Pure Biology
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…
apalazzo | July 8, 2006This world cup has been marked by beautiful games and people accusing refs of making bad calls. David Hirshey in today's NY Times OpEd section:
Several months before the 1999 Women's World Cup, I accompanied the United States national team to Brazil for a series of exhibition matches. One afternoon, at a training facility outside São Paulo, I was pressed into service to help officiate an intra-squad scrimmage. The team's coach, Tony DiCicco, handed me a red flag and told me to raise it if I detected any infractions.
The field was about 30 yards shorter than the regulation size, which is…
apalazzo | July 6, 2006I had read a couple of reviews about all the recent ruckus in this field. I was going to write something ... but I only have so many hours in a day. Now the newest paper has now surfaced. Pure Pedantry has the details. And so I guess I'll end up writing about it anyway.
So how did this all start? Because I'm lazy (and frankly have a ton of work to do) here is what I posted on Pure Pedantry:
...the big papers came out a couple of months ago. In the first paper a bone marrow from a GFP expressing mouse was transplanted into a native mouse. The native mouse developed GFP expressing oocytes (…
apalazzo | July 6, 2006No soccer today. So instead of spending time watching others run around, go read the two papers, published in last week's Nature on Golgi maturation.
Proteins that need to traverse, or be embedded, within membranes are synthesized on the surface of the endoplasmic reticulum (ER). At the ER membrane, proteins are cotranslationaly inserted through (or into) the memebrane via a pore called the translocon. Most of these "translocated" proteins are then delivered, through vesicular transport to the Golgi complex, where they are modified. How? Well sugars are covalently attached, sugars are…
apalazzo | June 30, 2006Every thought about how variable the expression of a particular gene is across an entire cell population?
That's what the Weissman lab described in a manuscript in a recent issue of Nature. Anytime you want to take on such a project - take my advice, you turn to yeast. The yeast field has created a library of strains, each containing a copy of GFP (Green fluorescent protein) fused to a particular gene within the genome. If you measure the fluorescence, you can quantify the level of protein expression. The next trick is to use flow cytometry to rapidly measure the brightness individual cells…
apalazzo | June 26, 2006Just read this Abstract from PLoS:
Mammalian genes are highly heterogeneous with respect to their nucleotide composition, but the functional consequences of this heterogeneity are not clear. In the previous studies, weak positive or negative correlations have been found between the silent-site guanine and cytosine (GC) content and expression of mammalian genes. However, previous studies disregarded differences in the genomic context of genes, which could potentially obscure any correlation between GC content and expression. In the present work, we directly compared the expression of GC-rich…
apalazzo | June 21, 2006Flipping through the latest issue of Cell:
Ujwal Sheth from Roy Parker's lab details the molecular mechanism that targets RNAs with premature stop codons to processing-bodies (or p-bodies) via the non-sense mediated decay (NMD) pathway. P-bodies are dense cytoplasmic granule-like structures that serve as sites of mRNA storage/degradation. P-bodies contain decapping enzymes, RNAses, and many other proteins of unkown function. In this paper the authors demonstrate that the NMD component, and RNA helicase, Upf1p, targets aberrant mRNA to granules. Upf1p's ATPase activity is then required to…
apalazzo | June 9, 2006Back in the fall of 2004, I submitted a prediction to TimeLine+25, a web based "cultural experiment" where random individuals were asked to predict near future events.
Here was my entry for the year 2025:
Plastic eating bacteria
Novel forms of bacteria which subsist solely on various forms of plastic come to life. Plastic around the world starts to decompose. Although plastic from garbage dumps "becomes" biodegradable, computers, airplane parts, CDs, DVDs and many everyday items start to rot. Panic sets in across the industrialized world.
OK so I was off by 19 years ... and I thought that…
apalazzo | May 31, 2006The nuclear membrane separates the nuclear space from the cytoplasm. This barrier is comprised of two membranes (Inner and Outer Nuclear Membrane) that are continuous with the endoplasmic reticulum. To cross the double membrane, molecules traverse the nuclear pore complex (NPC), a giant macromolecular complex that has an eight-fold symmetry and weighs over 100MDa. To date, only two components of the NPC have been identified: gp210 and Pom120. Interestingly many cells only express one of these proteins. Well it seems like Dirk Gorlich's group have been able to knock out BOTH genes from Hela…
apalazzo | May 23, 2006Sorry, I haven't been writing much in the past few days.
Here are some cool ER papers I've seen recently:
Direct membrane protein-DNA interactions required early in nuclear envelope assembly Sebastian Ulbert, Melpomeni Platani, Stephanie Boue, and Iain W. Mattaj JCB (2006) 173:469-476
When the nuclear envelope reforms after mitosis, ER vesicles must bind to the condensed chromatin, but how does this occur? Well about half of the nuclear envelope (NE) proteins have basic luminal domains that mediate electrostatic interactions with the DNA itself. (In comparison about 4% of general ER and Golgi…
apalazzo | May 18, 2006Yesterday I gave a talk. Everything was fine although I thought I was a little wordy.
So instead of writing something I'll throw you a few pictures.
