Sunday, October 15, 2006

From the smallest to the largest genome project

Clocking at a little under 160Kb, the carsonella rudii genome encodes 182 protein. Talk about streamlined. In fact this insect symbiont may be on the way to becoming an organelle. Still this is not as interresting as a free living organism in our quest to find the "minimum genome". Craig Venter (of the human genome fame) is interrested in finding this minimal genome to develop the new field of synthetic biology... "The Synthetic Biology Group is also interested in understanding and thus engineering new pathways ... Most genomes contain hundreds to thousand of genes necessary for adaptive living in complex environments. By synthesizing minimal genomes the team believes it is possible to construct simple cellular life with desirable synthetic properties... the team is dedicated to developing only synthetic organisms that completely lack the ability to survive outside the lab." Craig also recently announced the 10M$ X-prize genomics challenge (the same prize that was awarded for sub-orbital flights last year), to map 100 human genomes in 10 days. All you need is a few thousand summer students and lots of gels.


Bayman said...

inspired by a.c.'s branding initiatives, i pimped up the bayblab logo a bit...if anyone else wants to add I can send the source images and we can pimp it up open source style....think the layout might need a litle refining too...

Anonymous Coward said...

sweet! I like it.

rob said...

There is some talk about the X-prize on Quirks and Quarks this week where they speak with my former supervisor Dr. Steve Scherer from Sick Children's Hospital in T dot.

Bayman said...

Cool that its maybe on its way to being an organelle. The story linked to claims its the "smallest genome of a living oraganism", I would say is a bit misleading. The thing is an obligate symbiont, by this standard VSV (11000 bp) and many other viruses kick its ass for having small genomes.

Bayman said...

According to my calculations
you could get the X-prize by hiring 3x10^5 summer students for a rough profit of $8.75M. (minus the cost of agarose, elecricity and oligo primers)

If 1 student can prep and sequence 100 clones per day for an average sequence read of 1000 bp per clone:

(100x1000 bp/d/s.student)x(10 d)=
10e6 bp per student

3e9bp/genome x 100 = 3e11bp to sequence

3e11bp/10e6bp/student=300,000 s.students

cost of a s.student = 5000$/summer
$5000/120d=$41.66 repeating/day

$41.66/student x 300,000= $1.25M cost in student labor