This is the first of a two-part series in NWABR's bioinformatics curriculum, funded by a grant called Bio-ITEST: New Frontiers in Bioinformatics and Computational Biology, an Innovative Technology Experiences for Students and Teachers (ITEST) award from the National Science Foundation (NSF). This three-year award provided funding for education outreach programs and curriculum development that help secondary school teachers and their students learn about how information technology is used in biological research.
The Introductory curriculum unit explores how bioinformatics is applied to genetic testing. Specifically, the bioinformatics tools of BLAST and Cn3D are used to investigate the genetic and molecular consequences of a mutation to the Breast Cancer Susceptibility 1 (BRCA1) gene.
Students are also introduced to principles-based bioethics in order to support their thoughtful consideration of the many social and ethical implications of genetic testing.
Throughout the unit, students are presented with a number of career options in which the tools of bioinformatics are used.
In order for us to measure how our curriculum resources are being used, please take a moment to contact us and let us know the class or classes in which you're using our lessons. We also welcome feedback about our introductory bioinformatics curriculum. We will not share your contact information with anyone.
Major collaborators include Digital World Biology, EdLab Group, and Shoreline Community College. The program also draws on NWABR’s strong relationships with school districts, community groups, bioethicists and NWABR member research institutions.
The curriculum unit explores how bioinformatics is applied to genetic testing. Specifically, the bioinformatics tools of BLAST and Cn3D are used to investigate the genetic and molecular consequences of a mutation to the Breast Cancer Susceptibility 1 (BRCA1) gene. Students are also introduced to principles-based bioethics in order to support their thoughtful consideration of the many social and ethical implications of genetic testing. Throughout the unit, students are presented with a number of career options in which the tools of bioinformatics are used.
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Complete Lesson Plans
- Full "Using Bioinformatics: Genetic Testing" Curriculum
This PDF contains the entire “Using Bioinformatics: Genetic Testing” curriculum, including the overview, lessons, and appendix. For accompanying lesson PowerPoints, please download from the links above.
- Lesson One: Bioinformatics and Genetic Testing
A short topical play introduces students to the fields of bioinformatics, genetic testing, direct-to-consumer genetic testing, and ethical considerations. Students discuss some of the broad implications and ethical questions raised from gaining information through genetic testing. Students then consider a number of genetic tests and their potential usefulness and value and, as a class, explore the website of 23andMe, a company that offers direct-to-consumer genetic tests. The lesson wraps up as it began—by engaging students in a story. Through a short video, students are introduced to a family impacted by breast cancer. In Lesson One, students also learn how bioengineers might use bioinformatics tools in their career.
- PowerPoint for Lesson One
- Lesson Two: Navigating the NCBI
Students navigate parts of the National Center for Biotechnology Information (NCBI) website and work independently to explore databases, focusing on the BRCA1 gene and the bioinformatics tool Map Viewer. Through an analogy that compares two collections of databases (iTunes® and the NCBI), students connect with their own prior knowledge to better understand database structure and function. In Lesson Two, students learn how veterinarians might use bioinformatics tools in their career.
- PowerPoint for Lesson Two
- Lesson Three: Exploring Genetic Testing: A Case Study
In this lesson, students engage in a case study about a family with a history of breast cancer. Students consider ethical issues surrounding genetic testing as they decide whether or not family members should get tested for BRCA1 or BRCA2 mutations. Students then evaluate the case through the principles-based bioethics concepts of: Respect for Persons, Maximize Benefits/Minimize Harms, and Justice. Students apply the principles to help them reason through their decision as they participate in a Structured Academic Controversy. In Lesson Three, students learn how genetic counselors might use bioinformatics tools in their career.
- PowerPoint for Lesson Three
- Lesson Four: Understanding Genetic Tests to Detect BRCA1 Mutations
Students begin this lesson by working through a pedigree chart and Punnett squares for the Lawler family, attempting to track the BRCA1 mutation across generations. Based on the decisions as to who should be tested for the BRCA1 mutation, students then use the bioinformatics tool known as BLAST (Basic Local Alignment Search Tool) to compare individual DNA and protein sequences to reference sequences that are known to be free of BRCA1 mutations associated with cancer. At the end of the lesson, students compile class information from the Lawler family in order to revise their pedigree charts and Punnett squares. In Lesson Four, students learn how laboratory technicians might use bioinformatics tools in their career.
