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Cell and Microbial Engineering Laboratory Solving TSP on Lab-on-a-Chip 1 Jiyoun Lee
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Cell and Microbial Engineering Laboratory Solving TSP on Lab-on-a-Chip 2 Introduction TSP (Traveling Salesman Problem) –Graph with given vertexes, edges, and costs (weights) Hamiltonian paths containing the smallest sum of costs Airlines, transportation Graph dimension –7 vertexes, 24 edges, 5 costs
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Cell and Microbial Engineering Laboratory Solving TSP on Lab-on-a-Chip 3 1 0 3 2 5 6 4 0 1 2 3 4 5 6 0 (21) start 3 5 3 3 7 11 3 3 9 3 3 end 0 1 6 5 4 3 2 0 (31) 0 2 1 3 4 5 6 0 (27) 0 2 3 4 5 6 1 0 (31) 0 6 5 4 3 1 2 0 (27) 0 6 5 4 3 2 1 0 (21)
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Cell and Microbial Engineering Laboratory Solving TSP on Lab-on-a-Chip 4 vertexweight (with low GC) vertexweight (with low GC) vertex edge low melting temperature weight vertexweightvertexweightvertexweight low melting temperature more amplification by more denaturation
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Cell and Microbial Engineering Laboratory Solving TSP on Lab-on-a-Chip 5 ds DNA denaturation : more denaturation of DNA strands which have less weights primer annealing polymerization
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Cell and Microbial Engineering Laboratory Solving TSP on Lab-on-a-Chip 6 Procedure Generating random paths through the graph Keep only those paths that begin with v in Keep only those paths that enter exactly n vertices Keep only those paths that enter all of the vertices of the graph at least once Separation of the solutions Generating sequences & LIgation reaction PCR with v in as primers Gel electrophoresis separation by size Affinity-purification with a biotin -avidin magnetic beads system TGGE Figure out the pathSequencing & readout
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Cell and Microbial Engineering Laboratory Solving TSP on Lab-on-a-Chip 7 Procedure Generating random paths through the graph Keep only those paths that begin with v in Keep only those paths that enter exactly n vertices Keep only those paths that enter all of the vertices of the graph at least once Separation of the solutions Generating sequences & LIgation reaction PCR with v in as primers Gel electrophoresis separation by size Affinity-purification with a biotin -avidin magnetic beads system TGGE Figure out the pathSequencing & readout
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Cell and Microbial Engineering Laboratory Solving TSP on Lab-on-a-Chip 8 Affinity separation (7 nodes) Ligation (Connecting each ssDNA) PCR with Vin Hybridization (Generating all possible paths ) Size separation by electrophoresis Sequencing Temperature gradient in reservoir Isothermal reaction in reservoir Expected problems : buffer composition Ligation buffer Affinity separation buffer Cf) conventional method Purification of DNA by ethanol precipitation Paramagnetic separation using biotin-avidin interaction Temperature cycling in reservoir CE (or CGE)
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Cell and Microbial Engineering Laboratory Solving TSP on Lab-on-a-Chip 9 Affinity unit Reaction chamber for hybridization and ligation Reaction chamber for PCR Electrophoresis separation Buffer change Volume reduction? I wish to.. Eliminate the affinity step Change the buffers in flow
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Cell and Microbial Engineering Laboratory Solving TSP on Lab-on-a-Chip 10 Questions and Discussions… Danny’s idea: addition of salts.. –Not reservoir type, but channel type In English, please… Questions to Danny: –Method for inserting beads to channel. –Channeling effect or something… –TRIS,.. Some buffer names.. –Many beads – Yield of …
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