apalazzo | January 12, 2007I am the ideologue. The world is as I say. Little do you know that the universe follows the laws set down by my intellectual forefathers. It follows the rhythms of the idea that is swimming in my head. You may call me stubborn, but I am steadfast. You may call yourself "realists", but you are without principles. You are either with me, or you are my enemy, but I think that you all want to be my friend. Trust me this will all work out as it is predicted by my great idea, my ideals, by the thoughts that swim around in my head. All the great men were idealists (or at least that's what I've been…
apalazzo | January 10, 2007About a week ago I posted the original Powers of 10, here is the updated version:
Note that we can actually figure out where Springfield is ... and it ain't Springfield Massachusetts. Springfield Indiana perhaps? Or is it Illinois?
[HT: Jannet]
apalazzo | January 10, 2007Well the latest paper from the Reed lab (squeeking into Cell on its last issue of 2006) demonstrates that the cap is indeed promoting nuclear export of mRNA in vertebrate cells. (For more on mRNA export, click here.)
This idea that each step of mRNA metabolism is "coupled" to the following step of mRNA metabolism is an idea that has been going around quite a bit in the RNA world.
The cap, is a structure found at the start (or 5' end) of mRNAs, and consists of an inverted methyl-Guanosine linked by a tri-phosphate to the first nucleic acid, invariably guanosine. The role of the cap is to…
apalazzo | January 8, 2007From today's NY Times: Headhunters at Harvard May Put a Woman in Charge
(I know it's just wild speculation.) Here's an interesting bit:
There are suspicions, on the other hand, that the committee might be leaning toward the selection of a scientist to oversee the expansion of research in stem cells and other cutting-edge science on a new campus to be built in the Allston section of Boston.
That would be nice ...
apalazzo | January 8, 2007[Start dictation]
Believe it bore not this sentence was never typed by meet by a Secretary for a knee other human but by my trusty boys recognition system now this program is a meal fight and that's will make plenty of dictation Amherst but eventually it will learn to recognize my voice and hopefully make few were mistakes.
[Stop dictation]
OK I'm typing now ... what you read above was penned by my new "voice recognition software". Not bad, henh? I was inspired by this piece by Richard Powers (author of The Echo Maker) that appeared in yesterday's NY Times Sunday Book Review.
I proceeded to…
apalazzo | January 6, 2007From the latest issue of Science:
We demonstrated that despite their small size, specific miRNAs contain additional sequence elements that control their posttranscriptional behavior, including their subcellular localization. We showed that human miR-29b, in contrast to other studied animal miRNAs, is predominantly localized to the nucleus. The distinctive hexanucleotide terminal motif of miR-29b acts as a transferable nuclear localization element that directs nuclear enrichment of miRNAs or small interfering RNAs to which it is attached.
Cool.
Ref:Hwang HW, Wentzel EA, Mendell JT.
A…
apalazzo | January 5, 2007OK this week there is a theme ...
(Yeah I know, campus #3 has it's name in big white letters on a rooftop ... but it looked great on Google Earth, so I included it anyway ... and it seems like campus #3 has one of these too! Is there an infestation of such organisms in this area?)
As usual, leave all your answers in the comment section. (or email me)
apalazzo | January 4, 2007There is one particular comment written by BC with regards to a patent owned by Archemix that covers all RNA aptamers that I'd like to share with you:
My data point is talks with key a key scientific advisory board member of the company - they bought it from Gold's company, Gilead, IIRC (see wikipedia's aptamer page).
There are small companies such as Q-RNA that are based specifically on a single aptamer or class of aptamers (not clear to me from QRNA's site) and if they didn't get grandfather'ed then I'd say they're at the mercy of the patent holder.
I don't have the answer to the patent…
apalazzo | January 4, 2007
I saw this video while surfing on Sciencesque. It gives quite a ... perspective on our day to day existence.
apalazzo | January 3, 2007First the Wakefield scandal on a bogus link between MMR vaccine and autism, then the Chang scandal where a program error led to several erroneous x-ray crystal structures and five retractions. The first one caused by greed, the second by sloppiness.
(I'm trying to start the year on a good note, but it's hard.)
