MODEL-IN semi-annual meeting

Our group is part of a consortium that is funded by the European Union for a joint project on transcriptional regulation in inflammatory response. The title of the project is MODEL-IN, and you can learn more about it in its website.

As part of the project, we hold meetings roughly every six months. This is a great way to catch up on the progress in each group and also to get better working relationships. Most of the meetings were in the UK, and one was in Rome. This time the meeting was organized in Israel, which was a great opportunity to get project members to see Jerusalem.

We spent two intensive days in meetings going over scientific results.

On the afternoon of the second day we went for a tour around Jerusalem. This was a beautiful spring day (spring started early this year) and we got nice views of the old city and its interior.

Robotic NanoString Experiment

Today was finished our first large scale experiment using our robotic platform. 

Assaf programmed the robot to grow 90+ strains of yeast over two days to reach optimal conditions (as I previously described), then the robot stimulated them and harvested cells at 9 time points. Each harvesting step involved taking small amount of cells from the plate they were growing them and plunging them into a plate of cold liquid methanol. This immediately freezes the cells and "stops" them cold (literally).

Next, Assaf used the protocol he and Ayelet devised for extracting RNA from yeast cells, to process these 9 x 96well plates. These will be shipped to Ollie's lab for running the NanoString assay to measure exact RNA quantities.

This was the first time we had an actual experiment running from start to finish. Although we "debugged" various parts before, putting all of them together uncovered all types of problems. Assaf had to restart the growth several time before we had the whole thing running. But now we are smarter and know how to get things right the next time.

After few days of heavy robot use, Assaf collected all the plasticware he used. Here is a picture of triumphant Assaf at the end of the process.

Robotic Facility Kickoff

You may recall that we had an event to celebrate the opening of the first half of our lab. Now that the renovation is almost over (only missing few furnitures), we decided to have a more official kickoff. The idea was to say "Thank You" to all the people who helped us build this lab out of nothing.

The last week, Ayelet, Assaf and Avital (also known as "AAA Robotics") worked hard on setting up a demo of the capabilities of the robotic facility. The last two days, I recruited Tommy (who is still waiting for his J1 visa renewal) to help make a movie of this demo. Tommy turned out to to be a capable photographer and has the option of alternative career in the movie business. 

Yesterday afternoon, Naomi and I went to buy cheese, cherry tomatos and strawberries for the event. As usual, the selection of cheeses at our favorite fromagerie was tough, but we managed to negotiate it. This morning, Ayelet bought fresh bread from our favorite baker. We set up tables in the corridor leading to our lab, with sparkling wine, bread, cheese, and red tomatos and strawberries.

Since all the rooms are already in use, we had the event in the small meeting room/kitchen next to our lab. This meant very select company (we had space for 24 chairs). It was very emotional as it was a chance to thank so many people at once.

Moments before the 9:00am, we did a quick test of the demo, and Ayelet decided we needed another plate with YPD (media), so I rushed to do the job.

During the event I gave a short talk about the science we do, and then had a movie about the robot. 

We then moved to the corridor and had a toast. Sadly, the University President had to rush out before the toast. 

We then had real-life tours of the facility while other used the opportunity to chit-chat and catch up. Sometime even serious scientific discussions.

Photography at the event was courtesy of Roy.

Into the cold!

I am now in New England. I am visiting Ollie to write a grant and work on results. It snowed on the first day here. And now the clouds have cleared away, and it became colder. Today its about -10C and tomorrow it is supposed to get even colder.

Regulation of Blood Cell Differentiation

Another cause for celebration. A project that was active for several years has made it to publication. Today a paper with Noa as a first author appeared in Cell. This project was mostly done when Noa was at Aviv Regev's lab at the Broad Institute. She analyzed the expression profiles of genes through the differentiation of hematopoitic cell lineages --- how a bone marrow stem cell develops in to different types of blood cells.

                                                                          (Source: Cell)

The interesting part is that this analysis uncovered multiple "modules" --- groups of genes --- that are reused in different lineages. This shows that differentiation is much more complex than previously assumed about this system.

Congratulations to Noa!

NanoString Tryout

You might remember that previously I reported on our efforts on RNA extraction from yeast cells. Since then Assaf and Ayelet quantified the amounts and quality of RNA we get by doing RNA purification from the cell supernatant in Assaf's assay. They showed that the amount of RNA we get matches what literature reporters (about 1.2 pico-gram/cell), and that the RNA does not show any degradation.

Last week Assaf performed a time course experiment where he grew yeast, and then subjected them to salt stress, and collected cell at different time points following the stimulation. He froze samples of cells by droping them into very cold (< -40C) methanol, and then extracted supernatant using the technique I discussed in the previous entry. 

He packed the supernatant in a box with dry ice and we sent it to Ollie's lab at U. Mass. Medical School by carrier service. We were not sure if the samples will get there in good shape, and it was great to hear that they did, still frozen. Hsiuyi from Ollie's lab run the samples on the Nanostring nCounter machine they have there and sent us back the results.

Few words about the NanoString machine (you can read a nice overview on their website). The basic idea is that we order a set of probes that match genes we are interested in, and then using these probes can count individual molecules in a small volume sample. By counting how many times we see each type of probes we get a very accurate measure of the number of RNA molecules in the initial sample. The cool thing about this method is that it does not use any enzymatic reaction and thus does not have biases due to PCR preferences and such. Moreover, it is very simple to run and does not require RNA purification, labeling and such.

We were very happy that the results we got from Hsiuyi showed high degree of reproducability. Two repeats of the experiments looked almost identical (if they would have been more similar I would start being suspicious).

In this figure each dot correspond to a gene, and the x/y axis are the log (base 2) of the number of counts we had for that gene in the first or second replicate expriment. We can see that the dynamic range here is between 2 to 16, so we have 2^14 (= 4096) fold difference between the lowest probe and the highest one.

This success shows that Assaf's setup is ready for the big experiment of measuring many different mutants. Hopefully we will have this done in the next few weeks.

Visitors

This week the winter decided to give us a sneak visit. It has been a mostly sunny winter so far, but for a few days we had actual winter (rain and wind).

In the midst of this (mild) winter weather Tommy, an ex-student of mine who is now a postdoc at the Eisen lab at UC Berkeley, showed up for an interview. It was fun to spend time with Tommy again. He was involved with the early steps of thinking about the grant, and so it was nice to show off how much things have progressed.

We enjoyed a lull in the rain to sit outside among the fallen leafs and enjoy a simple lunch.

As part of his visit Tommy had to renew his visa, and seems that courtesy of the US embassy, we will have him visiting for a bit :-(

Here is a picture of wintery sunrise: