Pure Biology
apalazzo | May 9, 2007
Monday I saw an incredible lecture by U. Wash's Ning Zheng. (Yes Bil, I actually enjoyed a structure biology talk!)
I'll just summarize Dr. Zheng's last paper that was on the cover of the April 5th edition of Nature.
Intense studies on phototaxis in plants that began in part by Darwin (yup, that's right) led to the discovery of auxin, a diffusible signal that stimulates growth in plant cells. How do cells sense the growth factor? No one could identify the receptor until recently. It was known that auxin treatment promoted the degradation of the Aux/IAA transcription silencer, a protein that…
apalazzo | May 4, 2007Yesterday I saw Dr. Alan Cowman give a talk. He's a big guy in the Plasmodium field. Plasmodium is strange. It's the eukaryote parasite that causes malaria. But that's not why it's strange. Let's put it this way, if animals, plants and fungi are three siblings, Plasmodium would be their 6th cousin who lives in a trailer-park on the other side of the river. It's a distant relative, but deep down they're all related in an uncanny way.
Take the Plasmodium genome, about 60% of the genes have absolutely no discernible features. In other words we can't even ascribe a domain to more then half of…
apalazzo | May 2, 2007Joolya has been having some problems with contamination.
Now she needs your help. Can you identify the mystery organism that causes her tissue culture cells to bleb?
apalazzo | May 2, 2007In the lab we were discussing whether prokaryotes have true membrane bound organelles. By membrane bound organelles I mean that the membrane surrounding the organelle is not contiguous with the cell's delimiting membrane. Magnetosomes and other such organelles are though to be invaginations of the delimiting membrane, but this idea is controversial. Why should we care? Well we are not concerned about semantics (i.e. what is an organelle) but rather the implications of organellar biogenesis. You see once you have organelles composed of non-contiguous membranes you need to invoke a way to pinch…
apalazzo | May 1, 2007I have to say that I had never seen Eric Olson's seminar before, and it was awesome. Lately the Olson's lab has been looking at HDACs, i.e. histone deacetylases.
Don't forget that in the nucleus DNA is wrapped around nucleosomes that are composed of proteins called histones (see image, right). One important idea in biology today is that histones can get modified and this changes their regulates how they bind to the DNA. Thus by altering the histones you can regulate how accessible the DNA is for transcription (i.e. the conversion of DNA into RNA).
Histones are modified in many ways.…
apalazzo | April 13, 2007I've been writing my manuscript all week - hence the lack of posts. But this morning I flipped open the paper and read that they've sequenced by mass spec (proteomics in the new lingo) several proteins from the interior of a T. rex bone. So I'm reading the article in the NYTimes and then I stumble on to Lew Cantley's name. Lew's lab is into Dino bones? Interesting. From the article:
Lewis C. Cantley, a Harvard biology professor on the team, said he was satisfied that the findings were "unlikely due to contamination."
In a press release from Harvard, Dr. Cantley said, "Basically, this is the…
apalazzo | April 9, 2007How come no one told me about this site?
STRING is a database of known and predicted protein-protein interactions.
The interactions include direct (physical) and indirect (functional) associations; they are derived from four sources:
-Genomic Context
-High-throughput Experiments
-(Conserved) Coexpression
-Previous Knowledge
STRING quantitatively integrates interaction data from these sources for a large number of organisms, and transfers information between these organisms where applicable. The database currently contains 1,513,782 proteins in 373 species.
Check this out. An interaction…
apalazzo | April 3, 2007Well I tried some weird experiments on my cells, injecting fluorescent DNA. The result is some psychedelic images. The cells clearly were not happy.
Here is some fluorescent DNA molecules that aggregated in the cell's cytoplasm. Cellular chickenpox?
Note that we are simply viewing the fluorescence - hence the black and white image.
Here is another injected cell with giant DNA aggregates:
For non-cell biologists I've outlined the cell nucleus and the cytoplasm. Note that these structures are not in the nucleus but rather are on top of the nucleus:
Here's a closeup of those weird DNA…
apalazzo | April 2, 2007I've been struggling with eIF4E. You see eIF4E is the major cytosolic cap binding complex. When mRNA is synthesized in the nucleus the cap is loaded with nuclear cap binding complex, CBP80/20. Then (the story goes) the mRNA is exported to the cytoplasm where the ribosome engages the transcript and thus the pioneer round of translation begins. If there are problems such as premature termination codons, the RNA is degraded by nonsense mediated mRNA decay (NMD). If all is well, CBP80/20 is exchanged for eIF4E and now full scale translational synthesis can begin.
How does eIF4E promote…
apalazzo | April 2, 2007In this month's edition of Mendel's Garden we present to you the latest from the home office in Brno: Mendel's Premium Fish Flakes.
Guaranteed to invigorate your favorite genetic model organism, these flakes will work wonders.
Here are some testimonials:
Coturnix is wowed about how his massive aquarium has benefited from Mendel's fish flakes. With the latest genomic sequencing techniques that are discussed in a recent issue of PLoS - Biology, he can now analyze the genetic diversity in every corner of his huge aquarium. Coturnix points out how different DNA sampling procedures could tell us…
apalazzo | March 29, 2007Tuesday and Wednesday Dr Neupert was here at the medical school. The topic of his two seminars was mitos.