- PowerPoint for Lesson Four
- Lesson Five: Learning to Use Cn3D: A Bioinformatics Tool
Up to this point, students have seen the BRCA1 protein represented in a linear, sequential form. In this lesson, students are introduced to the high importance of a protein’s three-dimensional structure. Students first engage in a short activity in which they use a pipe cleaner to perform a simple function, as an analogy for the relationship between a protein’s structure and function. Students then learn to navigate between linear protein sequences and three-dimensional structures by using the bioinformatics tool Cn3D. Students begin by viewing and manipulating DNA—a familiar molecule to students—using Cn3D. When students are familiar with the program, students visualize parts of the BRCA1 protein to show how a specific mutation in the BRCA1 gene ultimately changes or destroys the protein’s function. In Lesson Five, students learn how 3D animators might use bioinformatics tools in their career.
- PowerPoint for Lesson Five
- Lesson Six: Evaluating Genetic Tests: A Socratic Seminar Discussion
In this lesson, students apply the ethical skills and scientific knowledge they have acquired over the previous lessons to determine (1) whether BRCA1 testing meets the standards of a useful genetic test, or (2) whether direct-to-consumer genetic testing should include genetic counseling of clients. Students or teachers may choose from one of two readings, after which students participate in a Socratic Seminar in order to deepen their understanding about genetic testing. Through the seminar discussion of the first reading, students become familiar with a framework for considering genetic tests in terms of their clinical validity and the availability of effective treatment. Through the seminar discussion of the second reading, students become familiar with issues and preliminary data regarding the effects of direct-to-consumer genome-wide screening. After the seminar, students are supported in coming to an individual position about genetic testing through the integration of scientific facts, stakeholder viewpoints, and ethical considerations. In Lesson Six, students learn how bioethicists might use bioinformatics tools in their career.
- PowerPoint for Lesson Six
- Lesson Seven: An Introduction to Bioinformatics Careers
In this lesson, students explore more deeply the information they have learned throughout the unit about people in various careers that use bioinformatics. Students choose one career they would like to learn more about. They further explore that career by reading a series of in-depth questions asked of the person highlighted in that career, as well as provided internet resources. Students then respond to a job posting for a summer internship in their chosen field, developing a resume for that position. Optional activities include peer-editing of resumes and socializing in a professional environment.
- PowerPoint for Lesson Seven
- Lesson Eight: Genetic Testing Unit Assessment: ALAD and SOD1
As an assessment of the unit, students revisit some of the bioinformatics tools they have used in prior lessons in order to locate a mutation in a protein associated with a genetic condition. Students also evaluate current genetic tests for the condition using the criteria of clinical validity and treatment options. Two conditions and their tests are presented: porphyria and amyotrophic lateral sclerosis (ALS).
- PowerPoint for Lesson Eight
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Supporting Materials
- Overview Unit Plan
- Appendix
Resource Materials FOR Introductory lessons
PowerPoints to accompany each "Using Bioinformatics: Genetic Testing" lesson are found on "Lessons" page, besideeach lesson title.
See our Student Career Center for career profiles, planning resources, and more.
Lesson Four: Understanding Genetic Tests to Detect BRCA1 Mutations
BRCA1 sequences
This Word document file contains Lawler family BRCA1 DNA and protein sequences.
Fluorescent Protein Extension Files:
Comparing Fluorescent Proteins Using BLAST Instructions (PDF)
Using BLAST to Analyze Proteins (PPTX)
DNA Sequences from Various Fluorescent Proteins
Protein Sequences from Various Fluorescent Proteins
These Word documents contain DNA and protein sequences of a variety of fluorescent proteins, including eukaryotic Green Fluorescent Protein (eGFP), the mCherry Red Fluorescent Protein (RFP), the mLemon Yellow Fluorescent Protein (YFP), and other members of the "mFruits" such as mGrape1, and mTangerine 1.5. This extension was first developed during the 2013 "Workshop C: Cloning DNA to Make Protein," part of the three-part partnership series between NWABR and Shoreline Community College's Amgen Bruce Wallace Biotechnology Program, "Easy as ABC: Applications of Biotechnology in the Classroom."
