Pure Biology
apalazzo | January 14, 2007Inspired by amnestic, I was perusing the videocasts of lectures given at the NIH, when I bumped into this lecture given by Thomas Silhavy on how the outer membrane of gram negative bacteria is synthesized. At the end of the lecture Dr Silhavy brought up some interesting statistics. In 1997, 38% of essential genes in E. coli were unannotated and thus have names that begin with "y". Now "essential" means that the knockouts of these genes give a lethal phenotype, and the products of these genes must serve key roles in various basic cellular functions. Unannotated, does not mean that we know…
apalazzo | January 10, 2007Well the latest paper from the Reed lab (squeeking into Cell on its last issue of 2006) demonstrates that the cap is indeed promoting nuclear export of mRNA in vertebrate cells. (For more on mRNA export, click here.)
This idea that each step of mRNA metabolism is "coupled" to the following step of mRNA metabolism is an idea that has been going around quite a bit in the RNA world.
The cap, is a structure found at the start (or 5' end) of mRNAs, and consists of an inverted methyl-Guanosine linked by a tri-phosphate to the first nucleic acid, invariably guanosine. The role of the cap is to…
apalazzo | January 6, 2007From the latest issue of Science:
We demonstrated that despite their small size, specific miRNAs contain additional sequence elements that control their posttranscriptional behavior, including their subcellular localization. We showed that human miR-29b, in contrast to other studied animal miRNAs, is predominantly localized to the nucleus. The distinctive hexanucleotide terminal motif of miR-29b acts as a transferable nuclear localization element that directs nuclear enrichment of miRNAs or small interfering RNAs to which it is attached.
Cool.
Ref:
Hwang HW, Wentzel EA, Mendell JT.
A…
apalazzo | January 3, 2007In this day, some biologist have to move beyond the simplistic view that the cell is a bag of M&Ms. What do I mean by that? It's the idea that enzymes and organelles are free floating entities within the cell.
On the other hand, don't tell me that the cytoskeleton provides a static skeleton that fixes each cellular component.
The cytoskeleton is a dynamic and sensitive cellular organizer that constantly reshapes itself in response to extra-cellular clues. And those M&Ms aren't nailed to some part of the cytoskeleton. No, in fact they are moved around and dynamically organized by…
apalazzo | December 27, 20062006 was (again) year of the RNA.
Two nobels. The RNA world expanded with the discovery of Piwi RNA. RNAi as a transmittable trait? (Lamarck is vindicated!) We also found out that much of the conserved parts of our genome do not encode protein. Now how many of these bits are regulatory elements and how many are non-coding RNAs is yet to be tabulated. However the most rapidly evolving gene between humans and chimps is one of these non-coding RNA. There are even hints that the lowly centrosome has it's own RNA (although flies apparently don't need centrosomes.) Also a nice theory was proposed…
apalazzo | December 24, 2006Check this out:
First-in-Human Experience of an Antidote-Controlled Anticoagulant Using RNA Aptamer Technology
From the paper:
A translatable platform for developing an optimal parenteral anticoagulant should consider several prerequisite properties: easy delivery, rapid onset of action, and predictable responses among the dose, pharmacokinetic profile, and pharmacodynamic effects to reduce the requirement for routine monitoring. Additionally, an optimal anticoagulant should be biologically selective and actively reversible.
What is in use currently?
Unfractionated heparin is currently the…
apalazzo | December 23, 2006Earlier this week you probably read the whole saga of how researchers tracked down some individuals who could not sense pain. They then identified the gene responsible as SCN9A, a voltage-gated sodium channel and that was published in Nature. But in Science there was another report of a gene, Catechol-O-Methyltransferase (S-COMT), that is critical for pain perception ...
Well it turns out that the data in the Science paper is much more interesting than the flashy (yet uninsightful) observations of individuals walking on hot coal and receiving knife stabs into their arms without even flinching…
apalazzo | December 12, 2006Apparently weak and strong signal sequences are differentially targeted to the ER acording to a new paper in Cell.
(For more on how proteins are inserted into the ER click here.)
Preprolactin has a strong signal sequence and is inserted into the translocon even when the unfolded protein response (UPR) is activated. Prion protein, which has a weak signal sequence, is only inserted when UPR is inactive. Remember that under stress (high heat or other nasty conditions) cells rewire protein production and turn off the insertion of most proteins into the ER while upregulating the production and…
apalazzo | December 8, 2006Yesterday Melissa Moore gave a talk at the School of Public Health here at Harvard Med School. She had lots of data - on nonsense mediated decay (how cells degrade mRNA transcripts with premature stop codons that arise through various mechanisms) and on nonfunctional ribosome decay (NRD). Here is some neat info from her intro on introns & NMD:
- Since 90% of the gene coding region is introns, exons are for all practical purposes modular. When DNA is duplication or swaped within a gene or between genes, chances are that genes will be cut and ligated at intronic sequences. (Thus the exons…
apalazzo | December 6, 2006As a grad student at Columbia, I once saw a talk by Joachim Frank at Rockefeller. Siting in the audience, I was wowed as Frank described the cryo-EM structure of the ribosome in many different conformations, each representing one step of the polypeptide chain elongation cycle. Compiling them together, he produced a little movie of a ribosome manufacturing a protein. While I was taking in this movie I remember thinking - wow, this is how the machine works!
