Introduction to Gene Mining: Part A--BLASTn-off!
Teacher Resources:
I. Lesson Summary
a. What students will do:
In this lesson, students will utilize bioinformatics tools and concepts to
propose a plant model that might prove useful in studying a human genetic
disease.
In Part A, students Engage prior knowledge of genetics and human
diseases using the Online Mendelian Inheritance in Man portal (www.OMIM.org)
to identify a sample gene which has a role in a human disease. They will briefly
write to expose their preconceptions of scientific models and of processes which
are common to both plants and humans. They next Explore using bioinformatics
tools. Students will find information about the sample human disease gene from
the www.NCBI.nlm.nih.gov portal. Students will then use the BLASTn tool to
align the human gene DNA sequence with Arabidopsis thaliana DNA sequences
and identify names of prospective plant versions of the human gene. They will
learn to interpret the BLASTn report to determine which is the most similar plant
gene to use in the disease study. During the Explain phase, students will discuss
those processes. They will Extend or Elaborate their learning by searching for
plant versions of disease-related genes of their own interest. They will Evaluate
their understanding about how to evaluate gene similarity through small group
and class discussions of the results of a “Gene Prediction Scorecard”.
b. Standards alignment: Part A
NGSS HS-LS4: Communicate scientific information that common ancestry and
biological evolution are supported by multiple lines of empirical evidence.
NGSS Science and Engineering Practices: Analyzing and interpreting data, using
mathematical and computational thinking, engaging in argument from evidence
AP Biology Learning Objectives LO1.9: The student is able to evaluate evidence
provided by data from many scientific disciples that support biological evolution.
AP Biology Learning Objective LO1.15: The student is able to describe specific
examples of conserved core biological processes and features shared by all
domains or within one domain of life, and how these shared, conserved core
processes and features support the concept of common ancestry for all
organisms.
1
c. Lesson learning objectives: By the end of Part A, students will be able to:
Provide examples of biological models and state why they are useful.
List characteristics of Arabidopsis thaliana that make it a useful model organism.
Use OMIM to find information about a genetic disease.
Explain why bioinformatics tools are needed to analyze large data sets.
Find information about a gene of interest on NCBI including FASTA sequence.
Perform a BLASTn comparison and identify which result has highest similarity
using E-value, scores, % query, graphics, description, and alignment results.
d. Student prior knowledge and skills, pre/misconceptions: Part A
Before the lesson, students should be able to:
Identify at least one scientific model.
Tell why/how scientific models are useful.
Describe Mendelian inheritance in a disease context.
Distinguish characteristics which are common to all organisms.
Use popular search engines to find scientific information.
Represent DNA sequences using double-stranded nucleotide models.
Understand scientific notation; for example, that 1 X 10-4 is 10,000 times larger
than 1 X 10-8.
II. Placement for Part A, within a high school or undergraduate course
Genetics, molecular biology, botany, evolution, experimental design, bioinformatics
III. Relevance to other concepts and to daily life
Models for disease studies, computer modeling is a human endeavor that frequently
modified
IV. Implementing the lesson
a. Time requirements and differentiation for mixed ability learners
The Pre-lesson assessment can be administered at any time prior to the lesson. Students
should take less than 15 minutes to complete this. Students need about 60 minutes for
the Engage and Explore sections. Students will need about 10-15 minutes to do the
Explain section. The Extend section can be assigned for homework and will take 30-45
minutes. For students who need more computer 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 the lesson to be
class facilitators. The post-lesson process assessment can check student ability to
2
perform a BLASTn search on a gene of their own interest (or from a teacher provided
list). Students should require about 20 minutes for the process assessment. The postlesson content assessment may require about 20 minutes.
b. Daily plans:
The teacher may involve the entire class in 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 computer-driven tasks.
c. Materials and equipment:
Students should work individually or in groups of 2 to complete the computerdependent sections of part A. 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 for links, it will be easier to backtrack if they make an
incorrect entry.
d. Advanced preparation
Teachers should provide computers for pairs of students and a copy of the student
handout per student. Pre-and post-lesson assessments should also be provided, 1 copy
per student.
III. Science Resources for Teachers
http://arabidopsisbook.org/ a free online information source
NCBI tutorials http://www.ncbi.nlm.nih.gov/home/tutorials.shtml
MIT Open courseware http://ocw.mit.edu/index.htm
BLAST results: Expect Values, part1 https://www.youtube.com/watch?v=nO0wJgZRZJs
Part 2 https://www.youtube.com/watch?v=Z7ek7UoP7Bg
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
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
3
“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