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ptschnack edited this page Feb 11, 2017 · 33 revisions

Welcome to the ministat-1 wiki

...a project formerly of the HiveBio community laboratory in Seattle, WA. Now hosted by

Building our own open-source lab equipment

A in-depth perspective and introduction to Open-Source, DIY Lab Equipment can be found in the great book from J Pearce (Professor at Michigan Technological University): Open-Source Lab, 1st Edition. The book is available for purchase in both paper and ePub format. In particular, chapters relevant to this project are:

  • Chapter 1 Open Licensing - Advanced Sharing (details the different Open-source Hardware licenses available)
  • Chapter 2. Open-Source Microcontrollers for Science: How to Use, Design Automated Equipment with, and Troubleshoot
  • Chapter 5. RepRap for Science: How to Use, Design, and Troubleshoot the Self-Replicating 3-D Printer

Evolution experiments

Chemostat,Turbidostat and Auxostat are all variants of the same concept: the idea is to build a piece of equipment that allows the culture of cells (or viruses/phages and the cells they infect) in a steady state condition. That is, the purpose is to guarantee that the conditions of culture are always exactly the same, no matter at what moment sampling occurs. The primary objective of SoundBio's project is to use a multiplexed chemostat system (the ministat) to conduct interesting evolution experiments.

The first order of business, once we have achieved a working prototype, is to devise a simple experiment to validate we can use our ministat and achieve similar results that have been obtained in the academic microbiology community. This will serve as a first "benchmark", as well as participate in the wide push for scientific reproducability. The criteria for choosing this first experiment in the context of the SoundBio community lab are the following:

  • Safety. We want to culture organisms and systems that are safe to use in the context of a community lab.
  • Cost. The experiment must use widely available strains, and the analysis of the population must be cheap enough
  • Reproducibility. In most complex evolution experiments, the different "evolutionary paths" found by individual cells or populations are such that vastly different solutions are "found", or "evolved" by the micro-organism(s) to the same problem. Because our first experiments are aimed at demonstrating that our SoundBio ministat will be performing well, we wish to pick an evolution experiment simple enough that we are statistically likely to find similar solutions, or at least mutations in the same genetic locus or gene.

Currently, we are considering repeating some of the E coli/lambda phage experiments from Rich Lenski's lab at Michigan State University. Here is a link to the paper describing the experiment we will attempt to reproduce at SoundBio. For a more general introduction to the lambda phage (a model system that historically was used to unlock some of the most fundamental principles of gene regulation in molecular biology), the book from Mark Ptashne A Genetic Switch (3rd edition) is an excellent introduction. I (Alex Zanghellini) will try to add more pointers as we define our experimental plan.

Turbidostat instrument development

We are inspired by work at the University of Washington Klavins Lab and Dunham Lab.