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EAU That Smell Jr

Compare two competing designs to optimize system performance

INTRODUCTION

Through hands-on laboratory work and interactive classroom sessions, you can put our most amazing technology (biology!) to work. After learning some of the tools and techniques for engineering cells, you will build and then measure a synthetic living system. In particular, you will modify a foul-smelling but harmless bacteria to make them look and smell like banana smoothies. You can’t drink these creations but you can use them to start imagining all that’s possible if we apply the living world to solve its problems.

LEARN

  • How engineers and scientists differ in their approach to living things
  • To work with DNA to prepare it for experimentation
  • To genetically engineer cells to smell like bananas
  • To use microbiological techniques to culture bacterial cells
  • To measure the smell output of their engineered system
  • To explore the applications of this approach to other, real world challenges

 

WORKFLOW FOR THIS EXPERIMENT

SampleWorkflow_EauThatSmell.pdf
Adobe Acrobat document [215.0 KB]

Procedure

  • Primer on cellular structures, especially any that will be referred to later.
  • Information on the characteristics of bacterial growth, i.e. the curve and terminology such as lag, log and stationary phases
  • Genetics/inheritance basic info
  • Vocabulary: competent, plasmid, promoter, etc.

GETTING READY

LAB MATERIALS TO HAVE AND TO KNOW

Before you begin your work you should put on personal protective equipment as deemed appropriate by your school. These may include:

  • Nitrile gloves
  • Eye protection
  • A lab coat

 TECHNIQUES TO LEARN

In advance of the transformation lab will need to learn sterile technique (shown in “liquid ONs” video), how to use the pipets and how to spread the bacteria on the plates. Videos for these three basic techniques are shown below:


ONE DAY BEFORE TRANSFORMATION LAB

At least one day before the transformation lab day, patch a small square of the bacterial strain called NB370 on an LB agar petri dish.

  • Q1: what do we know or notice about NB370? does it smell like bananas? does it stink?
  • Q2: what would you expect to happen if you patched these cells on LB media that has ampicillin or another antibiotic in it?

TRANSFORMATION WITH P-BNAN

E. coli strains will not normally take up DNA from the environment

  • Q1: why do you think cells may not want to take up DNA randomly?
  • Q2: are times when cells might benefit from uptake of DNA?

When they are treated with a CaCl2 salt solution, their outer membrane becomes slightly porous. The cells will become “competent” for transformation

VOCABULARY TO LEARN

  • “competent” = ready to bring DNA that’s external to the cell into the cytoplasm where the DNA code can be expressed.
  • “LB” = luria broth, food for bacterial cells
  • “ampicillin” = antibiotic, kills bacteria except those that carry gene for resistance
  • “selection” = genetic technique for killing all cells except those that carry particular genetic feature

The cells will also become fragile. Keep the cells cold and don’t pipet them roughly once you have swirled them into the CaCl2 salt solution.

Before you begin your work you should put on personal protective equipment as deemed appropriate by your school. These may include

  • Nitrile gloves
  • Eye protection and
  • A lab coat.

LAB PROTOCOL

1. Begin by labeling 1 small eppendorf tube “Cells”
2. Pipet 200 ul of CaCl2 into the eppendorf. This can be done by measuring 100 ul of solution twice. Place the tube on ice.
3. Use a sterile wooden dowel to scrape up one entire patch of cells, NOT including the agar that they’re growing on! Swirl the cells into the tube of cold CaCl2. NOTE: A small bit of agar can get transferred without consequence to your experiment, but remember you’re trying to move the cells to the CaCl2, not the media they’re growing on.
4. If you have a vortex, you can resuspend the cells by vortexing very briefly. If no vortex is available, gently flick and invert the eppendorf tube, then return it to the ice. Your teacher will explain how this step helps to make the bacterial membrane porous and how the cells are fragile at this point.
5. Label 2 small eppendorf tubes either “No DNA” or “+DNA”
6. Pipet 5 ul of DNA, called pBNAN, into the eppenforf tube labelled “+DNA.”
7. Place both the “No DNA” and the “+DNA” tube on ice
8. Find the “Cells” tube in your ice bucket and flick the tube with the competent cells to mix them.
9. Pipet 100 ul of the bacteria into the tube labeled “+DNA” and the remaining volume of cells into the tube labeled “No DNA.” NOTE: There may not be precisely 100 ul to add to the second tube and that’s OK.
10. Flick to mix the DNA and the cells in these tubes and return them to the ice for 2 minutes. You can use a timer or the clock to keep track of this incubation time.
11. While your DNA and cells are incubating, you can label the bottoms (not the tops) of the 2 petri dishes you’ll need. The label should indicate the name of the E.coli strain you’ve used (NB370) and the DNA you’ve transformed them with (“No DNA” or  “pBNAN”). You should also put on your name or initials and today’s date.
12. Heat shock all of your DNA/cell samples by placing the tubes at 42° for 90 seconds exactly (use a timer or the clock). Your teacher will explain how this step helps drive the DNA into the cells and closes the porous bacterial membranes of the bacteria.
13. At the end of the 90 seconds, move the tubes to a rack at room temperature.
Pipet 500 ul of room temperature LB into each of the tubes (“No DNA” “+pBNAN”). Close the caps, and invert the tubes to mix the contents.
14. Using a sterilized spreader, spread 100 ul of the transformation mixes onto the surface of LB+ampicillin agar petri dishes.
15. If desired the remaining volumes of transformation mixes can be plated on LB plates to show the effect of antibiotic selection on the outcome. What would you expect from this experiment if you did it?

16. Incubate the petri dishes with the agar side up at 37° overnight, not more than 24 hours– or at room temperature at least 2 days.


VIDEO VERSION OF LAB PROTOCOL


DATA TABLE FOR NEXT DAY’S RESULTS

  # of colonies (LB+AMP)
# of colonies (LB, if applicable)
No DNA
+DNA

GROWING BANANA-SCENTED BACTERIA

Check out how cells grow and why isoamyl OH must be added to the media

Before you begin your work you should put on personal protective equipment as deemed appropriate by your school. These may include

  • nitrile gloves
  • eye protection and
  • a lab coat.

LAB PROTOCOL

  1. Label a 15 ml screw-capped tube “Transformed Cells”
  2. Transfer 3 ml of Luria Broth (LB) + ampicillin + isoamyl alcohol to the tube.
  3. Using a pipet tip, scoop up a bacterial colony from the pBNAN petri dish and throw the tip into the media in the tube labelled “Transformed Cells.”
  4. Label a second 15 ml screw-capped tube “Starting Cells.”
  5. Transfer 3 ml of Luria Broth (LB) + isoamyl alcohol (NO AMPICILLIN) to the tube.
  6. Using a pipet tip, transfer a bit of bacteria from the “NB370” petri dish and throw the tip into the media in the tube labelled “Starting Cells.”
  7. Place the culture tubes on a shaker platform (?) in the incubator at 37°C (or Room Temp?) overnight.

Need to write up smell test day.