Category Archives: general post

The Bio-protocol experience

A few months ago, I joined Bio-protocol as an associate editor. The first  protocol I edited is now published, so I thought I’ll write about this experience.

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Bio-protocol is an open access, peer-reviewed e-journal which specializes, you guessed it, in publishing life-science protocols. Submission is almost exclusively by formal invitation and it is free of charge (i.e. no submission or publishing fees).

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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.

 

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 ].

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).

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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).

Corrigendum

It takes a lot of work to publish a paper. There’s the research itself, of course. Then there’s the writing and preparation of the figures for the paper, that are submitted to the journal for publication. Typically, most of the people who contributed to the research are involved in that, so the draft is circulated between at least 2 people, usually many more. There is one author (typically the 1st author, or the PI who is leading the research) who also needs to combine all the comments & changes into one coherent text.

The paper then goes through several rounds of  changes, following reviewers’ comments, editor’s comments, final proof-reading etc…

The accepted manuscript (MS) should be “perfect”. But mistakes can happen. Mistakes did happen for three of my recent papers.

For my Cell paper, I have prepared a nice schematic model to summarize the main highlights. It was nice, but we decided it is worth spending money on a professional artist to make a nicer one. Somehow, my scheme was uploaded for the accepted MS, instead of the more artistic one, and this is the one that was eventually  published  (you can see the artistic version in the blog post about the paper). I found that out after the fact, but since it was just a model, and the only difference was the art, we decided that publishing a correction just wasn’t worth the trouble.

Then, we published a paper in PLOS One. Only after it was published, I noticed that something happened to figure 4. Here it is:

Can you find the error?

Can you find the error?

Here, we had no choice but to publish a correction.

Recently we published a review paper, in Nature Reviews Molecular Cell biology. We worked very hard with lots of proof-reading and integrating each other’s changes to make sure it is perfect. Then, a few weeks ago, I was looking for some papers which I knew we referenced in that review. Strangely enough, those papers were mis-quoted in our review. Maybe its silly to publish a corrigendum just for a tiny mistake in references. But I think that it is important to keep science as mistake-free as possible, even with those tiny seemingly unimportant mistakes. So we published a corrigendum.

Here is also the place to thank the editors for handling these corrections pleasantly and efficiently.

I’m looking forward for my next corrigendum. What will that be?

Announcements

I am aware that it has been a while since I updated new posts on fluorescent microscopy. I blame life. And work.
Anyway, I have several papers piled up, waiting to get blogged.

In other news, I wrote a blog post for Addgene blog. Addgene, for those of you who do not know, is a non-profit organization that helps biologists share plasmids. Briefly, researchers can send Addgene their plasmids (which were featured in their publications) and other researches can order these plasmids from Addgene at a relatively small fee (relative to the amount invested in cloning a plasmid). My post is about how to choose the best suited fluorescent protein, something I wrote about in this blog sporadically. It should get published soon.

On May 22 I’m going to present my work at the annual meeting of the Israeli Society for Cancer Research.

On July 12-13 I’m going to present my work at the Gordon-Merck Research Seminar on Post-Transcriptional Gene Regulation  and the very next day at the Gordon Research conference on the same topic. You can still apply (for poster presentation only) for both of these.

On the publications’s front, a revised version of a paper I co-authored (which continues my work on the decay-transcription story) was recently sent back to the editors. We’re hoping for good news soon.

Am co-authoring review paper on mRNA localization for Nature Reviews Molecular & Cell Biology. Hope to submit within a couple of weeks.

And, the research I’ve been working on for the past two years is finally starting to take shape as a paper. Hope to submit within a month or so.

Also, for the first time, I’m now an official reviewer of a peer-reviewed journal ( RNA journal ).

protocols.io – Life Sciences Protocol Repository – a kickstarter project

The Protocols.io Kickstarter project looks like a very interesting and useful attempt to create an online, easy-to-use and easy to update protocol repository.

They have some great ideas, so I pledged some money for them.

An excerpt from the Kickstarter page:

“A free, up-to-date, crowdsourced protocol repository for the life sciences.

As scientists, we are constantly expanding the frontiers of research and knowledge. Yet, we are also constantly re-discovering knowledge that others have not had the time to publish and improving existing methods without the ability to share the improvements with the world. The mission of ZappyLab is to change this with the protocols.io repository.

Imagine you spend 3 months instead of a week to do a simple DNA transformation in a new species. After much frustration and many cups of coffee later, you discover that you need to do it at room temperature instead of the 42-degree water bath. This is a tiny but critical detail in a common technique. Unfortunately, there is no effective way to let others working with this species know about your discovery.

We started ZappyLab to create a free, central, up-to-date, crowdsourced protocol repository.

We just launched the beta version of protocols.io. This is where you will be able to share and discover changes, corrections, and optimizations of published methods. The trick is to make the sharing easy and crowdsourced. That’s why we have built a protocol checklist app, inside our mobile Bench Tools suite on iOS and Android.”

Go read the whole story and watch the video at their kickstarter page.

The blog turned 1!

Without me noticing, a year has passed and this blog turned 1.

green fluorescent birthday

Here are a few statistics of the 1st year:

I published 42 posts in 46 categories and used 73 different tags.

Usual traffic is >100 views on Mon-Fri,  with an average of visitor/view 1<x<2 (which means that many visitors are interested enough to read more than one entry, yay). Best day ever was Feb 12, 2013, with 154 views.

Most traffic comes from search engines,  though some get here through links from other sites (mostly researchblogging and twitter).

Top 6 most common search terms were:

fiash (143); phluorin (135); dtomato (129); mcherry spectrum(97) ; tagrfp657 (72) and mcherry (65).

I guess I should dedicate an entire entry to FIASH. Well, someday…

However, the top post ever (except homepage/archive) was on folding & maturation (part1), with 785 views, with next places fluorescence spectrum viewer (417), about (408), virtual cell biology (317), and the nature methods special series parts I, IIIV down the line.

I think that once I go ito live imaging, I will have more to write about the effect of folding/maturation time.

Writing in this blog assisted me in learning about microscopy and GFP biochemistry (doing literature research to write about subjects like FCSNA or folding & maturation really works).

It also helped me plan, organize, analyze and troubleshoot my experiments.

Some people even said that this blog is interesting, so I guess I’m doing good 🙂

I’m going to continue with the journal club entries (by far the most popular category) and, whenever I can, about my own experiments and experience.

Time to go back to work…