Tuesday, October 23, 2012

A functional selection model explains evolutionary robustness despite plasticity in regulatory networks

Its out on the Molecular Systems Biology website. Yay!

This paper summarizes quite a bit of work by Naomi and Ilan. It started with "here is a short 2-week project" and ended as big part of Naomi's PHD and a massive paper.

Highlights (from our synopsis):

By tracing the evolutionary history of transcriptional networks across 23 fungi, two seemingly contradictory trends are observed: rapid target turnover and conserved function. This is reconciled by a model that invokes strong selection to conserve the overall function of a motif, but not its individual targets.

  • The vast majority of cis-regulatory elements in genes’ promoters are rapidly gained and lost across species.
  • Despite this rapid turnover, most transcription factors are associated with a conserved function even at great evolutionary distances.
  • A functional selection turnover model reconciles these two phenomena by invoking a preference to conserve the overall function of the motif but not the individual target genes.
  • Our model fits the variation in measured transcription factor binding profiles across species in both yeasts and mammals.

Thursday, October 18, 2012

Another farewell party

It seems that we are facing a mass exodus. Today we had a small scale party to say goodbye to Michal who is returning to MIT/Broad to finish her PHD.

You might remember that Michal is long-term visitor in the lab who works with us the last few years. Next week she is flying back to Boston, and apparently next time she visit Israel will be after she will finish her PHD. In addition to that exciting event, she will also be a mom next time we meet her...

We had a small party. Due to experiments running on (more on that later), we switch the plan from going out to ordering food in. And since the options were limited, we had a Pizza Party! to remind Michal what she is about to enjoy a lot of in different meetings in the States :-)

Michal treated us to a very impressive (and tasty!) cake.

And also a surprise present of a ball. It turned out that the ball was a puzzle that required some effort.

Although we will continue collaborating with Michal, we will miss her presence at the lab.

Monday, October 15, 2012

Farewell to Naomi

The last week was marked with farewell events to Naomi. 

It started on Tuesday with a trip and picnic. Since Naomi is (was) a joint student of both Hanah Margalit and myself, we had a trip with the two groups.

On the road

Noa and Daniela

After the trip we had a nice lunch in a forest. Daniela was the star of the event, sitting in the middle and checking the choice of food.

Then came the more official part of the ceremony where we said our farewell wishes and exchanged cards and presents :-)

On Thursday afternoon we had the dissertation exam. Unlike the custom in many universities, in the Hebrew University the exam is a private event - the judges and the student without any audience.  Naomi surveyed the results from her dissertation and the judges asked questions.

Naomi at the start of the presentation

After the presentation and Q&A, the judges convened, and after a short discussion decided this was a great presentation and wonderful dissertation. We called Naomi to tell her the news.

Celebratory fresh PhD

Yesterday Hanah and I took Naomi for a lunch to have a chance for a more intimiate farewell. 

Today Naomi came to finish the TODO list on an ongoing project with Avital and Mor (from Hanah's lab). And at 3:30, she left, after tearful hugs with everyone. 

We wish Naomi easy move to Cambridge, MA, and much fun and success in her postdoctoral fellowship!