apalazzo | July 28, 2006I suppose it's that time of the week. Without further delay I present today's mystery campus:
Click here for a larger version.
And the hint:
Little Droplet of Lard
How to get in?
It'll take a tag-team effort!
Know what any of this means? Or the identity of the mystery campus? Well then leave a comment. (But hury, this one is a bit on the easy side.)
apalazzo | July 28, 2006From the pipeline:
Time is running out to enter Science Idol: The Scientific Integrity
Editorial Cartoon Contest-the deadline is Monday, July 31! We've
received some spectacular entries so far-from artists in their teens to
those in their nineties-but you still have a few days left. This is your
last chance to show off your artistic and comedic talents by creating a
one-panel or multi-panel cartoon that takes on the issue of political
interference in science.
Does the fact that hundreds of scientists at the Food and Drug
Administration report being asked to change technical information for…
apalazzo | July 27, 2006Well I was going to write about J. Weissman's new paper, but Pedro (from our lab) published his work TODAY (I knew it was coming out soon ...)
His paper and YET ANOTHER paper from the Weissman group made the cover of the latest issue of Cell:
They deal with the nitty-gritty of ERAD (to learn more on ERAD see this morning's post).
I won't go through the Weissman paper (the one in Cell that is), as I've yet to read it, but I can give you the summary of Pedro's work.
He discovered that ERAD works through three different complexes. Each complex is responsible for pulling a different class of…
apalazzo | July 27, 2006Need to analyze your DNA, protein or Gene (or do a one of a gadzillion other bioinformatic operations?) Well fortunately you live in the internet age.
But where to start?
From the Nucleic Acids Research Journal: A compilation of molecular biology web servers: 2006 update on the Bioinformatics Links Directory.
And the main database: http://bioinformatics.ubc.ca/resources/links_directory/narweb2006/ (If I were you I would bookmark this excellent site, it lists almost every web based application out there ...)
apalazzo | July 27, 2006OK today I'll talk about yet another paper from Jonathan Weissman's group at UCSF ... but I'll write it up in two parts. This post will be generally background about the ER and its ability to degrade proteins.
When many scientists think about "cellular functions", diagrams of the central dogma of biology (DNA=>RNA=>protein) pop into their head. But sorting out the good stuff (properly processed mRNA, well folded proteins) from the bad stuff (misprocessed mRNA, misfolded protein) is equally important.
Proteins can be divided into two classes, those that have to cross a membrane (membrane…
apalazzo | July 26, 2006And people think I'm down about the current situation.
In the last issue of Cell, Robert A. Weinberg is calling the current batch of postdocs The Lost Generation.
The abstract:
The funding policies of the NIH have made it increasingly difficult for young researchers to procure research funds. This threatens to drive a whole generation of young people away from careers in basic biomedical research.
First Paul Nurse, now Weinberg, I hope they are paying attention!
The numbers are striking. Over the past generation, the age at which American biomedical researchers with PhD degrees succeed in…
apalazzo | July 26, 2006In my last post, I forgot to link to these great movies of migrating fibroblasts (available as online supplements to the arginylation paper), that illustrate how beta-actin arginylation can alter cellular behavior.
So the assay is simple, grow fibroblasts until they fill up the coverslip as a single layer of cells (or monolayer). At this stage the cells will stop dividing (by a process known as "contact inhibition of cell growth"). Then the researcher can scratch the monolayer thus removing a strip of cells. The surviving cells present at the wound edge will at once migrate into the wound.…
apalazzo | July 26, 2006In cells, actin polymers dictate cell morphology.
Actin filaments can adopt several conformations, they can be bundled into large microfilaments (often called stress fibers; here "mf" - electron micrograph taken from the Borisy lab webpage) or arranged in a meshwork (as seen in the second electron micrograph). One actin isomer (gamma-actin) predominates in the stress fibers that are concentrated in the cell body, while another (beta-actin) predominates in the actin meshwork found in the leading edge of migrating cells. In fact, the generation of this meshwork right at the tip of the cell (…
apalazzo | July 25, 2006So today I was "shopping" online for cDNA clones from Open Biosystems (about 70-100$/cDNA clone) when I see this:
In case you can't read it here is a blowup:
So on the Open Biosystems website, some guy is blogging about podcasts and his daily commute? It would seem that everyone (and every website) has a blog.
apalazzo | July 24, 2006Overheard at the lab today:
"Only hookers work on weekends"
which was then followed by "and late nights."
