apalazzo | September 12, 2007(Disclaimer: this is not my field but the paper looked interesting so here goes ...)
Promoters, enhancers and other DNA regulatory elements that turn on or off gene transcription are important. We've known this for quite a while. Many would argue that metazoans all have the same major gene families. Getting closer to us, most vertebrates have the same types of cells and have very similar genes and gene counts. That is not surprising as most genes encode the different tools that go into making the each major cell type found in all vertebrates. To rephrase this idea in a different manner (so…
apalazzo | September 12, 2007PRISM (or the Partnership for Research Integrity in Science and Medicine) is a lobby against Open Access (OA) put together by the The Association of American Publishers (or AAP). Most Science Publishers are members of AAP, but since the unveiling of PRISM (and of their website) now many publishers are distancing themselves from this organization ... and rightfully so.
Mike Rossner, Executive Director of Rockefeller University Press (publishers of the Journal of Cell Biology) wrote an open letter to PRISM that most of us would agree with.
I am writing to request that a disclaimer be placed on…
apalazzo | September 11, 2007I usually don't comment on sensational science news (unless it has to do with basic cell biology) but this is just really ... bad. According to several news we can now use radio waves to convert water into hydrogen, which of course can be burned back into water. What exactly are these reports saying?
From an AP article:
The discovery has scientists excited by the prospect of using salt water, the most abundant resource on earth, as a fuel.
And read this, from Wired:
Rustum Roy, a Penn State University chemist ... called Kanzius' discovery "the most remarkable in water science in 100 years."…
apalazzo | September 8, 2007This summer has been bad on the book-side. I've picked up so many books that looked promising yet in the end disappointed. Recently I just finished Culturing Life, How Cells Became Technologies by Hannah Landecker, a book dealing with the history of tissue culture. I was please that someone had written about a topic rarely mentioned by the current crop of science journalists. Strange, considering that Cell Biology is currently one of the most active scientific fields.
Back to the book.
What to say ... I admit that it was a worthwhile read. Landecker is an anthropologist and so much of the…
apalazzo | September 7, 2007This morning, baymate and I were debating when would be a suitable time for coffee when we heard a giggle from the next bay. Here's what our neighbor saw on her transformation plate:
And here's a blowup:
As another postdoc said, "you probably don't have to sequence those colonies. They'll have what you're looking for."
apalazzo | September 7, 2007German Nihilist Postdoc: You know what we are?Me: No, what?GNP: Leibeigenschaft.Me: What's that?GNP: A serf, you know like in the middle ages.Me: You mean XXX is our lord and we follow his commands?GNP: Yup. Or a pawn, yes that is what we are.Me: Yeah, I guess XXX is the king or queen and we little guys move up the board square by freakin' square for the glory of the lab.GNP: Sometimes we kick to the right, sometimes to the left, battling the pawns from the other competing labs.Me: Some of us are sacrificed with risky projects.GNP: If we are not protected or backed up by the other pawns.Me:…
apalazzo | September 5, 2007At the end of September I'll be taking off for Italy to visit the land of my origins. At some point I'll be in Paris, visiting a good friend of mine and I'll be giving a talk at the Universite Pierre & Marie Curie entitled: The Signal Sequence Coding Region: promoting nuclear export of mRNA, and ER targeting of translated protein. I believe that the seminar is scheduled for October 12th at noon. See you then.
apalazzo | September 5, 2007Sorry for the lack of posts. I've been reconstructing the figures and the text of my manuscript and expect to resubmit the darn thing to PLoS Biology later this week. Until then here is an interesting paper that I've read recently:
Hitoshi Nakatogawa, Yoshinobu Ichimura, and Yoshinori Ohsumi
Atg8, a Ubiquitin-like Protein Required for Autophagosome Formation, Mediates Membrane Tethering and Hemifusion
Cell (07) 130:165-178
So what's this all about? Well the main player is Atg8, a protein that is essential for forming large multi-vessicular bodies (or MVBs).
What was that?
When cells are…
apalazzo | August 31, 2007I am sick and tired of quantitating my microinjection data. I've been doing this for two weeks and I'm going crazy. I've microinjected and quantified over 10,000 cells in this time period, all in the attempt to finish this damned paper. I've injected soo many cells that I've even accidentally microinjected the endoplasmic reticulum (ER) on several occasions (for anyone who has never microinjected, this is a very rare event). Want proof? Here's fluorescent dextran in the ER:
But I'm going crazy. I give up. I can do it anymore. I've put aside my blog, our policy paper, walking to work (too…
apalazzo | August 29, 2007A couple of weeks ago, Linda Wang from C&E News contacted me about my post on pipette tip usage methods (with a little side note on the Jesus Gel incident). Apparently the article came out August 20th and since then I've received emails containing people's pipette box artwork. If I get my act together I'll try to post a compilation of photos and testimonials.
