the cookers. This third party Android app does. It also has a simpler, faster interface than the official app and handles communications with multiple cookers much better than the official app.

Scavenging parts from the GAIIx vs the HiSeq

Imaging methods in Illumina instrumentsI’ve been wondering if there will be useful parts to be scavenged from HiSeq instruments when they reach the end of their lives. They have started showing up on Ebay but are still much too expensive to buy just for the sake of taking them apart.

This 2010 presentation (downloaded from here), in addition to schematics of the imaging compartment (p. 49-50) and an overview of the sequencing chemistry, also contains a slide which shows that the next generation of instruments are based on line scanning cameras. This means that, while there may be other useful parts in the newer sequencers, if you are building an imaging system and need a camera like the Coolsnap K4 then the GAIIx is the system to get your hands on.

Repurposing an Illumina GAIIx sequencer

GAIIx on EbayMy lab has been building custom high content microscopes using parts that turned out to come from Illumina GAIIx sequencers. In this blog I’ll be tearing down a GAIIx bought on ebay for a fraction of it’s original price ($350 to $500k, these kinds of instruments don’t come with a list price) to show you how to take it apart and how to repurpose the high quality parts it contains. The Greenleaf lab at Stanford (and possibly other labs) are also taking advantage of the cheap availability of retired GAIIx sequencers to enable innovative new experimental approaches. A teardown (but no repurposing) of an earlier version of the sequencer can be found here and here.

The GAIIx just arrived today. I’ll tear it down over the next couple of weeks and document what’s inside.