What Was In That Sandwich?

Overview & Concepts

Is it a case of food poisoning? Your students will have to figure out the cause of a man's illness.  After reading a mini case study, students will analyze the remains of the sub sandwhich to determine if there are prokaryotic organisms that caused the illness.  Students will use PCR analysis and gel electrophoresis. The students will then be presented with the gene sequences for the 6 bacteria that are found in the sample so a BLAST identification can take place.  Research about the specific bacteria will be completed to determine a positive match and identify which bacteria caused the illness.    

This activity is a slightly modified version of a protocol available at http://faculty.unlv.edu/wmojica/PCR_LAB2.htm.      

Grade Level: 

Concepts Covered: 

  • Pathogens
  • PCR amplification
  • Electrophoresis
  • Genome
  • BLAST

Prior Knowledge Required: 

  • How to use micropipetting techniques to transfer small amounts of liquid.
  • Being able to extract DNA from a cell.
Activity Notes

Days to Teach: 

This will take 3 days to complete.

Materials: 

  • Promega Master Mix
  • 1494 R primer
  • 530 F primer
  • Distilled Water
  • Electrophoresis Equipment (Gels, Power Supply, Chamber, Wires)
  • Micropipettes (10μL, 100μL)
  • PCR tubes
  • Master Mix tubes
  • GeneAmp PCR System
  • Eukaryote n Prokaryote Cell Sample
  • Permanent Marker
  • Ice
  • Vortex Machine
  • DNA Marker
  • Loading Dye
  • Computer with online capabilities

 

Teaching Tips / Activity Overview: 

Scenario:  Scott went to the local sub shop and purchased a turkey sub with lettuce, tomato, spinach, cheese and their special sauce on it.  He had the sub back at his house along with a glass of water for lunch.  Scott cleaned up his mess (he is a sloppy eater) and then went back to work outside planting the flowers his wife had bought at the store.  Five days later Scott became ill and was wondering what could have caused this. He went to the doctor next day because he was becoming dehydrated due to the events.  The doctor believes this could be some type of food poisoning but needs to identify the specific pathogen causing the illness.  The doctor is relying on you to identify the specific pathogen.  Time is of the essence.

Day 1:  Includes setting up the PCR tubes with their contents; cycling process will take place overnight

  1. Read through the case to determine what could have caused the illness
  2. Complete virtual lab on PCR from http://learn.genetics.utah.edu/content/labs/pcr/
  3. Set up the PCR tubes using proper techniques and protocol so that it can be amplified 

Day 2:  Students will be running the gel electrophoresis. Destaining will take place over night.

  • Students should practice using a micropipette at the very beginning by simply pipetting different amounts of dye onto filter paper.
  • The gels for the students will be made before Day 2 so the students do not have to create them and time can be saved.
  1. Complete virtual lab on electrophoresis using the link http://learn.genetics.utah.edu/content/labs/gel/
  2. Take sample and transfer contents to gel and run
  3. Stain the gel

Day 3:Students will be analyzing the data collected from the electrophoresis and be given the DNA sequences of six different bacteria they are to analyze using BLAST to identify the specific pathogen causing the illness.

  1. Analyze the gel to determine if prokaryotes are present
  2. Use nucleotide sequences to determine specific prokaryotes
  3. Research the 6 bacteria to determine which is pathogenic and could have caused the illness.  

Homework:  

  1. Work on the questions in packet
  2. Complete justification for selecting the one bacteria.

 

Both PCR and electrophroesis online animations can be used to help students understand what they will be physically doing.

Assessment: 

Students will be scored based upon the answers provided throughout the lab and their reasoning for their final answer to which bacteria caused the illness.

Extensions: 

You could take “non contaminated” food and determine if there are pathogenic bacteria on it.  Foods that are very high in causing food illnesses would be the first ones I would test, like raw chicken, eggs, and seafoods. Students could analyze the samples to see if they really are clean enough to eat.

Resources: 

This lab provided a guideline of how to set accomplish PCR amplification for a small sample of bacteria and then provided information on how to run what was produced through amplification using gel electrophoresis: http://faculty.unlv.edu/wmojica/PCR_LAB2.htm

This site was used to gather general information about the PCR and electrophoresis procedures.  The students will be using this to get a general overview of what they will be doing in class: http://learn.genetics.utah.edu/

General information on micropipetting was used to help explain the process of pipetting and the amounts each micropipette can hold.  Adapted lab from DNA Science, 2003 by Cold Spring Harbor Laboratory Press, purchased from Carolina Biological on Use of Micropippetors from the workshop on Bioinformatics

Acknowledgements: 

This lesson was modified from the lab created by N. Fester on November 7, 2005 and found on the website http://faculty.unlv.edu/wmojica/PCR_LAB2.htm. General procedures and specific diagrams were used and incorporated into this lab.

Academic Standards
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