Transcript CS584:Computational and Life Science

Life Science: Organisms
2 February, 2007
Genomics
“The genetic blueprints of all people generally have the same
information, with approximately 99% of one human genome
sequence being identical to all others. That makes the 1% of
places in the genetic code that account for human variation very
interesting…”
Momentum Winter 2006-2007, DNA Rubic
“Some geneticists have calculated the differences in human and
chimpanzee DNA as just over 1%, some at 1.6%, and others at
1.8%.”
Momentum Winter 2006-2007, What we learn from Chimpanzees
2 February, 2007
Genomics
Organism
Genome size
Number of genes
Human
3.2 Gb
25,000
Rat
2.7 Gb
25,000
Mouse
2.5 Gb
24,000
Dog
2.4 Gb
19,300
Puffer fish
390 Mb
25,000
Fruit fly
165 Mb
13,600
Arabidopsis (plant)
120 Mb
25,500
C elegans
97 Mb
19,000
Slime mold
34 Mb
12,500
Yeast
12 Mb
6,300
http://en.wikipedia.org/wiki/List_of_sequenced_eukaryotic_genomes
http://www.ornl.gov/sci/techresources/Human_Genome/home.shtml
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Biological Systems
http://www.innerbody.com/htm/body.html
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Cell types
The human embryonic
stem cells cultured have
been observed to
randomly differentiate in
culture into a variety of
different cell types,
including (A) gut, (B)
neural cells, (C) bone
marrow cells, (D)
cartilage, (E) muscle
and (F) kidney cells.
www.news.wisc.edu/packages/
stemcells/3327.html
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A Cell
http://micro.magnet.fsu.edu/cells/animalcell.html
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They are all the same cells –
They all have the same genetic material,
The only difference is what is turned on and what is
silent.
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Central Dogma
http://www.accessexcellence.org/RC/VL/GG/protein_synthesis.html
2 February, 2007
DNA
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DNA
2 February, 2007
RNA
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Central Dogma
http://www.accessexcellence.org/RC/VL/GG/protein_synthesis.html
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Translation RNA to Protein
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Proteins
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Gene to Protein
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Sites of Regulation
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Sites of Regulation
DNA
Protein
Chromosome packing
Methylation
Transcription factor binding sites
Post-translational modification
Structural modifications, cleavage
Protein-protein interactions
Co-factors
RNA
Metabolites
Capping, Poly adenylation
Editing, splicing
Transport from nucleus
Promotors, Ribosome binding
Co-factor and substrate concentration
Transport
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How do we measure it?
presence, concentration, activation state, etc. of specific biological
molecules.
How do we measure the variations?
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DNA
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Sequencing
Genomic library
Genome sequencing
PCR
SNPs
Linkage analysis
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Life Science
http://www.genomenewsnetwork.org/articles/06_00/sequence_primer.shtml
2 February, 2007
Life Science
http://www.genomenewsnetwork.org/articles/06_00/sequence_primer.shtml
2 February, 2007
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http://mekentosj.com/4peaks/science.html
Genomic Library
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2 February, 2007
Genome sequencing and Display
http://www.genomenewsnetwork.org/articles/06_00/sequence_primer.shtml
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BAC-to-BAC method
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whole genome shotgun sequencing
UCSC Genome Browser
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http://genome.ucsc.edu/
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2 February, 2007
Life Science
2 February, 2007
Microarray
Probe hybridization
to DNA on chips
Probes bind to unique
features on chips
Flourescent labels
highlight bound probes
http://www.affymetrix.com
2 February, 2007
RNAi :
RNA silencing
http://fig.cox.miami.edu/~cmallery/150/gene/how_siRNA_works.htm
2 February, 2007
Life Science
2 February, 2007
Proteomics: Mass Spectrometry
2 February, 2007
http://www.proteomesoftware.com/Proteome_software_ed_mass_spec.html
Proteomics: Mass Spectrometry
http://www.academysavant.com/cmsp.htm
2 February, 2007
Yeast 2 hybrid
used to measure
protein-protein
interactions.
2 February, 2007
Life Science
Flow of information
2 February, 2007
Life Science
Flow of information
2 February, 2007
NCBI Derivative Sequence Data
(Maureen J. Donlin, St. Louis University)
Curators
RefSeq
TATAGCCG
AGCTCCGATA
CCGATGACAA
Labs
Genome
Assembly
TATAGCCG
TATAGCCG
TATAGCCG
TATAGCCG
GenBank
UniGene
Algorithms
2 February, 2007