Tuesday, December 28, 2010

One Year Celebration

Today this blog celebrates its first year. With 102 posts during the year and many exciting events.

Just to remind everyone, a year ago we had two benches, one freshly installed FACS and two devices still packed in their boxes. Today we are past the renovations. The molecular lab has 6 working benches, and two more for equipment. We have a preparation room for making media and agar plates. And, most importantly, our robotics room is setup with all the devices up and running and integrated.

Now our efforts move from the renovation updates you have been hearing about to more scientific issues, such as setting up the experimental system and learning new exciting things.

Monday, December 27, 2010

Cameras and labels

We are slowly starting to check off the various little details that make a lab functional. Today we had two new improvements in the lab.

First, after long delays, we finally got proper printable labels, and Ayelet set off on the task of putting labels on drawers and cabinet doors. The long searches for where someone has placed a particular item will hopefully be easier now.

In the robot room we installed two IP webcams. These monitor the main Tecan stage and the peripheral area of the microscope and HyperCyt. We now need to hook these to a recording software so we can also browse back in time.

Here we see one of the cameras (the one watching the Tecan) and a view on the screen from the second one that watches the KiNEDx and peripheral devices.

This type of monitoring is important as we are starting to run the robot overnight and want to be able to analyze what went wrong if something does go wrong. Moreover, it will allow remote examination of the system when one of us is not around.

Saturday, December 25, 2010

You are what your father ate?!?

I have been lax at reporting papers coming out, but decided we need to change that. So here is a new type of post - talking about new publication.

This is culmination of a wild roller coaster ride over the last few years and months. The project has been one of Ollie's (Rando, OJ, that is) for quite few years and we were brought on to help.

For some reason Cell put a press release with the title "You are what your father ate" which seems a bit of an over statement. But it definitely managed to get the press interested. So far there is press coverage by the Time, and various other interesting venues, such as Pravda.

The basic story, is that Ollie and later his students have been feeding mice either control diet or one that is low on protein and high on suger. These mice where then mated with females and then removed from their cage. Ollie then examined gene expression in the offspring livers and found that they were different depending on the father. In particular, lipid metabolism in these mice was different.  

(source: Cell)

Our involvement was in trying to help Ollie make sense of the data. As usual he found the cool stuff by himself but needed reaffirmation from computational people :-) Naomi (Habib, N, that is) analyzed the expression data to make sure that the results made sense. She also compared the list of genes that changed in the offsprings to many relevant datasets in the literature and found connections that helped understand the nature of these changes. She also analyzed other datasets, including small RNAs in these livers, and gene expression in sperms from fathers of the two different groups. 

All by all, this project was one of the main things Naomi did over the last few years. It is great to have it come out, and in particular in such a prestigious venue.

Friday, December 17, 2010

Ariel sendoff

In quick succession of event, we moved from a lab retreat to a goodbye event to Ariel, who is going to Stanford to start his postdoctoral fellowship.

Ariel was a joint student of Hanah Margalit and myself, it was a great excuse to have the two groups meet together for a social event. We met in a nice pine grove in Jerusalem.

After a while we started a small BBQ to prepare hamburgers. Assaf, Jenia and Tal found themselves rotating as chief cooks.

In the meantime we all had a pleasant time.

Toward the end of the event we managed to embarrass the guest of honor by ceremonial goodbye speeches.

Clearly, Ariel was a leader in the group and one of the steadfast members who brought knowledge, critique, and useful suggestion to every interaction. We are sure he will have great success abroad, and already waiting for him to visit us.

Wednesday, December 1, 2010

Lab Retreat

The last two days we spent on our annual lab retreat. The idea is to go out of the university and spend two days in which we get a chance to hear what everyone has been up to and plans to do next. It is also a chance to bond socially.

This year we met in Netiv HaLamed-Heh, a kibutz south-west of Jerusalem.

In what used to be an old barn there is a site that now hosts weddings and seminars. We had a nice and specious room for the talks.

The talks covered a lot of materials, and so we needed some breaks to enjoy the sun.

In the late afternoon we had a special treat, a talk about therapy using puppets.

We then prepared food for the night. Moran found a yeast-shaped potato, which was clearly an important omen.

The potato went into the pot with all the other ingredients and onto the fire. After an hour or so, we had a tasty meal.

The next day we continued with the talks.

We then got into the cars and drove up to a nice hill, and had a lunch picnic, and a short trip to nearyby ruins.

