apalazzo | September 20, 2006There is a nice post by Coffee Mug at Gene Expression on non-coding RNAs (ncRNAs). This post was provoked by a paper in Annual Review of Neuroscience. In light of my post on the recent Eric Lander and David Spector's talks, here's a snippet:
There are more ncRNAs than you thought:
- Half of the "full-length long Japan" library of human cDNA clones appear to be non-coding. Anti-jargon: cDNA (complementary DNA) is sequence read off of RNA backwards. This group tried to take a very large scale unbiased picture of the RNAs floating around in human cells and did bioinformatics to guess whether…
apalazzo | September 20, 2006In yesterday's NY Times, James Gorman laments that lingo from molecular biology and cell biology hasn't yet permeated society. As Gorman states:
Molecular biology is the science of this century. We should be able to build some great clichés on it.
This topic reminds me of a conversation that I once had with my academic advisor and a certain Caveman. Why is that when you open the paper, you never read about all the cool developments in Cell Biology?
Lets face it. The paper is full of headlines such as "New Planet Discovered" or "Extinct Species Makes a Reappearance" or "Probing the Realm of…
apalazzo | September 19, 2006For those who don't know, John Yates is one of the most important mass spec (or "proteomics") guys out there (i.e. applying mass spectrometry to identify what protein you are analyzing). He developed tandem mass spec and is at the forefront of new technologies in this area. Yesterday he was in the Longwood area where he gave a seminar on the latest stuff coming out of his lab. The talk was OK, it would have been better if I was a mass spec guy as much of the talk was focused on the technology and how it has been used to probe biology ... rather than the biology itself. But I'd like to share…
apalazzo | September 19, 2006Biology is filled with feedback loops and other natural buffers to promote homeostasis. In the latest Nature, there is a ... cute ... paper about how the RNA export factor Tap (aka NXF1) mediates the nuclear export of an alternatively spliced form of it's own mRNA transcript. (For more background on the mechanism of nuclear export of mRNA, click here).
Viruses like the Mason-Pfizer monkey virus can exploit our mRNA export pathway by having their transcripts bind directly to export factors such as Tap. The RNA elements that bind Tap are called constitutive export elements (CTEs). In a hunt for…
apalazzo | September 18, 2006Well it looks like Stew has been souping-up his Science blog clearing warehouse, PostGenomic. A valuable source for searching the scientific blog-o-sphere (i.e. wasting time).
Interestingly there are stats for manuscripts floating round the blog-o-sphere and for many science blogs. Apparently The Daily Transcript is equivalent to Newsweek (does this mean that I'm the Fareed Zakaria of ScienceBlogs?)
For more on PostGenomic, visit Stew's blog Flags and Lollipops.
(Something really cool that I saw at Pg: HubMed, an alternative to PubMed. Click here to read the manuscript describing HubMed in…
apalazzo | September 18, 2006So Friday I posted a photo of an ad that went up in our lunchroom. The feedback was very indicative of the current mood of postdocs within the life sciences: frustration.
It all started with this ad:
And it sparked an interesting series of comments. The type of discussion that our profession needs. I'm not cheering for one side - but here are my two cents.
PIs, I understand, some of you look at this ad and you see passion, dedication and all these other virtues. And many postdocs (me included) see this ad as representative of an academic system gone amok. Sure we all value working hard and…
apalazzo | September 16, 2006From today's NYTimes:
Killing Off the American Future
America's domination of the global information economy did not come about by accident. It flowed directly from policies that allowed the largest generation in the nation's history broad access to a first-rate college education regardless of ability to pay. By subsidizing public universities to keep tuition low, and providing federal tuition aid to poor and working-class students, this country vaulted tens of millions of people into the middle class while building the best-educated work force in the world.
Those farsighted policies,…
apalazzo | September 15, 2006OK here is this week's mystery campus:
Hint:
Looking for the nugget in gold.
If you know the place or the event, leave a comment.
apalazzo | September 15, 2006Looks like this season's lecture series has started.
Yesterday evening I saw a talk by Eric Lander, head of the Broad Institute. Now normally I do not blog about my results and I do not blog about what I hear at seminars. It just doesn't feel right. Scientists work very hard at obtaining results and I don't want to start telling the world about their preliminary data. But I can give you some "factoids" from the talk ... very interesting stuff. (In addition, it would be very hard to scoop anything done at the Broad.)
