1. Genes and Chips

2. Genes….  The proper and harmonious expression of a large number of genes is a critical component of normal growth and development and the maintenance of proper health. Disruptions or changes in gene expression are responsible for many diseases.

3.  Gene expression is a highly complex and tightly regulated process that allows a cell to respond dynamically both to environmental stimuli and to its own changing needs.

4. In short…  Not only do genes have an ‘on’ and an ‘off’

5.  They also have volume control

6. This means…  All cells in an organism contain the same genes  Different genes are expressed in different tissues under different conditions

7. Induced (expressed) Gene: Gene A -------  Lots of mRNA A

8. Repressed (not expressed) Gene: Gene B ……..sadly, no mRNA B

9. To Determine which genes are expressed under which circumstances:  A microarray is 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.

10. How they work:

11. Why they are REALLY important….  Survey a large number of genes quickly or when the sample to be studied is small.  Assay gene expression within a single sample or to compare gene expression in two different cell types or tissue samples, such as in healthy and diseased tissue.

12.  Functions of new genes can be determined based on similarities in expression patterns with those of known genes.  Reveal new patterns of coordinated gene expression across gene families.  Knowledge of these inter- relationships among genes

13. Practical applications…  Comparative Genomic Hybridization --tumor classification, risk, and prognosis  Expression Analysis --drug and therapy development and response  Mutation/Polymorphism Analysis --tracking disease progression

14. In this experiment:  Identify the major steps of the chip process  Identify the primary colors that a chip shows  Understand the reasons for the presence/absence/intensity of a particular color

15. You will need:  Chip slide  Marker  Access to hybridization solutions

16. What to do: 1.DO NOT TOUCH surface of slide 2.Mark each spot with a number (1-6) 3.Move to water bath area 4.Use the dropper bottles to spot the appropriate gene solution onto each labeled slide spot 5.Successful print = hardened and dry spots

17.  6. Carefully drop 1-2 drops of hybridizing solution onto each spot, making sure not to touch tip of bottle to DNA spots  7. Visualize results by setting slide on white paper

18. How to read them…  The mRNA used in this lab was isolated from 6 genes found in both normal and cancerous lung cells  Expressed genes, because we are NOT using lasers, will be seen as either pinks, purples, and blues

19. Important Stuff….  Many students may have the view that only important cancer genes are those that are highly expressed, so it must be explained that: Highly expressed normal genes may prevent cancer Minimally expressed genes may be important “Housekeeping genes” may be expressed in either cell type

20. As the lab is written:  Everyone gets the same result, so basically everyone is testing the same individual  Students who don’t follow protocol can still “get the right results,” and therefore understanding is unclear

21. So….  Did some research and discovered how the solutions were produced…various combinations of water, phenophthalein, and thymolphthalein…by altering the combinations different “color” results can be achieved.  Student groups can have different “patients” to diagnose