Wednesday, March 31, 2010

Windows, doors, and tubes (a mid-passover report)

The last week or so I was on the road and did not get to see the building progress. On the few calls to the lab I heard in the background terrible noise. Turns out we finally got an electricity constructor and his workers were cutting tunnels to pass electricity wires in the walls.

Today I finally managed to get to see what this was all about.

The way the electricity layout is planned, we have a main board next to the door (the alcove that was built earlier on) from which electricity and communication cables will go up above the decorative ceiling, run along wireframe shelves, that will be hanged from these constructions

Then the cables have to reach the main service duct that will run just below window height (both below the windows and along the side walls). To reach that duct, the cables have to be routed through the walls, and the workers excavated wide passageways and prepared tubes, one per cable.


I am mystified why they cannot be routed through a normal duct (close to the windows), but I am not an electricity engineer.

The workers has started to seal off the tubes in cement and make them part of the wall.

Oh, and the new windows have been installed, except the ones on both ends that have to be build to fit. And we got a new door frame for the entry doorway (metal instead of wood, yay!).

Monday, March 29, 2010

On the road: Cold Spring Harbor (+Boston)

Devout followers of the Blog have probably noted the lack of updates the last week or so. I spent this time traveling. The goal of the trip was to attend the "Systems Biology: Global Regulation of Gene Expression" meeting at Cold Spring Harbor Labs (CSHL). This is one of the best meetings in the field, and I try to attend it when possible. For the last few years it has been scheduled for the week before passover, which meant busy flight schedule.

I started with a stop over in Boston. I landed on a crisp sunny day.

Ollie Rando (AKA "The Dude") a close collaborator and friend picked me up and took me to "The Barking Crab", one of the favorite waterfront places in town, for an afternoon light meal and scientific discussions. Bas van Steensel arrived a bit later (on a flight from Amsterdam) and joined us.

The next morning I took the train to Worcester and visited Ollie's lab. Heard a nice talk by Bas, and gave an informal talk about our lab in Ollie's group meeting. I had a good meeting with Marian Walhout, who uses the Singer RoToR for one-hybrid and two-hybrid screens in her lab. They are very happy with the RoTor and do not have the same issues we have.

The following day I visited Aviv Regev, another close collaborator and friend at the Broad Institute. It was nice to meet old friends in her group, and we also had productive discussions on various on going collaboration. Aviv and me then traveled together to CSHL for the meeting.

It was nice to meet many researchers I know, including ex-students Tommy Kaplan, Gill Bejerano, and Dana Pe'er. In addition I ended spending time with Arend Sidow, who I didn't see for quite a while. I won't list all the people I met, as the list would be long (and exhausting), but it suffices to note that I seem to know many of the attendees, which is a clear sign that I have been attending these meetings for a while (maybe too long?).

I shared a room in a wooden cabin with Tommy.  The room itself is very basic, and the cabin heating was either full blast or non-existent (so we alternated between severe heat shock to a mild chill). Moreover, our cabin was located in the furthest locaiton from the main meeting hall on the top of a hill, which meant that going there was a somewhat of a treck. However, by the nature of the meeting, one spends most of the time at lecture hall or in the pub (which is the main interaction hub).

On the last day of the meeting I learned to my surprise that my flight home is from Newark and not JFK as I thought. So I canceled the shuttle service I ordered to JFK, and instead took the train to Penn Station and then to Newark. I had a bit of time to get outside and get a sense of the feel of the big city.

We took off from Newark at sunset which left an impression.

Wednesday, March 17, 2010

Some lab updates

So its been a while since I had updates from the lab. The main reason is that things are going slow and I don't spend that much time there.

Nonetheless, few updates and some images. We finally got our very own ice-buckets (for some reason our lab-ware supplier had these in backorder for two months).

We are also testing a PCR machine. We got an offer to buy a machine from a reletatively unknown vendor that has good specs. To get a sense for it, we got a demo machine installed in our lab.

One of the nice features of this PCR machine is that has a detachable block, and so it can be either a 96-well block (for a full plate PCR or many reactions) or two 48-well blocks, allowing to run two reactions in parallel.

