2020(S11) Lecture:week 2: Difference between revisions

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=<center>Week 2 Tuesday </center>=
=<center>Week 2 Tuesday </center>=
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==<font color = blue> E. chromi </font color>==
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 similar from car to car, but often they 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.
 
You will compare the behavior of two genetic programs:
*[http://partsregistry.org/Part:BBa_K274002 pPRL], a purple color generator
*[http://partsregistry.org/Part:BBa_K274004 pGRN], a green color generator
These genetic programs were designed, constructed, and tested by the 2009 University of Cambridge [http://2009.igem.org/Team:Cambridge iGEM team.]
You will put these programs into two kinds of E. coli
*[http://www.neb.com/nebecomm/products/productE4104.asp Strain 4-1,] a K12 strain of E. coli
*[[http://www.neb.com/nebecomm/products/faqproductC2523.asp#1132 Strain 4-2,] a B-type strain.
===Procedure===
# Begin by reviewing [http://www.biobuilder.org/activities/bioprimer-7.html BioPrimer 7.] If you'd prefer you can download it [Image:BioPrimer 7.jpg here.] <br><br>Is it clear the differences are between the 4 strains of bacteria well be studying?
#Next we'll watch the animation about cell growth and division. Is it clear how log, lag, and stationary phase differ? Is it clear how you'd know what phase of growth the cells are in?
#Finally, you'll work in small groups to compare the turbidity and the banana-smell intensity for the four strains at each stage of growth. Give each strain a smell value and a density value.
#When you are done collecting your data, please wash your hands.
#Next, upload your data to the [http://www.biobuilder.org/submit-your-data/ BioBuilder website]
#Before you leave today, we'll consider these questions:
**Were we able to measure the population growth?
**Were we able to smell bananas?
**Did each device produce the same results?
**Did the genetic systems affect the growth curve of the bacteria? Explain your answers.
**How confident are you in the results?
**Are you equally confident in both the growth data and the smell data?
**Is using smell to measure the banana smell valid? Why or why not?
**What methods did you use to try to increase your confidence in the results?
**How might we try to change this system so that we can quantify the banana smell? Would we be better off using a different kind of signal? If so, what would you suggest?
**If you could construct a different genetic system, what might you construct? What would you need to do? 
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<center>'''Why are we doing this??'''</center>
<div style="padding: .4em .9em .9em">
You've now had some first hand experience with an engineered biological system. We'll return to this experiment a number of times during the term for different reasons but it's hoped that this first week has given you a taste (not literally!) of the kinds of creative solutions that are possible in biological engineering design.
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==<font color = blue>Why are we doing this?</font color>==
==<font color = blue>Why are we doing this?</font color>==
=<center>Week 2 Studio</center>=
=<center>Week 2 Studio</center>=

Revision as of 10:01, 27 January 2011

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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 similar from car to car, but often they 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.

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. You will put these programs into two kinds of E. coli

Procedure

  1. Begin by reviewing BioPrimer 7. If you'd prefer you can download it [Image:BioPrimer 7.jpg here.]

    Is it clear the differences are between the 4 strains of bacteria well be studying?
  2. Next we'll watch the animation about cell growth and division. Is it clear how log, lag, and stationary phase differ? Is it clear how you'd know what phase of growth the cells are in?
  3. Finally, you'll work in small groups to compare the turbidity and the banana-smell intensity for the four strains at each stage of growth. Give each strain a smell value and a density value.
  4. When you are done collecting your data, please wash your hands.
  5. Next, upload your data to the BioBuilder website
  6. Before you leave today, we'll consider these questions:
    • Were we able to measure the population growth?
    • Were we able to smell bananas?
    • Did each device produce the same results?
    • Did the genetic systems affect the growth curve of the bacteria? Explain your answers.
    • How confident are you in the results?
    • Are you equally confident in both the growth data and the smell data?
    • Is using smell to measure the banana smell valid? Why or why not?
    • What methods did you use to try to increase your confidence in the results?
    • How might we try to change this system so that we can quantify the banana smell? Would we be better off using a different kind of signal? If so, what would you suggest?
    • If you could construct a different genetic system, what might you construct? What would you need to do?
Why are we doing this??

You've now had some first hand experience with an engineered biological system. We'll return to this experiment a number of times during the term for different reasons but it's hoped that this first week has given you a taste (not literally!) of the kinds of creative solutions that are possible in biological engineering design.

Why are we doing this?

Week 2 Studio

Homework

Week 2 Thursday

Why are we doing this?

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