apalazzo | December 23, 2006Earlier this week you probably read the whole saga of how researchers tracked down some individuals who could not sense pain. They then identified the gene responsible as SCN9A, a voltage-gated sodium channel and that was published in Nature. But in Science there was another report of a gene, Catechol-O-Methyltransferase (S-COMT), that is critical for pain perception ...
Well it turns out that the data in the Science paper is much more interesting than the flashy (yet uninsightful) observations of individuals walking on hot coal and receiving knife stabs into their arms without even flinching…
apalazzo | December 20, 2006Chris Phoenix asked me to comment on his entry: Studying Molecular Biology. As someone who is constantly playing around with cells I'll add this advice to how biological systems differ from watches and the Antikythera Mechanism, biological systems are composed of adaptable platforms such as the cytoskeleton and the network of cell signalling molecules. When you think about cells, don't think cars ... think computer operating systems (yes insert pitch for systems biology here ...). What we are doing in the lab is figuring out what makes cells malleable. And to a certain extent the answer is…
apalazzo | December 19, 2006Last week was too stressful - although by Friday afternoon I had put together the pieces of the puzzle and it all makes sense (I'd tell you more about it, potentially I've stumbled upon a really cool little "cellular circuit", but I'd rather publish it first. Mother Nature has so many neat tricks up it's sleeve.) To relieve that stress, we took off on the Chinatown bus (actually we took the "Boston Deluxe" which travels between the Prudential and 86th street on the Upper East Side.
Highlights of this trip:
- Santa Con (i.e. a thousand drunk Santas running around central park). One of the…
apalazzo | December 15, 2006Here's one for you:
Last week's hint was fatal, this week's hint: deadly particle.
Leave your answers in the comment section, or if you don't want to ruin it for others, email me and I'll post all your answers over the weekend.
(And no, the forest on the left is not home to Willie the Wildcat.)
apalazzo | December 14, 2006From Kazuo Ishiguro's Never Let Me Go:
"When I watched you dancing that day, I saw something else. I saw a new world coming rapidly. More scientific, efficient, yes. More cures for old sicknesses. Very good. But a harsh, cruel world. And I saw a little girl, her eyes tightly closed, holding to her breast the old kind world, one that she knew in her heart could not remain, and she was holding it and pleading, never to let her go. That is what I saw. It wasn't really you, what you were doing, I know that. But I saw you and it broke my heart. And I've never forgotten."
apalazzo | December 13, 2006Here's a happiness scale for you (based loosely on this book). The listed numbers act as a point of reference:
10- Incredible result that explains all the data amassed by a field and resolves various conflicts between different models.
9.5- Fantastic result, all your pet theories are proven.
9- Great result indicating that you may have something interesting.
8.5- You've repeated that great result, it looks pretty solid.
8- You've successfully cloned a gene.
7- You're not sure, but your result might indicate that you have something interesting.
5- Making buffers.
4.5- Passaging cells in the…
apalazzo | December 13, 2006Time for a therapy session.
Man I hate this. My cortisol levels must be through the roof. I tested my clones and got weird results. I was racking my brain all weekend trying to figure out why. Then yesterday I tested a positive control, and got negative results. I feel like I'm trapped in the twilight zone. (I would have rather been at the ASCB meeting.)
What to do?
One advice that I got long time ago - if things don't work anymore, throw away all your reagents and start all over. It's the best advice that anyone has ever given me.
So today I'm doing exactly that.
apalazzo | December 12, 2006Apparently weak and strong signal sequences are differentially targeted to the ER acording to a new paper in Cell.
(For more on how proteins are inserted into the ER click here.)
Preprolactin has a strong signal sequence and is inserted into the translocon even when the unfolded protein response (UPR) is activated. Prion protein, which has a weak signal sequence, is only inserted when UPR is inactive. Remember that under stress (high heat or other nasty conditions) cells rewire protein production and turn off the insertion of most proteins into the ER while upregulating the production and…
apalazzo | December 9, 2006It's been a while since I did this. Baltimore on Dawkins. Three kingdoms? Skeptical publishing. Libertarians & adolescents? Kant vs. Archimedes. Yes they're all below the fold.
David Baltimore reviews Dawkins' The God Delusion. [HT: MM, FCD]
Larry Moran is writing a whole series of posts on Microbial Phylogeny and Evolution: Concepts and Controversies, or why the whole three kingdom description of life is flawed. Part 1, part 2, part 3, part 4, part 5.
PubSkep? You betcha. It even comes with it's own intro.
