Labs on a Chip

Background Knowledge: Students should be familiar with DNA structure and function, RNA structure and function, the central dogma

Do Now (teacher can explain this out loud)

Imagine you are a software engineer. You have written the program ‘Microsoft Word.’ On an individual computer, you aren’t sure which functions in the program are used most. For instance, a high school student, like you, might use the ‘Blank Document’ template of Microsoft Word to write papers for school. An administrative assistant in the office of the school might use the ‘Letters and Faxes’ template to type letters or faxes that he needs to send each day. Finally, your principal might use the ‘Memos’ template to type memos to the teachers each day.

Although each person uses the same program on his or her computer, each uses different pieces of the program to complete different tasks each day.

On the other hand, there are certain functions that all of the individuals who might use Microsoft Word would use. For instance, the student, administrative assistant and principal all use the spellcheck and save function.

How is the Microsoft Word computer program similar to DNA? How is each person who uses the program similar to different cells in your body?

Can we look at a copy of the program and tell which parts of it are being used by each person? Can we tell how often they are being used by each person?

Just like the computer program, DNA does not give us information about when and how much each part (gene) is used (transcribed). However, this information is extremely useful to a scientist or doctor. For instance, in many diseases, a part of DNA or a number of parts (genes) are being used/transcribed too much. In other diseases, an important part of DNA (gene) is not being used (transcribed) properly. How can a scientist find out which part or gene is going haywire in a cell that is sick?

The key is to look at the message that is made from the DNA. In other words, scientists are interested in the mRNA transcripts in a diseased cell and how they compare to the number and type of mRNA transcripts in a healthy cell of the same type. From that information, a scientist may look at the DNA sequence to see if there are any mutations and/or investigate the control mechanisms involved in the transcription of that gene.

Two things to note: mRNA has a sequence that is complementary to the DNA. Therefore, it can hybridize to the DNA sequence from which is it has been transcribed.

And, there is an enzyme called reverse transcriptase that can make DNA from RNA.

Introducing DNA Microarrays to Class

What if one of the computer’s is infected with a bug? Let’s say that this bug has messed up the code in Microsoft Word for the ‘Letters and Faxes’ template. Who is affected by this bug? When is this person affected by this bug?

In our example, unless we know who uses which template in our program, we can’t find out who needs the bug fixed. Similarly, until we know which cells in our body make products from which genes in our DNA, we can’t fix problems with DNA (mutations) or control mechanisms for transcription of DNA. For one cell, how can we determine what DNA is being expressed? What cellular products would give us an idea of gene expression?

mRNA is the key to our understanding of DNA expression. We need to look at the mRNA in a cell to determine which genes are being expressed. If there is a problem in the mRNA or more mRNA present than is in a healthy cell, we need to go back to the DNA code that made it to figure out what went wrong.

This is where DNA microarrays come in handy. Like in our example, it would take a lot of work to find the person who is affected by the bug. In cells, it takes a lot of time to figure out which genes are responsible for disease. DNA microarrays allow scientists to comb through a lot of cellular information to figure out areas that might be responsible for disease. DNA microarrays allow the process to occur quickly. However, the data has to be analyzed carefully.

There are three activities that make up this lesson. Each has directions and questions for the students on their worksheet.

First, you need to decide which genes (sequences of DNA) look interesting. Which genes are different in people with disease than in those without? Which genes are expressed only during certain times during development? Scientists continue to compile information about interesting DNA sequences in databases. The analysis of these databases is a fascinating area of science called bioinformatics.

Next, you need a short strand of the gene of interest (about 25 base pairs long). This strand will hybridize to the DNA or RNA that might be of interest when we run the microarray. Finally, the strands need to be attached to a slide.

(In an actual lab, the DNA microarray would be a slide with approximately 10,000 different gene sequences of interest in spots on a slide. Each spot has billions of the 25 base pair sequences attached.)

You have a sheet with 15 different DNA sequences that are available. You need to choose 4 of those sequences that you feel might be interesting. Cut out the 4 sequences from the sheet. Tape each in one of the four squares on your microchip sheet.