Yes this is what we've been reduced to ...
(P.S. Does this make my PI a pimp?)
apalazzo | July 24, 2006So a theme of my blog has been the conflicts between being a scientist and having a life. In my immediate environment, I'm surrounded by postdocs in their early to mid-30s, struggling to get their career going and thinking about starting a family. In some respects I'm lucky -- I'm male, and my wife is not an academic. I will never face the stress of pregnancy + facing the trials and tribulations of academia. But that is not to say that being a father and a postdoc/junior faculty will be easy. We are planning to have children eventually, however the longer we delay the hard it will be. This…
apalazzo | July 22, 2006GrrlScientist's entry on the new episodes of Star Trek, reminded me of something that I saw recently: Star Trek does the Knights of the Round Table. Best mashup ever? You be the judge.
apalazzo | July 21, 2006Scary comment in PLoS: Scientific Illiteracy and the Partisan Takeover of Biology by Lisa Gross.
It's mostly about Jon Miller's research on the public understanding of science. I've commented before on Miller's findings ... and it always scares me when I see any of these statistics. This time the focus is on public's understanding of "stem cells" and "evolutuion". (I will not comment on the recent Bush veto as SO MANY OTHERS here at SBs have done so.)
From the article:
As time went on, more people said they had a good understanding of stem cells--21% in 2004, up from 9% in 2003--but only 9%…
apalazzo | July 21, 2006Last week was tough, however it was solved in less than an hour. This week ... well we'll see how long this lasts.
So without further delay here is this week's mystery campus:
Click here for a larger image.
Hint: Black Capes
Good luck!
apalazzo | July 20, 2006I was interviewed by Hsien Hsien Lei, and the complete transcript is available at her fantastic blog, Genetics & Health.
(Hope my answers weren't to long winded ...)
apalazzo | July 20, 2006A couple of weeks ago I posted an entry on NIH funding rates, and how the increase in funding over the 90s led to an increase in the number of postdocs.
I went digging around for the numbers, and found this power point from the National Academies of Science Engineering and Medicine.
So here are some stats for all those interested:
The number of postdocs in the biomedical sciences has almost doubled between 1990 and 2000, following the increase in NIH funding.
And interestingly, most of these extra postdocs are foreigners (like me).
So it seems like the increase in postdocs could only be…
apalazzo | July 20, 2006From The Scientist: Public Concern for Private Funding.
More money generally means more science, and vice versa. But the source of the money - whether from public or industry well-springs - may be as important in determining the type of research that gets funded as well as the direction that research may take. During the last several years, the percentage of industry funding relative to public funding has grown (see Box). For example, industry funding of clinical trials rose from $4.0 billion in 1994 to $14.2 billion in 2003 (in real terms) while federal proportions devoted to basic and…
apalazzo | July 19, 2006I just read an EXCELLENT opinion in the July 6th edition of Nature, Illuminating the black box. Note to biologists: submissions to Nature should contain complete descriptions of materials and reagents used.
Sounds familiar? I've complained about it before.
From the Nature article:
This journal aims to publish papers that are not only interesting and thought-provoking, but reproducible and useful. In order to do this, novel materials and reagents need to be carefully described and readily available to interested scientists.
That might seem obvious. But despite the efforts of our editors and…
apalazzo | July 19, 2006From today's NY Times editorial section:
The national education reform effort has long suffered from magical thinking about what it takes to improve children's chances of learning. Instead of homing in on teacher training and high standards, things that distinguish effective schools from poor ones, many reformers have embraced the view that the public schools are irreparably broken and that students of all kinds need to be given vouchers to attend private or religious schools at public expense.
...
This point was underscored last week when the United States Education Department released a…
apalazzo | July 15, 2006I should have included these with my Golgi entry. Very cool movies explaining the difference between static Golgi and dynamic Golgi whose stacks (or cisternae) mature. From the Glick paper:
Movie1 Static Golgi (Black dots representing newly synthesized proteins traverse the Golgi by vesicular transport). After the recent results, this model of how the Golgi works is unlikely.
Movie2 Dynamic Golgi (Black dots STAY in a cisterna, and Golgi modifying enzymes - the green, orange, red - are transported from cisterna to cisterna, at the end the Golgi cisterna breaks apart into vesicles that are…