Lesson Five: Learning to Use Cn3D: A Bioinformatics Tool
BRCA1 Animation
Authored by the Bio-ITEST team at NWABR.
Animation by Beth Anderson (Arkitek Studios) and Jill DelSordi
DNA Structure File 1NAJ (save to your Desktop and open in Cn3D from the "File" menu)
BRCA1 Structure File 1Y98 (save to your Desktop and open in Cn3D from the "File menu")
BRCA1 VAST alignment: BRCA_BRCT_vastsrvalignment.val
Hemoglobin Structure Extension Files:
These structures can be used by teachers to illustrate the consequences of sickle cell mutations on the structure of hemoglobin. This extension was first developed during the 2012 "Workshop A: An Understanding of DNA: Making the Invisible Visible," part of the three-part partnership series between NWABR and Shoreline Community College's Amgen Bruce Wallace Program, "Easy as ABC: Applications of Biotechnology in the Classroom."
Wild-type Hemoglobin File 4HHB (the structure currently unavailable)
Note: This is structure is the multimer of four hemoglobin monomers.
(save to your Desktop and open in Cn3D from the "File" menu)
Sickle Cell Hemoglobin File 2HBS (the structure currently unavailable)
Note: This is structure is the multimer of four sickle-type hemoglobin monomers.
(save to your Desktop and open in Cn3D from the "File" menu)
Hemoglobin VAST alignment Hemoglobin_VAST_Alignment (the structure currently unavailable)
Note: This is an overlay of a single wild-type and a single sickle-type hemoglobin monomer.
(save to your Desktop and open in Cn3D from the "File" menu)
More information about how this sickle cell mutations leads to the sickle cell phenotype: http://www.ornl.gov/sci/techresources/Human_Genome/posters/chromosome/hbb.shtml
RFP and eGFP Structure Extension Files:
These structures can be used by teachers to illustrate the structural similarities between two unrelated fluorescent proteins: eukaryotic green fluorescent protein (eGFP) and red fluorescent protein (RFP). This activity can be used in conjunction with the fluorescent protein BLAST comparison activities developed as an extension of Lesson Four. This extension was first developed during the 2013 "Workshop C: Cloning DNA to Make Protein," part of the three-part partnership series between NWABR and Shoreline Community College's Amgen Bruce Wallace Biotechnology Program, "Easy as ABC: Applications of Biotechnology in the Classroom."
Eukaryotic Green Fluorescent Protein (eGFP) File 1GFL
Note: This is structure is a dimer of two GFP monomers.
(save to your Desktop and open in Cn3D from the "File" menu)
Red Fluorescent Protein (RFP) File 2H5Q
Note: This is structure is a RFP monomer.
(save to your Desktop and open in Cn3D from the "File" menu)
Fluorescent Protein VAST Alignment Fluorescent-Protein_VAST-Alignment
Note: This is an overlay of a GFP monomer and a single RFP monomer.
(save to your Desktop and open in Cn3D from the "File" menu)
Lesson Eight: Genetic Testing Unit Assessment: ALAD and SOD1
Porphyria and ALS amino acid sequences (download word file containing sequences)
Resource Materials FOR optional lesson extensions
- Comparing Sequences of Fluorescent Proteins Using BLAST (PDF)
This PDF contains the instructions for the Lesson Four extension activity, "Comparison of Fluorescent Proteins Using BLAST." The activity begins with a brief overview of the diversity and uses of fluorescent proteins in biological research, and then explains to students how to use the Introductory bioinformatics Lesson Four Student Handout, "Instructions for Aligning Sequences with BLAST," to compare sequences of flruoescent proteins. The goal is to determine whether the red fluorescent protein (RFP) included in the Amgen Bruce Wallace Biotechnology Laboratory Program is related to the famous GFP. This extension was first developed during the 2013 "Workshop C: Cloning DNA to Make Protein," part of the three-part partnership series between NWABR and Shoreline Community College's Amgen Bruce Wallace Biotechnology Program, "Easy as ABC: Applications of Biotechnology in the Classroom."
