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Catchy Title: Microarrays: Chipping Away at the Mysteries of Science and Medicine
Theme/Topic of Lesson: Introduction to Microarrays.
Time Commitment: Two 88-minute Periods
Subject Area(s):
Language Arts - Writing (composition)
Science - Environmental
Science - Biology
Science - Chemistry
Grade Level(s): 9,10,11,12
Standards Alignment:
Class Challenge Question: What are microarrays, how are they produced, and how do they work?
Overview:
The use of microarrays in medical research has the potential to revolutionize how disease is treated. This new technology may allow researchers to analyze the genetic effects of environmental agents (chemicals and medicines) quickly and accurately. Changes in DNA could be detected in the laboratory using a microarray without many of the uncontrolled variables found in living organisms. This direct link between cause and effect will allow data interpretation to be more precise and probably more accurate.
Students will be investigating what microarrays are, how they are produced and how can be used in research. The online Web Quest is designed to lead students in a directed path of inquiry through use of selected internet sites. Each of these sites has been chosen because of their clarity and accuracy and will allow student to develop an understanding of this new line of investigation. The final product of this activity will be an essay summarizing what they have learned. Teachers have the option of having the Web Quest and questions printed out to be evaluated as well.
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Environmental Science
(9-12) | Maryland Content Standards
Students will use scientific skills and processes to explain the interactions of environmental factors (living and non-living) and analyze their impact from a local to a global perspective. | Maryland State Indicators
6.12.5
investigate and analyze environmental issues from local to global perspectives (e.g., world population, food production and distribution, pollution and epidemics, biodiversity) to develop an action project that protects, sustains, or enhances the natural environment.
The student will identify an environmental issue and formulate related research questions. (CLG 6.4.1.)
The student will design and conduct the research. (CLG 6.4.2.)
The student will interpret findings to form conclusions and make recommendations to help resolve the issue. (CLG 6.4.3.)
The student will apply the conclusions to develop and implement an action project.(CLG 6.4.4.)
The student will analyze the effectiveness of the action project in terms of achieving the desired outcomes. (CLG 6.4.5.) | Social, ethical, and human issues
(Gr. 9-12) | ISTE Technology Standards
2. Social, ethical, and human issues
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Students understand the ethical, cultural, and societal issues related to technology.
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Students practice responsible use of technology systems, information, and software.
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Students develop positive attitudes toward technology uses that support lifelong learning, collaboration, personal pursuits, and productivity.
| ISTE Technology Performance Indicators
Identify capabilities
Identify capabilities and limitations of contemporary and emerging technology resources and assess the potential of these systems and services to address personal, lifelong learning, and workplace needs.
| Technology research tools
(Gr. 9-12) | ISTE Technology Standards
5. Technology research tools
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Students use technology to locate, evaluate, and collect information from a variety of sources.
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Students use technology tools to process data and report results.
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Students evaluate and select new information resources and technological innovations based on the appropriateness for specific tasks.
| ISTE Technology Performance Indicators
Routinely and efficiently
Routinely and efficiently use online information resources to meet needs for collaboration, research, publications, communications, and productivity.
| Technology research tools
(Gr. 9-12) | ISTE Technology Standards
5. Technology research tools
-
Students use technology to locate, evaluate, and collect information from a variety of sources.
-
Students use technology tools to process data and report results.
-
Students evaluate and select new information resources and technological innovations based on the appropriateness for specific tasks.
| ISTE Technology Performance Indicators
Investigate and apply
Investigate and apply expert systems, intelligent agents, and simulations in real-world situations.