Some great quote on libertarians found in the comment section of a tristero entry…
apalazzo | December 8, 2006Yesterday Melissa Moore gave a talk at the School of Public Health here at Harvard Med School. She had lots of data - on nonsense mediated decay (how cells degrade mRNA transcripts with premature stop codons that arise through various mechanisms) and on nonfunctional ribosome decay (NRD). Here is some neat info from her intro on introns & NMD:
- Since 90% of the gene coding region is introns, exons are for all practical purposes modular. When DNA is duplication or swaped within a gene or between genes, chances are that genes will be cut and ligated at intronic sequences. (Thus the exons…
apalazzo | December 8, 2006It's that time again.
Here is this week's mystery campus:
hint: fatal element.
As usual, leave your answers in the comment section.
apalazzo | December 7, 2006... is with me.
Two constructs to make.
Two colonies I had.
Each trial a single clone.
I cut them, they cut just the way I hoped.
Each clone was sequenced.
The sequence told me that I have what I need.
Although my hopes were low, I did succeed.
And now the clones are sent into the fire ...
Will they do my bidding?
Will they tell me the truth?
(I feel like Nick Cave)
PS Cloning = make an exact copy, in this case a DNA construct. Actually what I did was construct a a gene on a DNA vector and then introduce the newly made reagent into bacteria so that the cells would copy the novel DNA…
apalazzo | December 6, 2006As a grad student at Columbia, I once saw a talk by Joachim Frank at Rockefeller. Siting in the audience, I was wowed as Frank described the cryo-EM structure of the ribosome in many different conformations, each representing one step of the polypeptide chain elongation cycle. Compiling them together, he produced a little movie of a ribosome manufacturing a protein. While I was taking in this movie I remember thinking - wow, this is how the machine works!
Recently a few other labs have published the cryo-EM structures of the ribosome with every freakin' Ribosome cofactor. The latest…
apalazzo | December 6, 2006From today's Boston Globe:
Harvard has whittled down hundreds of nominees for its next president to a small list, including internal candidates and presidents of some of the nation's top universities, according to a source familiar with the process.
The source would not give a specific number, but said the university is considering a smaller group than the 30 names that the presidential search committee presented to Harvard's Board of Overseers on Sunday.
So who's on the list?
On the list of 30 candidates presented to the overseers were three Harvard leaders who worked for Summers: provost…
apalazzo | December 4, 2006The H-index was the brainchild of Jorge Hirsch. It's a method to quantify a researchers impact. (To read more on this, check this entry of mine: What's your h-index.)
I was just alerted that Michael Schwartzbach has written a program that can calculate your very own h-index quickly over the web by hacking into Google Scholar. I tried using it to get mine ... unfortunately "A Palazzo", is not unique and so I couldn't recalculate my own h-index. I finally got it to work by typing "A Palazzo" and Columbia and got 8 (the value I had the last time I checked). Go visit Epidemiologic Inquiry to use…
apalazzo | December 4, 2006Over this past summer I saw Dirk Görlich give a talk about how the multitude of FG repeats found within the nuclear pore complex (NPC), form a gel like matrix. This "elastic hydrogel" acts as the major barrier within the NPC. Although the gel can prevent the passage of most large molecules (>30kD), it is permeable to nuclear transport receptors (NTRs). Note that all this "story" was published in the November 3rd edition of Science Magazine (link). In that paper there's a nice diagram in the that explains it all:
An "FG repeat" is a long stretch of amino acids that form non-covalent…
apalazzo | December 3, 2006... came Stephane Dion to take the leadership of the Liberal Party in Canada.
Dion's platform ... (from the CBC)
"We cannot afford to miss out on the next industrial revolution: the sustainable economy," Dion said when he announced his bid April 7.
"For that reason, we must weave together economic growth, social justice, the environment and public health. That is why I want to become leader of the Liberal party and then prime minister of Canada."
From Robert Sheppard's blog at CBC:
Dion seemed to come out of nowhere. He had the least money and organization of any of the top tier…
apalazzo | December 1, 2006Earlier today I gave our weekly journal club. As usual there is some large scheme/model/godzilla image associated with the intro/summary. Here's mine ... mRNA nuclear export in yeast:
Highlighted are 3 major systems. Many proteins are listed, many more are not.
Nucleoplasm is on the bottom, cytosol on the top. The bilayered nuclear membrane is represented by the two black lines. The big red/blue thing with the purple basket is the nuclear pore complex (NPC).
In purple hue is the Mpl1/2 system. These proteins are the orthologues of TPR in mammalian cells and form the basket of the NPC.…
apalazzo | December 1, 2006Here is an easy one.
hint: Motor Wars.
We'll try something different this week. Now considering the readership of this blog I'm sure that many of you know this place very well. So if you know what it is, leave a clue, hint, or embarrassing incident that occurred there (in the comment section of course.) Good luck.