Introduction to Gene Mining: Part BHow similar are plant and animal versions of a gene?
Teacher Resources:
I. Lesson Summary
a. What students will do:
In this lesson, students will utilize bioinformatics tools and concepts to
examine whether a plant model has adequate homology to be a useful human
genetic disease model.
In Part B, students first Engage their prior knowledge of conserved
elements by using the metaphor of recipes handed down from one generation to
the next, identifying reasons that recipes might change over time. Students
transition the discussion from recipe metaphor to gene by comparing and
contrasting a gene with a recipe. Finally, they predict features of one gene that
might make it a version of another gene. Next, students Explore the process of
determining homology using NCBI BLASTp and data from Araport.org. by finding
conserved amino acid sequences, performing multiple alignments and
constructing distance trees for homologous proteins. From Araport, students
will gather data about gene function, expression, protein-protein interactions,
and functional protein domains. During the Explain phase, students will argue
for or against the proposed plant model using evidence gathered. They will
Extend or Elaborate their learning by researching similar work in the literature
and proposing an experiment or by repeating the homology-determining process
using a disease gene of their own interest. Learning will be Evaluated as
teachers and students use a rubric to assess their written arguments.
b. Standards alignment: Part B
NGSS:
HS-LS1-1.Construct an explanation based on evidence for how the structure of
DNA determines the structure of proteins which carry out the essential functions
of life through systems of specialized cells.
HS-LS4: Communicate scientific information that common ancestry and
biological evolution are supported by multiple lines of empirical evidence.
HS-LS3-2. Make and defend a claim based on evidence that inheritable genetic
variations may result from: (1) new genetic combinations through meiosis, (2)
viable errors occurring during replication, and/or (3) mutations caused by
environmental factors.
NGSS Science and Engineering Practices: Analyzing and interpreting data, using
mathematical and computational thinking, engaging in argument from evidence
1
AP Biology Learning Objective LO1.9: The student is able to evaluate evidence
provided by data from many scientific disciplines that support biological
evolution. LO1.16: The student is able to justify the scientific claim that
organisms share many conserved core processes and features that evolved and
are widely distributed among organisms today. LO1.17-1.19 The student is able
to (construct and evaluate phylogenetic trees) to determine evolutionary history
and speciation from a provided data set.
c. Lesson learning objectives: By the end of Part B, students will be able to:
Explain what conserved sequences are.
Discuss why some sequence parts might be conserved while other parts might
not be conserved.
Use NCBI protein BLAST, multiple alignment and distance trees to identify
potential homologous proteins.
Use Araport data to evaluate protein homology.
Define and provide and example of protein-protein interactions, co-expression
and gene expression.
Propose and defend their claim about the feasibility of using a plant model to
study a human genetic disease.
d. Student prior knowledge and skills, pre/misconceptions: Part B
Before the lesson, students should be able to:
Identify different scientific models and why they are useful
Conduct a BLASTn search.
Correctly describe transcription and translation.
Discuss types of mutations that would result in altered protein function.
Describe eukaryotic gene structure, including introns, exons, untranslated
regions and their functions.
Possible misconceptions:
Students may confuse the terms genotype and phenotype. Students are likely to
be unfamiliar with ways of finding phenotype, generally aware of only visible
phenotypic differences such as eye-color in Drosophila or pea shape (wrinkled or
smooth).
II. Placement for Part B, within a high school or undergraduate course
Genetics, molecular biology, botany, evolution, experimental design, research project
III. Relevance to other concepts and to daily life
Models for disease studies, scientific arguments must often be built with incomplete
evidence
2
IV. Implementing the lesson
a. Time requirements and differentiation for mixed ability learners
Part B will take about 60 minutes for the Engage, Explore sections. The Explain portion
can be assigned for homework or can be an in-class session of about 30 minutes for
brainstorming and outlining. The Extend portion may be assigned as an independent
project or an in-class continuation. For students who require more help, these the
Engage and Explain sections may be conducted in a Google Hangout or Skyping format
with other students. Alternatively, a teacher may wish to train one or two students
ahead of time to act as facilitators.
b. Daily plans:
The teacher may involve the entire class in the review of part A and the Engage section.
The Explore section may be completed with the teacher leading and facilitating
computer use if students need help. Alternatively, students may work in pairs or
individually by following the Powerpoint-Slideshare while performing the computerdriven tasks.
c. Materials and equipment:
Students should work individually or in groups of 2 to complete the computerdependent sections of part B. The school internet should support multiple student
users at once and should have a sufficient speed for reasonable progress. A projector
connected to a teacher computer may support student learning. If students select
“show in new tab” option, it is easier to backtrack if they make an incorrect entry and
get off-track.
d. Advanced preparation
Teachers should provide computers for students, and 1 copy per student of the handout
and the argument rubric.
III. Science Resources for Teachers
The Arabidopsis Book http://arabidopsisbook.org/
NCBI tutorials http://www.ncbi.nlm.nih.gov/home/tutorials.shtml
MIT Open courseware http://ocw.mit.edu/index.htm
Portal for Arabidopsis research including 50 years of Arabidopsis publications
http://www.Araport.org
ABRC educational outreach –lab materials and ideas http://abrcoutreach.osu.edu/educationalkits
The Partnership for Research and Education in Plants http://www.prepproject.org
One hundred important questions facing plant science research
http://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2011.03859.x/full
3
A model is a “simplified system that is accessible and easily manipulated”
.http://publications.nigms.nih.gov/thenewgenetics/poster.pdf
Living laboratories—model organisms poster from the NIH
http://publications.nigms.nih.gov/thenewgenetics/poster.pdf
“One More Way Plants Help Human Health”
http://publications.nigms.nih.gov/insidelifescience/plants-in-biomedicine.html
“The value of Arabidopsis research in understanding human disease states”
Xiang Ming Xu and Simon Geir Møller
Current Opinion in Biotechnology 2011, 22:300–307
4