V3 Loop Sequence Space Analysis Kasia Bo ek bozek@mpi-inf.mpg.de - PowerPoint PPT Presentation

Jan 16, 2024 •450 likes •613 views

V3 Loop Sequence Space Analysis Kasia Bo ek bozek@mpi-inf.mpg.de Max-Planck Institute fr Informatik, Saarbrcken AREVIR Bonn 24.04.2009 V3 loop sequence space analysis selection of V3 loop sequence variants for experimental imaging of

V3 Loop Sequence Space Analysis Kasia Bo ż ek bozek@mpi-inf.mpg.de Max-Planck Institute für Informatik, Saarbrücken AREVIR Bonn 24.04.2009
V3 loop sequence space analysis selection of V3 loop sequence variants for experimental imaging of the HIV cell entry understanding of the distribution of V3 loop sequences in their sequence space Kasia Bo ż ek AREVIR Bonn 24.04.2008
Data analysis Approach 2 sets of sequences from Los Alamos NSI/ SI CCR5/ CXCR4/ R5X4 distance distribution phylogenetical analysis using Splitstree hierarchical clustering Kasia Bo ż ek AREVIR Bonn 24.04.2008
Distance distribution – NSI/ SI NSI-NSI NSI-SI SI-SI Kasia Bo ż ek AREVIR Bonn 24.04.2008
Distance distribution – R5/ X4 R5-R5 R5X4-R5X4 X4-X4 Kasia Bo ż ek AREVIR Bonn 24.04.2008
Phylogenetical analysis - Splitstree Phylogenetical analysis evolution - not always is a branching tree-like process different phylogenetical signals in real data not always fitting into a unique tree Splitstree Splitstree – a tree-like network visualizing conflicting phylogenies Kasia Bo ż ek AREVIR Bonn 24.04.2008
Phylogenetical analysis - Splitstree Phylogenetical analysis Kasia Bo ż ek AREVIR meeting Bonn 24.04.2008
Hierarchical clustering Kasia Bo ż ek AREVIR Bonn 24.04.2008
Hierarchical clustering NSI R5 R5X4 SI X4 Kasia Bo ż ek AREVIR Bonn 24.04.2008
V3 loop sequence space analysis R5/ NSI: X4/ SI: conserved diverse forming clusters placed in distant parts of sequence space slow disease progression disease immune component of the V3 loop evolutionary pattern? R5/ NSI sequences under purifying selection of the immune system? Kasia Bo ż ek AREVIR Bonn 24.04.2008
Sequence space location vs. CD4 + T-cells Kasia Bo ż ek AREVIR Bonn 24.04.2008
Sequence space location vs. CD4 + T-cells 4 3 1 2 Kasia Bo ż ek AREVIR Bonn 24.04.2008
Conclusions conservation of CCR5/ NSI V3 loop sequences high variability of CXCR4/ SI viruses possible immune system selection pressure Kasia Bo ż ek AREVIR Bonn 24.04.2008
Conclusion Acknowledgements Alexander Thielen Rolf Kaiser Oliver Sander Saleta Sierra Aragon André Altmann Thomas Lengauer
Conclusion

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