Monday, November 29, 2010

Lab news - fixes and PCRs

Today we have quitely marked an important milestone. Itsik and Ami from the "fine mechanics shop" came to fix the Microscope, HyperCyt and KiNEDx rail to the tables. This means that from now we can assume that their relative positions with respect to each other are fixed (and thus the KiNEDx arm can return to the same position reliably). This is also an indication that we are happy with the temporary outline of devices we put down.

We were warned about the difficulties in drilling in the Terspa benchtop we have. It turned out that with a simple drill it was relatively easy to have holes in the benchtop. 

Ami threaded the holes, and then screwed in the equipment.

The HyperCyt is held in place by three machined blocks (two in front and one in the back). The Microscope had its holders that allow for screwing into the table and into the microscope body.

Finally the KiNEDx rail has holes in the rail itself, and it was screwed directly into the benchtop without external holders.

While Itsik and Ami worked in the Robotic room, we received a package.

Our new PCR thermocyclers. We got a deal on a pair of devices from Bio-Rad that combine 96-well head with two 48-well heads under a single controller. This was one of the missing large equipment on our "to get" list.

Wednesday, November 17, 2010

The army marches on its stomach...

... and science progresses on caffeine. Our newest addition to the lab is the new esspresso machine.

This was gift from Neotec to accompany the integration of the robotic facility.

This definitely improved our quality  of life and allowed us to discover new talents of our members. Without much practice, Ayelet created this nicely layered construction.

Blasting yeasts

In one of our projects we want to extract RNA from yeast for measurements using the nifty NanoString nCounter technology. One of the nice things about this assay is that it uses very small amounts of actual material to measure RNA quantities. Moreover, unlike other assays, we do not need to purify RNA before the assay, which saves a lot of headaches.

The challenge we posed to Assaf, who is about to do the experiment, is how to extract cellular material from a very small yeast sample. We actually need as few as 15,000 cells (just for reference, 1 microliter of happy growing yeast has about 1-2 x 10^7 cells). The problem is that yeast, like many other microorganisms, has a strong cell wall made from proteins. 

The classical way to break it is using mechanical action -- beating the yeast using small glass beads. This technique, however, does not scale down for small samples. And so, we decided to go with Plan B. Here we use an enzyme, Zymolase, that digests the cell wall. This creates spheroplasts -- cells without cell walls that are encapsulated by a thin membrane. We can then pop these open by diluting the sample with water with small amount of detergent.  This solution also includes protein denaturing agents that block any RNAses from breaking down the fragile RNA, and thus preserves our sample.

Assaf and Ayelet tried this technique, and it seems successful. The zymolase readily digested the cell wall and left with nice spheroplasts. Then when he dilluted these quickly disappeared. Assaf made a nice movie of this process under the microscope. What you see is a small drop with yeast spheroplasts, and midway through the movie this drop is dilluted.

Monday, November 15, 2010

Robotic Arm Integration (and other news)

The last week I was away on travel. During the week Shai (from Neotec) together with Avital & Assaf worked on robotic programing and hopefully we will have updates from that front.

In addtion, Udi and Yoram from Neotec manufactured a nice station for handoff between the Tecan Liquid Handling Robot and the KiNEDx robotic arm. Today Shai together with Amir and Moshe (also from neotec) worked on fine tuning the integration of the robotic arm into the Tecan control software.

At the end of the day we managed to film a demonstration in which using EvoWare (the Tecan control software) we can take a plate from the deck of the Tecan to the microscope/hypercyt and back. This means that we made a significant step toward integrating the system.

It is impressive to see the KiNEDx arm in action. Its movements are fast and fluid.

From the movie you will also notice that we hang the plastic curtains that surround the Tecan and keep it clean and sterile. We still need to tailor a hole for the KiNEDx to move through, so for now the enclosure is not complete.

Just to get a sense of the flurry of activity that led to these results, here is a time-lapse of part of that day.

Thursday, November 4, 2010

HyperCyt and Python Scripts

Today we had a long day in the robotic room. Yesterday Arik from Neotec came to calibrate the find details of the liquid handling arms on the Tecan which solves some issues we encountered on Tuesday.

Today Shai, who is responsible for "smart" robotic application came. We had a general discussion about different ways of integrating software to the robot controlling software. Afterward he, Avital and Assaf sat down and implement some pythons scripts that call the robot and others that the robot can call.

It seemed that this was very fast pace study as they reported success, and managed to fancy pipetting procedures on the fly.

In the meantime, Ariel and Jenia tried to get the HyperCyt to work in the new location. We decided to move the peristaltic pump onto the hypercyt deck. This however resulted in the arm pushing the pump off when the device was initialized. This was annoying, especially since the pictures of the device showed the pump sitting exactly where we put it. 

