Pure Biology
apalazzo | July 31, 2007I'm gone camping. Late last week I preprogrammed my blog to repost all these entries on microscopy. Enjoy!
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…
apalazzo | July 30, 2007I'm away in California - while I'm gone, I'm reposting all these old entries on microscopy, enjoy!
Here's a micrograph of a fibroblast (connective tissue cell) adherring to fibronectin coated coverslip. The cell was immunostained for regular microtubules (red) and modified detyrosinated microtubules (green, although since these are only partialy modified red+green = yellow).
apalazzo | July 29, 2007I'm off camping - so this week I'll be posting some old entries on microscopy, enjoy.
OK here's a post geared mostly to cell biologists. My big pet peeve about reading the scientific literature is ... colored fluorescent images.
Why do people insist on pseudo-coloring their images? I know that you want pretty pictures and as every kid knows the more colorful the picture the more adoration one gets from approving parents ... but we're talking about data and instructing/convincing your fellow peers about new findings.
So why is color bad for data presentation?
Your eyes are better at…
apalazzo | July 25, 2007I just wanted to post a brief entry on the newest paper from the Moore lab. I've already hinted at some of these results in a post from last year.
As you all know, mRNA is made and processed in the nucleus. During mRNA synthesis, all the introns must be removed and all the exon sequences must be glued together to produce mature mRNA. At each exon-exon fusion site (called exon junctions) a protein complex, called the exon junction complex (EJC), is deposited. Once processing is over and done, the mature mRNA is exported from the nucleus into the cytoplasm. Then ribosomes engage the mRNA and…
apalazzo | July 16, 2007I've been busy preparing for a lab meeting - I'm presenting tomorrow. These last few months have been weird - since I've submitted my paper, about 1+1/2 months ago, I've been testing various theories, and toying with some ideas. Recently I knocked down two related proteins using siRNAs. Unexpectedly this treatment resulted in a striking morphological change. The knockdown cells don't appear to be dying, and their doubling rate is only slightly altered as compared to control cells but they now have all these micro-blebs.
Bellow the fold are two pictures, the first being the knockdown cells,…
apalazzo | July 5, 2007Last week I posted an entry on Nature Publish Group, scientific publishing and web2.0. I'd like to add a couple of points, and throw out some links.
I would like to emphasize two points:
1) Feasibility. Yes we all want open information, but how to do it? And how to make it financially feasible? Publishing fees? Support from the NIH and other governmental assistance? Web based advertising?
2) Organization. Do we just dump everything on the web? Will this anarchy be great or will important research that is not directly relevant to your interests be lost? The web has been great to open up…
apalazzo | July 3, 2007After the last miRNA post, I was alerted to this paper that appeared in the June 15th edition of Nature:
Thimmaiah P. Chendrimada, Kenneth J. Finn, Xinjun Ji, David Baillat, Richard I. Gregory, Stephen A. Liebhaber, Amy E. Pasquinelli & Ramin Shiekhattar
MicroRNA silencing through RISC recruitment of eIF6
Nature (07) 447:823-828
How did I miss that? The basic story is that eIF6 was co-purified with the RISC complex. To remind you RISC is a protein agglomerate that helps miRNAs downregulate the translation of targeted mRNAs into protein. And eIF6 is not a typical eukaryotic translation…
apalazzo | June 25, 2007miRNA and RNA interference is so hot right now ...
I'm not in the field, but I do keep an eye on it. Right now the there is quite a few papers on how miRNAs regulate translation. There is some data that indicate that miRNA and the associated RISC complex (RNA Interference Silencing Complex) inhibits the ability of ribosomes from engaging targeted mRNAs. The initiation of protein synthesis would thus be blocked. Other data indicate that miRNAs inhibit the activity of ribosomes that are bound onto transcripts. In this second model miRNAs prevent the elongation step of protein synthesis. These…
apalazzo | June 23, 2007I was watching Science Saturday, over at bloggingheads.tv, where Horgan & Johnson were talking about the origin of life and RNA (among other things). Also mentioned was Robert Shapiro's article in Scientific American. Shapiro is an advocate of the cell first theory, which I have to say that I don't really get. How would that work? How would this entity self-perpetuate and evolve.
Another item at Science Saturday was a link to this article in the Economist on how RNA research is where all the action is ... from the article:
It is probably no exaggeration to say that biology is now…
apalazzo | June 9, 2007So last night we went out to watch the American Repertory Theatre's version of Eugene Ionesco's The Killing Game. Afterwards we ended up at Grafton Street for food, drinks and discussion.
Of course with Marius Wernig in attendance, the talk turned to this week's big news.
[In attendance as well was Mike Kharas, a postdoc in the Gilliland lab. In a weird coincidence, Mike worked on klf4 (krumpel-like factor4), the most mysterious of the four genes which are part of the cellular fountain of youth elixir.]
