apalazzo | May 19, 2007Lab work made sexy on primetime?
Don't you hate it when your BLAST searches turn up nothing!
apalazzo | May 18, 2007Over coffee we were flipping through the May edition of the Howard Hughes Medical Institute's Newsletter when we saw an article on riboswitches, RNA aptamers and the RNA World. The piece features Ron Breaker from Yale, who is most known for describing riboswitches. These RNA elements usually sit on the 5' end of an mRNA and can change conformation when they bind to various small molecules, such as metabolites. These structural changes can affect whether the downstream message on the transcript is translated into protein. So riboswitches are sophisticated versions of aptamers which are RNA…
apalazzo | May 18, 2007This is part 5 of the biomedical science serries on Charlie Rose, enjoy.
(P.S. Keep your eyes open, in a couple of months there will be a major revolution in this field.)
apalazzo | May 17, 2007Flipping through Nature, I stumbled onto this commentary: The good, the bad and the ugly. Here's a taste:
To correctly capture images using a modern microscope, researchers must have a good grasp of optics, an awareness of the microscope's complexity and an obsession for detail. Such skills can take months or even years to master, and yet, owing to inexperience or the rush to publish, are all too often squeezed into hours or days. Popular methods such as fluorescence microscopy are particularly fraught with dangers.
The problem? Here's more:
It is now a routine part of many studies to…
apalazzo | May 16, 2007Wow, yesterday was great! We had food, beer, wine and over a hundred people in attendance. There was plenty of conversation and I got a chance to talk to many people, although I wish we had more time to socialize.
Thanks to everyone who came. And thanks to our sponsors Alnylam and NEB.
Here is funny story for you. I started giving my power point presentation and everything seemed fine except that the room kept on getting hotter and hotter. It turns out that the thermostat was set to 85 degrees. So there I am in a long-sleeved shirt, drenched in sweat. By the end of my 30min talk (well closer…
apalazzo | May 16, 2007I finally got off of my butt and read the latest paper from the Hegde group at the NIH. They answered a fundamental problem in membrane biology: how do you insert tail-anchored proteins into the membrane.
When proteins are synthesized, any newly made signal sequence or transmembrane domain that pops out of the ribosome will be recognized by the signal recognition particle (SRP; click here for some beautiful SRP-signal sequence-ribosome images). This large complex will then inhibit further translation of the protein and target the newly made signal sequence or transmembrane domain and the…
apalazzo | May 15, 2007Wow, what a week. I finally submitted my paper to PLoS Biology and we finally got our RNA Data Club up and going.
This event/series was conceived in a drunken state at a happy hour about 1&1/2 months ago and now has become bigger then anyone of us originally imagined.
When we pitched this idea around there was much enthusiasm followed by fears from some who were worried that many research groups would not want to share their data due to the fact that the RNA field (and RNAi in particular) is so competitive. Well after we sent out a call for prospective presenters (postdocs and grad…
apalazzo | May 14, 2007From an email I just received:
RNA Processing Group (RPG) is intended solely for the person(s) who genuinely believe that RNA research is the coolest thing in the world. To become a member, you have to openly claim that RNA research is cooler than music, money, history, sex, engineering, more money, travel around the world, or sushi. Yeah, that's right!
- Anonymous RPG member.
apalazzo | May 11, 2007From the Federation of American Scientists for Experimental Biology (for all you non-biologists who are wondering who FASEB is):
Urge Congress to Support Research
Increase for NIH and NSF Depends On It!
ACTION REQUIRED NOW! The 2 Most Important Weeks for NIH and NSF Funding in FY2008
Dear FASEB Society Members:
The next two weeks are the most important for determining the level of appropriations that can be attained in FY2008 for the research agencies we support (NIH, NSF, DOE, VA, USDA and NASA).
The Budget Committees are meeting this week to finalize the level of discretionary spending…
apalazzo | May 11, 2007But this is no time to rest ... Tuesday I'm giving the first talk of our inaugural New England RNA Data Club (yes we've renamed it to the New England RNA Data Club ... we're having folks from out of state). There will be a total of 3 talks in this first assembly, mine + two on miRNAs.
I'll let you know how it goes.
But now that the paper is out, perhaps I can compose all these little entries I've been wanting to write.
1) Gunnar von Heijne's paper in Science from way back in February/March on how membrane proteins evolved. (I should add that Dan wrote something about it.)
2) The new Hegde…
apalazzo | May 9, 2007I once made an offer to this guy that I'd word for him if he offered me a permanent postdoc position with a 100% pay raise.
