Does bound MS2 coat protein inhibit mRNA decay?

Roy Parker recently sent a  “Letter to the Editor“, published in RNA journal, in which he suggested that the MS2 system might not be best suited for live imaging of mRNA in budding yeast. According to Parker, the MS2 system inhibits the function of Xrn1, the major cytoplasmic  5′ to 3′ RNA exonuclease in budding yeast, causing us to image mostly the remaining 3’UTR fragments. Thus, he claims, it is possible that interpertation of mRNA localization data using this system in yeast can be faulty. We wrote a response to his letter which just opened the debate even further.

But lets start with his Letter:

Continue reading

Imaging with CRISPR/Cas9

The hottest buzz-word in biology today is CRISPR: an adaptive immune system in bacteria and archea. At its basis is a nuclease, named Cas9, which is targeted to DNA by a short single-guide RNA (sgRNA). This turned out to be a very useful system for genome engineering in any organism due to its specificity (provided by the sgRNA) and its simplicity (all you need is to express the Cas9 and sgRNA in the cell). However, this system can also be used for other purposes. One such use is modulation of gene expression, for example by targeting a nuclease dead Cas9 (dCas9) fused to a transcription activator or repressor to promoter regions. Another such use is for imaging.

Here, I’ll described how Cas9 can be used to visualize specific DNA loci or specific RNA transcripts in fixed and live cells.

Continue reading

My 2nd grade science project

My daughter’s school has a tradition for 2nd grade, to celebrate 100 days of school.

So my daughter had to prepare something relating to the number “100”. At 1st grade they celebrated 50 days of school and my wife made a cake shaped like the number 50. So this year my daughter decided to spare her mother and not bring a cake (as several other kids did).

We pitched several ideas, and she chose my idea of using the microscope to enlarge 100x certain objects (hence, the relevance to this blog :-) ).

A few years ago I bought a microscope at AmScope to use at home with the kids. It is a 40x-400x compound microscope, and it has a digital camera that you can connect with a USB to your laptop. This allowed us to take really nice images of the objects we examined.

I brought E. coli and yeast samples from the lab and we imaged them 100x and 400x. We then imaged a single hair from her head. She got really excited about that and also took a hair from her dog, to compare.

She then brought me salt which gave a pretty picture of the cube-shaped crystal. Last, we imaged a leaf of strawberry and mold that grew on a cucumber.

We made a nice poster:

final poster


This was a great experience for both of us. She was really excited and we imaged for over an hour, late in the evening. She’s interested in science, particularly medicine. She’s rational, she’s smart and clever. She will do great things when she grows up.


ASCB15 – part 3

(part 1, part 2)

I ended part 2 Monday night. It was an exciting day with many excellent talks, but the best talk (mine, of course!) was due the next day.

Tuesday started with the seminar on engineering cells and tissues. There was the mandatory CRISPR talk as the great new thing in bio-engineering these days. Jennifer Doudna talked about the discovery, then went on to discuss new experiments (using Halo-tag to track Cas9 in live cell nuclei to study movement & binding kinetics) and improved technologies (transfect cells with pre-assembled Cas9-gRNA for quick editing & less off-target cleavage).

Continue reading

ASCB15 – part 2

I ended Part 1 after the morning session on pushing the boundaries of imaging.

After the amazing talks on imaging, I browsed the halls, visited some exhibitors, sampled a couple of exhibitor tech-talks. I later went to a mycrosymposium (#2: signaling in health & disease). This was mainly to see how this ePoster thing works, but also I promised Qunxiang Ong – with whom I discussed optogenetics the day before – to be at his presentation. He used a light-induced dimerization of signaling proteins to study the effect on neurite growth. The nice thing in his system was that the cells were plated in wells which were partly dark – so light-induction cannot take place in these regions. This allowed for analysis of neurite growth in lit vs “light-protected” regions of the same cell.

After this session, I attended my first “discussion table”. Continue reading

ASCB15 part 1

The ASCB meeting brings scientists from all levels to talk about cell biology, which is actually almost anything “biology”. But there’s also a full program dedicated to other matters, like science careers, science publishing, science communications and science policy. This is also a great venue for companies to show their products, and for organizations/institutions to recruit new members. If I remember the numbers correctly, there were over 550 oral presentations and over 2,700 posters. I overheard someone saying there were ~6000 people attending the meeting. I typically go to RNA meetings that are mostly in the lower 100’s of participants. So, to me, that’s a large meeting.


Continue reading

A funding experiment: force me to write

As some of this blog’s readers may have noticed, the number of posts published in 2015 has dramatically declined compared to previous years.

This past year, I found myself with less time to read papers, but mostly with less time to write quality posts the way I’d like to do that.  Typically, writing a post on a single paper takes me several hours, sometimes spread over a period of days. But I also enjoy writing about a new subject that encompasses several papers, which obviousely takes longer.

I have several drafts/ideas for such posts but I can’t find the time to actually do that.

Some of these topics include:

  • GFP-mimic RNA aptamers (e.g. Spinach, RNA-mango etc…)
  • Some more in depth posts on super-resolution methods.
  • New tools for imaging (e.g. Halotag, Snaptag, Suntag, CRISPR and others ).
  • A discussion on RNA detection by FISH vs RNA-seq vs PCR vs Northren (propmpted by  my upcoming response to Roy Parker’s Letter to the Editor on MS2 labeling, as well as discussions in Arjun Raj’s blog).

This semester I started to teach a seminar course on mRNA localization, and I had high hopes that after each seminar, I will write a post about “this week’s paper”. Well, that didn’t happen.

So, I thought of an incentive to get me to write, and what better incentive than money? [Particularly since I’m a poor postdoc with 2 kids, a dog and mortgage (my wages of 2400$/mo, including the teacher wages, barely covers it)].

I added Paypal “donate” buttons on the left “widget area” at the bottom  and also in the “about” post above.  [Edit] Here is a Paypal donation button. If you enjoy this blog, if you feel that you gain insight or just interested in the contents, you are welcome to support me. There is no minimum amount to donate.

PayPal Donate Button

If I get total donations of 600$, I will post at least once per month. If I reach 1000$ or more, I will try my best to publish every 2-3 weeks.  1500$ will be a great incentive to start the series of posts mentioned above.

For 1,000,000$ I will dedicate my life to this blog:-)

Those who donate also earn the right to suggest papers for future posts…

(Of course, I will continue to maintain this blog even without funding, but postings will be rare).


Next week I’m going to ASCB2015 meeting in San Diego, CA.  I’m presenting at the ePoster session on tuesday (Microsymposium 16: Cell biology of genetic information). If you’re interested in my research come and see what I do when I’m not blogging…. Or just come say hi.

I plan to write a summary post each day of the meeting (and maybe live-twitting).