- Using BLAST to Analyze Proteins (PPTX)
This PowerPoint provides and overview of the Lesson Four extension activity using BLAST to compare fluorescent protein DNA and protein sequences. It includes a brief history of fluorescent proteins, their uses as biological tools, and an introduction to their diversity. This extension was first developed during the 2013 "Workshop C: Cloning DNA to Make Protein," part of the three-part partnership series between NWABR and Shoreline Community College's Amgen Bruce Wallace Biotechnology Program, "Easy as ABC: Applications of Biotechnology in the Classroom."
- DNA Sequences from Various Fluorescent Proteins (DOCX)
This Word document contain DNA sequences of a variety of fluorescent proteins, including eukaryotic Green Fluorescent Protein (eGFP), the mCherry Red Fluorescent Protein (RFP), the mLemon Yellow Fluorescent Protein (YFP), and other members of the "mFruits" such as mGrape1, and mTangerine 1.5. This extension was first developed during the 2013 "Workshop C: Cloning DNA to Make Protein," part of the three-part partnership series between NWABR and Shoreline Community College's Amgen Bruce Wallace Biotechnology Program, "Easy as ABC: Applications of Biotechnology in the Classroom."
- Protein Sequences from Various Fluorescent Proteins (DOCX)
This Word document contain protein sequences of a variety of fluorescent proteins, including eukaryotic Green Fluorescent Protein (eGFP), the mCherry Red Fluorescent Protein (RFP), the mLemon Yellow Fluorescent Protein (YFP), and other members of the "mFruits" such as mGrape1, and mTangerine 1.5. This extension was first developed during the 2013 "Workshop C: Cloning DNA to Make Protein," part of the three-part partnership series between NWABR and Shoreline Community College's Amgen Bruce Wallace Biotechnology Program, "Easy as ABC: Applications of Biotechnology in the Classroom."
- Additional Fluorescent Protein Sequences (DOCX)
This Word document contains additional DNA and protein sequences of fluorescent proteins and their wild-type counterparts, to be used in extension BLAST analyses related to the above activities.
The Personal Genome Project is a public genomics research study that aims to improve our understanding of genetic and environmental contributions to human traits. They are enrolling members of the public who are willing to share their genome sequence and other personal information such as health and medical data with the scientific community and the general public for purposes that promote human welfare through the advancement of scientific and medical discovery. The mission of the Personal Genome Project is to encourage the development of personal genomics technology and practices that: are effective, informative, and responsible; yield identifiable and improvable benefits at manageable levels of risk; and are broadly available for the good of the general public. To achieve this mission they are building a framework for prototyping and evaluating personal genomics technology and practices at increasing scales. Each year additional people are recruited to participate.
A Series of articles written by Emily Singer for MIT's Technology Review detailing the rationale behind the Personal Genome Project, and how the project has grown tremendously during just the past few years.
Biochemistry and Molecular Structure Resources
3D Molecules
Protein Data Bank (PDB)
Search for the protein structures and either print, view online, or download to view with an appropriate plug-in (some of which can be downloaded from the site). Features a "molecule of the month." Also, visit the extensive Educational Resources Section.
NCBI's Structure Page allows you to view structures with a simple view, Cn3D, available for download from the site. It also maintains its own structure database, MMDB, which is a subset of the PDB.
Genetic Science Learning Center
Offers many valuable resources for teaching and learning about biotechnology.
Iowa State Biotechnology Resources for Educators
Includes thirteen laboratory activities, curriculum units, and more. Topics include DNA extraction, fingerprinting, bacteria transformation, bioluminescence, plant micro propagation, a PCR activity, and a soybean flavor demonstration.
National Centre for Biotechnology Education (United Kingdom)
NCBE Publications--Download curriculum to teach biotechnology in the classroom, including plant biotechnology and fermentation.
Beyond Discovery: The Path from Research to Human Benefit
Real life case studies illustrate how recent medical and technological advances arose from basic laboratory research. Some of the areas covered are Hepatitis B, polymers, designer seeds, and human gene testing.
Fred Hutchinson Cancer Research Center SEP Program Science and Education Links
An extensive collection of science links is available at Dyanna's Picks. The downloadable resource list is especially valuable for Washington State educators.
NCBI
The National Center for Biotechnology Information has links to a wealth of resources for learning about biotechnology, including information on human genome resources, model organisms, and outreach/education. Begin at the "About NCBI" section for a good overview of resources. PubMed is a valuable resource for locating scientific research articles.
