Designing our future overlords or: How I Learned to Stop Worrying and Love Robotics
Decoding our bacterial overlords - Melbourne Knowledge Week - tue 28 oct 2014
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Transcript of Decoding our bacterial overlords - Melbourne Knowledge Week - tue 28 oct 2014
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Decoding our
bacterial overlords
Dr Torsten Seemann
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A bacterium
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Bacteria are diverse
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5,000,000,000,000,000,000,000,000,000,000,000
000,000,000,000,000,000,000,000,000,000,000,
000,000,000,000,000,000,000,000.
Bacteria run the show
100,000,000,000,000
1,000,000
90% microbial
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Help digest
our food
Essential for human life
Immune systemSynthesize
vitamins
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“Good” E.coli “Bad”
(colon) (bladder)
Bacteria are not malicious
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6,000,000,000
letters
The blueprint of life
GenomeA T G C
4,000,000
letters
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Extract
the DNA
Reading the genome
Chop it into
small piecesRead DNA of each piece
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We had a bunch of nice long DNA(each 4 million letters long)
We got back millions of short DNA (each only 200 letters long)
We want our nice long DNA back!(please)
Can’t always get what you want
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Reconstruct the DNA of the chromosome(s)
Genome assembly
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● No box
● Millions of pieces
● Missing and duplicate pieces
● Broken pieces
● No corner or edge pieces
→ Usually end up with ~200 sequences
Like a jigsaw puzzle, but ...
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Contains ~4,000 genes
Each gene is ~800 letters long
Genes start and end with special triplets
Finding genes
←ATGCATGATTAGCTTTTAGTCTTATAATGTCTTATATATCGCATTTAAGCCCTGATTCTATGAATG→
Genome is ~4,000,000 letters long
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● Identify new species
● Find resistance genes
● Understand evolution
● Trace outbreak origin
Applications
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2000 finished genomes
10,000 assembled draft genomes
200,000 downloadable genomes
2,000,000 sitting on USB disks?
Genome assembly is different
- RAM more useful than CPU
Computational challenge
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