| Writing
(9-12) | Maryland Content Standards
Students produce informational, practical, persuasive, and narrative writing that demonstrates an awareness of audience, purpose and form using stages of the writing process as needed (i.e., pre-writing, drafting, revising, editing and publishing). | Maryland State Indicators
3.12.1.2
support thesis or judgments with techniques such as analogies, paraphrases, quotations and opinions from authorities (CLG 2.1.1, CLG 2.1.2, CLG 2.1.3, CLG 2.2.1, CLG 2.3.4, CLG 3.1.1 CLG 3.2.1, CLG 4.1.1)
| Writing
(9-12) | Maryland Content Standards
Students produce informational, practical, persuasive, and narrative writing that demonstrates an awareness of audience, purpose and form using stages of the writing process as needed (i.e., pre-writing, drafting, revising, editing and publishing). | Maryland State Indicators
3.12.3.2
self-edit and refine writing using knowledge of standard English conventions of language and appropriate print and non-print resources (e.g., dictionary, thesaurus, spell-check software) (CLG 2.2.2, CLG 2.2.3, CLG 2.2.5, CLG 2.2.6, CLG 3.1.6, CLG 3.1.7, CLG 3.1.8, CLG 3.1.9, CLG 3.3.1, CLG 3.3.2, CLG 4.3.1, CLG 4.3.2, CLG 4.3.3)
| Writing
(9-12) | Maryland Content Standards
Students produce informational, practical, persuasive, and narrative writing that demonstrates an awareness of audience, purpose and form using stages of the writing process as needed (i.e., pre-writing, drafting, revising, editing and publishing). | Maryland State Indicators
3.12.6.1
write expository texts for an intended audience and purpose that define, inform, explain or some combination, including essays of analysis and research papers that
- marshal evidence in support of a thesis and related claims
- include information on all relevant perspectives, considering the validity and reliability of primary and secondary sources
- make distinctions about the relative value and significance of specific data, facts, and ideas
- anticipate and address a reader's potential biases, misunderstandings, and expectations
(CLG 2.1.1, CLG 2.1.2, CLG 2.1.3, CLG 2.1.4, CLG 2.2.1, CLG 2.2.2)
| Writing
(9-12) | Maryland Content Standards
Students produce informational, practical, persuasive, and narrative writing that demonstrates an awareness of audience, purpose and form using stages of the writing process as needed (i.e., pre-writing, drafting, revising, editing and publishing). | Maryland State Indicators
3.12.2.1
use clear research questions and coherent research methodology to elicit and present evidence from primary and secondary sources using available library, electronic, and human resources (CLG 2.2.1, CLG 2.3.1, CLG 2.3.2, CLG 2.3.3, CLG 2.3.5)
| Writing
(9-12) | Maryland Content Standards
Students produce informational, practical, persuasive, and narrative writing that demonstrates an awareness of audience, purpose and form using stages of the writing process as needed (i.e., pre-writing, drafting, revising, editing and publishing). | Maryland State Indicators
3.12.1.1
establish a controlling impression or coherent thesis that conveys a clear and distinctive perspective on the subject and maintains a consistent tone and focus throughout the piece of writing (CLG 2.1.1, CLG 2.1.2, CLG 2.1.3, CLG 2.2.1, CLG 2.3.4, CLG 3.1.1 CLG 3.2.1, CLG 4.1.1)
| Writing
(9-12) | Maryland Content Standards
Students produce informational, practical, persuasive, and narrative writing that demonstrates an awareness of audience, purpose and form using stages of the writing process as needed (i.e., pre-writing, drafting, revising, editing and publishing). | Maryland State Indicators
3.12.2.3
use appropriate conventions for in-text documentation, notes, and bibliographies, adhering to style manuals (CLG 2.2.1, CLG 2.3.1, CLG 2.3.2, CLG 2.3.3, CLG 2.3.5)
| Writing
(9-12) | Maryland Content Standards
Students produce informational, practical, persuasive, and narrative writing that demonstrates an awareness of audience, purpose and form using stages of the writing process as needed (i.e., pre-writing, drafting, revising, editing and publishing). | Maryland State Indicators
3.12.2.2
synthesize information from multiple sources and identify complexities and discrepancies in the information and how each medium offers a different perspective (CLG 2.2.1, CLG 2.3.1, CLG 2.3.2, CLG 2.3.3, CLG 2.3.5)
| Life Science
(9-12) | Maryland Content Standards
Students will use scientific skills and processes to explain the dynamic nature of living things, their interactions, and the results from the interactions that occur over time. | Maryland State Indicators
3.12.4
explain how traits are inherited and passed from one generation to the next (i.e., from parental DNA, RNA to gross anatomical traits of offspring).
