Gene ExpressionGene Expression

Group Awesome (aka Team Water Spill)Group Awesome (aka Team Water Spill)Geoduck Land Summer Institute, 2012Geoduck Land Summer Institute, 2012

Group MembersAmy Oakley Katie Clark Sharsti SandallJim Burnette Sarah StockwellKrissi HewittLori KayesSteve Chordas

Background Information

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

Students will already…

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

Unit Learning GoalsStudents will:

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

Learning Outcomes for Teachable TidbitsStudents will be able to:

Teachable Tidbit 1You 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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Type of Finch Species

Gen

e E

xpre

ssio

n L

evel

s o

f Bmp4

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Bea

k S

ize

(cm

)

Type of Finch Species

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A

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C

Hypothesis to explain relationship between

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B

2 min!

Abzhanov, A. et al. Science 2004

Design an Experiment

Based on the class hypothesis, design an experiment with at least 1 control.

Predict the outcome.

Would this outcome support your hypothesis?

5 min!

Bmp4

The Bmp4 signal changes gene expression which changes phenotype

Bmp4

The Bmp4 signal changes gene expression which changes phenotype

Transcription factors turn genes on or off

Bmp4

The Bmp4 signal changes gene expression which changes phenotype

The cell changes!

Transcription factors turn genes on or off

Bmp4

The Bmp4 signal changes gene expression which changes phenotype

The cell changes!

Transcription factors turn genes on or off

Cell changes can include:• Cell growth and division• Cell death• Pausing the cell cycle• Cell movement

Bmp4

The Bmp4 signal changes gene expression which changes phenotype

Teachable Tidbit 2

New York Times Article--for Tomorrow

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Main Points of Article (for SI)

2 classes of ocular melanoma: after treatment

Class 1 --> 100% survival

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 earB) hyperpigmentation of the skinC) skin cancer of the eye D) sleeping disorder

2. Describe the new test that distinguishes between Class 1 and 2 ocular melanoma

A) measure tumor sizeB) gene expression testC) DNA sequence testD) no test needed; there is no difference

Clicker Questions

How does the article relate to finches???

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5 min!

Small group discussion

Onken M D et al. Cancer Res 2004

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Onken et al J Mol Diagn. 2010

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Teachable Tidbit 2Think-Pair-Share

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Onken et al J Mol Diagn. 2010

Ethical Implications for Genetic Testing

Doctors in New York Times article conflicted

Imagine you are a doctor. Individually reflect on whether you would offer this test to your patients.

First list the pros and cons…

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

Indicate your original position on the top of the paper

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?