Our preliminary work studying the telomere biology of planarians received widespread media attention. As a result we have received a lot of questions from people (non-scientists) who were excited by the media reports.

We've launched the new version of the Aboobaker lab website. We are using PivotX to power our backend CMS (content management system). Most of the content is still not filled in yet. We will be doing that throughout the week. Please check back in a couple of days for more content.

I recently had to write a Summary of our work on telomere biology in planarians for the public, so I thought I would post it here as well, as its likely to missed on a dusty beurocratic website somewhere.

From my own conversations with experts in pluripotency they tend to always use the "contributes to the three germ layers" definition of pluripotency. I wouldn't argue with that as it is a definition with some teeth, and excludes the germ line which I believe is reserved exclusively for "totipotency' (you can get all three germ layers and the germ line from these cells- and this might be important -and we'll come back to it). In any case useful and meaningful definitions are absolutley crucial if you want to understand how things evolved using a comparative method. The definition(s) of the character(s) you are comparing will decide the scope for your questions. Assuming you might want your questions to be important, interesting and tractable...  a strong definition helps. 

When thinking about the evolution of pluripotency it is a molecular definition of the key components of stem cell pluripotency rather than a cellular funcion definition that I would find most useful (my students too) for subsequently asking the right questions, and performing the right comparsions. This definition would have a different  function from an evolutionary perspective than the stricture of a cell function test of germlayer contribution. I guess this might be a fairly obvious point to make for most of us interested in this. (-For those of you for whom this is a heresy- stop reading now is my advice, it gets worse!)

We had a lot of great questions/comments posted in the comments section of the youtube video released a month ago. I've copied and categorized all the relevant questions and comments in this entry. There were a lot of people asking the same questions, so I've also filtered the questions for redundancy (what do you expect from the computer guy -Aziz). We will answer them as we get to them. Check back often for updates to this Q/A.

The ability of stem cells to differentiate and form other cell types is not only a key area of practical interest for biomedical science it also underpins animal evolution. Thus it seems strange that a formal framework for studying how pluripotency evolved is not in place (I missed that particular EU Framework grant obviously). While investigating embryogenesis, formation of the germline and the nature of stem cells in a variety of organisms provides evidence, are there key experiments in key taxa that would tell us how fixed or free to evolve the machinery controlling pluripotency is? Are there distinct pathways controlling pluripotency present in some taxa and not in others?

I gave an overview of the 3 planarian transcriptomes in my last blog post. Since we do not have immediate access to all the raw data that went into the transcriptomes, we have to resort to merging the assembled transcriptomes according to their strengths and weaknesses.

Here are some thoughts on the 3 transcriptomes that'll need to be address when performing the merge:

• The BIMSB transcriptome contains the most full length, non redundant set of transcripts, but it also has the least amount of transcripts.

• The AAA and Heidelberg transcriptomes have better coverage of the transcriptome due to high depth of sequencing.

• The BIMSB and AAA transcriptomes both have a small population of very short sequences. It looks like Heidelberg discarded transcripts below 100 base pairs.

• The Heidelberg transcriptome contains a lot of Ns.

• There maybe some isoform information contained in all the transcriptomes.

• The AAA transcriptome may contain elements of both asexual and sexual sequences since the SOLiD reads were reference assembled.

• Strandness in BIMSB and Heidelberg transcripts are mainly based on ORF or homology evidence.

Read the rest of this entry here.