The student will demonstrate that the sorting and recombination of genes during sexual reproduction has an effect on variation in offspring (meiosis, fertilization). (CLG 3.3.1.)
The student will illustrate and explain how expressed traits are passed from parent to offspring (phenotypes, dominant and recessive traits, sex-linked traits, genotypes, punnett square). (CLG 3.3.2.)
The student will explain how a genetic trait is determined by the code in a DNA molecule (definition of gene, structure of DNA, sequence of bases directing protein formation, proteins). (CLG 3.3.3.)
The student will describe the effect of gene alteration on an organism and/or a population (mutations, chromosome number, cloning, genetic recombination). (CLG 3.3.4.) | Life Science
(9-12) | Maryland Content Standards
Students will use scientific skills and processes to explain the dynamic nature of living things, their interactions, and the results from the interactions that occur over time. | Maryland State Indicators
3.12.3
describe the abnormal functioning in cell regulation, such as cancer, as it relates to cell growth, division, and response to environment. |
Learning Objectives:
The Students will:
- describe the uses of a microarray.
- explain why microarrays are important to genetic research.
- describe the history of microarrays and how they are constructed.
- clarify how a microarray is analyzed.
Assessment
At the end of the activity students will be required to construct an essay which will demonstrate their understanding of microarrays and how they are used in environmental research.
Teachers will have the option of printing out the Web Quest for evaluation of the student responses to the questions included in the document.
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Resources
| Internet Sites | National Center for Biotechnology Information This site is used as an introduction to microarrays. | | http://www.ncbi.nlm.nih.gov/About/primer/microarrays.html | | DNA Home This is a description of how scientist manipulate and use DNA sequences. | | http://www.dnai.org/b/index.html | | Howard Hughes Medical Institute Gene Chip Manufacturing
In this segment from the 2002 Holiday Lectures on Science, "Scanning Life's Matrix: Genes, Proteins, and Small Molecules," Dr. Eric Lander describes the process used to manufacture gene chips. An animation accompanies this description and illustrates the methods used to synthesize unique DNA sequences at specific locations on the chip. | | http://www.hhmi.org/biointeractive/genomics/video.html | | Howard Hughes Medical Institute Using Small Molecules to Modulate a Protein
This animation illustrates how a small molecule binds to a protein. As a result of the binding, the protein alters its shape and becomes inactivated. | | http://www.hhmi.org/biointeractive/genomics/animations.html | | Affymetrix Chip-Basic Concepts The oligonucleotide arrays, developed by the Affymetrix Company , are a new approach in microarray technology, based on hybridization to small, high-density arrays containing tens of thousands of synthetic oligonucleotides. | | http://cnx.rice.edu/content/m12387/latest/ | | Affymetrix Corporation This is the homepage of the Affymetrix Corporation, a leader in microarray technology. | | http://www.affymetrix.com/index.affx | | Affymetrix Corporation - Outreach GeneChip® Microarrays: Teaching Curriculum | | http://www.affymetrix.com/corporate/outreach/lesson_plan/index.affx | | Affymetrix Corporation - Outreach, Student Manual The student manual includes 5 independent activities that stress different aspects of microarray technology and the application of genetics to society. This section also contains a DNA-basics refresher and a genetics glossary. | | http://www.affymetrix.com/corporate/outreach/lesson_plan/student_manual.affx | | Laser Scanning Confocal Microscopy This site is a primer on Laser Scanning Confocal Microscopy | | http://www.microscopy.fsu.edu/primer/techniques/confocal/ | | Confocal Laser Scanning Microscopy and Digital Image Analysis Here the confocal laser scanning microscope comes to rescue,
because it allows recording very sharp and clear images even of those labelled bacteria that live in aggregates and are embedded in thick and complex structures like biofilm. | | http://www.microbial-ecology.net/clsm.asp | | Microarrays: Chipping Away at the Mysteries of Science and Medicine This is the WebQuest that will guide students through the lesson. | | http://www.fastol.com/~renkwitz/microarray_chips.htm |
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Materials
Per classPer student team/group of 2
Vocabulary
- DNA - Deoxyribonucleic acid. One of two types of molecules that encode genetic information
