Mitochondrial DNA: Where Chemistry, Biology and Anthropology Meet

Transcription

1 Mitochondrial DNA: Where Chemistry, Biology and Anthropology Meet Meredith Knight, Rocco Cieri, Medford High School

2 Presentation Overview Concept Science Development Experiment Dissemination Questions

3 Concept From spit to SNP Develop an experiment to allow high school and college students to determine their deep ancestry using the mtdna in their saliva. Advantages Engaging for students Real world application Genetics Challenges Keeping cost low Limited time Limited equipment

4 Science Background Mitochondria are in all cells Wikipedia - File:Biological_cell.svg Mitochondria contain DNA Wikipedia - Animal_mitochondrion_diagram_en_(edit).svg

5 Science Background Mitochondrial DNA is only inherited from mother; does not recombine

6 Science Background Mitochondrial DNA (mtdna) Human mtdna = 16,569 base pairs long Different mutation rate than nuclear DNA No recombination but faster mutation! Scan loop for SNPs Wikipedia File:Mitochondrial_DNA_en.svg

7 Science Background - SNPs Single Nucleotide Polymorphism ACCTTGCGCGCTATA ACCTTGGGCGCTATA Occur throughout the genome Nuclear and mitochondrial DNA Are used as genetic markers Wikipedia - Dna-SNP.svg

8 Understanding Haplogroups

9 How to create a haplogroup 1. Identify multiple SNPs from multiple people 2. Create Haplotypes 3. Tag SNPs are identified make identifying process easier Person 1 Person 2 Person 3 Person 4

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11 Interdisciplinary Learning Opportunities Migration of ancient peoples Identification of students with their deep ancestry Challenge ideas of race/ ethnicity Immigration/ assimilation Make science relevant Link to social issues current and historical Very engaging!! These are some of the 30 Tufts students who have worked on the HHMI project

12 Classroom Implementation Medford High School Day 1: Saliva collection Day 2: PCR Day 3: Gel electrophoresis Articulate students ideas about race Race: The Power of an Illusion Compare mtdna sequence to world population GeneticOrigins.org Bioservers 400 bp band Send to Dolan they sequence Class results go on server Students can access results

13 Ligation Developed by Tufts Undergraduates Saliva collection DNA purification PCR (mtdna) Biosensor readout Ligation Gel electrophoresis Control line Ligation No ligation T G

14 Ligation-based Assay Common probe AAAA AAA B SNP specific probe T A Ligation! Mitochondrial DNA sample #1 Common probe AAAA AAA B SNP specific probe A G No ligation Mitochondrial DNA sample #2

15 Biosensor Readout Control Streptavidin B TTT.TTT AAA. AAA Sample flow Students create the biosensors Control line poly A oligonucleotides Experimental line streptavidin If 2 probes ligate, 2 red lines appear biotin binds to streptavidin *and* poly T beads bind to poly A tails

16 Examples of Working SNPs on Biosensors Haplogroup F? expect G at SNP site Haplogroup T? expect T at SNP site Haplogroup M? expect C at SNP site F-G10310A T-T10463C M-C10400T Allele Sample ID G A G A T C T C C T C T = no 54 = yes 48 = no 15 = yes 21 = no 2 = yes

17 Understanding Haplogroups

18 Running the Assay in the Classroom 7 high school juniors and seniors (Feb vacation 2010) 7 Post-Docs, graduate and undergraduate students From start to finish: 9am-6pm Students were eager to learn Students had good ideas for simplification Streamlining protocols ready in late spring 2010 M-C10400T PrC M-C10400T PrT

19 CO-OP Dissemination Plan Developed by HS teachers & Tufts Staff Summer Workshop at Tufts Equipment Lending Library Tufts maintains equipment Scheduled Times for Experiments Google calendar Tufts staff & undergrads help in classroom Teacher feedback about experiments Teachers networking between high schools Generate new ideas next year s workshop Resource Sharing Model

20 CO-OP Somerville High School Medford High School Malden High School Josiah Quincy HS (Chinatown)

21 Acknowledgements Funded by Professor s Award Professor David Walt Tufts Undergraduate student developers (see below) Graduate student mentors (see below) Post Doctoral mentors Medford High, Malden High, Somerville High, Chinatown High

22 Interested in this project? Sign up on our list Take a one page flyer about the project Links to developed activities We ll be in touch!