Recently a few other labs have published the cryo-EM structures of the ribosome with every freakin' Ribosome cofactor. The latest…
apalazzo | December 4, 2006Over this past summer I saw Dirk Görlich give a talk about how the multitude of FG repeats found within the nuclear pore complex (NPC), form a gel like matrix. This "elastic hydrogel" acts as the major barrier within the NPC. Although the gel can prevent the passage of most large molecules (>30kD), it is permeable to nuclear transport receptors (NTRs). Note that all this "story" was published in the November 3rd edition of Science Magazine (link). In that paper there's a nice diagram in the that explains it all:
An "FG repeat" is a long stretch of amino acids that form non-covalent…
apalazzo | December 1, 2006Earlier today I gave our weekly journal club. As usual there is some large scheme/model/godzilla image associated with the intro/summary. Here's mine ... mRNA nuclear export in yeast:
Highlighted are 3 major systems. Many proteins are listed, many more are not.
Nucleoplasm is on the bottom, cytosol on the top. The bilayered nuclear membrane is represented by the two black lines. The big red/blue thing with the purple basket is the nuclear pore complex (NPC).
In purple hue is the Mpl1/2 system. These proteins are the orthologues of TPR in mammalian cells and form the basket of the NPC.…
apalazzo | November 30, 2006There was some minor controversy for the RNAi Nobel ... should Rich Jorgensen's have been acknowledged? and the miRNA people?
Here is what Rich Jorgensen has to say (from the latest edition of Science):
I feel that the Nobel committee's decision to focus on the central role of double-stranded RNA (dsRNA) was quite appropriate; it was this specific discovery that broke an obscure field wide open and brought it to the attention of all biologists. The publication of RNAi (1) catalyzed new interactions between plant and animal geneticists that led directly to all kinds of discoveries about the…
apalazzo | November 29, 2006OK I finally did that experiment that people asked for ... and more.
If you want to know why I performed this experiment, read this post on RNA treatments for autism. Here I present to you evidence that your body is secreting enzymes, called RNAses, that will chew up your RNA in minutes.
So the experiment:
500ng of RNA was mixed with either
- control buffer (100mM KCl, 10mM Tris buffer pH7.4)
- 1ul of DNAse (1mg/ml), this is what you would call a negative control - no degradation should be seen here
- 1ul of water applied to sweaty skin
(After working a bit with my latex gloves, I puled off…
apalazzo | November 29, 2006
When I was a grad student, eukaryotes had all the neatest toys ... actin, microtubules, kinesins, dynein, myosin, dynamin, SNAREs ...
OK that's not totally true - bacteria had their version of tubulin (the constituent of microtubules), and it's called FtsZ. Then others found that bacteria had a version of actin, the most known is called MreB. The latest is that prokaryotes have dynamin. (Click here for previous dynamin entries.)
From the paper:
Given the presence of large GTPases with predicted dynamin-like domain organization in many members of the Eubacteria such as E. coli and Bacillus…
apalazzo | November 20, 2006In my work, I've investigated mRNA distribution in cells. Many aspects of mRNA metabolism and regulation seem dependent on splicing. And so I've been doing some digging with respect to the survey of intronless genes that I wrote about yesterday. According to their bioinformatic analysis of the human genome, there are over 3000 coding genes that do not contain introns. Here's a comment on this survey from RPM:
From the website you link to:
1. Single exon genes are identified using the CDS FEATURE definition in the genome data.
It seems like they're ignoring introns located in the 5' and 3'…
apalazzo | November 19, 2006Introns are parts of the gene that do not contain coding information, they have to be spliced out of precursor RNA to form mature messenger RNA (mRNAs). But ask most biologists and they'll tell you that in "higher eukaryotes" all genes have introns. All? They may reply, "well not quite". The most famous examples of intronless genes are the histone genes. Also many tRNA genes are intronless. But just how many intronless genes are there in the human genome? Well I just stumbled onto this site: Genome SEGE - Intronless Genes in Eukaryotes.
Here's a couple of graphs from the SEGE (Single Exonic…
apalazzo | November 17, 2006It's been a while since I've written about mRNA and mRNA export. There has been lots of CPEB papers (cytoplasmic polyadenylation element binding protein), but nothing fundamentally new at the molecular level. As for mRNA export, the Reed lab will have a big paper out soon, and when that comes out I'll write a blog about how each step of mRNA metabolism is thought to promote the next step in mRNA metabolism (so that mRNA transcription promotes splicing which in turn promotes nuclear export.)
But for now lets turn our attention to a new JCB paper that claims that a subset of mRNAs, which…
apalazzo | November 16, 2006A couple of weeks back I wrote about dynamins and mitochondrial fusion. Well the latest piece of the puzzle came in ... I just saw a paper in the latest issue of Nature Cell Biology on this very topic. Apparently a mitochondrial version of phospholipase D (MitoPLD) may act downstream of the dynamin like molecule Mfn1 to promote fusion of the outer mitochondrial membrane.
Now remember mitos have two membranes. If two mitos want to get together they must fuse the outer membranes. This requires a dynamin protein (Mfn1 in mammals). After this fusion the two inner mitochondrial membranes can come…
apalazzo | November 14, 2006
This is for cell motility aficionados.
How do cells crawl? Well most in the field would say that actin polymerization generated by the Arp2/3 complex at the leading edge acts to generate an actin meshwork (see pic). The addition of actin monomers right under the membrane (arrows) act as a Brownian ratchet to push membrane forward. But for anyone who has actually monitored cell motility in the microscope, you must think that this idea is ludicrous. First of all, motility is more that pushing membrane, it's about transporting all your organelles and cytoplasmic components forward while…