Headed to Santa Fe

I had almost forgotten the pain of designing and printing a poster 24 hours before a conference! I am heading to Santa Fe for Keystone Symposium on long non-coding RNAs. This would be my first attendance at Keystone symposia, which is supposedly one of the very focused conference series. I am show casing one of the lncRNAs that I have been working on for the past year. This lncRNA is a divergent transcript from a protein coding gene. This lncRNA is particularly interesting to us as it seems to be relevant to the context of pluripotency and differentiation. I will be presenting some of our findings on characterization and functional analysis of this long non-coding RNA. More importantly, I will present some of the tools that I have developed, during my postdoc, for studying non-coding RNAs.

Science apart, I am excited to visit Santa Fe! It is going to be my second visit to New Mexico, but my first visit to Santa Fe! looking forward to it.

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New section being built

You might have noticed that there is a entirely new section in my website, dedicated to genome editing tools. This page is a work in progress and it is intended to be a simple guide for beginners on the choice of genome editing tools and a practical start for anyone who wants to use them. Materials and notes are being added to this page on daily basis! Let me know what you think! 

More on genome editing tools

It's been a while since I wrote about the new generation of genome editing tools TALENs and CRISPR/Cas. I have been trying these two systems side-by-side to test their efficiency in my mammalian cell culture system. After about five months of trying out different versions of these tools and multiple rounds of optimization on various levels, I finally got the CRISPR system to work. The simplicity of the CRISPR/Cas system, compared to TALENs, in design and time of generation is amazing. However, how specifically CRISPR/Cas target genome is still a huge question. This is mainly because the targeting part of the CRISPR/Cas system is a short RNA (20 nucleotides) that is complementary to the target DNA. This short guide RNA (gRNA) directs the Cas9 nuclease to a particular site of genome, which eventually makes a double-strand break at that site. It is not entirely clear whether or not a partially bound RNA-DNA can cause a double strand break in an unwanted region of genome.

A recent paper by Ann Rann (Feng Zhang lab) show that the specificity of the CRIPSR/Cas system can be significantly improved by using a nickase Cas9, instead of double strand nuclease Cas9. Using this system, one needs to design two guide-RNAs (gRNA or sgRNA) to direct two Cas9 nickases to the site of interest to make two adjacent nicks in DNA, which can ultimately cause a double strand break. This is a particularly exciting new for the community as it might eventually make majority of scientists to switch to CRISPRs form TALENs. 

I am looking forward to take the final steps of optimization of TALENs and CRISPR/Cas in our system and come back here with more information! 

Notes on ISSCR 2013 meeting

This past weekend, I attended the 13th International Society of Stem Cell Research (ISSCR) meeting in Boston. Living and working in Boston, I ended up shuttling back and forth between the lab and the meeting. This made it a little hard as I had to attend many of the talks and take care of my research and our team as the same time. The conference was amazing. Besides all the good talks, It was a perfect place for networking. I was definitely excited to talk to the scientists who are using the same techniques and technologies as us. Of course, the TALEN and CRISPR/Cas system were among the popular methods for genome editing (I will have more to say about these two very soon). Another highlight of the meeting for me was meeting Dr. Shinya Yamanaka (discoverer of induced pluripotent stem cells and 2013 Nobel laureates in physiology and medicine). I mentioned to him how his paper, along some of the brilliant works in epigenetics between 2007 and 2010, changed my research path. 

I am looking forward to the next ISSCR meeting next year in Vancouver. 

Events in boston area and impact on research

From the last Monday to Friday, we have been witnessing a lot of crazy events in Boston and Cambridge area. Regardless, we have been doing our routine lab work. However, after the city lockdown on Friday, I was a bit worried as to whether or not I would be able to make my way to the lab and feed the cells! Finally, the ban was lifted and the public transportation stared functioning in the evening  That made me able to go to the lab and inspect the cells and everything else. Everything is back to normal again and hopefully we will have a week of progress. 

On Harvard Catalyst

Earlier, I asked if there is an integrated system in Harvard or any other research institute in Boston and Cambridge that lists all the biological and biomedical talks that are held in the region. I would randomly come across flyers and would receive emails about some of talks, but I thought an accessible calendar that lists all the events in one place would be very useful. Last week, while looking for a microscopy core facility, I came across the "Harvard Catalyst". This website is made to make it easier to find scientists and recourses and, in general, to initiate more collaborations. Also, the events section of the Harvard Catalyst lists some of the talks scheduled by Harvard Medical Schools. While this section is very interesting, it still needs more comprehensive listing of the relavant talks in other schools and departments. 

On a separate note, I was amazed by the number of imaging cores in different parts of the Harvard campus and Harvard Medical School. I will be confocaling for the next few weeks (back to the old PhD habits!). 

More genome editing tools

There is an increasing number of articles being published about the new methods of genome editing. Zing finger nucleases, TALENs and now the CRISPR/Cas system, which takes advantage of the RNA-guided Cas9 to make a double-strand break in targeted DNA. I can envision that all the three options (ZNF, TALEN and CRISPR) would coexist and researchers' choice of them would be cell/context/design specific.

Using TALEN for knocking out genes

I became familiar with the concept of TALEN (Transcription Activator-Like Effector Nuclease) few months ago. It has been quickly developing since its introduction in 2011-2012. So much so that it was runner up for the breakthrough of the year, chosen by AAAS. Being able to direct a protein to specific location with a sequence of up to 17 nucleotide gives any molecular biologist all the tools they need for their genome modification studies. Knock-outs are only the beginning. I bet we will hear more and more about the new enzymes coupled to these effectors and doing amazing manipulations that once was a dream. I am so excited that I will use TALEN in few weeks! 

End of an era

After 13 years of being a student in college or university, my formal education came to an end few weeks ago. Basically this semester is the first semester of my life being in a school, but not as a student. Last semester was a quick transition, or somehow an overlap, between a being a graduate student and a postdoc. Not to mention the transition from a small cozy town-like southern city to the dense area of Boston and its hectic life style. Things happened so fast that I can't believe it's been only 3 months since I started here. Speaking of the moving to Boston, it's hard not to mention the climate. I experienced a good -19 Celsius last week. Last time I experienced something close to this, was about 22 years ago.

Personal SNPs and more papers to review

Few days to Christmass and the weather in Boston is already cold and snowy. This is the time that most people of the lab-sphere work in limited hours and I sometimes find myself working alone in a huge room with no one around. In the past few days, I have been reading more on genomic profiling of SNPs and its applications. Two unrelated things made me enthusiastic about the topic. First, I found out the "23andme" (the company the runs microarray for personal profiling of SNPs) has dropped the prices from $300 to $99. This made me study their technology, which is apparently an array based profiling, and think about profiling my own SNPs. Second, I received another manuscript for peer-review! This is the third one so far and it is going to take a lot of time. No need to mention that it's about the SNPs! That makes my Christmas semi-break.

Cheers from Cambridge.