New furniture

The remaining open item in our lab renovation was furniture for the common kitchen/meeting room and for the offices. Since we were not sure about the amount of surplus budget, we left these for later stages of the renovation. 

Once the major experimental areas were finished, we started on this mini-project. As usual, the planning stage took longer than expected, and then we had to get quotes, issue a purchase order, and wait for the carpenter to make the furniture. 

Last week this process ended, and Benny our carpenter showed up to install the furniture. As part of the renovation of the kitchen he also had help in installing new kitchen top and sink. 

The end result was a brand new room with much nicer table to sit around, areas for storage, and kitchen top for the coffee machine and water dispenser. Below the counter there is a place for several refrigerators so that each group can keep its own stuff separately.

On his next visit Benny installed the office (when I was away for the retreat). The new office design looks much better and provides area to sit and work. 

CSLS Retreat

I am one of the heads of the Computer Science and Computational Biology dual-major program at the Hebrew University. The unofficial name more often used is Computer Science - Life Science (CSLS). As part of our activities we hold a yearly retreat with all the undergraduate students in the program, teachers, and some of the program graduates. 

During the retreat the third year students present their senior year project, we have some social activities, discuss the program and issues raised by students at different stages, and have a guest lecturer. 

Our guest lecturer this year was Roy Kishony from Harvard Medical Center who talked about bacteria, anti-biotics, and forces that shape they evolution of anti-bacterial resistance.

The location of the retreat is on the beach in Hof Dor (also known as Tantura, see a wikipeida article on the complex history of the place), south of Haifa, which hosts a very beautiful settings for activities. The location is northen border of the sandy beaches of southern Israel, which are formed by sand from the Nile. From here to the north there are hills of sandstone that form ragged beaches. The location was the southern-most Phoenician  city of Dor, which served as a port for various sea-routes of the Phoenician traders. They also had an active industry for collecting sea shells from which the "Royal Purple" color was manufactured (a very rare and expensive dye in the ancient world). 

Today, the natural lagons are a harbour for fishing boats and a public beach.

We finished the retreat with a short trip in Ramat Hanadiv, a park established by the Baron Edmund de Rothschild Foundation in his memory at the southern part of the Carmel mountain. This includes very nice gardens and a large area for nature conservation 

Full-length transcriptome assembly from RNA-Seq data without a reference genome

Just hot off the press - a new paper appeared in advanced online publication in Nature Biotechnology. This paper describe a new computational pipeline to recover RNA transcript sequence and abundance (aka the "transcriptome") from RNA-seq data without using the genome as a reference.

This paper is a joint work of Moran from our group and Brian Haas and Manfred Grabher, both from the Broad Institute. The three of them (Brian, Manfred and Moran) developed a three-part tool to handle massive number of sequencing reads and assembling them to accurate account of the transcriptome. They also applied a very thorough evaluation of our method and how it compares to most of the state of the art methods in the field. This evaluation  by itself is of interest to the this emerging area of analysis.

The basic problem is that RNA-seq returns many (millions) of sequences of different fragements of the original RNA molecules from the sample. To make sense of it, we need to assumble it (like puzzle) into longer pieces. The two general strategies for doing so are nicely illustrated in this figure (from a review by Haas and Zodie):

The "straightforward" approach is to align reads to the reference genome, and then use this mapping to guide reconstruction. The less obvious approach, that we took here, is to first assemble the puzzle, and then map to the genome. This turns out to be often as accurate (or even more), since it is less suceptibles to problems in mapping to the genome, differences between the reference genome and the actual sample, and partial/fragmented references.

Our strategy is based on three steps, each processing the data very efficiently while maintaining information and dealing with sequence errors and rare events.

London and Oxford

I just returned from a quick three day visit to the UK. I was invited to participate in a symposium on "Integrative Network Biology and Cancer" at Institute for Cancer Research in London. This was an excuse to visit collaborators at the Wellcome Trust Centre for Human Genetics in Oxford and at the Imperial College in London. As such, I found myself giving three different talks in three days :-) Nonetheless it was fun and interesting meeting with multiple colleagues and friends, and also hearing some very interesting talks.  

Although I didn't have time for serious touristic activities, I did get few chances to take pictures. 

Oxford, in particular, was very picturesque.

In London I had fewer chances to go around, but the I still managed to catch few images that I like.

Tuneups and a small (but important) improvement

The observant readers of the blog would have notice that conspicuous pink block of hard foam showed up at some point. We used it to stabilize the handoff position of the incubator. The problem was that the incubator is shaking (to aerate the plates inside). These vibrations are then transferred to the attached rail. Since that rail is long, it amplifies the vibrations, leading to unstable pickup by the robotic arm.

Sticking a block of foam beneath the rail damped the vibrations. However, the good people at Neotec, where not happy with it as a long term solution. So today they replaced it with a proper support, that is both sturdy and professional.

More than that, Yoram and Moshe also realigned the "LiHa" arm that has individual pipettes. We have been using the four fixed pipettes a lot, but haven't used the four disposable ones that much. These were haven't been properly tuned yet, and now that we started working with 384 well plates this has become an issue.

It turned out that this tuneup required disassembling part of the fixed tips. Aligning the disposable ones, and then realigning the fixed ones relative to the alignment of the disposable ones. 

The alignment involved a special pin that replaces the tip and has to align to a specific point on the work table.

Once the head is aligned, the actual tips are aligned to be straight down. This requires examining from all possible angles and adjusting the small screws at their base.

Hotels in actions

Last week we installed a new external hotel to hold plates. Yesterday Shai Kaplan and Assaf programmed the KiNEDx to recognize the hotel coordinates. Today Assaf put the new device to use by building a program to perform cherry-picking from individual wells from the whole yeast library. Thus, saving himself the need to go into specific wells in 16 plates, each with 384 wells.

The program worked nicely, and we can see a short part of it in this movie.

We did learn few important lessons about hotels. First, manually loading places onto it can be tricky. If you are not careful it is easy to drop a plate. Second, the installation is a bit too close to the KiNEDx rail, and so we might try to move the hotel back a bit.

In addition, Assaf will try to parallelize the program so it brings the next plate while working with the previous one, and so on.

Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells

An "online" version of a paper appeared in Nature Biotechnology. This work of Michal Rabani, a Hebrew University graduate who is now a PhD student in Aviv Regev's lab at MIT. Michal is also a member of our group, spending several months a year here. This work also included Ido Amit, a postdoc at Aviv's lab who is starting a new lab at the Weizmann later this year.

In this work Michal and Ido used a new method to label newly synthesized RNA using a modified version of uridine that can be later used to separate it from the total RNA pool. This way they measured and sequenced "new" RNA. Michal then used these measurements to estimate the production rate of RNA in cells that respond to an external stimuli. Moreover, by contrasting the production rate of RNA and total RNA she could reconstruct what are the degradation rates through the process.

The main takeaway message from the paper is that RNA degradation rate (or stability) differs between different RNA species. However, for most genes, it did not change dramatically during the response. Thus, most of the shape of RNA level was regulated by production. We did find that for some genes changes in degradation rate was important to modulate the response.

Weekend getaway

After a break of almost three months I went for a weekend of diving in the Red Sea with Matan, my ex-student and dive buddy. Few pictures.