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

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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.  
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.  
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. <br>
 
You will compare the behavior of two genetic programs:
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_K274002 pPRL], a purple color generator
*[http://partsregistry.org/Part:BBa_K274004 pGRN], a green 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.]
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
In small groups, 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/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.  
*[http://www.neb.com/nebecomm/products/faqproductC2523.asp#1132 Strain 4-2,] a B-type strain.  
===Procedure===
===Procedure===
# Begin by reviewing [http://www.biobuilder.org/activities/bioprimer-7.html BioPrimer 7.] If you'd prefer you can download it [[Media:BioPrimer 7.jpg| here.]] <br><br>Is it clear the differences are between the 4 strains of bacteria well be studying?  
# Begin by reviewing [http://www.biobuilder.org/activities/bioprimer-7.html BioPrimer 7.] If you'd prefer you can download it [[Media:BioPrimer 7.jpg| here.]] <br><br> Is it clear what the differences are between the 2 strains of bacteria we'll be studying? What about the genetic programs?
#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?
# Next we'll watch a short animation about the technique of [http://www.dnalc.org/view/15916-DNA-transformation.html DNA transformation.] Is it clear what the steps are and why they are performed?
#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.
#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 [[BioBuilding: Synthetic Biology for Students: Lab 4| here.]]
#When you are done collecting your data, please wash your hands.
#When you are done performing these manipulations, please wash your hands.
#Next, upload your data to the [http://www.biobuilder.org/submit-your-data/ BioBuilder website]
#The petri dishes will be incubated at 37° overnight and you will examine the results of your work tomorrow.  
#Before you leave today, we'll consider these questions:
#Before you leave today, we'll consider these questions:
**Were we able to measure the population growth?
*Did you make any mistakes that might affect the outcome of this experiment?
**Were we able to smell bananas?
*How confident are you in the results you'll see tomorrow?  
**Did each device produce the same results?
**Are you expecting colonies on all the plates? Are you expecting the same numbers on all plates?
**Did the genetic systems affect the growth curve of the bacteria? Explain your answers.
**Are you expecting the colonies to all look the same?
**How confident are you in the results?  
*If there are differences tomorrow, how will you explain them?  
**Are you equally confident in both the growth data and the smell data?  
*If there are differences tomorrow, what could you do to test your explanations?
**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>
<center>'''Why are we doing this??'''</center>
<div style="padding: .4em .9em .9em">
<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.  
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 bacteria growing on the petri dishes. This technology has been used routinely for a generation or so. Consider, though, what it will mean, as we get better at both reading DNA programs that exist in nature, and also MAKING 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. [[Media:SyntheticCell Sci2010.pdf| The article]] describes what the authors terms a "synthetic cell."
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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>=
#Next, upload your data to the [http://www.biobuilder.org/submit-your-data/ BioBuilder website]
==<font color = blue> '''Homework'''</font color>==
==<font color = blue> '''Homework'''</font color>==
=<center>Week 2 Thursday</center>=
=<center>Week 2 Thursday</center>=
==<font color = blue> </font color>==
==<font color = blue> </font color>==
==<font color = blue>Why are we doing this?</font color>==
==<font color = blue>Why are we doing this?</font color>==

Revision as of 13:06, 27 January 2011

<html> <style>#en2020 a {color:black;}</style> </html>

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.
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. In small groups, 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 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 bacteria growing on the petri dishes. This technology has been used routinely for a generation or so. Consider, though, what it will mean, as we get better at both reading DNA programs that exist in nature, and also MAKING 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 terms a "synthetic cell."

Why are we doing this?

Week 2 Studio

  1. Next, upload your data to the BioBuilder website

Homework

Week 2 Thursday

Why are we doing this?

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