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.
Monday, March 15, 2010
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).
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
Starbrusts
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.
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.
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.
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.
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.
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.
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