- Gene expression - the term used to describe the transcription of the information contained within the DNA, the repository of genetic information, into messenger RNA (mRNA) molecules that are then translated into the proteins that perform most of the critical functions of cells
- microarray - a tool for analyzing gene expression that consists of a small membrane or glass slide containing samples of many genes arranged in a regular pattern
- Mutation - A permanent change, a structural alteration, in the DNA or RNA
- mRNA - a type of RNA that reflects the exact nucleoside sequence of the genetically active DNA. mRNA carries the "message" of the DNA to the cytoplasm of cells where protein is made in amino acid sequences specified by the mRNA
- nucleotides - A subunit of DNA or RNA. To form a DNA or RNA molecule, thousands of nucleotides are joined in a long chain
- oligonucleotides - a short fragment of a single-stranded DNA that is typically 5 to 50 nucleotides long
- Sequencing - Learning the order of nucleotides (base sequences) in a DNA or RNA molecule or the order of amino acids in a protein
- Single Nucleotide Polymorphism - a small genetic change or variation that can occur within a person's DNA sequence
- tRNA - a short-chain type of RNA present in cells. There are 20 varieties of tRNA. Each variety combines with a specific amino acid and carries it along (transfers it), leading to the formation of protein with a specific amino acid arrangement dictated by DNA
Procedures
The students will construct meaning through using the text features supplied through the medium of the lesson's Internet-based WebQuest. Students will maximize learning through cooperative interaction. Student will be expected to work in teacher-selected collaborative pairs. The technology configuration will be one connected computer per student collaborative team of two. Teacher may have to reserve a computer lab for this lesson's activities. Oral reading accommodations should be provided for those not meeting grade level criteria by the instructor or the special education department.
1: Microarrays
Daily Challenge Question: What is a microarray and how are they used to further research in medicine?
88 minutes
Set-up Directions:
Students should be organized by the teacher into their cooperative groups of 2, based on computer skills, and assigned a computer. Each Internet-ready computer should be addressed to the proper URL:
Teacher Presentation & Motivation:
This presentation is meant to be an introduction to new techniques used to experiment on gene sequencing using microarrays. The use of these techniques will allow experimentors to quickly determine mutations that can be caused by the application of chemical stresses upon human genes.
Wrap Up:
Have students save their work and shut down the computers. Elicit student comments and thoughts about what they have discovered so far from research through the WebQuest.
1: Microarray Essay
Daily Challenge Question: Students will compose an essay of at least 300-500 words to explain what microarrays are, how they are made, and how data is collected from them. Statements should be supported with the facts presented in this presentation.
88 minutes
Set-up Directions:
All students will still need access to an internet ready computer to refer back to their document while writing the essay. The computer's word processing program will be used to construct the document.
Teacher Presentation & Motivation:
Students should be instructed to access the word processing program as well as their completed Web Quest for reference.
Activity 1 - Essay
Student will construct meaning from Day 1 activity by composing their essay.
Wrap Up:
Essay should be saved to computer and then printed to be turned in.
Enrichment Options
Parent-Home Connection
The WebQuest is available on the Internet and could be worked through by both students and their parents at home, heightening the awareness on nuclear power.
Cross-Curricular Extensions
History - Following the progress over the past 50 years in human gene research.
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As a reflective practitioner, note how this lesson could be adjusted after its initial implementation. How successful were the students? What did the assessment demonstrate about the students’ learning? What skills do the students need to revisit? What instructional strategies worked and what made them successful? What will you change the next time you use this lesson? Why?
Author: Arthur Renkwitz and Doug Becker
Program: EnviroHealthLink
Author's School System: Dorchester County Public Schools
Author's School: Cambridge-South Dorchester High
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