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!

Monday, September 24, 2012

A week of visitors

This week we had several visitors to the lab.

On Sunday we hosted a delegation from the Helmholtz Association. This delegation included the president of the association as well as directors from several research centers. They did a whirlwind tour of Israel. Their schedule at the Hebrew University was for half a day, and included a general introduction and then topic-oriented meeting. I was chosen to host the Biology meeting in the lab. The guests included the President of the association, the Director of Research of the Helmholtz Zentrum Munich and the Director and Vice-Director of Research of the Max Delbruck Center in Berlin. 

As you can guess this was a very important crowd, and we assembled a team of scientists (established and new) to meet with them. The meeting ended up crowding 16 people in our small meeting/kitchen room, and as consequence was very informal. We also had a short tour of the robotics room.

This visit was a an excuse for us to do a thorough cleanup day on Thursday last week. I think that since it was open the lab never was so clean. The cleanup included also out of sight areas, such as the cold room, which was reorganized by Amit and Noa, who sorted through all the shelfs, removed old and outdated plates, and rearranged things in an accessible way.

On Monday, we were part of the country-wide "Scientists Night" events. The event at the Hebrew University included tours in labs, and our lab was one of the advertised tours. Each group was of 10 teenagers that didn't know much about labs and biology. Avital and Noa took charge of hosting the visit and explaining to the energetic youth why we have robotics.

One last, unexpected and less prestigious, visitor was a chameleon that started visiting my office window regularly. 

The first sighting of this science-curious lizard was when we had a meeting with five people in the room, and suddenly I noticed that everyone was focused on the window behind me. 

Since then it revisited almost every day, and finally I decided that it is calls for some pictures. The window is not 100% clean, but that ended up giving the images a bit of interesting blurs.

Wednesday, August 29, 2012

Evolution of Transcription Factors Binding paper is accepted!


Just got email that a paper by Naomi, Ilan Wapinski, Aviv Regev, Hanah Margalit and me was accepted to Molecular Systems Biology. This paper represents almost two years of work by Naomi and Ilan, and undergone several dramatic ups & down during this time. So it is great to hear that it is officially accepted.

It made just in time for Naomi to print her dissertation listing this paper as "accepted for publication" instead of "in review".

We celebrated by an impromptu toast in the lab.

More details once the paper appears....

This is also a good chance to add a picture of Naomi & Ilan from a trip to CSHL at the time we started talking about this project.

Friday, August 24, 2012

Light box

As you may recall from early posts, we use agar plates for growing and manipulating libraries of yeast strains. We also keep "replicating" copies of these plates to maintain a "live" copy of the libraries.

One of the potential problems is that we mis-copied a plate, or introduced a contamination. One way to check that is to examine the plate pattern. Basically, each library plate has different set of empty spots. This means that we can easily identify plates by these "finger prints". Moreover, a contamination would fill the empty spaces by new colonies. 

Thus, it was clear early on that we need a tool for taking pictures of plates and recording/analyzing the colonies. We could use the standard gel camera we have in the shared room, but that was both unwieldy and exposed our plates (and us) to ethidium bromide (which is used by other labs for dying DNA on gels).

Instead we aimed for a dedicated station for imaging plates. We found some solutions by commercial companies. These however, were very very expensive. And so we decided for a Do It Yourself solution. We consulted with the local electrician, and helped by Meretz, a retired electrician built our own solution.

The box is an old wooden box that was originally for a nikon microscope. The local workshop built us a device to hold the plate in a precise location. Since the plate is asymmetric this ensures that the images are of the correct orientation. We bought a Nikon camera that can have external power supply and remote operation. It is an overkill for the image quality we need, but it does work without battery replacement or manual operation.

As a light source, Meretz suggested using a led strip. He built these leds below the plate holder. This meant that the image colonies showed up as silhouettes.

Image with background light - colonies are dark circle on light background

I wrote a simple program that identifies colonies, their location and their size (which is useful for estimating the fitness of different strains). Eli Peker, who worked as a summer student, wrote a program for uploading images and storing them in a database. This interface allowed different people in the lab to keep track of libraries and compare to previous versions.

Recently, Amit (who deserve his own post soon) suggested we also examine the color and texture of the colonies. This appears to be a known phenotype. However, since the light source was below the colonies we could not use our box. We again contacted the local electricians who installed additional led strips for forground lighting.

"Disco" foreground lights

As you can see, the forground lights turned out to be a bit excessive ("disco" as Amit put it). Now we could make out the color and the texture of the colonies.

Same plate, with foreground lighting
However, now some of these disco lights are reflected in the image and look like small colonies (top part of the image). To deal with this, we added our own DIY screen (paper) to soften the light. 

Foreground lights with diffused screen
Which lead to removal of the annoying reflections on the agar.

Same plate, with diffused foreground lighting

Notice that in this plate there are few white colonies (two small ones) and some that are more yellow. These differences are easier to see if zoom in on a region of the image.

Moreover, some colonies have a different texture, these differences are enhanced when we examine a gray-level version.

For now we use the lightbox to record the plates with different strains. We didn't yet write an automated color classifier (relatively easy) or a texture classifier (a bit harder).

Wednesday, August 22, 2012

Robot Updates

As part of ongoing attempts to get the system to work to our liking we run into two problem.

First, many of the steps in our yeast growth protocols use individual pipetting actions for each well. For this reason we have an arm with individual pipettes. Initially we configured the arm with four fixed tips and four disposable pipettes. The fixed tips are easier to use and do not consume plasticware. On the other hand to get perfect sterility we need to use plastic tips.

So far we learned that the fixed tips (with a wash between uses) is sufficiently clean for our purposes. And so we use these a lot. The problem is that the time it takes to "process" a plate (e.g., remove individually tailored amounts per well for growth dependent dilutions) was too long. The main time consuming steps is the tip washing. 

After consultation with Neotec people, we decided to switch two of the disposable pipette heads with fixed tips. This will give us more tips and thus less washes (as the washes are done in parallel and take the same amount of time for 4 or for 6 tips).

Six fixed tips in action
The second problem is much more serious - the robotic manipulation arm kept getting out of alignment. This lead to serious of failure in our longer experiments. The blame fell onto the plate shaker, which we use a lot in our protocol. The design of the shaker has to allow a robotic arm to place/remove a plate, but at the same time hold the plate firmly during the shaking. The solution in the shaker we had was a spring that held the plate in place. Every time the arm came down to the shaker it would press on a lever and release the plate from the spring. Apparently these repeated presses moved the arm out of place (not by much but sufficiently to cause problems)

The solution was to replace the shaker head to one with a different locking mechanism based on a higher stand that kept the plate sitting down. This required adaptation of a solution Tecan built for arms that hold the plate from above (and not from the side like ours).

New shaker head
So far it seems that the system is indeed more stable. It worked for two days without issues and we are counting.