Category Archives: DIYBiology

This work envisions new systems to scaffold non-professional participation in biology.

Antibiotic-responsive bioart art class for junior and high school students

DSC_0813.JPGAs part of the Digital Culture Summer Institute, the SANDS lab organized a bioart module for junior and high school students. Working with Cassandra Barrett and Kat Fowler, we developed a week-long summer camp course that invites students to create petri dish art using bacteria and antibiotic substances. 

Our design studio was recently approved for BSL-1 (biosafety level 1) clearance, which means we can now (officially) work with minimally risky bacteria and procedures. Fun fact: we might be the first design lab to get this clearance through the ‘proper’ layers of paperwork and inspections at our University!

Our work embraces the DIYbio movement, which aims to make biology accessible outside of professional laboratories. So during the first day of camp, we showed the students how to sterilize lab equipment with a pressure cooker. According to the CDC guidelines, this means the materials must be kept at 121°C and 15psi for 30 minutes. It’s usually a pretty exciting 30 minutes to be watching the pressure cooker.

The next few days of the camp were spent practicing aseptic (sterile) lab technique to streak plates with different pigmented bacteria. We used our trusty old DIY incubator that we made in-house to culture our art at 26C.

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We used several regular antibiotics (Ampicillin and Streptomycin) as well as antibiotic items the students brought from home to shape the growth of the bacteria. Essentially, we did the Kirby–Bauer diffusion test for antibiotic sensitivity, whereby growth is hindered around the effective antibiotics.

Our students brought an impressive and very creative range of substances to test for antibiotic properties, including handsoap, pennies, dog antibiotics, neosporin (very effective), tylenol, and toothpaste (not very effective at killing bacteria it turns out!).

We also added food coloring to our media to add a background color to the petri dish art.

For the final project, we asked the students first to sketch out the layout for their bacteria art piece, including what bacteria, background color, and antibiotic substances they wanted to use on their petri dishes. Can we say we did rapid lo-fi prototyping for biology 🙂 ?

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The resulting bacteria images inspired us to write bioart haikus, and some of these were pretty deep.

 Finally, the students used a graphic design program to convert their favorite petri dish images into stencils for vinyl cutting and screenprinting. The last day day of screenprinting was chaotic and messy, but order emerged just like the haiku said 😉

Huge thanks to everyone who helped run this awesome class, and to the creative and thoughtful students who are now excited to take a bio course at their schools even if they don’t get a printed T-shirt out of it next time.

 

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Bio workshop at HeatSync

Hi folks, as we are continuing our work in DIY biology with general public and non-professional biology hobbyists, last week Cass, Stacey and Me conducted a DIY bio workshop at HeatSync Labs in Meza, Az. HeatSync is a community driven maker-space, one of the coolest places I’ve ever been in Arizona. Unfortunately Matt couldn’t make it this time, even though he immensely contributed in organising and planning the workshop.DSC_0414.JPG

The first part of the workshop was about yoghurt fermentation. Cass explained the steps of yoghurt fermentation process and worked closely with the participants in the process. Here are some images.

Then we moved to the second part of the workshop – Gram staining. In this activity participants were asked to follow instructions printed on the card given by us, as well as Cass’ guidance. Everyone was so excited to see the microscopic images of the slides they have created, actually results were awesome!

 

While everyone was partying with bacterias in the downstairs, I was busy connecting the camera of our DIY incubator to the HeatSync WIFI network. Yes, now we have a WIFI camera inside our incubator as we promised in one of our earlier posts!

We left our incubator and some basic materials at heat syncs lab, so that they can play with them in the summer. Hopefully we will get some useful feeds from the camera too!DSC_0411

I’m Piyum, signing off and running to catch the flight to CHI 16 to present our Bio work there. More on that later! Thanks for reading.

Update:

Here we were at CHI 16 poster session.

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A low cost and accurate incubator for DIY biology

DSC_0958DIYbio, (Do It Yourself) biology is a growing movement that aims to make biology accessible outside of professional contexts. Over the past few years, platforms such as OpenPCR and Pearl Biotech transilluminator have been designed to support biology work in schools and maker spaces for a fraction of the cost of professional lab equipment. These exciting developments pave the way for crowdsourcing biology research amongst students, hobbyists, and non-experts. (Matt wrote a nice article introducing our work on DIYBio at SANDS.)

This post is about our contribution to the growing number of open source biology tools by developing a low-cost, yet relatively precise and easy-to-use incubator. An incubator is an essential tool for a number of biological experiments and is often used in bacterial cell culture experiments. Given the higher price range of the commercially available incubators (upwards of several thousand dollars), non-professional biology enthusiasts might not afford to add an incubator to their stock of DIYbio tools. In our instructable, we describe how to build a low cost (under $70), yet accurate ( +/- 0.25C) DIY incubator using simple materials and some basic electronics components.image

The goal of the incubator is to keep a constant temperature inside. On the most basic level, we are using a temperature sensor and a light bulb as our heating element. The change in temperature inside the incubator is proportional to the amount of heat emitted by the tungsten bulb minus the heat loss through the walls of the incubator. In other words, to increase the temperature, the bulb needs to emit more heat than the heat loss through the walls. Once the desired temperature is reached, the bulb should emit the same amount of heat as what’s lost.The amount of heat emitted by the tungsten bulb is proportional to the power applied to the bulb. Hence, we can control the temperature inside the incubator by controlling the AC input supplied to the bulb. Our design contains a custom built AC phase control circuit, an Arduino Uno, an Adafruit Max31855 thermocouple amplifier and a K-type thermocoupler, an Olimex LCD Shield (16×2 LCD with 4 buttons).

