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Problem 36: Different genes are active in different kinds of cells.

Use DNA arrays to determine the best treatment for breast cancer.
HI! Herceptin and taxol are two drugs used to treat breast cancer. Some women respond better to one vs. the other, and some women respond best to a combination treatment. Using DNA arrays, scientists can test which genes are expressed in tumor and normal tissues under different drug treatments. Let's try this example. You print a DNA array with six cDNA samples labelled A to F. You then do four sets of experiments. You take normal and tumor cells from a woman after treatment with 1) herceptin, 2) taxol, 3) herceptin and taxol, 4) no treatment. You isolate mRNA from the tissues, label them with fluorophores, and incubate the DNA arrays with the mRNAs. The computer can convert the "color" into a numerical value. Red = 0; Yellow = 50; Green = 100. Gene A is not expressed in any of the tissues under any condition. (No, gene A is expressed in these cells.) Gene A is the control. It is always expressed to the same level in cells. (That is correct.) The experiments didn't work. The colors should be only green or red. (No, if normal and tumor mRNAs bind fairly equally to gene A, then "yellow" can occur.) None of the above. (No, there is a correct answer.) Both normal and tumor cells have mRNA that bind to gene A. The color intensity of the combination of green and red fluorophores is yellow. Gene A is a control that is expressed the same way in all kinds of cells. In general, what does the pattern of expression of gene B mean? Gene B is highly expressed in normal cells after Herceptin treatment. (No, a low number, red, means more tumor mRNA is binding.) Gene B does not respond to treatment. (No, a low number, red, does not mean there is no response.) Gene B is highly expressed in tumor cells after herceptin treatment. (That is correct.) Gene B is not expressed in normal cells. (No, gene B is expressed in normal cells.) Gene B is more highly expressed in tumor cells after treatment with herceptin, because it bound more "red" mRNA. You plot a graph of the data that you have, and you notice that genes B and D have similar profiles. Are there other samples with similar profiles? Genes B and D are the only ones with a similar profile. (No, genes B and D are not the only ones with a similar profile.) Genes C and F have similar profiles. (That is correct.) Gene E has a similar profile to B and D. (No, gene E does not have a similar profile to B and D.) Genes C and F bound normal and tumor mRNAs similarly under all the treatment conditions. The expression of genes C and F are "clustered" as is the expression of genes B and D. cONGRATULATIONS!!! YOU'RE SO SMART!
dna arrays, tumor cells, color intensity, breast cancer, combination treatment, kinds of cells, taxol, cdna, genes, tissues, fluorophores, expression, colors, drugs
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