First you need to choose a type of cell to study. For example, you may want to study cells that have been exposed to certain pollutants and compare them to cells that have not been exposed. Maybe you would like to investigate which genes are turned on in cancer cells versus normal cells. Or you may want to study which genes are turned on in a developing egg versus an adult chicken.

A scientist must first isolate the mRNA from the cells of interest. Then, a fluorescent label is used to label the mRNA. That way, if the mRNA hybridizes with the DNA sequences on the microchip, it will be visible using a fluorometer.

This activity requires groups of 3 or 4 students. Take a pair of envelopes of mRNA transcripts from the front table. Each is labeled with the cell type from which the mRNA was isolated.

First, check to see if any of the normal envelope sequences would hybridize with the DNA sequences on your sheet. Next, check to see if any of the abnormal envelope sequences would hybridize with the DNA sequences on your sheet. Fill out the table on your worksheet.

Note: These sequences are arbitrary as are the mRNAs for the cell types. The teacher may wish to create other sequences of cells/mRNAs of interest depending on what has been studied in class prior to this activity.

These examples may seem easy for students to interpret. However, as the next activity will show, DNA microarray results are difficult to interpret because in any cell some genes are always on or always off. Finding causation from just the microarray data is virtually impossible. However, it does help scientists narrow down their focus to a number of interesting genes. Then, a scientist can use other biotechnology techniques to investigate the importance of those genes in more depth.

Now we will begin to analyze the results from DNA microarrays. As you saw in the second activity, depending on the cell type chosen, additional mRNA transcripts may have been present, no mRNA transcripts may have been present or different ones may have been present in one cell as compared to another. This type of data makes it difficult to analyze and interpret results from DNA microarrays. To demonstrate the process of analyzing data we will complete the following activity.

We will investigate the role of 10 different genes in a type of cancer in 5 patients (five microarrays were run). I need 10 volunteers (10 genes were tested on each array). Each volunteer will represent a gene or DNA sequence on a DNA microarray. In a cell of any type, each gene can either be on or off. I will give each person/gene a list of the five patients who we have tested and whether the gene is on or off for that patient. If the gene is on, the person who represents that gene will stand. If the gene is off, the person will remain seated. We will compile the data for five different patients. (Call out each person and have those genes that are ON stand. Then have a student compile the data in the following table on the board (X means ON). It should be copied onto each student’s worksheet.)

Patient #	1	2	3	4	5
Genes ON	2	2	1	2	1
	4	3	3	3	4
	5	4	4	4	6
	8	8	5	8	7
		10	6	10	10
			7
			10

Have students share answers to help everyone understand how the data is interpreted. You may then assign the homework that involves using DNA microarrays to understand how patients will respond to drug treatments or use the activity as a follow-up lesson on the next day.

National Standards

Teaching Standard A: Teachers of science plan an inquiry-based science program for their students.

Content Standard A: As a result of activities in grades 9-12, all students should develop abilities necessary to do scientific inquiry, understandings about scientific inquiry

Content Standard C: As a result of their activities in grades 9-12, all students should develop understanding of the cell, molecular basis of heredity, biological evolution, interdependence of organisms, matter, energy, and organization in living systems, behavior of organisms

Program Standard A: Teaching practices need to be consistent with the goals and curriculum framework.

New York City Science Standards

Standard S5 (a-f) The students demonstrates scientific inquiry and problem solving by using thoughtful questioning and reasoning strategies, common sense and conceptual understanding from Science Standards 1-4, and appropriate methods to investigate the natural world.

	Blank Document	Letters and Faxes	Memos	Spellcheck	Save
Student	X			X	X
Administrative Assistant		X		X	X
Principal			X	X	X

	Gene 1	Gene 2	Gene 3	Gene 4	Gene 5	Gene 6	Gene 7	Gene 8	Gene 9	Gene 10	Chip
Person 1		X		X	X			X			1
Person 2		X	X	X				X		X	2
Person 3	X		X	X	X	X	X			X	3
Person 4		X	X	X				X		X	4
Person 5	X			X		X	X			X	5

Gene		1	6	7	9	2	8	4	10	3	5
Patient	1					X	X	X			X
	2					X	X	X	X	X
	3					X	X	X	X	X
	4	X	X	X				X	X	X
	5	X	X	X				X	X		X