Team:Austin Texas/human practices

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ELLA/Someone else

Add images of us
- at SXSW
- collecting samples
- Specific data from poster

Content - some data, some of the discussions/outreach we had with people.

credit Ashley and Mike for assisting in sample collection.

Caffeinated Coli

Ella collecting coffee sample from Austin Java

In the spring of 2014, [http://www.kareningram.com Karen Ingram], a representative of the SXSW festival, invited the UT Austin iGEM team to create a presentation for the [http://sxsw.com/exhibitions/sxsw-create/participants-2014 South By Southwest (SXSW) 2014 Create event]. The SXSW festival is an annually held set of music, film and interactive events in Austin. The Create event was an interactive event that showcases up and coming maker/hacker/DIY culture. There were many relatively new team members, so the we saw this as an opportunity to not only teach the new members essential research techniques, but also to reach out to the community and raise awareness for the emerging field of synthetic biology. We decided to revive an old iGEM project, the

Jordan discussing our project with Matt Bolick, co-owner of Flat Track Coffee

"Caffeinated coli," and thought it would be interesting to measure the caffeine content of various different local house coffees. The [http://www.ibuyaustin.com Austin Independent Business Alliances'] slogan of [http://www.keepaustinweird.com "Keep Austin Weird,"] is a widely shared sentiment of Austinites, and emphasizes the need to promote local businesses. We thought it would be a great community outreach project to work with local vendors of Austin, and do our part to "Keep Austin Weird!"

Jordan, a senior member of the group, took charge and assembled a map of about 40 local coffee shops in Austin. The team took a Saturday and split up to visit dozens of coffee shops, collecting samples of their house coffee. We were met with much enthusiasm by the coffee shop owners and employees, who's interest had been peaked when we described our experiment.

[http://www.google.com/maps/d/viewer?mid=zlUDhks6KHxI.ketDvlvg6zis Click here for an interactive map of coffee shops we visited!]

Back at the lab, the team members got to work. Senior members divided their attention to mentor the new members in the techniques necessary to start cultures, work with the lab equipment, and other general laboratory safety.

The beginning of something great! Special thanks to Razan Alnahhas, Mike Hammerling, and Ashley Kessel for assistance

Measuring Caffeine Content

Cultures of knockout strain grown with collected coffee samples.

The E. coli we used are a synthetic strain, previously made by the 2012 UT Austin iGEM team. This strain has had its normal guanine synthesis pathway knocked out, but contains a plasmid with a set of genes that enables the organism to synthesize guanine from xanthine and many of its derivatives, including caffeine. Without caffeine (or other xanthines), the strain cannot grow. When caffeine is added, the strain can demethylate the caffeine molecules to make guanine. It then grows normally until the caffeine is completely metabolized, at which point the cells can no longer synthesize guanine, and cease to grow.

Standard growth curve of knockout strain grown with different amounts of caffeine.

Thus, by looking at the relative growth of the strain with different samples of coffee and comparing it to a standard curve of growth in solutions with known amounts of caffeine, we could somewhat accurately measure the amount of caffeine in the coffee.

The protocol was simple: We provided our Caffeinated coli with a diluted sample of coffee we had acquired from the various shops, and then compared the relative growth rates by taking an OD600 value at a time point. The simplicity of the project was the key its success. It provided a glimpse into the exciting new world of synthetic biology for the new members, and allowed them to learn vital skills that were used in day to day research during the summer. The results we found can be seen in Figure 1. below.

Figure 1. Relative levels of caffeine in house coffee samples from around Austin.

SXSW Create

A couple of weeks later, we presented this data set at the SXSW festival. As part of this outreach, we explained our project and synthetic biology to a wide range of people. Many people who came by had little to no background in science or technology, and even most of the ones who did had not heard about synthetic biology. By discussing our experiments with bacteria and coffee, an interesting and easy to understand application, we were able to explain what synthetic biology is and how it can be used in a beneficial way. Occasionally, these conversations would branch out into wider topics of science and technology.

change to picture of team member presenting poster at event

This included a follow up conversation with one of the owners of Wright Bros. Brew & Brew, whose coffee seemed to have significantly more caffeine. The owners concluded, after discussing our project and the coffee brewing process, that the specific pot of coffee was probably just not fully drained, i.e. there was less water in the batch than normal, resulting in a higher caffeine/volume content. However, similar conversations were had between the entire team and the various coffee shops and baristas during the collection and presentation processes.

@@ Line 85: / Line 85: @@
 [[file:UT_Austin_E._coli_coffee_cultures.jpg|300px|thumb|left| Cultures of knockout strain grown with collected coffee samples.]]
-The ''E. coli'' we used are a synthetic strain, previously made by the [https://2012.igem.org/Team:Austin_Texas 2012 UT Austin iGEM team].  This strain has had its normal guanine synthesis pathway knocked out, but contains a plasmid with a set of genes that enables the organism to synthesize guanine from xanthine and many of its derivatives, including caffeine. Without caffeine (or other xanthines), the strain cannot grow.  When caffeine is added, the strain can demethylate the caffeine molecules (and other derivatives) to make guanine. It then grows normally until the caffeine is completely metabolized, at which point the cells can no longer synthesize guanine, and cease to grow.[[file:UT_Austin_caffeine_growth_standard_curve.png‎|200px|thumb|center| Standard growth curve of knockout strain grown with different amounts of caffeine.]] Thus, by looking at the relative growth of the strain with different samples of coffee and comparing it to a standard curve of growth in solutions with known amounts of caffeine, we could somewhat accurately measure the amount of caffeine in the coffee.
+The ''E. coli'' we used are a synthetic strain, previously made by the [https://2012.igem.org/Team:Austin_Texas 2012 UT Austin iGEM team].  This strain has had its normal guanine synthesis pathway knocked out, but contains a plasmid with a set of genes that enables the organism to synthesize guanine from xanthine and many of its derivatives, including caffeine. Without caffeine (or other xanthines), the strain cannot grow.  When caffeine is added, the strain can demethylate the caffeine molecules to make guanine. It then grows normally until the caffeine is completely metabolized, at which point the cells can no longer synthesize guanine, and cease to grow.[[file:UT_Austin_caffeine_growth_standard_curve.png‎|200px|thumb|center| Standard growth curve of knockout strain grown with different amounts of caffeine.]] Thus, by looking at the relative growth of the strain with different samples of coffee and comparing it to a standard curve of growth in solutions with known amounts of caffeine, we could somewhat accurately measure the amount of caffeine in the coffee.
-The protocol was simple: We provided our Caffeinated coli with a diluted sample of coffee we had acquired from the various shops, and then compared the relative growth rates by taking an OD600 value at a time point.
+The protocol was simple: We provided our Caffeinated coli with a diluted sample of coffee we had acquired from the various shops, and then compared the relative growth rates by taking an OD600 value at a time point. The simplicity of the project was the key its success. It provided a glimpse into the exciting new world of synthetic biology for the new members, and allowed them to learn vital skills that were used in day to day research during the summer.
 The results we found can be seen in Figure 1. below.