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.

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.

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.

Today, Cell published a paper "Paternally induced transgenerational environmental reprogramming of metabolic gene expression in mammals" by Carone BR*, Fauquier L*, Habib N*, Shea JM*, Hart CE, Li R, Bock C, Li C, Gu H, Zamore PD, Meissner A, Weng Z, Hofmann HA, Friedman N, Rando OJ. 

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.

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.

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.