We searched the manual high and low, and finally realized that one of the figures mentions an L-shaped piece that serves as a stopper in such a configuration.  We used this as evidence that this is the right solution and installed the stopper, which indeed solved the problem.

However, now the coordinates of the arm were totally off. And so we learned how to "teach" it where the different locations are. This involved moving the tip of the needle very slowly with mouse controls until it was in the right location.

In the end the system was working, and we even managed to film it. As you can see the sampling needle goes into each well in succession. This means that it creates alternating bubbles of media (+ cells) and air in the tube. If you look carefully in the movie you can see these tubes.

After lunch break and group meeting Jenia run his nifty analysis software to break the long FACs stream of events to specific wells. It worked like a charm and immediately gave him detailed summary of each well. The investment in this software was definitely worth while.

Monday, November 1, 2010

First steps with the robot

Today we had our first training session with the Tecan robot. We learned how to create a script for doing various steps (e.g., pipetting, moving plate from one device to another and such). The concepts were relatively simple and intuitive, and by lunch we had our first working protocol. It takes a plate, seed it from another plate. Move the plate to the shaker for a minute and then measures optical density.

After lunch we moved to more complex protocols that used multiple plates (e.g., when you want to run something on a large number of plates). At the end of the day we felt that we can start making use of this device.

We also had a our down moments, including a crash when the robot arm that moves plates decided to go to the first available position, which was not available....

Tuesday, October 26, 2010

Busy busy day (Robots, FACS, cabinets and sinks)

So another one of these crazy days. So what did we have today.

* David and Ariel from Merkel Technologies came to move the FACS and HyperCyt into the new robotic room (see movie).

* Udi and Shy from NeoTec continued installing the KiNEDx robotic arm. They managed to move a plate from the Tecan to the microscope and back (see movie again).

* We had our first wet-lab group meeting in the room next to robotic room. The furnishing need some work, but the room is usable.


* Yoel, the carpenter from "Wooden Horse" (סוס עץ) brought the new storage cabinets/lockers for the corridor. He also brough cabinets for the robotic room, which made it interesting to work there for a while. The workmanship of the new cabinet was impressive.

* The plumbers came to install a water heater in small yeast preparation room. They also finished the sink in the robotic room.

* We had a regular group meeting in the CS building as well :-)

* And most importantly, Yael came to visit the lab to approve it.

And movie of some of the installation around the robot.... Note the sequence at the end where the arm moves the plate from Tecan to Microscope.

Monday, October 25, 2010

Robot is (finally) installed!

After two delays, today was finally the day. Early in the morning Udi and Arik from Neotec showed up for installation. After re-checking that the tables are flat, we set out to install the robot.

The first step was to unbox the robot from the huge shiping box.

All empty space inside the device was full of a box with various accessories. It took a while to realize that we don't have any hope of pulling it out as one box, and we resorted to removing the contents one-by-one.

Now we could start seeing the shape of the device, Tecan Evo 200, and admire it.

Next, Udi and Arik connect special handles to the robot frame.

We recruited Alon from the lab and Ayelet and set out to lift the Tecan (220kg according to Udi) onto the smallish cart that the Neotek people brought with them. 

Somewhat surprisingly, the cart held the weight, and we slowly moved the procession into the room and next to the table.

A bit of a coordinated heave, and the Tecan was on the table. Few more adjustments and it was located into place.

The curious people could now examine the details of the labels.

We then had a small unwrapping ceremony where we got a chance to remove all plastic protectors from the robot outer shell. 


Shy, who is the main software integrator showed up and joined the party. Arik set out to installing the device. This involved removing safety brackets and unlocking the  arms. It didn't take long for him to get to a stage where he set the device on a "Random Walk" mode. In this mode the robot tries moving the arms to different X/Y/Z locations to see that there are no obsticles or mechanical problems. It was fun to watch and gave a good impression of what the machine can do.

While the main Tecan was playing at random walk, Udi and Arik started assembling the movable arm. Its called Peak Robotic KiNEDx. It has a flexible gripper that can hold plates and move them from the Tecan to the microscope.

Once Udi managed to get the arm to move, we tested how far it can reach. We had to move the microscope a bit, but now the stage is in reach of the arm.
During this whole procession, Shy started working on interfacing with the external device. He had a quick success in interfacing with the microscope and in no time managed to show that he can control it from the driver he wrote. So, we are hopeful that the integration would be smooth.

And finally, the obligatory stop-motion film of the day's highlights. Given requests from the audience, I edited the sequence to be short and include the main interesting points. Enjoy!