Monday, June 21, 2010

Renovation Halftime Celebrations

Today we celebrated the opening of the first half of the renovated lab.

The day started by a trip to the Market to buy cheeses, bread, fruits and vegetables. We started by buying breads at Teler Bakery, which is considered the best in Jerusalem, and one of the best I know.

We then moved to Basher's Fromagerie. This is best Fromagerie I know outside France, maybe competing with The Cheeseboard in Berkeley. Eli Basher, the owner, is a very welcoming man, who puts on a show for recommending cheeses, cutting samples with the big knife and giving customers a taste.

We asked Eli for his advice, and he sent one of his workers to check prices for wood-boards to serve the cheese on. We then went through a long (and tasty!) project of tasting and choosing cheeses. Eli recommended serving them with Kava and fruits. So, we bought some Kava bottles from him, and then he packed the cheese.

My respect for Eli's professionalism, which was already high, reached new heights today. His estimate of what is needed was right on target, the cheese and the wine was sufficient with a bit left over, but not excessively so.

After buying fruits and serving dishes we returned to the lab. With the help of Drorit we arranged the place for a reception.

At one o'clock the place was empty, and I was getting worried that we will have to eat all the cheese ourselves. But in few minutes the room was packed. We raised a toast, and then cut the improvised ribbon that Avital and Ayelet prepared (picture credit to Zohar Markovich).

The room was packed with guests and seemed like everyone had a good time.

I gave a tour of the lab to the visitors from Computer Science (I seem to be a tour guide quite often lately).

After the party, we stayed to enjoy the aftereffect and the remains of the cheese and wine. Some of us were in elated mood. Avital claimed a desk and made sure it was her's.

Not to waste any time, we started the move. The first item to move was the Singer RoToR. Avital and I secured it, as per instructions, and then with the help of few neighbors we moved it to its new temporary home.

An hour later we called on the same neighbors to help move the cabinets. To get a sense of the action, see the follow stop-animation taken during the move:

By the end of the afternoon we were very tired, but managed to move quite a bit into the lab, and now it starting to look like a real lab.

New (old) person in the lab

Congratulations to Assaf! He submitted his M.Sc., got a final grade, and his latest paper with Ollie was sent to the journal.

Now Assaf embarks on a new career and set out to tackle some experimental stuff in the lab. Today he got his official induction into the lab stuff. He donned gloves and cherry-picked ~380 strains from the knockout library for his first experiment.  This means picking colonies from the original library plates to a fresh plate with media. The challenge is to maintain concentration as each colony must be identified by row/column address and then copied to the right target position.

Avital kept a close eye on him to help ensure that no mistakes creep in during this crucial step.

Thursday, June 17, 2010

Acceptance Tests

Today we had a semi-celebratory event. We performed acceptance tests for the lab. This involved all the contractors, planners, and various university representatives that showed up to examine the work and make a list of accept/reject.

Early in the morning various crews showed up for last minute touches. The electricity folks were in a good mood while testing each circuit breaker.

In the meanwhile the construction workers continued to work on the small Yeast Mating room.

At 10am people started to show up at the lab.

Some of the checks were very thorough and involved detailed examination of every pipe and faucet.

We tested the A/C heating function and nearly suffocated from the heat.

At times the place seemed like a cocktail party.

One of the tests involved the emergency circuit breaker.

There were arguments as to the language on the breaker. And, as expected by some, it did not work the first time around.

Some of the rejects we had

* We didn't have a phone line
* The hot water boiler was leaking and not tightly connected to the beam (!)
* The fire alarm detector system was not properly connected and so couldn't be tested
* The electricity ports below the computer benches are too bulky and could cause knee damage

Most of these will be fixed by Sunday. And so we are about to move into the lab next week!

Tuesday, June 15, 2010

Clean up

At the finish line of work to the "release" of the molecular lab, the cleaning crew came in today. They removed all the wraps over the tables and other accessories (thereby taking some of the fun of "new" furniture). Then they cleaned everything to a polish.

The place looks brand new :-)

In other renovation news, the work on the small Singer room is progressing at a fast rate.

We now have a closet for the electricity board of the room.

The plaster wall is standing and mostly finished.

New windows are installed

And later in the afternoon the working crew started with the floor tiles. This meant a lot of tile cutting in the corridor.

Catching them midway of the work shows the room taking shape.

Monday, June 14, 2010

Touch ups

We are now into the last touch ups in the new molecular biology room. Now that there is proper light, various small defects are noticeable and the workers are fixing them.

One of the funny fixes is dealing with the ceiling. When the ceiling was installed there were noticeable deformation in the tiles.

To fix these, the workers brought small aluminum pieces that they installed at the end of each tile.

This fixed the problem, and now we have nice and even lines.

Singer RoToR Fixup

You may remember the Singer RoToR, our colony replicator. This is a great device, but recently it has been erratic in lifting on of the plate lids.

We contact the nice people at Singer who sent us instruction on how to tune the sensor on the arm. This is very similar to an issue we had in the past with device after it was filled with agar. Tuning the sensor solved the problem but it would reappear.

