apalazzo | December 4, 2007Well I'll give you our "author's summary", a feature that accompanies every PLoS paper so that it can be better understood by the lay person:
In eukaryotic cells, precursors of messenger RNAs (mRNAs) are synthesized and processed in the nucleus. During processing, noncoding introns are spliced out, and a cap and poly-adenosine sequence are added to the beginning and end of the transcript, respectively. The resulting mature mRNA is exported from the nucleus to the cytoplasm by crossing the nuclear pore. Both the introns and the cap help to recruit factors that are necessary for nuclear export…
apalazzo | December 2, 2007... and I'm not there. If there's anything noteworthy, please leave a comment.
P.S. This is one of the biggest science meetings of the year, but no press ever goes there and most pop-science journalists are unaware of the meeting's existence. In contrast, both Nature and Science are featuring the Cell Nucleus on their covers, no doubt just in time for ASCB. Are there any ideas out there why this major meeting is under the radar?
P.P.S. Those reviews and papers on the nucleus are pretty impressive - I'll try to blog about them in the near future. Also you should check out Tom's review on…
apalazzo | December 1, 2007Wow! One of the biggest findings of the year! I'll have to read the article more carefully before I comment on it - previously, I wrote a post on the paper that led to this new discovery that was just published online in Science.
Switching from Repression to Activation: MicroRNAs Can Up-Regulate Translation.
Vasudevan S, Tong Y, Steitz JA.
AU-rich elements (AREs) and microRNA target sites are conserved sequences in mRNA 3'-untranslated regions (3'UTRs) that post-transcriptionally control gene expression. Upon cell-cycle arrest, the ARE in tumor necrosis factor-alpha (TNFalpha) mRNA is…
apalazzo | November 29, 2007This week, I haven't had too much time to blog, but I would like to point out two posts written about a paper that I briefly mentioned in a post that appeared last week. It's on that that fabulous result concerning ribosomes from budding yeast.
Background: the S. cerevisiae genome underwent a duplication event - as a result many ribosomal proteins are now encoded by two distinct genes. Two groups located here at Harvard Medical School (the Silver and Roth labs), have found that these critters take advantage of the many duplicate genes that encode ribosomal proteins to construct at least two…
apalazzo | November 27, 2007
(Yeah, I know, luck ... at least I feel better after staying in the lab until 9:00PM purifying DNA from 40 mini-preps and then preparing 40 DNA digestion reactions.)
apalazzo | November 25, 2007I woke up yesterday, made myself a cup of coffee and sat down with the New York Times, and a left over piece of corn bread from Thanksgiving.
It was a beautiful morning and I was at peace.
Then I read this (I will try to be polite) by Paul Davies.
Apparently scientists operate on faith. Faith that the world is rational and non-changing. Apparently scientists are no different than theists. Apparently science is distributed as theistic dogmas which are never to be questioned.
My morning went from a 10 to a 2. I've been grumbling for 2 days now. But I need to get this off my chest. And so ...…
apalazzo | November 23, 2007This week we learned about the latest results from the emerging field of induced pluripotent stem cells (IPS cells). I just wanted to give a few links and my latest thoughts on the subject.
What this field has given us is the ability to study how cells are programmed and how they are deprogrammed. I agree with Thomas Robey who writes:
.... most of science is not about designing cures! It's about asking questions and answering them. Goal-oriented science and translational research is what pays the bills because it captures our imagination. But when it comes down to the bottom line in…
apalazzo | November 23, 2007After skipping a week, it's back.
Here is today's mystery campus:
Hint:The other stem cell story.
This should be pretty easy, even for Northwestern alumni ...
apalazzo | November 21, 2007Yesterday was an action packed day. I got to lab early and made a major discovery. Then last night we had an excellent NERD Club meeting. Then as I walked into the front door at 9PM last night, my wife asks me "Did you hear the news?" Sure enough they have been able to make induced pluripotent strem cells (IPS cells) from human cells. Fantastic. As a biologist, I consider the very first and second experiments on mouse cells to be much more important, and the extension of the technique to another mammalian cell as being secondary.
Now a couple of additional points.
