BioBuilding: Synthetic Biology for Students: Lab 1

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PDF of this page LAB 1: Eau that smell Compare 2 competing designs to optimize system performance Acknowledgements: This lab was developed with materials and guidance from the MIT 2006 iGEM team, as well as technical insights and help from Ginkgo Bioworks Objectives By the conclusion of this laboratory investigation, the student will be able to: Explain how synthetic biology as an engineering discipline differs from genetic engineering. Explain the population growth curve of bacteria. Culture bacteria using proper microbiology methods. Measure the growth of a bacterial population. Define and properly use synthetic biology terms: Part, Device, Inverter. Define and properly use molecular genetics terms: Promoter, ribosome binding site ("RBS"), open reading frame ("ORF"), Terminator, Plasmid. Introduction BioPrimer #1 pdf For the 2006 iGEMcompetition, MIT students designed eau d’ e coli, E. coli that smell like bananas when their population is in the stationary phase. They did this by inserting device that contains a stationary phase sensitive promoter coupled to a banana smell device, a device that contains a ribosome binding site (RBS), an open reading frame (ORF) that codes for the ATF1 enzyme and terminator sequences. The ATF1 enzyme converts isoamyl alcohol to isoamyl acetate, the molecule that gives bananas their characteristic smell. It has been suggested that a device that generates the banana smell during the bacteria’s log (or exponential) phase of population growth will be helpful. There are two ways to accomplish this. Both methods will continue to use the banana smell device but alter the function of the promoter. One method involves coupling the banana smell device to a new part, a log phase promoter. The other method involves using the same promoter but adding an inverter. Synthetic biologists have constructed these devices for us and transformed bacteria with them. We have been sent four different E. coli colonies. Each contains a different device: Sample 1. The original Eau d’ Coli device Sample 2. The banana smell generator coupled to the log phase promoter Sample 3. The original Eau d’ Coli device but with an inverter added between the promoter and the RBS. Sample 4. A strain of E. coli that has no smell generating devices. Our task will be to grow these bacterial populations and test for the banana smell as the population moves through the log phase and into the stationary phase. We will determine the population growth by using a Spec 20 to measure the density of the bacteria in liquid culture. As the population increases we can assess the increasing banana smell. Procedure Day 1 We will be receiving our bacteria with the plasmid already inserted. This culture will come in the form of a "stab" or "slant", a test tube with a small amount of bacteria on a slanted media. To continue the experiment we will have to further culture the bacteria by streaking out the stabs onto LB+amp plates. The plates will be incubated 37° overnight. Using a sterile toothpick or inoculating loop, gather a small amount of bacteria from the stab and transfer it to a petri dish containing Luria Broth (LB) agar plus ampicillin medium. Repeat with the remaining stab samples, streaking out each onto a different petri dish. Place these cultures in a 37°C incubator overnight. This video illustrates the technique used for this transfer: Day 2: Using a sterile inoculating loop, transfer a bacterial colony from one of the petri dishes to a large sterile culture tube containing 5 ml of Luria Broth and 5 μl of ampicillin. Repeat for each strain you will inoculate. Place the culture tubes in the roller wheel in the incubator at 37°C overnight. Be sure to balance the tubes across from each other to minimize stress on the roller wheel. This video illustrates the general technique for setting up overnight liquid cultures, though you’ll be transferring cells from the petri dish to the Luria Broth. Day 3: Procedure if using a spectrophotometer Prepare a solution with 300 mL Luria broth 300 μL Ampicillin 250 μL isoamyl alcohol Vortex this solution up and down two times to mix it. Move 2 mL of this mixture into a small sterile culture tube. Set this aside, it will be the blank for the spectrophotometer. Move 50 ml of the broth solution to 100ml sterile erlenmeyer flask and add 2mL of bacteria from one of the overnight cultures. This will be one of your the sample tubes. Repeat the mixing of 2ml of bacteria with 50 ml of broth for each of the overnight cultures. If you are testing all 4 samples you should now have 5 small test tubes (4 with bacterial dilutions and one blank). Prepare the spec 20 by setting it to OD600. Note the time and take an "initial" density reading for the bacterial samples by removing 1-2 mls (follow your teacher's direction) from each culture and adding each to a cuvette. Please note that your teacher may have carried out the preceding steps in advance of the lab. If that is the case, the teacher will tell you how much time has elapsed. That time will be your T0. Add a stir bar to each culture flask and place onto stir plates. Stir slowly. Cover the flasks with foil. After 20 minutes, remove 1 ml from each sample and place in a cuvette. Note: the volume you use here will depend on the size of the cuvette appropriate for your spec. Please follow the teacher's instructions. Read the blank and adjust the % Absorbance to zero. Read the sample tubes and record the % Absorbance. Sniff the flask for any evidence of a banana smell, comparing the odor with the standards. Be sure to shake the tubes before sniffing. Record your data. At 20 minute intervals repeat steps 10-12. Between time points, you can calculate the bacterial population: 1 OD600 unit = 1 x 109 bacteria. Procedure, if no spectrophotometer is available The OD 600 can be estimated using the Turbidity Standards. This method uses suspensions of a 1% BaCl2 in 1% H2SO4 at various concentrations and is modeled after the McFarland Turbidity Scale. These suspensions appear visually similar to suspensions of E coli. Data Table In your lab notebook, you will need to construct a data table as shown below for each of the samples. Lab Report As you write, be sure to define and properly use all highlighted terms throughout the introduction and other parts of the lab. I. Introduction Provide a brief introduction describing the field of synthetic biology. Briefly describe the purpose of the lab. What are we trying to do here? Explain how the banana smell generator functions. Why are we using optical density to measure the population? Explain each phase of the bacterial population growth curve. Presume that a reader of your lab report has not read the assignment. II. Methods You do not have to rewrite the procedure. Explain why you did each step of the protocol. III. Results Present the data tables in clear format. Draw population growth curves of the class mean data for each sample. Indicate on each curve when you could smell bananas. IV. Discussion Describe the results: 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. Analyze the data: Be sure to discuss how each part of the experiment adds to your conclusion. Discuss errors and other reasons for data variability. How confident are you in the results? Are you equally confident in both the growth data and the smell data? Explain. Is using smell to measure the banana smell valid? Why or why not? What did 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 genetic system, what might you construct? What would you need to do? V. Citations and references Be sure these are of good quality. Embed citations. Follow proper reference format. Navigation BioBuilding: Synthetic Biology for Students BioBuilding: Synthetic Biology for Students: Lab 1 BioBuilding: Synthetic Biology for Students: Lab 2 BioBuilding: Synthetic Biology for Students: Lab 3 BioBuilding: Synthetic Biology for Students: Lab 4 BioBuilding: Synthetic Biology for Students: Essay BioBuilding: Synthetic Biology for Students: Design Assignment BioBuilding: Synthetic Biology for Students: Glossary Lab Report Rubric ( pdf) and Lab Report ScoreSheet ( pdf) Essay Rubric ( pdf) and Essay Scoresheet ( pdf) BioBuilding: Synthetic Biology for Teachers