Exploring transcription regulation through cell-to-cell variability

Yay! A paper that was in the works for two years, including more than six months in review, finally appeared in Proceedings of National Academy of Sciences, USA.

This describes Ruty's MSC dissertation, which was done with help from Ariel and me. In this work she took a very large dataset collected by Martin Jonikas and Maya Schuldiner at Jonathan Weissman's lab, and reanalyzed it to uncover new findings.

The key point of the paper is the use of "noise" or variability in expression levels of the same protein between genetically identical cells as a phenotype for genetic screen. Ruty shows that mutations that lead to abnormally high or abnormally low variability are involved in key processes in regulating transcription. Moreover, by using double knockouts she can pinpoint some mechanisms on these defects.

This work is cool as it shows that promise for the general theme that we want to pursue in the lab, of using genetic perturbation and examining effect on protein expression in single cells.

Funny/Sad Moments

Part of learning to program a complex robot involves learning to debug programs that actually manipulate the real world. As a consequence "bugs" often have more impact than a simple error message on the screen.

Most these bugs are our fault, and so really have no one to blame. Once in a while there is one that seems to come out of the blue, and it took a while to find out what happened. Today, Ayelet tried a simple protocol that worked fine before, and it had dramatic results. I came in to check if this error was reproducible and so got it onto a movie (although a bit out of focus).

After some soul searching, finger pointing, and checks. We realized that the incubator was slighly moved when the FACS was being serviced. As a result the programmed position for lifting the plate was off, and thus the dramatic consequences.

Once we figured this out it was easy to recalibrate the position (we are getting good at that). Moreover, we had the incubator fixed into place the next morning. (We have had the request to do so out for a while, but now we made it clear this was urgent.)

Sooner than expected

Any installation that involves water flowing in pipes is prone for leaks. We got the first one in our robotic room. Much sooner than we would have hoped.

In the middle of a discussion with Assaf I noticed that the ceiling outside my window was "weeping" water .

A quick examination showed that the whole shelve above the window was flooded with water. We tracked this to a leaking pipe in the water-based A/C unit in the robotic room. 

We called the emergency maintenance hotline, and soon someone showed up. He called the person responsible for A/C maintenance who showed up after half an hour. Together they blocked the in & out lines for this unit (and neighboring room) and drained the pipes to avoid additional leakage. 

Update from this morning. The contractor who connected the A/C showed up. The fault was a fracture in valve that connected the old (pre-existing) pipes to the new installation. He replaced the valve, and now we hope that the ordeal is behind us.

For leakage, the damage was quite minimal. We might need paint renewal in few spots, but overall all equipment are intact.

Dry Ice Shipping Revisited

After the catastrophic results of our last attempt to send samples on dry ice, we went back and did research on packaging materials for ice. We learned that we need to use foam and strings as plastic tend to be brittle. We also checked various tubes to see how they hold up in cold temperature.

We finally selected tubes that were less brittle and better packaged in their box. Only the larger version was available, and so we ended using tubes that were much larger than needed, but we decided that this would not harm the content.

Assaf re-run the whole experiment again. This time it went smoothly and he got samples without any probelms (so we do learn from experience).

This time each box was padded both inside and outside, and securely wrapped in foam. 

We then packaged them in the box, and wedged them into place with pieces of styrofoam. We broke the big blocks of dry ice to small piece to ensure that there is no big hard mass bumping around during shipping. Since we didn't have a large box, we sent the samples in two separate boxes.

To our relief, the two boxes arrived safe and sound.

Site visit to new Engineering Building

As you know, I am a member of the School of Engineering at the university. The school was established more than ten years ago, and it was immediately clear that it needs a physical venue. I was part of a committee that helped define the functional specifications for the building with the architects (a collaboration of a Canadian and an Israeli firm, AJ Diamond, and Kolker, Kolker, and Epstein). The result was plans for a very nice building with multiple functions (offices, research, teaching, student lounges, etc.)  You can learn more about it here.

Due to complex circumstances, the construction of the building was delayed quite a bit, but in the last two years it has been going on in full steam, and hopefully it will be ready for opening in about a year. Today I was invited for a tour of the construction site to see how the interior will look like. I took the opportunity to take some photos of the place. It was raining last week, and so there puddles still on the roof and in some of the large empty spaces (which will become lounges).

It is a cold harsh world: Lessons in shipping with dry ice

Two week ago Assaf completed a large scale experiment with the robot. The next step was sending all the samples to Ollie's lab for running the NanoString assays. This involved sending cellular extracts with RNA from ~900 samples. Since the samples are sensitive, they need to be kept cold, and so should be shipped expediently packaged with dry ice to keep the temperature.

It turned out that this is a non-trivial exercise. In our previous iteration, we learned where to order dry ice. Now, however, we needed a much larger box as we were sending hundreds of tubes. 

Assaf used the robot to move the samples into 12-strips of small tubes, organized in 96-well format by using tip boxes.

Ayelet and Assaf then sat down and labeled the strips and packed them in boxes. They sealed the boxes with parafilm to keep everything in place. 

Assaf and I packed the insulating polystyrene box with blocks of dry ice, and arranged the boxes on top of them. Finally we sealed the box tightly and shipped it to UMass.

After three days, we get an email titled "Disaster!". When the UMass people opened the box they found small rocks of dry ice and many fragments of plastic scattered throughout the box (although few boxes remained intact).

(pictures courtesy of Ollie's iPhone)

The lessons we learned from the exercise is a harsh one. Turns out that the plastic strips we use are extremely brittle at cold temperature. Moreover, parafilm no longer binds when cold. Moreover, as the ice blocks evaporate, there is room for play inside the box, and things start to jump around, leading to havoc.