...happily ever after.

4 May 2011

Hello everyone, and welcome back for the final installment of the BioBoard blog! Today is the last day of the Great Global Hackerspace Challenge 2011, and thus our last chance to tell you about all the cool stuff we've been doing on this project over the last 6 weeks. In all fairness, those of you who've kept up with the blog already know most of this, but since this is our last post, please bear with us as we do a quick run-down of the project once again.

Our initial target with the BioBoard was to build a set of sensors that would allow us to monitor several different, biologically relevant parameters in luquid microbial cultures, such as bacterial or yeast fermentation. The parameters we settled on were temperature, biomass / cell density, acidity (pH), and oxygen levels.

Temperature is the key parameter in this context, as almost all biological reactions and processes are strongly temperature-dependent, and in many cases almost linearly proportional to temperature, too, at least up to a certain point. Essentially, at low temperatures, the limiting factor in any reaction in a liquid medium is the rate of molecular movement; at high temperatures, the ceiling is usually set by the the denaturation (unfolding) of proteins, a process which rapidly causes the cessation of biological activity in any form. There are numerous exceptions, but none which are relevant in this context, nor in general for most DIY biologists. However, as well as explaining why refrigeration and / or heating works for preserving foodstuffs, temperature is also an important factor in pH and oxygen measurements. Both pH and oxygen sensors basically detect the concentration of chemical species in the medium - H+ for pH and O2 for oxygen - and the solubility of these varies with temperature, i.e. more oxygen can be dissolved in cold than in warm water.

The idea of measuring biomass / cell density was obviously motivated by a strong desire to be able to visually convey this simple dependence on temperature. Furthermore, for many purposes, knowing which growth phase your culture is in can be crucial - a lot of conjecture in microbiology is based on the assumption of exponential growth, and mathematical models based on such assumptions are obviously only valid when the culture in question actually is in the exponential growth phase. Last, but not least, the rate of biological growth is what determines when your homebrew will be ready for harvest, and thus of prime importance to the much-famed kombucha fermentations that were the original inspiration for this entire mad scheme.

The kombucha was also our main reason for including pH, at least at first. Along with the aerobic yeast fermentation, the bacterial acidification process that takes place during kombucha production is what creates the distinctive, acidic flavour, and also what makes your kombucha turn into vinegar if you leave on the shelf for too long. In order to achieve consistent, reproducible results from our production, we first need to know how the acidification co-varies with temperature and biomass - not necessarily a linear relation! That way, we'll know which parameters to change in future set-ups to optimize our results.

Because yeast only make alcohol in the absence of oxygen, measuring dissolved oxygen is a lot more relevant in anaerobic fermentations, such as ethanol production. It's also often a limiting factor in aqautic environments, where (as Sean put it) oxygen levels basically determine whether you're going to get fish (need it!) or algae (don't need it) in your pond. Especially during the exponential growth phase of a bacterial or yeast culture, oxygen can very quickly become depleted, resulting in the formation of unwanted by-products, or even the eventual demise of your culture.

Monitored over time and displayed together, these parameters should give most students a basic understanding of the interdependence of several co-variable with a single independent key variable. However, over time we also hope to accumulate enough base-line data for mathematical modelling (and - perhaps someday - automation) of the biological processes we study. If you are interested in making your own BioBoard, and using the supporting software we've developed for it, you can use the documentation wikis and how-tos we've made for this project:

https://www.noisebridge.net/wiki/BioBoard - the initial project description and overview; also contains links to all the other pages

https://www.noisebridge.net/wiki/BioBoard/Documentation/Temperature - DTS and thermistor documentation and how-to

https://www.noisebridge.net/wiki/BioBoard/Documentation/pH - DIY pH electrode run-down

https://www.noisebridge.net/wiki/BioBoard/Documentation/Oxygen - how to build an optode

https://www.noisebridge.net/wiki/BioBoard/Documentation/Optical_loss - a home-built NIR sensor for <$10

https://www.noisebridge.net/wiki/BioBoard/Documentation/Arduino_protocol - microcontroller assembly and schematics

https://www.noisebridge.net/wiki/BioBoard/Documentation/PC_Software - documentation on the datalogging and visualization

Most of the pictures we've taken during the challenge can be found on Picasa: https://picasaweb.google.com/rikke.c.rasmussen/BioBoard20110412#

Last, but not least, we've finally managed to make a short video of the project which we've uploaded to YouTube. Here you go, hope you've all enjoyed this challenge as much as we have! This is Noisebridge and the BioBoard team signing off for now, and reminding you, as always, to be excellent to each other, dudes!