First it looks like everyone in the Jaenisch lab is jumping onto this project - turning…
apalazzo | June 8, 2007Here's another video for you where Dr. Jaenisch discusses this week's incredible findings:
Also check out this new feature at the Nature website on stem cells and a new stem cell blog called the niche. (NT: pimm)
PS I'll be meeting up with Marius tonight if you have any questions you would like to ask on stem cells let me know.
apalazzo | June 6, 2007
Today three papers came out, two in Nature, and one in the inaugural edition of Cell Stem Cell, that basically confirm the results from last year's landmark manuscript by Kazutoshi Takahashi and Shinya Yamanaka (for details on this paper, see this post).
Just to remind you, in that original publication Takahashi and Yamanaka describe how they reprogrammed connective tissue cells (called a fibroblasts) into stem cell like entities, by introducing four active genes (Oct3/4, Klf4, Sox2 and c-Myc). The resulting iPS cells (induced pluripotent stem cells) could differentiate into any number of…
apalazzo | June 3, 2007
Welcome to the 15th edition of Mendel's Garden.
This month Gregor wanted to compile a summer reading list for all those going to the beach. But watch out, a sandy keyboard is never good!
So here we go:
First off, Gregor would like to point out this very interestin peice on what exactly caused wrinkling in his peas, you remeber don't you - the wrinkled versus smooth phenotype. Well Larry Moran at Sandwalk informs us that the wrinkling phenotype was cause by a defect in a gene that encodes a starch branching enzyme. How very interesting.
For some great summer reading, Gregor suggests that you…
apalazzo | May 31, 2007Soon it will be clear that this year old manuscript by Kazutoshi Takahashi and Shinya Yamanaka will be the basis of a future Nobel Prize.
The paper is how to transform any cell into a stem cell. In the paper the authors took an "I'm so smart" approach to the whole problem. These smart guess approaches rarely work, but it's always worth trying. This paper demonstrates why.
So let's get back to the problem. Reprogramming cells so that they can become totipotent. How to proceed? From the paper:
We selected 24 genes as candidates for factors that induce pluripotency in somatic cells, based on…
apalazzo | May 25, 2007In the past 15 years, the two biggest technical advances that have helped us Cell Biologists are RNAi and green fluorescent protein, aka GFP.
You see before the advent of GFP, researchers could only analyze the distribution of proteins in a living cell by first fixing and thus killing the sample. No information could be collected from a protein within it's natural envioronment, that of active cytoplasm. We could figure out where proteins were at a certain point in time, but not how they behaved over time. You see we were missing the temporal dimension. Sure there were exceptions, Yuli Wang…
apalazzo | May 24, 2007This is a cleaned up version of a comment I left on Larry Moran's blog.
As a cell biologist, I view genes as tools that contribute to the building and maintenance of different cell types. Vertebrates all have the same types of cells and thus it is no surprise that most of our genes have counterparts in all other vertebrates and all vertebrates have similar gene counts. Invertebrates such as worms and flies have almost the same number of cell types that vertebrates have and thus it is no surprise that invertebrates have almost (if not the same) number of genes that we have.
If one were to…
apalazzo | May 22, 2007This idea that most of your DNA is continuously transcribed has been floating around scientific circles.
I've blogged about it at least twice, and Coffee Mug at GeneExpression has mentioned it.
Keeping this in mind, here is some more interesting data from Danesh's lab.
Background: Certain small siRNA produced from the genes within the centromeric portion of S. pombe's chromosome will inactivate neighboring genes found in these regions. These siRNAs accomplish this task by binding to the RITS complex. In the new paper, Marc Buhler describes exactly how the RITS complex silences nearby genes…
apalazzo | May 21, 2007
A few days ago I wrote about Ron Breaker and Riboswitches, and today I was alerted to this really neat advanced online publication by the Breaker group on how a riboswitch in Neurospera regulates alternative splicing. Wow.
So what is happening?
When the fungi Neurospora crassa is exposed to thiamine, it takes up this vitamin B1 precursor and phosphorylates it to form thiamine pyrophosphate (TPP). This small metabolite then binds to an RNA element found within an intron in the NMT1 pre-mRNA. These RNA folds that bind to small molecules are called aptamers and when these aptamers regulate how…
apalazzo | May 21, 2007From a new Science paper:
Centrioles duplicate once in each cell division cycle through so-called templated or canonical duplication. SAK, also called PLK4 (SAK/PLK4), a kinase implicated in tumor development, is an upstream regulator of canonical biogenesis necessary for centriole formation. We found that overexpression of SAK/PLK4 could induce amplification of centrioles in Drosophila embryos and their de novo formation in unfertilized eggs. Both processes required the activity of DSAS-6 and DSAS-4, two molecules required for canonical duplication. Thus, centriole biogenesis is a template-…
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…