Last week we got an email from Ian at Singer that he believes the problem is with a faulty relay in the electronic board. It turns out that the device (which is very thoughtfully  designed) comes with a spare relay. Ian sent us detailed instructions on how to fix this. The only problem was that it required opening the back panel --- meaning that we need to move the device.

We opened the instructions for securing the arm and plates. Fixed everything in place, again the design was such that given the instructions it was a piece of cake. We then moved the whole device onto a table.

Removed the back panel,

and switched the old relay with the spare one.

In 10 minutes we had the device back on the original table and working.

I can't say enough how impressed I am with the design and operation of the RoToR. It looks as though every aspect was thought of in advance, including how to best guide remote operators in dealing with issues and fixing problems. I'd wish some of the other devices we bought were that well thought out.

Ian also noted that they came up with a new board that does not requires these relays which can fail. So sometime soon we will do an upgrade to the new board. Given the ease of maintenance of the device, I am looking forward to that.

Renovations updates - "Yeast Mating Room"

As we wait for the final touches on the main molecular lab room, the workers started working on a small side room.

This room will serve as the "Yeast Mating" room. It will have a place for the Singer RoToR, the MasterClave and agar preparation station, an incubator, and supplies for all of these. The idea is that the room will be a more or less autonomic workstation for researchers interesting building and manipulating yeast libraries.

Since this is a small room, we hope the work will progress quickly. The workers tore down the existing interior. Then they rebuilt the foundations of the wall with the neighboring office (to support shelves and to allow for insulation).

The following day the electricians came in and put the tubes for placing the electricity wires.

Today, the plaster wall was finished, and tomorrow we should have tiles in place.

Tuesday, June 8, 2010

Let there be light!

After long delays, today the new lab was connected to the electricity system. The electricity crew came in at 6am and was supposed to be done by 10am.

At 3pm when Ilan and me came in, we found them still working on the main board.

Turned out that the 30+ year switches failed and had to be repaired. This meant that the internet connection for the whole wing was disconnected throughout the day and that our lab and neighboring lab had limited electricity.

Nonetheless, and by that time against all expectations, the crew managed to fix the board, and we got to see lights going on in the new lab!


Ilan Wapinski, a long time collaborator, is visiting Israel for Naomi's wedding. Today we spent several hours together. First we had technical chat with Naomi.

Then we went for lunch at one of the nicest places in town for food - MachneYuda restaurant. This was a combination of cool discussion and tasty food. We sat on the "chef bar" and so also had the whole kitchen staff as entertainment.

Friday, June 4, 2010

Naomi's Wedding

Last night we (all the group) attended Naomi's wedding. It took place in a meadow in a wooded parks on the hills south-west of Jerusalem. We arrived there toward sunset and had a chance to see the forest view and the rolling hills, and then the sunset. The ceremony was at twilight time with the first stars coming out.

It was a happy, energetic and and fun event. We mostly concentrated on the dance "floor" which was full of people, young and older, with an eclectic mix of dance music.

Thursday, June 3, 2010

Short renovations update

Nothing much happened on site this week. But still some updates.

* Next week, we hope, the electricity board will be connected and maybe the new molecular lab would be declared "done".

* Next Sunday work on the small equipment room, where the Singer and the MasterClave will reside, starts. Due to the delays in the renovations on the robotic room, the contractor promised to make fast progress here.

* The one piece of missing furniture in the molecular lab - storage cabinets for consumables - has been finally designed and call for proposals is out. Hopefully we will have it done in two-three weeks.

* We are starting advanced stages of the furniture and electricity design for the robotic room.  

Wednesday, June 2, 2010

Our first GFP-RFP strain

On aspect of the lab that I haven't wrote about much is our Scan^R microscope. The problem is that I planned to explain it with a lot of details, which meant that this post was being postponed everytime.

In the mean time, however, we have been using it quite a lot. For our purposes, we need strains that contain the right fluorescent markers. We relay on the use of  proteins, such as the Green Fluorescent Proteins (GFP) that are inherently fluorescent. This means that when the protein is expressed (made by the cells) we can measure it.

To setup experiments we need to make sure the cells express these proteins in response to the conditions we want to test. As our first attempt in that direction we combined strains expressing GFP attached to different native proteins (one per strain) with a strain that Avital built that expresses a protein called mCherry (a variant of Red Fluorescent Protein or RFP) in a constitutive way. This means that all cells are marked in red, which helps focusing on them and also defining the area of the cell.

We had some set backs with getting the mCherry strain to work, but after some detective work by Avital, she overcame the technical issues. Last week Avital managed to get her mCherry strains to mate with the GFP strains. And next week we are supposed to get the final product of haploid cells with the two markers. In the mean time she took images of the diploid cells, and they look good.

In red:

In Green:

And an image made by overlaying these two images:

You can see that (almost) all cells are red (with varying degrees). Some cells have green in the nucleus (sharp points in the middle of the cells), suggesting that this protein is nuclear one and has variable level of expression under the conditions we measured.