Next week we will get another machine for a demo, and then we will decide which one to keep.

As part of our work we often have to grow bacteria or yeast in colonies. When starting with very small amount of cells that can grow on the media, we often want to spread them on the plate. The common way of doing so is with a bunch of sterile beads. You pour some onto the agar

and then add the bateria dilluted in water (or liquid media)

and shake well.

After wards we discard the beads into a collection bottle for recycling, and move the plate to incubator for overnight growth.

Pipes, Windows, and Sky

Last week the renovation work slowed down a bit, but now we are starting to pick up the pace. We had a window contractor come in to install a window for demonstration

Eyal, our project manager, approved the window with some additional modifications, and so soon we will have the whole row of windows replaced.

Yesterday our new A/C and installation contractor started working. His worker replaced the temporary pipes with new ones.

Outside the hazy warm days were replaced by clear and windy ones. Walking today from the lab back to my CS office I saw the potential for impressive sky.

(The crane is the building site for the new engineering building that should be finished in about a year and half.)

Monday, March 15, 2010

Live Imaging Day

Today we had at the institute a meeting of the Israeli Live Imaging Forum. This included talks from groups from all over Israel, and one international keynote. Many talks with extremely cool movies, ranging from intra-nuclear bodies moving, yeast dividing, cells migrating during development, to flying bats. (That is not a joke, the welcome speech by the institute head had an example of imaging without a microscope :-)

It was good to see Ifach, my ex-student who is now starting his one lab at Tel-Aviv University. (Incidentally, he arrived in August, and his lab renovations, that included rebuilding everything from scratch, are finished, and cost in terms of $/m^2 less than half of our renovations. It will remain a big mystery why renovations here are so expensive.)

I showed Iftach the lab, and we had interesting discussion about PCR machines, the MasterClave, and the the other toys. Funny that I didn't think that would be our main chatting point, back when he was student. Iftach made the point that they had problems with agar going too soft due to high acidity of the water they used. This might explain some of the issues we had recently with soft agar.

Another attendant was Nir Friedman of the Weizmann Institute (AKA as "the other Nir Friedman"). His student gave a very good talk, where the original few slides were very in step with the kind of questions we plan to ask in the lab. In this sense, it seems that we are drawing closer in terms of our scientific interests.

Thursday, March 11, 2010

Short renovations update - another meeting

The progress of the renovations is measured by meetings, each one bringing us a bit closer to the end of the road. Nothing is done until it is chewed upon from all directions.

Today we had another meeting with Itsik and Eyal (no pictures). We went over the comments on the revised furniture plans (after the first round of comments). This should be the final specification for the first stage of the lab.

Then we talked about the expected schedule for completion of this first stage. The current prediction is somewhere in May. This means that the second stage will take another 1-2 months after that. I got to place where I am not upset about these things, just try to make sure that everything progresses forward. I wonder whether this is giving up, or growing up.

Finally we talked about the plans for the second stage. We made some progress in defining what we want, and it seems that our plans for the robotic room are doable. Next we will move to more refined definition of the furniture (coming up soon).

Wednesday, March 10, 2010


The track to learning how to use the tools in the lab leads us with surprising turns. For example, the Singer RoToR is something we thought we understood and start using with reliability. Every time we believe we sorted out the problems we run into new one.

Yesterday, Ayelet decided to copy the GFP-tagged library so that we can have fresh copies to use for picking up strains. What worked fine the previous day, suddenly decided to cause problems. Once again the de-liding arm didn't pick up a plate lid. Unlike the previous event which lead to a cascade of escalating problems, this time the resetting worked fine. But only on the forth attempt (with a complete reset after each one) things went back to normal.

In previous rounds of copying, we had problems with the colonies at the corners of the plate. Our thinking was that the agar is starting to dry and thus is no longer flat. To avoid this problem, Ayelet increased the pressure of the tips onto the agar. This solved the corner problem, but lead to a new one. Since we used fresh plates, the extra pressure on the target plate caused the pins to puncture the agar. Instead of putting cells on the surface, we now have them in small craters. Today, after some growth the colonies look more like starbrusts than the disk shape they should take.