Washington Biotechnology and Medical Technology Online
The home page of WBBA, the Washington Biotechnology and Biomedical Association (WBBA), provides information about biosciences in Washington State, as well as Education Materials such as a lab on gel electrophoresis and DNA fingerprinting.
WhyBiotech.Com
An informational site from the Council for Biotechnology Information.
Cell Biology Resources
Biology4Kids: The Cell Biology Pages: These pages cover all major cell organelles in detail with gorgeous color graphics and helpful analogies for understanding cellular functions. Not just for "kids," this site would provide a terrific review for high school students as well.
The Biology Project provides cell biology resources in addition to addressing other aspects of biology. It also offers activities, lesson plans, and tutorials.
Cells Alive provides a wonderful microscopic images of cells. Check out the cell model tutorial and the cell gallery!
NCBI Bookshelf: Search topics directly in the online versions of the classic texts of cell biology,Molecular Biology of the Cell, and Molecular Cell Biology. This is an amazing resource!
Stem Cells
MedlinePlus: Latest news on stem cell research from the National Library of Medicine.
PBS Newshour Online: Human Stem Cell Research: After reviewing background and a research interview on this controversial topic, view a three-minute animation on how human stem cells are cultured. Embryonic stem cell issues are debated by medical ethicists.
Science Magazine: Original article on "Embryonic Stem Cell Lines Derved From Human Blastocysts" in the October 1998 issue.
Stem Cell Primer from the NIH provides an overview of stem cells and issues related to their growth.
Virtual Cell, An Education Index Top Site. Zoom into the cell, cut sections, and learn about different organelles in this highly interactive site.
Neurobiology Resources
Digital Anatomist Interactive Atlas (Neuroanatomy): This is an advanced program provided by the University of Washington that can be taken for credit, used in a classroom, or enjoyed for individual learning purposes. Graphics and photos illuminate many components of the nervous system. Online movies are available for every subject. The overview details how to customize the program, label photos and diagrams, navigate the site, and how to use quiz mode.
Neuroscience for Kids--This home page has been created for all students and teachers who would like to learn more about the nervous system. Enjoy the activities and experiments on your way to learning more about the brain and spinal cord. This includes a scavenger hunt to help familiarize students with the site and nervous system.
Drugs and the Brain
Alcohol and Drug Abuse Institute, University of Washington
A Multidisciplinary Center at the University of Washington, whose mission is to support and facilitate research and research dissemination in the field of alcohol and drug abuse. There is information about research being conducted and local clinical trials; in addition, there is an extensive list of links related to drug and alcohol abuse, treatment, and recovery.
American Council for Drug Education
National Institute on Drug Abuse (NIDA)
NIDA provides easy-to-use powerpoint "Slide Teaching Packets" on several topics related to drugs and the brain, including: The Brain and the Actions of Cocaine, Opiates, and Marijuana, The Neurobiology of Drug Addiction, and the Neurobiology of Ecstasy (MDMA). NIDA and NIH also offer a free curriculum supplement called "The Brain: Understanding Neurobiology through the Study of Addiction."
General Online Resources
Action Bioscience provides readings and curriculum ideas for topics such as biotechnology, the human genome, and a variety of other topics in biology.
The Biology Project provides activities, lesson plans, and tutorials, especially strong on problem sets, and tutorials.
The DNA Files--Experts and public radio watchdogs explore cutting edge topics in biomedical research.
Online Texts
The bookshelf is growing number of biology reference boks that can be searched directly. Several important biology reference texts, such as" Molecular Biology of the Cell" by Alberts et. al, and "Immunology" by Janeway et. al, are available.
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http://www.personalgenomes.org/
The Personal Genome Project is a public genomics research study that aims to improve our understanding of genetic and environmental contributions to human traits. They are enrolling public for purposes that promote human welfare through the advancement of scientific and medical discovery. The mission of the Personal Genome Project is to encourage the development of personal genomics technology and practices that: are effective, informative, and responsible; yield identifiable and improvable benefits at manageable levels of risk; and are broadly available for the good of the general public. To achieve this mission they are building a framework for prototyping and evaluating personal genomics technology and practices at increasing scales. Each year additional people are recruited to participate. A Series of articles written by Emily Singer for MIT's Technology Review detailing the rationale behind the Personal Genome Project, and how the project has grown tremendously during just the past few years.