Please refer to our Instructable post for detailed implementation details.

Last week me, Matt and Stacey tried an experiment to culture E.Coli  in our DIY Bio lab and used our incubator at constant 37C temperature for around 24 hours. Happily, everything went super smoothly this time. (Even though we had few hiccups in testing stages because of some firmware bugs!)DSC_0886

In next steps, we plan to build a shaker and add a camera to the incubator to have a “live feed” of what’s happening inside. We will keep you updated about new developments of this project via SANDS blog. Until then, thanks for reading, I’m Piyum Fernando here, signing off.

Welcome to DIYbio!

Hello everyone! My name is Matthew Pandelakis and welcome to SANDS’ DIYbio blog page. So, we have been working on a DIYbio branch for a couple of weeks now. This blog post is supposed to bring you up to speed on what we’ve been up to lately and give you a bit of information about DIYbio.

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So, let’s start with some general information; DIYbio stands for do-it-yourself biology and it is a fairly new field that as of today hasn’t necessarily been well defined quite yet. The general idea of it is to bring biological research to the public, instead of it being something that is exclusive to large research universities and pharmaceutical companies. It is a much more collaborative and public endeavor than traditional biological research, at least from what I’ve seen so far. Right now, our involvement in DIYbio is still very much in its infancy, but we hope to help bring biological science research to the public in hopes that we can help create a more science literate world, and helpbring people bring their own ideas to life (heh, science pun).

We are just setting up our lab space which has been a bit difficult. One of the biggest challenges that our group has run into has been trying to do everything as cheap as we possibly can. Traditional biological research is a remarkably expensive endeavor, especially when it comes to purchasing equipment. Basic pieces of tech can run for thousands of dollars, and is a big barrier to entry for the average joe interested in participating in biological research. So to get around that we have been working with some open source technology like OpenPCR, and we’ve built our own homegrown incubator… at least we’re trying to.DSC_0892

The last one we built kind of melted and I’ll post some pictures of that. Once we get a fully functional incubator going we are going to be moving in to doing some basic cell culturing work which has all kinds of challenges associated with it, but I think it’s doable. We hope to run a workshop by the end of the semester that will and teach individuals aseptic technique and some cell culturing methods. Next semester we hope to look into doing some PCR work and some genetic engineering work, which I am very excited about!DSC_0886

DIY DNA Extraction

Hello SANDS followers, we had an exciting day at SANDBOX (our unofficial name for the space) last week because we were trying out a new DNA extraction protocol for the first time. As you may know, one of our projects focuses on interactive platforms for DIY biology.
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Earlier in the semester, we’ve been developing a few interfaces. We have designed an acoustic-based interactive table and the iPad web application as education and outreach tools for performing bio experiments outside of professional labs. Recently, we got our lab sink installed (thank you!), and today was the first day for us (Pat & Jennifer) to get our hands wet!
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Here is all of the material that we used for the DNA extraction. Most of the stuff beside some chemicals from the DNA extraction kit are just regular off-the-shelf things. For example, the pot and hot plate to incubate our samples.

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For this DNA extraction, we used a protocol from Carolina’s barcoding kitBarcoding is a process by which you can identify the species present in your sample and it can be very useful for studying biodiversity and local ecology. DNA extraction is the first step for this type of analysis. To test out this protocol, we used the unknown plant as a sample. As you can see below, Jennifer was using a plastic pestle to chop down some plant tissue in order to increase the surface area that came in contact with the lysis buffer. This process is the very important because DNA is found in the nucleus of the cell, so the DNA yield depends on the amount of cell that we can break.
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 Normally, after we break down the tissue we need to incubate our samples in a water bath. However, to make it DIY, we decided to use just a warm water in the pot instead because the purpose of having a tube in the warm temperature is just to speed up the lysis process (lysis is a process of breaking down the cell membrane), so any way that can warm up the tube is good to go.

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Here is another exciting part, centrifuge (a process for separating solid particles from the liquid solution by rapidly spinning a sample). Again, we used a dremel instead of a real centrifuge, but the result is pretty acceptable. However, the dremel generates a lot of noise and is a little bit distracting.

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At the end we used almost three eppendorfs (small tubes) in order to extract a DNA of a plant that we picked. The process is really fun because we got to use a lot DIY tools. We spent around one hour for this extraction, but we have learned a lot for our project. We will keep blogging as we do more exciting things at the sandbox, so keep checking this out!

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-Pat Pataranutaporn & Jennifer Weiler