Keynote: Webb Miller - Bioinformatics Methods to... - ISMB/ECCB Stockholm 2009

10 Steps to Success in Bioinformatics - sebi

has been 40 yrs in computers, 20 yrs in bioinformatics: but doesn't have enough money to retire (tongue-in-cheek) - Michael Kuhn

Step 1: Become a biologist. - sebi

http://www.iscb.org/index... - Peter Menzel

extinction - Venkata P. Satagopam

Extinction: How to save endangered species - Peter Menzel

which species are in trouble? - Venkata P. Satagopam

Here's the article "10 steps to success..." http://www.iscb.org/iscb-pu... - Michael Kuhn

3 stories - Venkata P. Satagopam

(out of batteries, not sure the iPhone is adequate for this. So far a great intro :) ) - Oliver Hofmann from iPhone

3 studies: Tasmanian tiger, Mammoth, ... - Peter Menzel

explains how DNA can be found in hairs. - Peter Menzel

For extinct species, mitochondrial genome is easier to sequence, as it is up to 1,000 times more abundant than genomic DNA - sebi

aDNA = ancient DNA - Peter Menzel

background of ancient DNA ... - Venkata P. Satagopam

what can be learned from aDNA? - Venkata P. Satagopam

1. phylogenetics - Peter Menzel

2. population genetics - Peter Menzel

This has some parallels to the last talk in today's session in T1 by RE Green: Neandertal mitochondrial DNA to place them (and us) in the phylogenetic tree - sebi

3. directly observe evolutionary rates - Peter Menzel

genes - Venkata P. Satagopam

4. observe evolution of function - Peter Menzel

short reads are good enough for aDNA junks - Peter Menzel

next-generation seq of aDNA - Venkata P. Satagopam

aDNA from hairs can easily be decontaminated - Peter Menzel

aDNA from hair shafts enclosed in a plastic bag like .... - Venkata P. Satagopam

Tasmanian tiger: extinction date 7/9/1936 - Peter Menzel

over 700 know specimens - Venkata P. Satagopam

http://thylacine.psu.edu - Peter Menzel

thylacine = tasmanian tiger - Peter Menzel

attempts to study thylacine DNA - Venkata P. Satagopam

observations - Venkata P. Satagopam

2 mitochindrial genomes in GenBank - Peter Menzel

in GenBank two genes 12S, cytb both were wrong - Venkata P. Satagopam

both wrong at 10% of nucleotides - Peter Menzel

tasmanian devil closest relative to tiger - Peter Menzel

split at ~40m years ago - Peter Menzel

30% of new sequence data are from nuclear genome - Peter Menzel

-> maybe sequence whole genome? - Peter Menzel

one imp question ... did an epidemic contribute to extinction? - Venkata P. Satagopam

Epidemic probable cause of extinction - Peter Menzel

(the quiet comments are hillarious. 'we sequenced one from Stockholm swimming in alcohol. Long way from home, extinct, drowning his sorrows...') - Oliver Hofmann from iPhone

story 2 wooly mammoth - Venkata P. Satagopam

Mammoth: - Peter Menzel

hair sample from eBay - Peter Menzel

we found sample on ebay - Venkata P. Satagopam

for 90$ :-) - Peter Menzel

most samples are from Sibiria - Peter Menzel

have now 18 different complete mtDNA sequences - Peter Menzel

what we draw from this analysis ....mammoth separated from living elephants 6m years ago - Venkata P. Satagopam

like chimp and human - Peter Menzel

want to sequence the full nuclear genome - Peter Menzel

already got 0.7-fold coverage - Peter Menzel

= 3.3 billion bp - Peter Menzel

assuming real size of genome is 4.7Gb - Venkata P. Satagopam

aa identitiy is nearly 99.8% between mammoth and elephant - Peter Menzel

99.4% overall nucleotide identity - Peter Menzel

This equals 1 mutation per protein - sebi

(all this excluding indels) - Peter Menzel

90% seq from the sample from the wooly mammoth - Venkata P. Satagopam

Mammoths differ from all other vertebrates in some highly conversed genes, such as MRTO - Venkata P. Satagopam

maybe due to living in cold places - Peter Menzel

extinction scenario ...human killed them all - Venkata P. Satagopam

certainly not - Venkata P. Satagopam

extinction szenario: killed by humans.. become to warm... -> but thats' not true - Peter Menzel

humans arrives to late in Siberia - Peter Menzel

3rd story Tasmanian devil - Venkata P. Satagopam

tasmanian devil now - Peter Menzel

threatened by extinction due to cancer - Peter Menzel

cancer cells passed around by biting each other - Peter Menzel

cancer is passed through infection (biting other individuals, spreading cancer cells) - sebi

some resistant individuals - sebi

Trying to preserve the species, keeping the gene pool large enough - sebi

compared two individuals: one who is resistant, one who died - Peter Menzel

Finding out about the resistance: considering an ortholog of a human tumor supressor gene - sebi

the guy who died, has a mutation at an extremely conserved position - Peter Menzel

but not much is known what it means.. - Peter Menzel

want to look at non-coding nuclear SNPs - Peter Menzel

closest sequenced relative is oppossum - Peter Menzel

90m years of separation - Peter Menzel

-> computational problem: SNPs without a reference genome - Peter Menzel

produce sequences from many individuals instead - Peter Menzel

and compare SNPs there - Peter Menzel

-> extract population structure - Peter Menzel

seems to work.. but no final data... - Peter Menzel

Quick summary: Bioinformatics very helpful, but much more data needed - Peter Menzel

Role of genetic diversity in extinction still not really known.. no simple story - Peter Menzel

but genetic diversity not necessary a good indicator for risk of extinction.. - Peter Menzel

e.g. panda has high diversity, but endangered - Peter Menzel

TV documentary from Australia: http://www.abc.net.au/catalys... - Peter Menzel

(only to get the blog on top of the ISCB portal site; the figures messed up our layout) - Reinhard Schneider

Related: 11 Extinct Animals That Have Been Photographed Alive: http://ecoworldly.com/2009... - Peter Menzel