PS I was chatting with BTM and some other local "structure people" about the Geoffrey Chang. Apparently he was a prodigy ... assistant prof at 28(?), won the Presidential Early Career Award for Scientists and Engineers. That's the type of award that is presented to you at the White…
apalazzo | January 3, 2007Yestetrday we recieved an email asking us to vote on the new coffee bar at the NRB (NRB = New Research Building = No rich person has yet donated money to Harvard Medical School for this structure)
NAMING THE COFFEE BAR AT NRB
(Vote for your favorite name)
*Atoms
*Carbon
*Javium
*Particles
*Aliquots
*Catalyst Café
*CoffeeOmics
*Eureka (café)
*Synapse
*Oasis
(in my opinion they could have spiced up the list by replacing "Aliquotes" with "Ali-G-quotes")
apalazzo | January 3, 2007In this day, some biologist have to move beyond the simplistic view that the cell is a bag of M&Ms. What do I mean by that? It's the idea that enzymes and organelles are free floating entities within the cell.
On the other hand, don't tell me that the cytoskeleton provides a static skeleton that fixes each cellular component.
The cytoskeleton is a dynamic and sensitive cellular organizer that constantly reshapes itself in response to extra-cellular clues. And those M&Ms aren't nailed to some part of the cytoskeleton. No, in fact they are moved around and dynamically organized by…
apalazzo | January 2, 2007... don't bet on it!
I read far too many papers where the author claims that their favorite protein "localizes to the leading edge in migrating cells". Then they show a pretty picture like this one:
The problem is that the cell thickens right at the leading edge. So if your protein is freely floating around, there will ALWAYS be more of it (in absolute terms) at the leading edge then in the nearby lamella. To underline this point, the image above is of fluorescent dextran microinjected into the cytoplasm of a fibroblast. Dextran is a molecule that is certainly not a marker of the leading…
apalazzo | December 31, 2006(This is back dated as I would like to start the new year on a brighter note.)
After a long day of skiing in the green hills of Vermont, my brother , cousin and I decided to go for a swim followed by a dip into the jacuzzi at the back of the hotel. I haven't seen my cousin in 4 years. He was living in Osaka, now he's studying international affairs in London. We talk about our lives, our plans the status of the world. We talked about how over the years the winters have changed quite visibly. When we were kids, growing up in Montreal, the city street cleaners would dump all the street snow into…
apalazzo | December 29, 2006Let's end this year with a bang!
Here is this week's mystery campus:
hint: It's getting cold.
As usual, leave your answers in the comment section.
(although I screwed up last time, don't worry, Willie is warm!)
apalazzo | December 28, 2006(I wish)
I though I could spend a day or too relaxing ... but it seems like I can't do it. Today was spent cleaning the apartment in preparation for a family visit down from Montreal.
We're actually meeting up with my parents, brother, aunt and cousins in Burlington Vermont for some skiing (thank FSM for the recent snowfall in northern New England!). We'll be leaving in about an hour or so.
But while I was cleaning I was redesigning our humble Boston Book club blog and trying to give it a nice new style (what do you think?).
Yes we have a bookclub in up here. It's a great excuse to get…
apalazzo | December 27, 20062006 was (again) year of the RNA.
Two nobels. The RNA world expanded with the discovery of Piwi RNA. RNAi as a transmittable trait? (Lamarck is vindicated!) We also found out that much of the conserved parts of our genome do not encode protein. Now how many of these bits are regulatory elements and how many are non-coding RNAs is yet to be tabulated. However the most rapidly evolving gene between humans and chimps is one of these non-coding RNA. There are even hints that the lowly centrosome has it's own RNA (although flies apparently don't need centrosomes.) Also a nice theory was proposed…
apalazzo | December 24, 2006Check this out:
First-in-Human Experience of an Antidote-Controlled Anticoagulant Using RNA Aptamer Technology
From the paper:
A translatable platform for developing an optimal parenteral anticoagulant should consider several prerequisite properties: easy delivery, rapid onset of action, and predictable responses among the dose, pharmacokinetic profile, and pharmacodynamic effects to reduce the requirement for routine monitoring. Additionally, an optimal anticoagulant should be biologically selective and actively reversible.
What is in use currently?
Unfractionated heparin is currently the…
apalazzo | December 23, 2006Sorry this week has been hellish. I've had no time to blog (but I did see a great two-man performance of The Importance of Being Earnest at ART). Anyway, this week was filled with work. I've been microinjecting my brains out. And then whatever is left was fried on the microscope. During one of the sessions I was listening to NPR where they were discussing the bonus that Goldman Sachs gave to its CEO, Lloyd C. Blankfein, a record of $53.4 Million. Some one called to say:
What did he do to get that, cure AIDS?
And I was thinking to myself, the one who cures AIDS will probably be earning a…