It is amazing how many protein shuttling mechanisms there are in mitos. Mitos only make about a dozen proteins from their own DNA, the rest are synthesized from nuclear genes. These nuclear derived gene products have to be imported into the mitos and this is where all the protein transport comes in. There's the TIM and TOM complexes to shuttle proteins from the cytoplasm into the intermembrane space and matrix, the TOB complex the Oxa transport system, the stop transfer system all working…
apalazzo | March 21, 2007OK here's a refresher ...nuclear export of mRNA in yeast:
Nucleoplasm is on the bottom, cytoplasm on the top. The bilayered nuclear envelope is represented by the two black lines. The top line is the outer nuclear envelope the bottom line is the inner nuclear envelope. The big red/blue thing with the purple basket is the nuclear pore complex (NPC).
In green is the TREX mRNA nuclear export system (TREX = transcription, export). These proteins are loaded sequentially during transcription in yeast and during splicing in higher eukaryotes. In most cases the Tho complex, which is comprised of…
apalazzo | March 15, 2007So Sir Paul Nurse gave a talk today where he discussed the 5 big ideas in the Life Sciences.
Instead of going through the talk, I'll just say that he ended it with his 5th big idea - biological organization. It reminds me of discussions I've had with colleagues on cell polarity. And in someways it's no surprise as this is Paul Nurse's current topic of interest. To generate a front and a back, cells must have a large interactive cellular network full of scaffolds and feedback loops that enforce a differentiation within a cell. Cell polarity cannot be explained simply in describing the polarity…
apalazzo | March 8, 2007... finally. Sign up http://www.cellpress.com/misc/page?page=podcast> here. Or enter http://podcast.cell.com/cell.xml into your podcast subscription.
It has a nice summary of a new Hannon paper on the role of piRNA in suppression of transposons in germ cells, another summary of how WASP is anchoring actin in the lamellipodium to the membrane at the leading edge (and which fits in to the model of membrane buckling postulated in the paper that I eluded to a couple of days ago), and a paper from Gerhard Wagner's lab on a new small molecule inhibitor of eIF4E, a factor involved in the…
apalazzo | March 8, 2007There's a new paper in Dev Cell with a nice reconstruction of a fission yeast cell (S. pombe) with all its microtubules.
From the abstract:
Here, we describe a large-scale, electron tomography investigation of S. pombe, including a 3D reconstruction of a complete eukaryotic cell volume at sufficient resolution to show both how many microtubules (MTs) there are in a bundle and their detailed architecture. Most cytoplasmic MTs are open at one end and capped at the other, providing evidence about their polarity. Electron-dense bridges between the MTs themselves and between MTs and the nuclear…
apalazzo | March 6, 2007In the Februray 6th issue of Cell there is an indept study by the Borisy & Sheetz labs that describes how crawling cells push and ruffle and bend the membrane at the very front with the aid of actin dynamics. Very cool stuff, very cool movies. I'll blog (or attempt to blog) about the actual paper in the near future. For today I have some background on actin dynamics in migrating cells.
Just to remind you what we're talking about, here is a movie of a migrating keratinocyte (skin cell) from the Borisy lab webpage.
Note that at a certain point the cell is fixed and lysed. We then zoom…
apalazzo | February 27, 2007Well last night I was invited to dine at Clio's with our Seminar Speaker, James Manley and some of the local transcription gurus, Kevin Struhl, Danesh Moazed, Steve Buratowski and Miriam Bucateli, a postdoc in the Buratowski lab. Unfortunately Dr. Manley had to leave early to catch a flight back to NY. But the rest of us had a nice conversation about that 70% of the genome being transcribed. (For past discussions click here and here).
So all the transcription guys firmly believed that the whole bit about 70% of the genome being transcribed is true. In fact Kevin Struhl pointed out a review…
apalazzo | February 23, 2007I guess prokaryotes are looking more and more like eukaryotes.
It turns out that their DNA is moved around by cytoskeletal filaments. The most recent (and one of the most dramatic) examples can be seen in a recent article in G&D where Fogel and Waldor describe how ParAI polymers yank the DNA around by being attaching to ParBI proteins that are anchored to specific sites called parSI sites. Although ParAI is shares structural features with MreB and thus actin, it is the functional analogue of our microtubules, ParBI would be like our kinetochores and parSI is the equivalent of our…
apalazzo | February 10, 2007I haven't done one of these in a while. Last Thursday, Stephan and I "imaged" some macrophages being infected with a vicious strain of vibrio, here's a cool image of one of the poor suckers:
The macrophage is on the top right, a few vibrio cells can be seen on the lower left. Note that the macrophage has all these funky tubes coming out of it.
(Yet again tubes ... my thesis adviser's lab would refer to microtubules as "tubes" too. They're everywhere!)
apalazzo | February 8, 2007MDR: Multi Drug Resistance Protein. It's an ABC (ATPase Box Cassette) Transporter. In other words, this gene encodes an energy utilizing pump that sits on the plasma membrane and actively transports (mostly hydrophobic?) compounds out of the cell. As I wrote yesterday, a silent change in this gene at the nucleotide level alters the transporter's specificity. According to a paper in the Jan 26th edition of Science, the altered MDR protein is just fine at transporting most compounds but is defective in the transport of a particular compound. The silent mutation does not affect mRNA levels or…