Wednesday, April 27, 2011


One of the big issues in running large experiments on the robot is managing plasticware. As the experiment progresses we need to use new plates, and these have to be stored somewhere until then.

To solve this issue, we decided to introduce hotels -- racks that can store multiple plates. Since we have an external arm (the KiNEDx), we ordered a hotel that can be accessed by the arm. This allows us to have a larger hotel and make it also more accessible for humans. 

We decided to start with a single hotel to see how it works. Several weeks ago we received it, and then had a meeting with the nice people from the mechanical workshop to discuss how to mount it. Today they showed up with the "stage". It is large enough to hold five hotels in the end. 

After installation, we have a nice hotel standing up. Next, we need to teach the robotic arm to access it.

Sunday, April 24, 2011

Comparative Functional Genomics of the Fission Yeasts

Fresh off the press: An online version appeared on the Science Express website (pre-publication online release of Science articles). This is a genome paper where the main result is the sequencing of a genome. In this case, actually two new species, both related to the fission yeast, S. Pombe

(figure from Nick Rhind's website)

The fission yeast is well studied model organsim. As its name suggests, it divides in half during growth (unlike the budding yeast). It is also closer to humans than the budding yeast (aka Baker's yeast) in terms of many mechanisms. And so, many important discoveries in fission yeast in the areas of cell cycle, silenced genomic regions (heterochromatin) and other regions, were more directly related to mammalian cells.

(figure from )

The new world of genomes allows to compare related genomes and use these comparisons to understand what part of the genome are functional. Such comparative genomics has proved immensely fruitful. However, so far very few related species of S. pombe were sequenced. The sequencing of the new genomes, and functional annotations of the genes in the these two genomes provide fresh insights into S. pombe genetics. 

As you can see in this evolutionary tree that contains most of the currently sequenced yeast genomes, the "neighborhood" of S. cervisiae (bakers' yeast) and C. albicans (a species of Candida, a human pathogen) are well populated (horizontal branch lengths correspond to evolutionary distance). With the addition of S. japanicus and S. octosporus, the branch leading to S. pombe is now better explored.

(figure courtesy of Naomi and Ilan)

This project was spearheaded by Nick Rhind (UMass Medical School) and Chad Nusbaum (Broad Institute). Our contribution was in helping make sense of functional data and comparative analysis. Moran helped in identifying transcribed genes in the two new species based on samples collected at Aviv Regev's lab. She discovered many antisense transcripts that regulate some of the key genes in developmental decision making in these yeasts. Naomi and Ilan used comparative methods to find regulatory elements in these genomes, and showed how regulatory elements that are conserved throughout the tree of ascomycota yeasts change their function in these yeasts to match their life style.

Tuesday, April 12, 2011

Spring time in Boston

I got invited by the students of The Computational and Systems Biology program (CSBi) at MIT to give a seminar talk and meet with them. It is a great honor to be chosen by the students. This involved two days of meetings with many interesting people at MIT, especially many of the graduate students in the program.

We had a roundtable lunch discussion where Michelle Chan, who coordinated my visit, led with a series of questions about how to choose career paths, scientific problems, and such. I was somewhat unsure as to my qualifications to answer such questions, but the discussion did raise interesting points.

This was also a chance to catch up with many people at the Boston area. I want to thank Michelle for making intensive effort to get the visit perfectly organized, and making sure that everything works smoothly.

Unlike my previous visit to Boston, the weather was definitely show that spring has arrived, and many of the trees were starting to bloom.

The new courtyard between Biology, CS (the (in)famous Stata Center) and the new Koch Institute (cancer research center)

I had a chance to take an afternoon walk toward Boston

A somewhat curious squirrel in the Botanical gardens

Tuesday, April 5, 2011

Multi-Color FACS

As you may remember, we are using the Flow Cytometer (FACS) to measure the fluorescence levels of individual cells. Our FACS is an older BD FACSCalibur that has gone through several updates. Almost exactly a year ago, we had all the electronic boards refurbished. At the same time we already had plans to replace the old 488nm laser with two lasers at different colors. These lasers arrived with the electronics, but we decided to hold off on their installation that until we stop using GFP markers (that need 488nm excitation). 

After few months we realized that this will not happen so fast, and ordered a third laser with 488nm capabilities. Due to many reasons the delivery of this upgrade was postponed for a long while. Finally, last week, all the necessary parts arrived. Last week Ariel and David from Merkel Technologies installed these upgrades and today we had a training session to go over the capabilities of these devices.

As part of the installation, Ariel removed the old (big and heat generating) laser, and put in a stack of three lasers instead. These required a panel of one-way mirrors to focus the beams onto the light path of the flowcytometer.

You can see the lasers here (with Ariel explaining) on the left side as small boxes. They are really tiny, but sit on aluminum blocks to disperse heat they generate.

The new light path involves mirrors that take the beams from the lasers

More schematically, the new light path configuration is shown below, where each line segment is either a bandpass filter (that allows only small "window" of wavelengths to pass through) or a half-mirror (that reflect certain wavelengths and passes others). As a result each sensor (FL) measures different area of the spectrum.

The consequence of this design is that we now can measure either GFP and mCherry  (a type of RFP) together, or YFP and mCherry. We cannot operate measure together both GFP and YFP since the YFP excitation is very close to the GFP emission.

As before, when the FACS is serviced all the covers come off, and it is a great chance to take pictures of the light beams going through the prisms and mirrors


and finally hitting the target area in the flow cell