One worry is that copying from these plates will be difficult since the colonies are not growing upwards but rather inwards.

Tuesday, March 9, 2010

Shaking (and grinding)

One of the cool devices we have in the lab is our incubated plate shaker. The job of this device is to shake plates while maintaining constant temperature for fast growth (30C in the case of yeast). During this growth the yeast has to be shaken for two reasons. First, to aerate the media which maintain a constant environment (releasing ethanol from fermentation and mixing in oxygen), and second, since yeast tend to precipitate (settle down) in media, it has to be resuspended to ensure that all cells are exposed to similar microenvironment.

As we are using dense formats (96 and 384 well microtiter plates), we need to shake the plates at a high frequency and a small orbit, which usually is not achieved by standard shakers. Since we bought a dedicated shaker, it was a nice bonus that it has its own built-in incubation environment.

Yesterday Ayelet inoculted plates with samples from a library that we got from Ollie Rando's lab. Since there were multiple plates, she stacked them up in two levels. The plates are molded so that the top plate is anchored to the lid of the plate below, and thus does not fall off during the shaking. However, we discovered a curious fact this morning. The plates were dirty with a fine white powder.

Turns out that the high frequency shaking motion was slowly grinding the plates against each other, resulting in this plastic dust. While the grinding does not seem to wear down the edge of the plate in a significant manner, it does create unpleasant source of potential contamination. We need to see whether to stop using two-levels of plates, or figure a way to buffer the grinding.

Renovations update

The last two weeks I have been mostly busy with start-of-semester issues, various committees, meeting with students, and such. At the same time the renovation work has continued in its own pace.

Yesterday the workers were busy in the last stage in building(?) the floor. They put a special cement to seal the gaps between the tiles.

This morning the floor was clean and done. The workers already put protective surfaces (dry wall sheets) along the windows to protect the floor during the installation of the  A/C units and replacement of the window panes. The only missing part in the floor are the two tiles in the entry way. They will be installed only after the door frame is rebuilt.

On other fronts, we now have an A/C contractor. I am still unsure as to when he will start the operations (we are still waiting for an electricity contractor), but this is a good sign.

Tuesday, March 2, 2010

Floor & plans

The work on the renovations progress forward and yesterday the worker started laying down the floor of the lab.

On other matters, the I am posting the current furniture plans as we got them from PVPlast. As you can see, this is less colorful than what I posted before, but hopefully more precise.

The last two weeks were the start of the second semester, and I had personal meetings with about 45 students. All very interesting but taking most of my time. Hopefully next week will be better and I will have more interesting updates.

Monday, March 1, 2010

Rainy day - outside and inside

Today is the second day of Purim - a holiday, in which the children are on vacation. The university operated in a limited capacity (as a weekend day). Nonetheless, some of us continued working. The strong rainy spell of the last few days brought over 200mm of precipitation in the Jerusalem area, and throughout the day there spells of harsh rain.

After lunch I got a call from Ariel who was in the lab (working with Ariel from Merkel on the HyperCyt) that there was a leak in the cold room that we share with other labs on the floor. I immediatly worried that the leak was due to some work on our renovations (as the cold room is neighboring the renovated lab). I came over, and Ariel and Sebastian (our neighboring PI) showed me the source of the leak --- behind the cold room there is a pier that runs pipes from our floor to the top floors. The whole pier was dripping with water running all along the walls. By the time I got there Ariel already called security to let them know, and I called again to verify that they are sending plumbers to the scene.

The pictures did not manage to capture the immense flow of water.

The two temperture rooms next to the pier had puddles on the floor and leaking wall.

I went up to the fourth floor and there the rooms were closed, but the corridor was one big puddle.

In our own lab there was a little leak from the pier, but no real damage. It was a reminder of the fragility of the building. It is hard to tell whether this is due to condition of the systems or just unlucky break - I guess all building new and old suffer from problems, but older ones are more susceptible.