Microarrays allow scientists to analyze expression of many genes in a single experiment quickly and efficiently. They represent a major methodological advance and illustrate how the advent of new technologies provides powerful tools for researchers. Scientists are using microarray technology to try to understand fundamental aspects of growth and development as well as to explore the underlying genetic causes of many human diseases.
-EnablingTechnologies MICROARRAYS: CHIPPING AWAY AT THE MYSTERIES OF SCIENCE AND MEDICINE
Read the instructions that follow below and begin your investigation of microarrays and their applications in science and medicine. Answer the questions, according to your instructor's directions, to demonstrate your understanding of this new and important technology
You are about to begin an Envirohealth WebQuest. Instructions will appear in RED and questions to be answered in BLACK. Read the directions carefully before going to any sites. Look at the questions that are to be answered from the information at a site and use the questions as objectives to direct your reading and examination of any pages. Toggle back and forth between the specified sites and these pages. Use the BACK and FORWARD button on your browser bar. Your instructor will explain to you how they want your data displayed for grading.Let's begin! Click the green heading above each section of questions below. It will take you to your destination.
When you arrive there, read MICROARRAYS: CHIPPING AWAY AT THE MYSTERIES OF SCIENCE AND MEDICINE. The headings over each of the questions below will indicate in which section of the page the information is found to answer the questions.
DNA Microarrays: The Technical Foundations1. The two recent complementary advances in knowledge and technology were the Human Genome Project and DNA microarray technology.
2. A microarray works by exploiting the ability of a given _______molecule to bind specifically to, or hybridize to, the ______ template from which it originated.
3. By using an array containing many mRNA samples,
scientists can determine, in a single experiment, the expression levels of hundreds or thousands of genes within a cell by measuring the amount of DNA bound to each site on the array.
Why Are Microarrays Important?4. The use of microarrays could speed the identification of genes involved in the development of various diseases by allowing scientists to examine greater number of genes.
5. Microarrays are an insignificant advance both because they may contain a very large number of genes and because of their small size.
What Exactly Is a DNA Microarray?6. DNA Microarrays are
DNA Arrays-The historyClick on the link DNA Arrays-The history. You will arrive at a page on the DNAi web site called MANIPULATION. Scroll to the bottom of the page and Click on Techniques. The next page will contain the Index for the section on Techniques. Click next on Large-Scale Analysis at the top of the page. Click on the first listing in the list of presentations, Gene Chips. Move through the presentation and answer the questions below on the history of the gene chip.
Use the key below to match the microarray related term with a description of its function: Key:1. Stephen Fodor
2. Affymetrix
3. special glass
4. Photolabile protective group
5. UV light
6. polymerization
7. filter
8. 20 nucleotides long
9. cDNA
7. Gene chip arrays are printed on this.
8. The length of the nucleotide sequences on the chip.
9.The energy source used to remove the protective agent.
10. The company that was formed to manufacture gene chips.
11. The probe that is used to identify the nucleotide sequences on the chip.
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."-Howard Hughes Medical InstituteNow click on the link labeled Gene Chip Manufacturing .You will be taken to a page on the Howard Hughes Medical Institute's web site. The page is identified as a BIOINTERACTIVE page of movies. Scroll down until you see GENE CHIP MANUFACTURING. Click on the graphic and another window will open and Download the movie on Gene Chip Manufacturing. The movie explains how DNA microarrays are made. When you have run the movie and feel you understand it, then answer the four questions listed below.
12. There is a different twenty-five letter DNA sequence in every square on a DNA microarray chip.
13. The microarray chips are produced by a method that is completely different from the process used to make computer chips.
14. Light and masks are used to deprotect certain squares on the microarray allowing DNA letters to attach to them.
15. The build up of a DNA sequence on any microarray square is limited to only seven letters per square.
Small Molecule Microarray"To screen many small molecules at once, microarray technology is useful. Automated devices have made it possible for thousands of different small molecules to be printed as an array of spots on a glass slide. A single type of protein which has been tagged with a fluorescent marker can then be washed across the array. Any small molecule that binds to the protein can be detected by scanning for spots that are fluorescent.One technique for screening small molecules uses glass slides that have been machine-printed with an array of dots, each dot containing different small molecules. This is known as a small molecule microarray. Each slide contains 12,000 small dots, corresponding to 12,000 different small molecules. The slides are then washed with a single known protein that has been tagged with a fluorescent marker. If the protein binds with a small molecule on the slide, it will glow, indicating that the small molecule contained in that particular dot is a potentially useful one for studying that particular protein function."
-Howard Hughes Medical Institute
Now click on the link labeled Small Molecule Microarray . You will be taken to a page on the Howard Hughes Medical Institute's web site. The page is identified as a BIOINTERACTIVE page of animations and movies. Scroll down until you see SMALL MOLECULE MICROARRAYS. Click on the graphic and another window will open with the link to the movie on Small Molecule Microarrays. The movie and animation explain how microarrays are made and how they can be used as a probe for molecules. When you have run the movie and feel you understand it, then answer the four questions listed below.
16. The microarray robot is very much like the robot that is used to print the New York Times.
17. There are forty-eight quill pen-like structures spotting a one nanoliter solution of these small molecules on the microarray slides.
18. When finished, the slide will have 20,000 different small molecules attached to it. Two molecules per spot.
19. The slide is washed with protein and if there are any complmentary shape matches, then there is a new small molecule probe of one of those proteins.
Now that you have some understanding of how microarrays are created, let's take a look at their cost and how they are "read", or scanned, to interpret the data they contain. Read the BLACK TEXT below. Answer the questions following the reading to indicate your understanding of the information.Cost and Analysis of Microarrays
Microarray technology is highly cost-intensive. Setting up a system ranges in price from
$60,000 to 500,000. The cost of each chip ranges from $50 for self-made chips to $2,500 for ready made ones. The computational hardware and software can range in cost from $10,000 to more than $100,000.
Microarrays allow for the simultaneous monitoring of the behavior/expression of thousand of genes, proteins, or whatever molecules are attached to their surface. They provide a functional aspect to sequence information.
Specifically, the data from microarrays is composed of several layers. Once experimental data have been obtained, the data have to be normalized in order to standardize all experiments to variations in microarray quality, sample handling and biological diversity. The data must be stored in relational databases linked to publicly available genomic and functional databases as well as the results of previous experiments, allowing easy data retrieval and manipulation. Advanced analysis tools such as clustering applications and data mining tools are needed in order to retrieve all functional information stored in the data. Standardization of the data (raw and processed) is a major problem due to the vast number of available technologies. Standard expression database management systems are being developed to permit data sharing by scientists worldwide.
20. The cost of setting up a microarray system is not very expensive considering that the cost is only $100 each for ready made chips and the analysis software comes free when you purchase the chips.21. One of the short-comings of microarray chips is that they can only be used to do DNA analysis.
22. Data from microarray chips requires considerable statistical analysis. Standardization of and correlation of the results to relational databases requires advanced analysis tools such as clustering applications and data mining tools.
Continue your Quest with the images and text that follows. Read the BLACK TEXT below. Answer the questions following the reading.Scanning DNA Microarrays
Here's an example of the process of scanning microarrays. There are many different types of customized DNA microarrays for clinical and research use. Let's examine gene expression in tumors from cancer patients. The first approach in creating a microarray for tumor analysis is to use the chemically synthesized form of DNA called COMPLEMENTARY DNA (cDNA). These probes contain only the coding part of the DNA sequence, complementary to its corresponding mRNA transcript. The microarray we are buiding is in the form of a microscope slide containing hundreds to thousands of immobilized DNA samples that are hybridized in a manner very similar to other previously used assay methods. The main function of this microarray is to detect the level of mRNA transcript of genes of interest from the tumor cells. The microarray plates are incubated in the solution containing the genetic material under consideration. The mRNA transcripts floating in the solution will hybridize to their complementary cDNA, previously placed on the microarray chip. Since the cDNA on the chip is fluorescently labeled, every spot will emit a light in an ultraviolet environment, intensity of which depends on the amount of hybridized mRNA. The differentiation of the cDNA's ultraviolet dye allows the comparison of the gene expression under different experimental conditions.
Coding the gene expression by means of colors is used for building genetic maps and graphical data processing. An *expression gene map is created in the form of a table; the rows of which will correspond to the consecutive genes and the columns will represent different samples.
*cDNA maps: Shows the locations of expressed DNA regions ( exons ) on the chromosomal map. Because they represent expressed genomic regions, cDNAs are thought to identify the parts of the genome with the most biological and medical significance. A cDNA map can provide the chromosomal location for genes whose functions are currently unknown. For disease- gene hunters, the map can also suggest a set of candidate genes to test when the approximate location of a disease gene has been mapped by genetic linkage techniques.[Primer on Molecular Genetics, Oak Ridge National Lab, US] 23. The first approach in creating a microarray for tumor analysis is to use the chemically synthesized form of DNA called CONTIGUOUS DNA (cDNA).
24. The differentiation of the cDNA's ultraviolet dye allows the comparison of the gene expression under different experimental conditions.
25. Data from microarray chips can be used to create gene expression maps.
This completes the investigation on microarrays. Now, 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. Support your position and choices with the facts presented in this presentation.Open your word processing application and create your essay. Your instructor will explain the format. Good luck!
Part 2
