November 2010 - Time to move!

We started packing for our move to the Engineering "&" Research Building. The new labs/offices look amazing! We're going to have some down time while stuff is moved, but most will happen over the holiday and we should be fully functional by early January.

Anna has done some prelim analysis comparing Tcon and Tcas (~800 gene frags). Ks values are much lower than expected based on Angelini and Jockusch's handful of genes. If it holds up this'll be a very good thing for us. Really wich I had some money to sample Tcas polymorphism and Tfreemanii.

September 2010 - Brian joins the EPA; Anna joins the lab

Brian got a job! It works out pretty well that Kevin Preuss started in Indiana with the Wade lab at about the same time. Anna Williford (Ph.D. 2010 from Iowa) will also join us as a new postdoc. She worked with Josep Comeron at Iowa and will probably work on molecular evolution of sex biased genes. Would be nice if we had more T. confusum sequence!

July 2010 - T. confusum update

It goes slowly. We have ~20% coverage of T. castaneum chromosomal scaffolds in the reference assembly. We did a new extraction from the same inbred line after curring them of Wolbachia. Will start generating reads from the new libraries soon (I hope).

May 2010 - Sex-bias paper in GBE; T.confusum update

The first microarray paper is now "in press" at Genome Biology and Evolution:
Lots of firsts in this paper. Most importantly it looks like both sexes hyperexpress the X chromosome resulting in "too much" X in females. It's very interesting since C. elegans and mammals (except maybe platypus) also hyperexpress the X in both sexes but have independently evolved female "counter-compensation" mechanisms to get X:A = 1:1 in both sexes. Tribolium seems to get away without doing that (female X:A > 1:1 for most genes on the X). I'm looking for a good student or postdoc to come pursue what's going on with the Tribolium sex chromosomes.... contact me if you're interested.

Initial sequences of T. confusum and its Wolbachia parasite:
We got pretty poor results from the first 454 run for T. confusum, but the core is still working out kinks with the new machine/protocols/chemistry. The confusum assemble is pretty worthless, although my bioinformatics course did some nice repeat content analyses just on the ~6 Mb we got. We also got about ~20% of the Wolbachia parasite's genome. We knew before hand that our beetles were infected so the class screened it out of the confusum reads pre-assembly. Shouldn't be long before we have "real" sequence to work on.

March 2010 - NIH supplement awarded!

We were awarded an ARRA administrative supplement to the NIH speciation grant it provides ~$110,000 for additional grad student and postdoc support. If you fall into one of those categories and you want to work on Tribolium speciation genetics, send me your CV and a brief statement of your specific interests.

February 2010 - Sequencing T. confusum

2/20 - Just waiting on inbred beetles at this point. Ellen Pritham's lab course is going to do EST and paired end preps for us and my bioinformatics course is going to do the analysis. We should get 10-12X coverage including EST and paired ends. Let's hope Burns "The best laid schemes o' mice an' men Gang aft agley..." isn't prophetic.

January 2010 - New 454 Promises Happy New Year!

1/20 - Looks like sequencing Tribolium confusum might actually happen. Trying to get Roche to buy into "Sequencing a complex eukaryotic genome becomes a classroom project"

1/7 - Santa brought us a new 454 sequencer (thanks NSF)! I think I'll sequence a genome and have my Bioinformatics class analyze it for their course projects.

 


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