If you want to contribute a story or a photo, email me.
apalazzo | August 27, 2007This was to be expected. Remember how Elsevier and American Chemical Society hired Eric Dezenhall? (click here for more) Well apparently under Dezenhall's direction these guys have formed Partnership for Research Integrity in Science & Medicine or PRISM, a lobby group against open access.
As I've mentioned before, there is a concern about how open access (OA) is to be funded. It takes lots of money to hire editors and a production team to produce a top tiered journal such as Science, Nature, Cell and even PLoS Biology. And it is not only the peer review and production, but also the…
apalazzo | August 27, 2007From the last week's issue of Nature, More biologists but tenure stays static. From the article:
The data, compiled by the Federation of American Societies for Experimental Biology (FASEB) (opa.faseb.org/pages/PolicyIssues/training_datappt.htm), are from many sources, including the US National Science Foundation (NSF), the Council of Graduate Schools and the National Institutes of Health (NIH). And one message is clear: increasing numbers of bright young students are eager for a career in biology and biomedicine, but fewer than before will gain the coveted tenured academic positions.
Although…
apalazzo | August 25, 2007I moved to the US.
To commemorate this event here's The Immigrant Song, as performed by the original mash-up group, Dread Zeppelin:
apalazzo | August 24, 2007Nature Network Boston is having another pub night on Tuesday. From Corie:
It will be next Tuesday, August 28 at 6pm at the Middlesex Lounge in Cambridge (315 Mass Ave, near Central Square/MIT). Come out and meet other members of Boston's scientific community.
We're doing something a little different this time. Starting at 6pm, we're holding a brief, informal discussion about Nature Precedings (http://precedings.nature.com), Nature's new website where biologists, chemists, clinical researchers, and earth scientists can post pre-publication manuscripts, presentations and other documents. The…
apalazzo | August 22, 2007that Sigma-Aldrich advertises on it.
(ht: baymate)
Rout 65 bus info (MBTA).
PS if anyone else sees this send me some photos.
apalazzo | August 22, 20077AM, up out of bed. I prepare breakfast, two slices of focaccia with salmon and olive spread with an espresso to wash it all down. I quickly flip through the paper. For once the NY Times Science section has an article on some basic molecular biology (it must have been the evolution angle). After jumping in and out of the shower, I throw some clothes on and walk to the lab listening to the latest Nature podcast. 8AM, I prepare my tissue culture cells for the final round of experiments and spin down several samples of DNA for microinjections. 9AM-2PM, five hours of brain numbing microinjection…
apalazzo | August 16, 2007Sorry about the lack of posts. The lost week spent roaming around the California wilderness has really taken a toll. I have been microinjecting my brains out, but fortunately it looks like I'll be able to get the last piece of data that the reviewers asked for. In addition there has been much post-scifoo activity that I have yet to contend with. And then yesterday I sacrificed a day's worth of work to be with a dear friend who is leaving town this morning. We'll miss you, pumpkin seeds.
As for posts that I wanted to write include the new Singer paper, the Vault paper, the incredible imaging…
apalazzo | August 14, 2007I just sent out this email:
Hello All,
We are soliciting speakers for the November and December meetings. If you are a postdoc or grad student, and would like to present your work in a 20-25 min talk, please let us know and we will add you to the roster.
The next meeting of the New England RNA Data Club will take place September 11th starting at 5:30 in the Cannon Room of Building C at Harvard Medical School. Our speakers will be
-Chris Hammell, from the Ambrose Lab, Darthmouth Dartmouth Medical School
-Natalie Gilks Farny, from the Silver Lab, HMS
-Sebastian Kadener, from the Rosbash Lab,…
apalazzo | August 12, 2007Yesterday I surrendered to the gods of the electronic world as I finally got a cellphone (now people can reach me where ever I may be, yikes!) and I registered with facebook where I will forever be eating plums (don't ask, this has to do with last night and it's a long story.)
Well it could be worse, I could have been a citizen of Shenzhen (aka Canton). From today's NYTimes:
Starting this month in a port neighborhood and then spreading across Shenzhen, a city of 12.4 million people, residency cards fitted with powerful computer chips programmed by the same company will be issued to most…