2020(S11) Lecture:week 2

Week 2 Tuesday

E. chromi

Let's start with an analogy that's a perennial favorite for engineers: consider a car....A car is a highly engineered system of interconnected parts. Many car parts are similar from car to car, but often the parts must be tailored to the size and function of the car. The chassis of a truck, a GTO muscle car and a Toyota hybrid are different, and so are many of the internal parts that make up the engine and the drive train. We might be able to move a radio from a truck chassis to a sports car chassis, but not much else. The car manufacturers are comfortable with this complexity, and it has little effect on the user of the car.

Now think about building a DNA program that runs a cell. We saw last week how a yeast gene could be moved to bacteria, allowing those cells to smell like bananas under certain growth conditions. From this one experiment you might be inclined to think that DNA parts will run reliably, independent their cellular context. Today you will explicitly test that notion.

Genetic Programs

You will compare the behavior of two genetic programs:

• pPRL, a purple color generator
• pGRN, a green color generator

These genetic programs were designed, constructed, and tested by the 2009 University of Cambridge iGEM team.

Cellular Chassis

In small groups, you will put these programs into two kinds of E. coli

• Strain 4-1, a K-12 strain of E. coli
• Strain 4-2, a B-type strain.

If you are curious about the ancestry of these two "breeds," there is an interesting article linked here. The short version of the story is that the K-12 strain was isolated from a stool sample of a dipthertia patient in Palo Alto, CA and domesticated for the lab by Tatum and Lederberg around 1922. By contrast, a B-type strain was used in the early 1900s by the Phage Group at the Institute Pasteur. Both types of E. coli are still widely used in research labs today.

Procedure

1. Begin by reviewing BioPrimer 7. If you'd prefer you can download it here.Is it clear what the differences are between the 2 strains of bacteria we'll be studying? What about the genetic programs?
2. Next we'll watch a short animation about the technique of DNA transformation. Is it clear what the steps are and why they are performed?
3. Finally, you'll work in small groups to transform the purple or the green color generators into Strains 4-1 or 4-2 as described here.
4. When you are done performing these manipulations, please wash your hands.
5. The petri dishes will be incubated at 37° overnight and you will examine the results of your work tomorrow.
6. Before you leave today, we'll consider these questions:

• Did you make any mistakes that might affect the outcome of this experiment?
• How confident are you in the results you'll see tomorrow?
  • Are you expecting colonies on all the plates? Are you expecting the same numbers on all plates?
  • Are you expecting the colonies to all look the same?
• If there are differences tomorrow, how will you explain them?
• If there are differences tomorrow, what could you do to test your explanations?

Why are we doing this?? You've taken some seemingly simple steps today and done something pretty awesome, namely intentionally imbued a bacterial host with properties you've chosen. Tomorrow, if all has gone well, you'll see colorful, antibiotic-resistant bacteria growing on the petri dishes. This transformation technology has been a routine lab procedure for a generation or so. Consider, though, what it will mean, as we get better at reading DNA programs that exist in nature, and also better at writing DNA programs that we dream up. DNA synthesis is a key enabling technology in synthetic biology, one we'll hear a lot more about tomorrow. In advance of that discussion, you might watch the DNA synthesis animation on the BioBuilder website, and also look at the journal article we'll be discussing. The article describes what the authors call a "synthetic cell."

Week 2 Studio

E. chromi, Day 2

You'll remember that yesterday we transformed the purple or the green color generators into Strains 4-1 or 4-2. Record the following data: Consider again these questions from yesterday:

• Did any mistakes you made seem to affect the outcome of this experiment?
• How accurately did you predict the outcome you see?
  • Do you see colonies on the plates you expected? Do you see the same numbers of colonies on all plates?
  • Do all the colonies look the same?
• If you see differences, how can you explain them?
• If you see differences, what could you test your explanations?

1. Finally, before we leave this exercise about chassis effects, upload your data to the BioBuilder website

Introducing Synthia!

from [1]

Let's begin by looking at another comic strip. This one is from the ETC group, an international civil society. This comic reacts to the plan by the J. Craig Venter Institute for building a synthetic cell.

Next, let's consider in detail the primary journal article that describes this technical feat and the reactions to it. The review slides for today are here. Our conversation will cover:

• the technical accomplishment itself (May 2010)
• the reaction to the announcement, including Barack Obama's call for a BioEthics Panel to review the field (May 2010)
• the work of the BioEthics Panel, including the procedures for gathering information and the recommendations that the panel ultimately offered (December 2010)
• reactions of government, scientists and watchdog groups to the recommendations

Why are we doing this?? These are current events, some happening only weeks ago. These current events will affect the progress of the field of synthetic biology. The events model how a civil society can address contentious issues. Finally, this lesson should inform your thinking and help you plan your work in 20.020 and your life in 2020 and beyond.

Your Turn!

Last week you chose some areas for biotechnology that seemed important/interesting to you. These areas were:

• Food or Energy
• Environment
• Health or Medicine
• Manufacturing
• New Application Area
• Foundational Advances
• Information Processing

You will be grouped now according to areas of common interests. Once in your groups you should do the following:
First, introduce yourselves if you don't already know eachother.
Second, appoint a note-taker in the group.
Next, talk about any topics in your area that you find especially interesting. These could be motivated by an article you've read, a personal experience, a research project you know about. Be sure everyone speaks, even if it's to say that no ideas really jump out just yet. You will need at least three ideas on the list, though, before moving ahead.
Finally, listen to the following podcast. The file itself can be accessed here. This podcast is about 1/2 an hour long. As you listen, take notes about how the ethics considerations might impact the projects you collected. Take a few minutes before you go to rank the projects on two lists.

• List one: topics of greatest interest to your group
• List two: topics that raise the greatest ethical concerns

HOMEWORK Tomorrow we are lucky enough to have one of the premier genome engineers coming to speak with us. Pete Carr has done remarkable work in the MIT Media lab as part of the Center for Bits and Atoms, and has collaborated with George Church at Harvard Medical School on an ambitious genome rewriting project called "Re.coli." In advance of his talk tomorrow, please spend one hour looking at the following review article. Also, before Friday, please add some thoughts to the class blog. This will be the first of 6 entries you'll make this term.

Week 2 Thursday

Welcome Pete Carr!

Dr. Peter Carr

Thanks for coming to talk to our class today.