What will we gain from this lab?
1. Relate science to our everyday life.
2. Real World Relevance in our DCHS Classroom. We are the only AP Bio class in the district doing this.
3. We will be able to isolate Fish DNA. Use PCR (Polymerase Chain Reaction) to amplify a portion of a specific gene. PCR is only available in college labs. We are very lucky. We will analyze the PCR products with gel electrophoresis in our lab and send off our samples for sequences to iBOL (the International Barcode of Life project) to compare to other sequences in the database.
Why?
1. Market substitution
2008 New York Times student experiment
1. Relate science to our everyday life.
2. Real World Relevance in our DCHS Classroom. We are the only AP Bio class in the district doing this.
3. We will be able to isolate Fish DNA. Use PCR (Polymerase Chain Reaction) to amplify a portion of a specific gene. PCR is only available in college labs. We are very lucky. We will analyze the PCR products with gel electrophoresis in our lab and send off our samples for sequences to iBOL (the International Barcode of Life project) to compare to other sequences in the database.
Why?
1. Market substitution
2008 New York Times student experiment
|
|
|
|
|
|
|
b
An overview of our lab:
Designated people will collect fish samples. You will need baggies marked with fish sample name and location you obtained the sample. Between the two classes we have the materials to run 16 samples. These will be obtained from grocery stores, sushi resturants, fishing trips, etc.
Take samples from the interior and use gloves between samples. .
We will be examining the COI gene. Highly conserved, part of the electron transport chain of the mitochondria. Essential to energy flow. (Bacteria have this gene also, so we have to think and do sterile).
Molecular biology skills, sterile technique skills, proficiency in running gels and micropipetting are not negotiable.
We will need 16 samples. We will not need 16 people to bring them in. If you are interested in acquiring samples next weekend, please discuss this with me. At this moment, the following people are collectors:
1. Laurence Dela Luna
2.
Also, a selected team will possibly be going to FSC Biotech lab with me after school to take pictures with a UV Transilluminator if I can work it out.
An overview of our lab:
Designated people will collect fish samples. You will need baggies marked with fish sample name and location you obtained the sample. Between the two classes we have the materials to run 16 samples. These will be obtained from grocery stores, sushi resturants, fishing trips, etc.
Take samples from the interior and use gloves between samples. .
We will be examining the COI gene. Highly conserved, part of the electron transport chain of the mitochondria. Essential to energy flow. (Bacteria have this gene also, so we have to think and do sterile).
Molecular biology skills, sterile technique skills, proficiency in running gels and micropipetting are not negotiable.
We will need 16 samples. We will not need 16 people to bring them in. If you are interested in acquiring samples next weekend, please discuss this with me. At this moment, the following people are collectors:
1. Laurence Dela Luna
2.
Also, a selected team will possibly be going to FSC Biotech lab with me after school to take pictures with a UV Transilluminator if I can work it out.
What is DNA Barcoding? Reading
Suggested Background Reading:
dna-barcoding.blogspot.com
phe.rockefeller.edu/barcode/sushigate.html
ibol.org
Tips and Helpful Hints we must adhere to:
Each individual fish sample is processed with a NEW (not washed or wiped old one) plastic knife. Why?
Robust amplified DNA samples best from these FRESH fish samples:
Catfish
Shark
Sturgeon
Trout
Rock Cod
True cod
Tilapia
Mackerel
Yellowfin tuna
Sea bass
Opah
Imitation crab
Flying fish roe
Bonito flakes
Our schedule:
Pre-read and answer Lesson 1 and Lesson 2 Student Manual (there is an extra page 39 and 40. I will delete these from your hard copy in lab.)
Monday, December 7:
Lesson 1: DNA extraction
Lesson 2: Set up PCR reactions (and pour gels)
Run PCR reactions (4 hours)
Pre-read and answer Lesson 3 and Lesson 4 Student Manual above.
Tuesday, December 8:
Lesson 3: Gel electrophoresis
Lesson 4: DNA sequencing
Results back in 3-5 days
During Evolution unit: Bioinformatics
Suggested Background Reading:
dna-barcoding.blogspot.com
phe.rockefeller.edu/barcode/sushigate.html
ibol.org
Tips and Helpful Hints we must adhere to:
Each individual fish sample is processed with a NEW (not washed or wiped old one) plastic knife. Why?
Robust amplified DNA samples best from these FRESH fish samples:
Catfish
Shark
Sturgeon
Trout
Rock Cod
True cod
Tilapia
Mackerel
Yellowfin tuna
Sea bass
Opah
Imitation crab
Flying fish roe
Bonito flakes
Our schedule:
Pre-read and answer Lesson 1 and Lesson 2 Student Manual (there is an extra page 39 and 40. I will delete these from your hard copy in lab.)
Monday, December 7:
Lesson 1: DNA extraction
Lesson 2: Set up PCR reactions (and pour gels)
Run PCR reactions (4 hours)
Pre-read and answer Lesson 3 and Lesson 4 Student Manual above.
Tuesday, December 8:
Lesson 3: Gel electrophoresis
Lesson 4: DNA sequencing
Results back in 3-5 days
During Evolution unit: Bioinformatics