Here is a picture of a two cells that were microinjected with mRNA. The mRNA encodes a protein that is cotranslationally inserted into the endoplasmic reticulum (ER), and thus the mRNA itself is targeted to this same intracellular location. The cells were fixed 2hrs post-injection and then stained using a fluorescent probe the hybridizes against the exogenous transcript. This technique of labelling mRNA is called fluorescence in situ…
apalazzo | April 19, 2006A new paper out in Nature, brakes through the diffraction barrier to see things that have never been seen before. Using this novel fluorescence-microscopy technique called STED (stimulated emission depletion), Willig et al., see Kiss and Run. And yes they see it!
OK ... I know, you have 2 questions. How does STED work? and What is Kiss and Run?
Rayleigh's law of resolution maxima, which says that you can never resolve two dots that are closer together than the ~size of the wave-length of light used to probe the sample, defines how small we microscopists can see in the two dimensional plain of…
apalazzo | April 18, 2006OK I haven't been writing anything on papers I've read recently, to make up for this here is a brief summary of a neat paper on Sad1:
1- Sad1 is a homologue of the SUN proteins in S. pombe (fission yeast). In higher eukaryotes the SUNs are inner-nuclear membrane proteins that link to KASH domain containing proteins that reside in the outer nuclear envelope. These KASH containing proteins, such as Nesprins, then link to cytoskeletal elements in the cytoplasmic space and are involved in moving the nucleus to various intracellular spaces.
So what is Sad1 doing in pombe? During Meiosis the ends…
apalazzo | April 12, 2006Spurred on by some comments left by Coturnix on the Three Types of Experiments entry, and by the Microparadigm paper (see my entry, and another discussion of this paper at In the Pipeline), I now present to you ... the significance of negative data.
Now most of the older (and well read) philosophers of data such as Kuhn, Popper and Feyerabend were obsessed with the physical sciences, and as Ernst Mayr has pointed out in several books, they're ideas are less applicable to the life sciences. Even the principle of Occam's Razor often fails biology. The main mechanisms that operate within a…
apalazzo | April 10, 2006
I just came back from a Wade Harper talk where we were subjected to an obscene amount of ubiquitin biology and even more ubiquitin nomenclature. This blasting of your brain with technical terms is becoming more and more common with big Biology talks.
But to be honest Prof Harper gave a good talk about an RNAi screen to identify new cell cycle regulators. He's a pretty smart guy (although he needs to take a little more caffeine). A major focus of the talk was on the modulation of Ubiquitination by E3s.
Ubiquitin as you know, is that small peptide that gets conjugated to proteins that are…
apalazzo | March 29, 2006OK after making fun of System Biologists out comes Peter Sorger's latest paper in Cell.
In this paper, Sorger's team collected almost 8000 intracellular measurements (they collected some of the data directly and got the rest from the literature - I'll have to check on that) plugged it into an algorithm or a ...
... compact representation of the entire compendium by using discriminant partial least squares regression (DPLSR; Janes et al., 2004). A DPLSR map was created such that the signaling proteins and cytokines were projected onto a set of "principal components" that maximized covariation…
apalazzo | March 27, 2006The van Oijen lab (here at HMS) had a nice paper in Nature where they indirectly observe single T7 DNA polymerase complexes copying DNA.
How do they do it? One end of the DNA is fixed while the other side is coupled to a bead that can be visualized. A laminar flow is applied to the reaction causing the DNA strand to stretch out. Thus the bead becomes a marker for the length of the DNA.
As the T7 complex duplicates the leading strand, the uncopied lagging strand agglomerates. Since the lagging strand is fixed to the cover slip, the DNA shortens and this reels in the bead like a fish on a line…
apalazzo | March 23, 2006I was notified of this review in PLoS-Biology by Richard Robinson. It gives a nice outline of the current thought in the field and delineates the genes first vs. metabolism first views (although in my not-to-much-of-an-expert opinion, I don't think that the "metabolism first" theory is likely ... but what do I know.)
Ref: Richard Robinson. Jump-Starting a Cellular World: Investigating the Origin of Life, from Soup to Networks. PLoS Biology (2005) DOI: 10.1371/journal.pbio.0030396
apalazzo | March 20, 2006Although there is a trend in the life sciences towards big Biology, recently all the greatest insights have come from studies of single molecules. Some of the best work has come from Stephen Kowalczykowski's group. They have used single particle imaging to monitor how a single RecBCD complex unfold DNA.
Now in the latest issue of Nature, the Xie group, monitor the expression product of single genes in E. Coli. They perform this Herculean task by affixing the cells to small wells. When the gene (beta-galactosidase) is turned on, mRNA is produced and then translated into a secreted enzyme. In…
apalazzo | March 17, 2006After posting some microtubule stuff, it's time for an entry about mRNA.
RNA granules are very intriguing. They are thought to transport RNA in some cell types such as neurons or Oocytes, and store/degrade mRNA in other cell types. Recently the RNAi machinery is thought to localize to some of these dense structures too. How are the granules/processing bodies formed? Well it turns out that proteins thought to have prion like properties (TIA-1 and CPEB) may serve as scaffolds that support these granules. To read more check out this review in the latest JCB.
Ref: Paul Anderson and Nancy Kedersha…