1. ALU Polymorphisms Unit Questions 1.What does DNA tell us about ourselves? 2.In what ways can DNA be altered and what effects can alterations have? 3. What gear and skills are needed to study DNA?

2. Co-authored by… Chris Munzert – Mt. Hope Marcia King – Mt. Hope Janet Butler – Davies Career and Tech. John Wemple – Providence Schools Chris Moon – Providence Schools

3. PART I: Neurofibamatosis: A human genetic disorder caused by a mutation in the Neurofibromin Gene (NF-1) PART II: Alu Insertion Lab

4. OPTIONAL GUEST SPEAKER DAY – Career Connection Genetic Counselor

7. WHAT IS RESPONSIBLE FOR THE SYMPTOMS JUST OBSERVED? Genetic Disorders

8. Neurofibromatosis Information Souce:http://www.emedicine.com/derm/topic287.htm Souce:http://www.emedicine.com/derm/topic287.htm Background: Neurofibromatosis is an autosomal dominant disorder that affects the bone, the nervous system, soft tissue, and the skin. Race: All racial groups are affected equally. Sex: Women and men are affected equally by neurofibromatosis. Frequency: Worldwide, NF-1 occurs in approximately 1 of 2500- 3300 live births. Mortality: Patients with NF-1 have an estimated 3-15% additional risk of malignant disease in their lifetime. (The mortality rate is higher than that of the healthy population because of the increased potential for malignant transformation of diseased tissues and the development of neurofibrosarcoma.)

9. Meet Joseph Merrick – For a long time, it was thought that he had neurofibromatosis

11. Class Articles: Pair Share Joseph Merrick: “The Elephant Man” –Article #1: History of Joseph Merrick http://myhomeoflove.tripod.com/shortstories/merrick.html –Article #2: A comparative analysis of “Elephant Man’s Disease” http://www.dartmouth.edu/~dujs/1999S/03_Merrick.pdf Living with Neurofibromatosis: Real people, real stories…Living with Neurofibromatosis

12. DAY 2 Assessing Prior Knowledge DNA  RNA  Protein – Overview AnimationsDNA  RNA  Protein –Details on Transcription - AnimationDetails on Transcription –Details on Translation - AnimationDetails on Translation

13. DAY 3 What does the normal NF-1 gene do? Animation of NF-1 Gene comparing normal function with mutated functions.Animation of NF-1 Gene comparing normal function with mutated functions. Rotate a 3-D model of the NF-1 protein

14. DAY 4 How do the versions of the genes differ? Sequence Alignment Activity Normal DNA Sequence vs. Mutant DNA Sequence LALIGN – Genomic DNALALIGN Teacher Comment: Details on Mutation: Alu element inserts into an intron; this changes the splicing pattern that ultimately results in the deletion of exon #6.

15. DAY 5 PRE-LAB NOTES Mutation Refresher Activity –Deletions –Insertions –Duplications –Etc…

16. DAY 6 What caused the NF-1 mutation? Meet Alu… A de novo Alu insertion results in neurofibromatosis type 1 Nature 353, 864 - 866 (31 October 1991); doi:10.1038/353864a0A de novo Alu insertion results in neurofibromatosis type 1 Nature 353, 864 - 866 (31 October 1991); doi:10.1038/353864a0 What other diseases are caused by Alu insertions?What other diseases are caused by Alu insertions?

17. Source Document Source Document http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WNG-45FSDCM- 25&_user=489286&_coverDate=07%2F31%2F1999&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000022678&_version=1&_urlVersion=0&_useri d=489286&md5=1c3c2d942c3aae40e11b4ceddb92223f Source Document

18. Why should I not think Alu is only associated with disease? The vast majority of “Alus” are located in introns, where they appear to have no phenotypic effect…The vast majority of “Alus” are located in introns, where they appear to have no phenotypic effect… Alu insertions in the primate genome have been occurring for millions of years…Alu insertions in the primate genome have been occurring for millions of years… Alu insertions have been used to study patterns of human migration.Alu insertions have been used to study patterns of human migration.Alu insertions have been used to study patterns of human migration.Alu insertions have been used to study patterns of human migration. Follow this link to an interesting animation of human migrationFollow this link to an interesting animation of human migration

19. DAYS 7  Alu Insertion Lab DAY 7 –Extract DNA and freeze DAY 8 –Setup PCR –Flex Time Teacher Note: Drop off PCR samples today to Megan. DAY 9 –Guest Speaker: Applying Bioinformatics to answer real questions

20. LAB Continues… DAY 10 –Electrophoresis and Photography –Possible Results and Explanations HW: Alu within an Alu gel anomaly DAY 11 –Discuss Homework: Alu within an Alu gel anomaly –Analyze Gels Expected movement of the bands What does it mean if they have at least one Alu-element? Utility of Alu Insertion information in Evolution Studies DAY 12 –PANEL DISCUSSION: Kary Mullis and Craig Venter and Francis Collins