Now everywhere I turn, I see his face.
Open Nature, and there are back to back papers with his name as a co-first-author. Skimming through HMS's Focus magazine, and there is an article on his latest accomplishments. Flip open JCB, and there is a two page spread on the guy.
And read to this comment (from that JCB article), from someone who has figured out big puzzles within the cell cycle field:
What was your initial aim in your postdoc?
I didn't like the cell cycle too…
apalazzo | May 9, 2007
Monday I saw an incredible lecture by U. Wash's Ning Zheng. (Yes Bil, I actually enjoyed a structure biology talk!)
I'll just summarize Dr. Zheng's last paper that was on the cover of the April 5th edition of Nature.
Intense studies on phototaxis in plants that began in part by Darwin (yup, that's right) led to the discovery of auxin, a diffusible signal that stimulates growth in plant cells. How do cells sense the growth factor? No one could identify the receptor until recently. It was known that auxin treatment promoted the degradation of the Aux/IAA transcription silencer, a protein that…
apalazzo | May 6, 2007So apparently I'm a month late on this item.
*** CORRECTION ***
Keepon was developed by Dr. Kozima and Dr. Nakagawa at NICT in Japan (see comments). Marek Michalowski, a robotics student at Carnegie Mellon University, has developed the rhythm recognition, hence his thesis:
the use of rhythm in human-robot social interaction.
Michalowski did not develop the robot per se. Sorry 'bout that.
*** END OF CORRECTION ***
What is Keepon? Here is a taste:
But this robot not only responds to audio stimulation. Watch how it responds to various visual stimuli:
To get a sense of how Keepon works, here…
apalazzo | May 5, 2007We arrived in New York last night and we joined a friend for dinner in Williamsburg at a joint called Tacu Tacu, a Peruvian/Thai place (they had an excellent ceviche platter). Eventually talk drifted to biotechs. Apparently Bloomberg in collaboration with Alexandria Real Estate initiated a project to develop some land on the Island of Manhattan for biotech companies. It will be located on the east river near NYU.
It's about time.
In Boston, biotech and big Pharma are everywhere. Partnerships between academic institutions and private industry are plentiful, and researchers in both settings…
apalazzo | May 4, 2007Yesterday I saw Dr. Alan Cowman give a talk. He's a big guy in the Plasmodium field. Plasmodium is strange. It's the eukaryote parasite that causes malaria. But that's not why it's strange. Let's put it this way, if animals, plants and fungi are three siblings, Plasmodium would be their 6th cousin who lives in a trailer-park on the other side of the river. It's a distant relative, but deep down they're all related in an uncanny way.
Take the Plasmodium genome, about 60% of the genes have absolutely no discernible features. In other words we can't even ascribe a domain to more then half of…
apalazzo | May 3, 2007There's a little "Leading Edge" review by Laura Bonetta on scientists who blog. I spoke to her last week and some of our conversation is in the peice. Some other ScienceBlogs mentioned are A Blog Around the Clock, Pharyngula, Aetiology, and Framing Science. Larry Moran is also quoted. Go check it out.
Ref:Laura Bonetta
Scientists Enter the Blogosphere
Cell (07) 129:443-445
doi:10.1016/j.cell.2007.04.032
apalazzo | May 2, 2007Joolya has been having some problems with contamination.
Now she needs your help. Can you identify the mystery organism that causes her tissue culture cells to bleb?
apalazzo | May 2, 2007In the lab we were discussing whether prokaryotes have true membrane bound organelles. By membrane bound organelles I mean that the membrane surrounding the organelle is not contiguous with the cell's delimiting membrane. Magnetosomes and other such organelles are though to be invaginations of the delimiting membrane, but this idea is controversial. Why should we care? Well we are not concerned about semantics (i.e. what is an organelle) but rather the implications of organellar biogenesis. You see once you have organelles composed of non-contiguous membranes you need to invoke a way to pinch…
apalazzo | May 1, 2007I have to say that I had never seen Eric Olson's seminar before, and it was awesome. Lately the Olson's lab has been looking at HDACs, i.e. histone deacetylases.
Don't forget that in the nucleus DNA is wrapped around nucleosomes that are composed of proteins called histones (see image, right). One important idea in biology today is that histones can get modified and this changes their regulates how they bind to the DNA. Thus by altering the histones you can regulate how accessible the DNA is for transcription (i.e. the conversion of DNA into RNA).
Histones are modified in many ways.…