1) From initial rumours it…
apalazzo | November 19, 2007It's incredible. You finish with one project, and the next set of experiments pops up. No time to blog, no time to read papers ... although there are several interesting ones: transcriptional regulation by an endogenous antisense RNA in yeast, ribosomes composed of slightly different subunits translate different messages, how the endoplasmic reticulum is inherited in yeast and how this act helps organize the septins, and this very complicated paper about the energetics of protein folding and how this relates to vesicular transport. If anyone has had the time to sift through these, please let…
apalazzo | November 17, 2007Sorry about the lack of posts, I've been a bit busy as of late. On Thursday I had to look over the proofs for my upcoming paper: The Signal Sequence Coding Region Promotes Nuclear Export of mRNA. It is due to come out December 4th in PLoS Biology.
If also been busy with two other projects that have recently yielded fantastic results. As a result it will be a while before I take another weekend off (yes I'm in the lab, PCRing up genes, RNAi treating cells, and performing the obligatory acts of cutting and pasting DNA).
But don't get me wrong, I am very excited about these new results. It is…
apalazzo | November 14, 2007Bellow the fold:
Fellow science enthusiasts,
I am sending you this email to alert you that ACS has a plan in place if Open Access passes in Congress. I've been told by multiple colleagues that ACS executives are creating a bogus controversy that Open Access will impede scientists' copyright privileges in regards to the studies they publish. ACS has already begun to "educate" scientists about intellectual property rights, with hints that this "education" will help them protect the integrity of their studies.
In reality, this is little more than a stealth campaign to sow confusion and doubt…
apalazzo | November 13, 2007Here's a general email message that I just sent out for next week's New England RNA Data Club.
Hello All,
The next meeting of the New England RNA Club will take place Tuesday, November 20th starting at 6:00PM in the Cannon Room of Building C at Harvard Medical School. Our speakers will be:
- Caryn Navarro, Lehmann Lab, NYU
- Ruthie Zearfoss, Ryder Lab, U Mass Worcester
- William Abraham Pastor, Rao Lab, HMS
We will email out a flyer of the meeting by the end of the week.
Food and beverages will be served after the talks. This meeting is sponsored by MERCK, Qiagen and The Department of Cell…
apalazzo | November 13, 2007
Friday, after Bora's visit, my wife calls me up and informs me that we are off to NYC for the weekend. So we spent Saturday and Sunday roaming around our old stomping ground, looking for stimulation (Soho, PS1, some off-off Broadway theatre, Central Park ...) Fortunately Terri and Matt, had made reservations about the much talked about WD-50. Just last week it was featured in the New York Time's Science Section. Yes this is haute cuisine for geeks.
The joint is the brainchild of Wylie Dufresne (hence WD) located on 50 Clinton street (explaining the 50) in NY's lower east side. And yes I'm…
apalazzo | November 11, 2007There is one small event from the conference (Publishing in the New Millennium: A Forum on Publishing in the Biosciences) that I would like to share with you. I asked Emilie Marcus, head editor of Cell, a few questions. But before we go there I'd like to delve into one aspect of the whole open access debate.
When you think about who pays the publishers to produce all these journals, the answer is simple - the NIH. And it does not matter whether the journal requires a subscription or whether it is open access (i.e. author based subscription).
Lets see how this works.
Subscription based…
apalazzo | November 9, 2007This week's mystery campus. What could it be?
hint:1) Husband and wife team.
2a) Husband and wife team.
2b) .ma et ef iw d na dna bs uH
Know what this means? I'll confirm any correct answers by tomorrow.
apalazzo | November 8, 2007A micrograph of some wacky crystals I found.
Sometimes even crap looks cool.
apalazzo | November 7, 2007Bora (from A Blog Around the Clock) will be in Boston tomorrow. If anyone is interested you can meet us at the Miracle of Science Bar - we'll try to get there by 8PM. Friday, Bora will be discussing the future of science communication at the mini conference entitled Publishing in the New Millennium: A Forum on Publishing in the Biosciences. For more details click here or visit Anna Kushnir's blog.
apalazzo | November 7, 2007If you have the time, pick up a copy of the latest Nature. There is a paper that describes how a lab, based here at Harvard Medical School, used a random gene splicing strategy to express various fluorescent proteins in each neuron inside of the brain of a transgenic mouse. As a result of the random splicing event (using a cre/lox recombination system), each neuron expressed a different subset of the fluorescent proteins. Here is an example of the brainbow mouse's mosaic brain:
So, how many distinguishable colors did the different cells express?
To determine [the number of distinguishable…