He started off his talk with the neatest analysis of the 20th century. Gregor…
apalazzo | September 14, 2006Why am I making all this fuss over the latest stats on acceptance rate of general RO1 grants distributed by the National Institute of Health (NIH) ? This is the money that keeps the biomedical/life sciences alive in the US. The numbers indicate that fewer grants are aproved on the first submission. To get your grant funded, you have to resubmit more and more. The longer it takes to get your grant approved, the more your career is in jeopardy. Every time your grant request is turned down, it's another 3-4 months until you can resubmit it to the NIH. If you spend all your time writing and…
apalazzo | September 14, 2006One 18 year old girl is dead. Eight others are in serious condition. It could have been worse, but I think that the Montreal Police learned from the 1989 Ecole Polytechnique massacre that you should try to confront and disable anyone who walks into a public area and intends to commit mass murder.
This had to take place at Dawson, of all places. I have some of my best memories there. For those of you not familiar with education in Quebec, after high school, all students are required to go to CEGEP (or college) for two years before entering university. As we have one year less of both high…
apalazzo | September 13, 2006I just heard about this. A guy started shooting at random people in the cafeteria, and then shot himself. (I was a student there in the early 90s.)
I don't get it, the murder rate in Montreal is low, but at educational institutions we've had quite a few horrible events (the Ecole Polytechnique murders, Valery Fabrikant at Concordia).
apalazzo | September 13, 2006... (or where did all the funding go???)
From The Scientific Activist, Mike the Mad Biologist (and Science Mag, where the article was published - I must have missed this). And now PZ Myers and Orac have commented as well.
Look at the drop in total first time RO1s and the drop in the rate of funding.
{Update} From the article:
We have collected data (6, 7) on the fate of "unamended" (unsolicited) R01 applications. The unamended R01 represents the original application and does not consider resubmissions. NIH classifies R01 applications into type-1 (new) and type-2 (renewals). Revision and…
apalazzo | September 13, 2006I gave lab meeting yesterday and I'm exhausted. Here something I presented.
(First the images then the explanation)
Image 1:
Image 2:
Signal sequences are short stretches of protein that are recognized by the signal recognition particle and direct the protein to be inserted into the endoplsmic reticulum (ER). Similarly there are protein stretches that target newly synthesized proteins to mitochondria. Signal sequences are hydrophobic, while mitochondrial targeting sequences are amphipathic helices.
What is an amphipathic helix? Poly-peptide chains tend to either line up next to each other…
apalazzo | September 12, 2006A web based survey developed by Marc Hauser and coworkers Try it. Then read more about it at Gene Expression. Click here to read about Marc Hauser's book Moral Minds.
apalazzo | September 12, 2006A good friend Claudia, posted a picture on her photoblog (aroundaboutme) that reminded me of something ...
One day, summer of 2002 I think, I decided to take the day off and walk down the Hudson River by myself from the Upper Westside to ... well as far as I could go. It was a time in New York when things felt unhinged. We were all zombies, the world felt different and we were unsure of what to do next. But there was much solidarity between New Yorkers. At some point a woman who was also strolling down the river edge just started talking to me. We walked about 20 blocks together. Her son was…
apalazzo | September 11, 2006It does not seem like 5 years have gone by.
I remember waking up that morning in our apartments in Washington Heights. I was washing the dishes and there were all these sirens. I looked out the window and saw police cars, firefighters and ambulances going down the Henry Hudson Parkway. I was thinking that there must be some big fire somewhere and that we would hear about it later in the day. Then I got a phone call from my father in Montreal. A plane crashed into the Twin Towers he told us. Strange. That Friday we were suppose to see the Cirque du Soleil performing a free show in the Twin…
apalazzo | September 11, 2006This would be an appropriate summary of Matthew Scully's review of E.O. Wilson's latest book, The Creation: An Appeal to Save Life on Earth for the NY Times book review.
So here we have Professor Wilson, writing to his intended audience, a southern baptist minister. He asks the minister to join him in a quest ... to help preserve our environment, help protect endangered species ... help rescue "God's Creation" from the excesses of human activity ... and what does Matthew Scully (a former speech writer for Bush) write?
In his own defense, however, the pastor might reasonably wonder just how…
apalazzo | September 8, 2006That time again.
Here is this week's mystery campus (and it's not Northwestern!):
Hint:
Neutron blast!
Leave your answers in the comments.