1
We are fascinated with the question of human origin.
Palaeontology and archaeology are the branches
that traditionally d...
HUMAN GENOME DIVERSITY PROJECT
HUMAN GENOME DIVERSITY PROJECT SEEKS TO UNDERSTAND
THE GENETIC RELATIONSHIP BETWEEN DIFFERE...
TWO HYPOTHESES REGARDING EVOLUTION OF MAN
OUT OF AFRICA THEORY
MULTI REGIONAL THEORY
MITOCHONDRIAL DNA IS COMMONLY USED ...
MITOCHONDRIAL DNA WAS FIRST RECORDED BY
ELECTRON MICROSCOPY IN 1963 BY NASS & NASS
IT WAS ISOLATED FROM YEAST MITOCHONDR...
CIRCULAR MOLECULE OF 16569 BP LENGTH
37 GENES
13 CODING PROTEINS
2 rRNAS, 22 tRNAS
THE ONLY NON-CODING REGION IN THE ...
MITOCHONDRIAL DNA MAP
THE CONTROL REGION IS HIGHLY STRUCTURED,
WITH A CONSERVED CENTRAL REGION (CCR)
FLANKED BY TWO HIGHLY DIVERGENT
PERIPHERAL...
THESE FEATURES OF mtDNA HAVE BEEN EXPLOITED FOR
EVOLUTIONARY AND POPULATION GENETIC STUDIES
MAKING IT A SUITABLE CANDIDAT...
ISOLATION OF DNA
QUANTIFICATION OF DNA
DILUTING THE DNA SAMPLES
AGAROSE GEL ELECTROPHORESIS
POLYMERASE CHAIN REACTION
PCR FOR 9bp
PCR Reaction Mixture
Requirement
PCR Buffer
MgCl2
dNTPs
Primer A
Primer B
Taq
Polymerase
DDW
DNA (10ng/μl)
Vol...
POLYMERASE CHAIN REACTION
HVR I PRIMER
PCR Reaction Mixture
Requirement Volume(μl)
PCR Buffer
MgCl2
dNTPs
Primer F
Primer ...
SEQUENCING PCR
THESE PCR PRODUCTS ARE SEQUENCED IN ABI PRISM 3700
AUTOMATED DNA ANALYSER
Requirement
BigDye™
Primer F
DDW
...
THE SEQUENCES WERE ASSEMBLED IN AUTOMATED DNA
SEQUENCER
ANALYSIS OF FLOURESCENT LABELLED DNA MOLECULES.
THIS INSTRUMENT...
NOTE ALL THE MUTATION SITES AFTER ASSEMBLING THE
DNA SEQUENCES WITH THE ANDERSON SEQUENCE .
MJ NETWORK ,THE NETWORK WAS ...
MEDIAN JOINING NETWORK OF CHENCHU TRIBE
NJ NET WORK
NEIGHBOUR JOINING TREE WAS CONSTRUCTED WITH
THE DATA FROM 44 CHENCHU INDIVIDUALS WITH THE
DATA FROM THE INDIVI...
NJ NETWORK OF CHENCHU TRIBE
Masters dissertation work - Human genome diversity
Upcoming SlideShare
Loading in …5
×

Masters dissertation work - Human genome diversity

556 views

Published on

Human geneome diversity of Chenchu tribe of Andhra Pradesh - India

Published in: Education, Technology
0 Comments
1 Like
Statistics
Notes
  • Be the first to comment

No Downloads
Views
Total views
556
On SlideShare
0
From Embeds
0
Number of Embeds
1
Actions
Shares
0
Downloads
3
Comments
0
Likes
1
Embeds 0
No embeds

