Transcript gene expression group, northwest 2012

Gene Expression
Group Awesome (aka Team Water Spill)
Geoduck Land Summer Institute, 2012
Group Members
Amy Oakley
Katie Clark
Sharsti Sandall
Jim Burnette
Sarah Stockwell
Krissi Hewitt
Lori Kayes
Steve Chordas
Background Information
Students will already…
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Have had a brief introduction into gene
expression
Know how transcription and translation work
Know that there are technologies to measure
gene expression, both genome-wide and for
specific genes
Have been introduced to experimental design
Unit Learning Goals
Students will:
1. Understand that gene expression regulates
cell function
2. Understand the flow of genetic information
from DNA to phenotype
3. Appreciate the relevance of gene
expression to science and society
4. Effectively work in groups to model the
collaborative process of science
5. Think critically about how experimental
evidence answers a scientific question
Learning Outcomes for Teachable Tidbits
Students will be able to:
1. Describe how a change in gene expression can
lead to changes in phenotype
2. Analyze and interpret graphs and scientific images
3. Synthesize data into a hypothesis to connect gene
expression and phenotype
4. Apply a similar hypothesis to a real situation
5. Develop, articulate, and defend a position on the
ethics of genetic testing
Teachable Tidbit 1
You are a scientist wandering the Galapagos Islands, and you
notice that finches have different beak sizes. You think this might
be based on differences in gene expression. Upon returning to
your island laboratory, you find that a gene called bone
morphogenic protein 4 (Bmp4) varies across finch species.
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A
B
C
Hypothesis to explain
relationship between
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2 min!
Type of Finch Species
Gene Expression Levels of Bmp4
Beak Size (cm)
Abzhanov, A. et al. Science 2004
Type of Finch Species
Design an Experiment
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Based on the class hypothesis, design an
experiment with at least 1 control.
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Predict the outcome.
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Would this outcome support your hypothesis?
5 min!
The Bmp4 signal changes gene expression which changes phenotype
Bmp4
The Bmp4 signal changes gene expression which changes phenotype
Bmp4
The Bmp4 signal changes gene expression which changes phenotype
Bmp4
Transcription factors
turn genes on or off
The Bmp4 signal changes gene expression which changes phenotype
Bmp4
Transcription factors
turn genes on or off
The cell
changes!
The Bmp4 signal changes gene expression which changes phenotype
Bmp4
Transcription factors
turn genes on or off
The cell
changes!
Cell changes can
include:
• Cell growth and
division
• Cell death
• Pausing the cell cycle
• Cell movement
Teachable Tidbit 2
New York Times Article--for Tomorrow
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Main Points of Article (for SI)
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2 classes of ocular melanoma: after treatment
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Class 1 --> 100% survival
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Class 2 --> 20% survival
Previously, the only way to determine prognosis
was by tumor size…but this wasn’t very accurate
Researchers then compared gene expression
between tumors
12 signature genes can differentiate tumor class,
thus predicting survival
Knowing tumor class does not change treatment
or outcome
Doctors are split as to whether to offer this test
Clicker Questions
1. What is ocular melanoma?
A) skin cancer of the ear
B) hyperpigmentation of the skin
C) skin cancer of the eye
D) sleeping disorder
Clicker Questions
2. Describe the new test that distinguishes
between Class 1 and 2 ocular melanoma
A) measure tumor size
B) gene expression test
C) DNA sequence test
D) no test needed; there is no difference
How does the article relate to finches???
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Small group
discussion
5 min!
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Onken M D et al. Cancer Res 2004
Onken et al J Mol Diagn. 2010
Teachable Tidbit 2
Think-Pair-Share
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Onken et al J Mol Diagn. 2010
Ethical Implications for Genetic Testing
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Doctors in New York Times article conflicted
Imagine you are a doctor. Individually reflect on
whether you would offer this test to your patients.
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First list the pros and cons…
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Choose a position and be prepared to defend it.
5 min!
Discussion
Students who would
offer the test stand by
the chalkboard
Students who would
NOT offer the test stand
by the corkboard
Write your reasons for your
position on the board/paper
Write your reasons for your
position on the board/paper
Come back as a group and discuss
each position and reasons
1 minute reflective paper
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Indicate your original position on the
top of the paper
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Defend the opposite side
Summative Assessment (SI)
Assuming that there are multiple classes of ovarian
tumors, and some are treatable and some are not, what
information would you need to know to design a test to
determine whether a tumor is treatable or not?
List and describe at least 3 (of the 5) critical components:
Answer:
1. Gene expression levels of different classes of tumor
2. What genes are changing, which aren’t?
3. Tumor vs normal tissue samples
4. Long-term survivorship of patients
5. Genome-wide expression
Summative Assessment (SI)
Assuming you find a good candidate gene to determine
tumor class, draw a graph showing the difference in gene
expression between the 2 tumor classes and a graph of
survivorship by tumor class.
If you had ovarian cancer, would you want your tumor
tested? Why or why not?