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Cw nelson scarcii
Cw nelson scarcii
Cw nelson scarcii
Cw nelson scarcii
Cw nelson scarcii
Cw nelson scarcii
Cw nelson scarcii
Cw nelson scarcii
Cw nelson scarcii
Cw nelson scarcii
Cw nelson scarcii
Cw nelson scarcii
Cw nelson scarcii
Cw nelson scarcii
Cw nelson scarcii
Cw nelson scarcii
Cw nelson scarcii
Cw nelson scarcii
Cw nelson scarcii
Cw nelson scarcii
Cw nelson scarcii
Cw nelson scarcii
Cw nelson scarcii
Cw nelson scarcii
Cw nelson scarcii
Cw nelson scarcii
Cw nelson scarcii
Cw nelson scarcii
Cw nelson scarcii
Cw nelson scarcii
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Cw nelson scarcii

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  • 1. Using GIS to analyze genetic variationin pathogen populations: a case studywith Plasmodium falciparumCHASE W. NELSONUSC, Department of Biological SciencesAdvisor: Dr. Austin L. Hughes11 FEBRUARY 2012
  • 2. Background Gene: a stretch of DNA that encodes one product (i.e., RNA or protein)
  • 3. BackgroundDNATranscriptionTranslationProteinmRNARNA
  • 4. Background Central DogmaGene 2Gene 1 Gene 3Copyright © Roche Genetics Education Program.
  • 5. Background Gene: a stretch of DNA that encodes one trait Mutation: random changes in DNA sequence Synonymous changes: “silent” neutral changes Nonsynonymous changes: functional divergence
  • 6. The code is redundant
  • 7. Background Gene: a stretch of DNA that encodes one product (i.e., a ncRNA or protein) Mutation: random changes in DNA sequence Synonymous changes: “silent” neutral changes Nonsynonymous changes: functional divergenceCTA  LeucineCTC  LeucineCTG  LeucineCTT  LeucineAGA  ArginineAGC  SerineAGG  ArginineAGT  Serine
  • 8. Natural selectionNATURAL SELECTIONPURIFYINGSELECTIONPOSITIVESELECTIONMUTATION
  • 9. Background Malaria Major global health issue Kills 1 million per year >216 million cases in 2010 (Howitt et al. 2012) No effective vaccine Sporozoite stage Circumsporozoite protein (CSP) 5’NR – NANP repeat region – 3’NRImage obtained from: Cowman & Crabb (2006).
  • 10. Background Malaria Major global health issue Kills 1 million per year >216 million cases in 2010 (Howitt et al. 2012) No effective vaccine Sporozoite stage Circumsporozoite protein (CSP) 5’NR – NANP repeat region – 3’NRImage obtained from: http://www.pnas.org/content/109/4/999/F1.large.jpg
  • 11. Literature Jongwutiwes et al.2010
  • 12. Methods Obtained P. falciparium circumsporozoite protein (CSP) sequences BLAST Dame et al. (1984) GI:160160 448 / 665 hits had 100% coverage 1 full chromosome 443 could be located by exhaustive literature review Bioinformatics Alignment with ClustalW
  • 13. Data All 447 sequences were traced to geographic origin by: GenBank annotations Extensive literature review Contact with study authorsCOUNTRY NO. REGION(S) Lat LongBrazil 2 Manaus, Amazonas -3.1292 -60.0214Cameroon 9 Yaounde 3.8667 11.5167China 1 Hainan Province 19.1067 109.5675El Salvador 1 Cangrejera 13.4667 -89.1753Gambia 44 Farafenni 13.5667 -15.6Ghana 1 Accra 5.55 -0.2167Honduras 1 Honduras 14.7806 -87.4384India 11 Assam 26 93Kenya 18 Asembo Bay, Western Kenya -0.1831 34.3839Laos 1 Laos 18.2912 103.6069Nigeria 1 Lagos 6.45 3.3833P.N. Guinea 2 Madang Province -5.2269 145.7939Thailand 335 Kanchanaburi, et al. 14.0225 99.5317Unknown 4 NoData NoData NoDataVanuatu 6 Malakula -16.3 167.5Venezuela 10 Amazonas, etc. 3.5 -66TOTAL 447 27 distinct regions + NoData
  • 14. Model Two goals DNA sequence interpolation Nearest Neighbor Detect spatial autocorrelation Moran’s IdPij =
  • 15. Moran’s I Spatial autocorrelation
  • 16. Model User provides ArcGIS with: Basemap, e.g., World Street Map (WGS 1984) Land map, e.g., World Continents (WGS 1984) Spreadsheet with sequences Latitude and Longitude Proportion difference (e.g., pRefDiff) 443C2 = 97,903 Nucleotides at each site (e.g., Site_i)
  • 17. Add XY DataDraw ThiessenPolygonsClipGenetic TableWith XYSampleLocationsSequencePolygonsLand LimitedPolygonsLand AreaAdd fieldsConcatenate SitesFull Sequenceand dP FieldsFull SequenceJukes-CantorCorrectedDistance (dP)Moran’s I0147 8 952+/- .36/*-+CE C0147 8 952+/- .36/*-+CE CMoran’s I
  • 18. Sources: Esri, DeLorme, NAVTEQ, USGS, Intermap, iPC, NRCAN, Esri Japan, METI, Esri China (Hong Kong), Esri(Thailand), TomTom, 2012
  • 19. Sources: Esri, DeLorme, NAVTEQ, USGS, Intermap, iPC, NRCAN, Esri Japan, METI, Esri China (Hong Kong), Esri(Thailand), TomTom, 2012
  • 20. ResultsALLNo NW RedundNo Redund
  • 21. Discussion Model extremely brittle: implement wild cards for sites in Python Incorporate sequences without full coverage Thiessen polygons for each site? Devise strategy to handle thousands of nucleotide sites Define another reference sequence or all pairwise comparisons
  • 22. Discussion Moran’s I across or within specific regions Moran’s I interpretation Ultimate: use genetic and spatial data to control malaria
  • 23. Acknowledgments Dr. Austin L. Hughes USC Geography Department Michael E. Hodgson Erica Pfister-Altschul Lynn Shirley
  • 24. finis

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