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& MUTATIONS IN HUMAN MITOCHONDRIAL PHYLOGENY COMPARING MITOCHONDRIAL DNA ACROSS SPECIES Alessa Moscoso OEB 275br Module Presentation.

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Presentation on theme: "& MUTATIONS IN HUMAN MITOCHONDRIAL PHYLOGENY COMPARING MITOCHONDRIAL DNA ACROSS SPECIES Alessa Moscoso OEB 275br Module Presentation."— Presentation transcript:

1 & MUTATIONS IN HUMAN MITOCHONDRIAL PHYLOGENY COMPARING MITOCHONDRIAL DNA ACROSS SPECIES Alessa Moscoso OEB 275br Module Presentation

2 NUCLEOTIDE ONLINE DATABASES A prime tool for analyzing molecular data Accessible from anywhere Incorporate archeological specimens (Neanderthal data)

3 MODULE OBJECTIVES Students will learn how to use online databases for gather molecular data Will learn how to analyze molecular data with phylogenetics (creating gene trees and species trees) Finally, will use comparative genomics to address human disease. Where do these alleles arise?

4 ONLINE DATABASES/PROGRAMS Ensembl – gather Human mtDNA, orthologs BLAST- find Neandertal data TranslatorX – align sequences SeaView – compare sequences Mitomap – disease mutations in mtDNA PAUP – builds phylogenetic trees, analysis Fig Tree – builds phylogenetics trees

5 NEANDERTHAL DATA Data found using BLAST search

6 MITOCHONDRIAL GENES Looking at ATP6, ATP8, COX1, COX2, COX3, CYB, ND2, ND3

7 ORTHOLOGS Primates Chimp Gorilla Orangutan Macaque http://ec.europa.eu/health/opinions/en/non-human-primates/glossary/pqrs/primates.htm

8 TREE CREATED FROM 8 COMBINED GENES

9 ATP6 ALIGNED SEQUENCES

10 ATP6 PHYLOGENY IN PAUP

11 BOOTSTRAPPING

12 ATP6 MUTATIONS GeneDiseaseAllele Nucleotide Position Nucleotide Change Amino Acid Change Status MT-ATP6 NARP/Leig h Disease/MI LS/otherT8993C8993T-CL-PCfrm references MT-ATP6 NARP/Leig h Disease/MI LS/otherT8993G8993T-GL-RCfrm MT-ATP6 FBSN/Leig h DiseaseT9176C9176T-CL-PCfrm references MT-ATP6 Leigh Disease/Sp astic ParaplegiaT9176G9176T-GL-RCfrm MT-ATP6 Leigh Disease/At axia syndromes/ NARP-like diseaseT9185C9185T-CL-PCfrm

13 DISEASED HUMAN ATP6 GENES

14 DISEASE CAUSING ATP6 MUTATION ONLY IN HUMANS *What does this tell us?

15 ATP8 GENE TREE *no difference between this tree and the ATP6 tree

16 ATP8 MUTATIONS GeneDiseaseAllele Nucleotide Position Nucleotide Change Amino Acid Change Status MT-ATP8 MIDD / LVNC cardiomyopat hy-assoc.A8381G8381A-GT-AReported MT-ATP8 Reversible Brain Pseudoatrop hyC8393T8393C-TP-SReported MT-ATP8 Severe mitochondrial disorderA8411G8411A-GM-VReported

17 *ATP8 disease mutations in humans

18 ND2 BOOTSTRAPPED TREE

19 ND2 MUTATIONS GeneDiseaseAllele Nucleotide Position Nucleotide Change Amino Acid Change Status MT-ND2 LHON/Insulin Resistance/A MD/NRTI-PNA4917G4917A-GN-D Reported; haplogroup T marker MT-ND2 NIDDM helper mutation; AD, PDA4833G4833A-GT-A Reported; haplogroup G marker MT-ND2LHON C4640A4640C-AI-MReported MT-ND2 Longevity; Extraversion MI/AMS protection; blood iron metabolismC5178A5178C-AL-M Reported; haplogroup D marker

20

21 COX1 MUTATIONS

22 GeneDiseaseAllele Nucleotide Position Nucleotide Change Amino Acid Change Status MT-CO1 Prostate CancerC5911T5911C-TA-VReported MT-CO1 Prostate CancerG5913A5913G-AD-NReported

23 * COX1 Mutations In Humans


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