No notes for slide

Masters dissertation work - Human genome diversity

  1. 1. 1
  2. 2. We are fascinated with the question of human origin. Palaeontology and archaeology are the branches that traditionally deal with the reconstruction of human origin and history. Molecular biology is contributing to this area through DNA analysis.
  3. 3. HUMAN GENOME DIVERSITY PROJECT HUMAN GENOME DIVERSITY PROJECT SEEKS TO UNDERSTAND THE GENETIC RELATIONSHIP BETWEEN DIFFERENT POPULATIONS BY USING STANDARD DNA MARKERS LIKE mtDNA “Y” CHROMOSOME HGDP IN INDIA- CCMB IS ONE OF THE PIONEER INSTITUTE WHICH IS ANALYSING PRIMITIVE TRIBES AND CASTE AT MOLECULAR LEVEL. AROUND 6000 BLOOD SAMPLES OF DIFFERENT POPULATIONS HAVE BEEN ANALYSED FOR THEIR GENETIC DIVERSITY
  4. 4. TWO HYPOTHESES REGARDING EVOLUTION OF MAN OUT OF AFRICA THEORY MULTI REGIONAL THEORY MITOCHONDRIAL DNA IS COMMONLY USED IN THE CONSTRUCTION OF EVOLUTIONARY TREES. EVOLUTION OF MAN
  5. 5. MITOCHONDRIAL DNA WAS FIRST RECORDED BY ELECTRON MICROSCOPY IN 1963 BY NASS & NASS IT WAS ISOLATED FROM YEAST MITOCHONDRIA BY SCHATZ IN 1981 THE MITOCHONDRIAL GENOME WAS COMPLETELY SEQUENCED BY ANDERSON et al. mtDNA IS MATERNALLY INHERITED [GILES ET AL 1980] mtDNA IS A SEMI-AUTONOMOUS MOLECULE, WHICH DOES NOT UNDERGO RECOMBINATION.
  6. 6. CIRCULAR MOLECULE OF 16569 BP LENGTH 37 GENES 13 CODING PROTEINS 2 rRNAS, 22 tRNAS THE ONLY NON-CODING REGION IN THE MTDNA IS SITUATED BETWEEN THE GENES CODING FOR tRNA-PRO AND t-RNA-PHE. IT IS ABOUT 1120bp IN HUMANS
  7. 7. MITOCHONDRIAL DNA MAP
  8. 8. THE CONTROL REGION IS HIGHLY STRUCTURED, WITH A CONSERVED CENTRAL REGION (CCR) FLANKED BY TWO HIGHLY DIVERGENT PERIPHERAL DOMAINS.  IN HUMANS THE TWO PERIPHERAL REGIONS ARE CALLED HYPER VARIABLE REGIONS ONE AND TWO (HVR-I AND HVR-II). THE CONTROL REGION IS RELATIVELY TOLERANT OF HIGH MUTATION RATE, THE MT GENOME IS INHERITED INTACT OVER THOUSANDS OF GENERATIONS, WITHOUT THE CONFOUNDING EFFECT OF CROSSOVER WITH A PATERNAL CHROMOSOME.
  9. 9. THESE FEATURES OF mtDNA HAVE BEEN EXPLOITED FOR EVOLUTIONARY AND POPULATION GENETIC STUDIES MAKING IT A SUITABLE CANDIDATE FOR THE STUDY. THIS PROJECT AIMS TO FIND GENOMIC DIVERSITY WITHIN AND BETWEEN ENDOGAMOUS POPULATIONS BY EVOLUTION USING A STANDARD DNA MARKER –mtDNA
  10. 10. ISOLATION OF DNA QUANTIFICATION OF DNA DILUTING THE DNA SAMPLES AGAROSE GEL ELECTROPHORESIS POLYMERASE CHAIN REACTION
  11. 11. PCR FOR 9bp PCR Reaction Mixture Requirement PCR Buffer MgCl2 dNTPs Primer A Primer B Taq Polymerase DDW DNA (10ng/μl) Volume(μl) 1 0.6 0.8 1.0 1.0 0.5 1.1 4 PCR Conditions Steps 1 2 3 4 5 6 7 8 Conditions 950 C for 5min 950 C for 1min 550 C for 1min 720 C for 1min Go to 2, 35 times 720 C for 5min 40 C for ever End THE PRODUCTS WERE THEN RESOLVED IN 6% POLYACRYLAMIDEGEL . NO DELETIONS AND INSERTIONS WERE OBSERVED.
  12. 12. POLYMERASE CHAIN REACTION HVR I PRIMER PCR Reaction Mixture Requirement Volume(μl) PCR Buffer MgCl2 dNTPs Primer F Primer R Taq Polymerase DDW DNA (10ng/μl) 1 0.6 0.35 0.2 0.2 0.5 3.15 4 PCR Conditions Steps Conditions 1 2 3 4 5 6 7 8 940 C for 1min 940 C for 30sec 600 C for 45sec 720 C for 2 min30sec Go to 2, 34 times 720 C for 7min 40 C for ever End
  13. 13. SEQUENCING PCR THESE PCR PRODUCTS ARE SEQUENCED IN ABI PRISM 3700 AUTOMATED DNA ANALYSER Requirement BigDye™ Primer F DDW DNA (10ng/μl) Volume (μl) 1.8 0.1 2.1 1 PCR Reaction Mixture PCR Conditions Steps 1 2 3 4 Conditions 950 C for 10sec 500 C for 5sec 600 C for4min, 30cycles 40 C for ever & end
  14. 14. THE SEQUENCES WERE ASSEMBLED IN AUTOMATED DNA SEQUENCER ANALYSIS OF FLOURESCENT LABELLED DNA MOLECULES. THIS INSTRUMENT COMPRISES OF A ELECTROPHORETIC APPARATUS WITH A 5000 V POWER SUPPLY. ARGON ION LASER. CCD CAMERA. MACINTOSH COMPUTER WITH SOFTWARE SUCH AS AUTO ASSEMBLER.  THE SEQUENCES WERE ASSEMBLED AND COMPARED WITH ANDERSON mt DNA SEQUENCE AND MUTATION SITES WERE NOTED.
  15. 15. NOTE ALL THE MUTATION SITES AFTER ASSEMBLING THE DNA SEQUENCES WITH THE ANDERSON SEQUENCE . MJ NETWORK ,THE NETWORK WAS DRAWN USING HVR 1 SEQUENCES THROUGH NETWORKING 3.0 VERSION SOFTWARE OF FLUXUS ENGINEERING. A TOTAL OF 15 HAPLOTYPES WERE OBTAINED . OUT OF 15 ,10 ARE UNIQUE AND REST FORM COMMON SETS OF HAPLOTYPES. MJ NET WORK
  16. 16. MEDIAN JOINING NETWORK OF CHENCHU TRIBE
  17. 17. NJ NET WORK NEIGHBOUR JOINING TREE WAS CONSTRUCTED WITH THE DATA FROM 44 CHENCHU INDIVIDUALS WITH THE DATA FROM THE INDIVIDUALS OF OTHER INDIAN POPULATIONS USING CLUSTAL X, ARLEQUIN ,PHYLIP SOFTWARES . THE CHENCHU POPULATION HAS CLOSE RELATOION WITH DUNGRI BHILS ,DUNGRI GARASIAS, IRULA NILGIRIS
  18. 18. NJ NETWORK OF CHENCHU TRIBE

×